DHS Science and Technology Directorate | MOBILIZING INNOVATION FOR A SECURE WORLD
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DHS SCIENCE
AND TECHNOLOGY
Master Question List for
COVID-19 (caused by
SARS-CoV-2)
Weekly Report
04 August 2020
For comments or questions related to the contents of this document, please contact the DHS S&T
Hazard Awareness & Characterization Technology Center at HACTechno[email protected].gov.
REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
Updated 8/04/2020
i
FOREWORD
The Department of Homeland Security (DHS) is paying close attention to the evolving Coronavirus
Infectious Disease (COVID-19) situation in order to protect our nation. DHS is working very closely with
the Centers for Disease Control and Prevention (CDC), other federal agencies, and public health officials
to implement public health control measures related to travelers and materials crossing our borders
from the affected regions.
Based on the response to a similar product generated in 2014 in response to the Ebolavirus outbreak in
West Africa, the DHS Science and Technology Directorate (DHS S&T) developed the following “master
question list” that quickly summarizes what is known, what additional information is needed, and who
may be working to address such fundamental questions as, “What is the infectious dose?” and “How
long does the virus persist in the environment?” The Master Question List (MQL) is intended to quickly
present the current state of available information to government decision makers in the operational
response to COVID-19 and allow structured and scientifically guided discussions across the federal
government without burdening them with the need to review scientific reports, and to prevent
duplication of efforts by highlighting and coordinating research.
The information contained in the following table has been assembled and evaluated by experts from
publicly available sources to include reports and articles found in scientific and technical journals,
selected sources on the internet, and various media reports. It is intended to serve as a “quick
reference” tool and should not be regarded as comprehensive source of information, nor as necessarily
representing the official policies, either expressed or implied, of the DHS or the U.S. Government. DHS
does not endorse any products or commercial services mentioned in this document. All sources of the
information provided are cited so that individual users of this document may independently evaluate the
source of that information and its suitability for any particular use. This document is a “living document”
that will be updated as needed when new information becomes available.
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REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
Updated 8/4/2020
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Table of Contents
Infectious Dose – How much agent will make a healthy individual ill? ..................................................................................... 3
The human infectious dose of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown by all exposure
routes. Studies from other animal models are used as surrogates for humans. Based on primate models, the inhalation
median infectious dose (ID
50
) in humans is likely less than 10,000 PFU, and possibly less than 1,000 PFU.
Identifying the infectious dose for humans by the various routes through which we become infected is critical to the
effective development of computational models to predict risk, develop diagnostics and countermeasures, and effective
decontamination strategies. Animal studies are a plausible surrogate.
Transmissibility – How does it spread from one host to another? How easily is it spread? ...................................................... 4
SARS-CoV-2 is passed easily between humans, likely through close contact with relatively large droplets and possibly through
smaller aerosolized particles.
Individuals can transmit SARS-CoV-2 to others before they have symptoms.
Undetected cases play a major role in transmission, and most cases are not reported.
661
Individuals who have recovered clinically, but test positive, appear unable to transmit COVID-19.
285
The relative contribution of different routes of transmission, such as close contact and droplet transmission versus aerosol
transmission and contaminated objects and surfaces (fomites), is unknown and requires additional research.
Host Range – How many species does it infect? Can it transfer from species to species? ......................................................... 5
SARS-CoV-2 is closely related to other coronaviruses circulating in bats in Southeast Asia. Previous coronaviruses have
passed through an intermediate mammal host before infecting humans, but the presence or identity of the SARS-CoV-2
intermediate host is unknown. Current evidence suggests a direct jump from bats to humans is plausible.
58
SARS-CoV-2 uses the same receptor for cell entry as the SARS-CoV-1 coronavirus that circulated in 2002/2003.
To date, ferrets, mink, hamsters, cats, deer mice, and primates have been shown to be susceptible to SARS-CoV-2 infection.
It is unknown whether these animals can transmit infection to humans.
The best animal model for replicating human infection by various routes is still unidentified.
Incubation Period – How long after infection do symptoms appear? Are people infectious during this time? .......................... 6
The majority of individuals develop symptoms within 14 days of exposure. For most people, it takes at least 2 days to
develop symptoms, and on average symptoms develop 5 days after exposure. Incubating individuals can transmit disease for
several days before symptom onset. Some individuals never develop symptoms but can still transmit disease.
While the incubation period is well-characterized overall, the duration of infectivity is poorly understood in different patient
populations (e.g., age, disease severity).
Clinical Presentation – What are the signs and symptoms of an infected person? ................................................................... 7
Most symptomatic cases are mild, but severe disease can be found in any age group.
4
Older individuals and those with
underlying conditions are at higher risk of serious illness and death.
Approximately 40% of cases are asymptomatic.
433
The case fatality rate is unknown, but individuals >60 and those with comorbidities are at elevated risk of death.
562, 675
Minority populations are disproportionately affected by COVID-19.
Children are susceptible to COVID-19,
155
though generally show milder
105, 361
or no symptoms.
Both the duration and prevalence of debilitating symptoms that inhibit an individual’s ability to function are not understood.
The true case fatality rate is unknown.
Protective Immunity – How long does the immune response provide protection from reinfection? ........................................ 8
Infected patients show productive immune responses, but the duration of any protection is unknown. Initial evidence
suggests that the neutralizing antibody response does not last more than a few months, though this varies by severity.
Currently, there is no evidence that recovered patients can be reinfected with SARS-CoV-2.
As the pandemic continues, long-term monitoring of immune activity and reinfection status is needed.
Clinical Diagnosis – Are there tools to diagnose infected individuals? When during infection are they effective? .................... 9
Diagnosis of COVID-19 is based on symptoms consistent with COVID-19, PCR-based testing of active cases, and/or the
presence of SARS-CoV-2 antibodies in individuals. Confirmed cases are still underreported.
234
Testing is available to
individuals with or without a doctors referral based on state and local guidelines.
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Validated serological (antibody) assays are being used to help determine who has been exposed to SARS-CoV-2. Serological
evidence of exposure does not indicate immunity.
In general, PCR tests appear to be sensitive and specific, though confirmation via chest CT is recommended. The sensitivity
and specificity of serological testing methods is variable.
Medical Treatments – Are there effective treatments?...........................................................................................................10
Treatment for COVID-19 is primarily supportive care,
220, 381
and no single standard of care exists. Drug trials are ongoing.
Remdesivir shows promise for reducing symptom duration
45
and mortality
205
in humans.
Hydroxychloroquine is associated with risk of cardiac arrhythmias and provides limited to no clinical benefit.
120
Dexamethasone may significantly reduce mortality in severely ill and ventilated patients.
Other pharmaceutical interventions are being investigated.
Additional information on treatment efficacy is required, particularly from large randomized clinical trials.
Vaccines – Are there effective vaccines?.................................................................................................................................11
Work is ongoing to develop and produce a SARS-CoV-2 vaccine (e.g., Operation Warp Speed).
42, 225, 228-230, 421
Early results are
being released, but evidence should be considered preliminary until larger trials are completed.
Published results from randomized clinical trials (Phase I – III) are needed.
Non-pharmaceutical Interventions – Are public health control measures effective at reducing spread? .................................12
Broad-scale control measures such as stay-at-home orders are effective at reducing transmission.
Research is needed to help plan for easing of restrictions. Testing is critical, and synchronized interventions may help.
As different US states have implemented differing control measures at various times, a comprehensive analysis of social
distancing efficacy has not yet been conducted.
Environmental Stability – How long does the agent live in the environment? .........................................................................13
SARS-CoV-2 can persist on surfaces for at least 3 days and on the surface of a surgical mask for up to 7 days depending on
conditions. If aerosolized intentionally, SARS-CoV-2 is stable for at least several hours. The seasonality of COVID-19
transmission is unknown. SARS-CoV-2 on surfaces is inactivated rapidly with sunlight.
Additional testing on SARS-CoV-2, as opposed to surrogate viruses, is needed to support initial estimates of stability. Tests
quantifying infectivity, rather than the presence of viral RNA, are needed.
Decontamination – What are effective methods to kill the agent in the environment? ..........................................................14
Soap and water, as well as common alcohol and chlorine-based cleaners, hand sanitizers, and disinfectants are effective at
inactivating SARS-CoV-2 on hands and surfaces.
Additional decontamination studies, particularly with regard to PPE and other items in short supply, are needed.
PPE – What PPE is effective, and who should be using it? .......................................................................................................15
The effectiveness of PPE for SARS-CoV-2 is currently unknown, and data from other related coronaviruses are used for
guidance. Healthcare workers are at high risk of acquiring COVID-19, even with recommended PPE.
Most PPE recommendations have not been made on SARS-CoV-2 data, and comparative efficacy of different PPE for
different tasks (e.g., intubation) is unknown. Identification of efficacious PPE for healthcare workers is critical due to their
high rates of infection.
Forensics – Natural vs intentional use? Tests to be used for attribution. ................................................................................16
All current evidence supports the natural emergence of SARS-CoV-2 via a bat and possible intermediate mammal species.
Identifying the intermediate species between bats and humans would aid in reducing potential spillover from a natural
source. Wide sampling of bats, other wild animals, and humans is needed to address the origin of SARS-CoV-2.
Genomics – How does the disease agent compare to previous strains? ..................................................................................17
Current evidence suggests that SARS-CoV-2 accumulates substitutions and mutations at a similar rate as other
coronaviruses. Mutations and deletions in specific portions of the SARS-CoV-2 genome have not been linked to any changes
in transmission or disease severity, though modeling work is attempting to identify possible changes.
Research linking genetic changes to differences in phenotype (e.g., transmissibility, virulence, progression in patients) is
needed.
Forecasting – What forecasting models and methods exist? ...................................................................................................18
Forecasts differ in how they handle public health interventions such as shelter-in-place orders and tracking how methods
change in the near future will be important for understanding limitations going forward.
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Infectious Dose – How much agent will make a healthy individual ill?
What do we know?
The human infectious dose of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown by all exposure
routes. Studies from other animal models are used as surrogates for humans. Based on primate models, the inhalation
median infectious dose (ID
50
) in humans is likely less than 10,000 PFU, and possibly less than 1,000 PFU.
Non-human primates
• A total dose of approximately 700,000 plaque-forming units (PFU) of the novel coronavirus SARS-CoV-2 infected
cynomolgus macaques via combination intranasal and intratracheal exposure (10
6
TCID
50
total dose).
490
Macaques did not
exhibit clinical symptoms, but shed virus from the nose and throat.
490
• Rhesus and cynomolgus macaques showed mild to moderate clinical infections at doses of 4.75x10
6
PFU (SARS-CoV-2
delivered through several routes), while common marmosets developed mild infections when exposed to 1.0x10
6
PFU
intranasally.
360
• Rhesus macaques are effectively infected with SARS-CoV-2 via the ocular conjunctival and intratracheal route at a dose of
approximately 700,000 PFU (10
6
TCID
50
).
147
Rhesus macaques infected with 2,600,000 TCID
50
of SARS-CoV-2 by the
intranasal, intratracheal, oral and ocular routes combined recapitulate moderate human disease.
415
• African green monkeys replicate aspects of human disease, including severe pathological symptoms (exposed to 500,000
PFU via intranasal and intratracheal routes),
626
mild clinical symptoms (aerosol exposures between 5,000 and 16,000
PFU),
232
and acute respiratory distress syndrome (ARDS), with small particle aerosol exposure doses as low as 2,000 PFU.
56
• Aerosol exposure of three primate species (African green monkeys, cynomolgus macaques, and rhesus macaques) via a
Collison nebulizer resulted in mild clinical disease in all animals with doses between 28,700 and 48,600 PFU.
276
Rodents
• Golden Syrian hamsters exposed to 80,000 TCID
50
(~56,000 PFU) via the intranasal route developed clinical symptoms
reminiscent of mild human infections (all hamsters infected).
533
In a separate study, immunosuppressed Golden Syrian
hamsters showed severe clinical symptoms (including death) after exposure to 100-10,000 PFU via intranasal challenge.
64
• Golden Syrian hamsters infected with 100,000 PFU intranasally exhibited mild clinical symptoms and developed
neutralizing antibodies,
100
and were also capable of infecting individuals in separate cages. In another study, older
hamsters had more severe symptoms and developed fewer neutralizing antibodies than younger hamsters.
435
• Mice genetically modified to express the human ACE2 receptor (transgenic hACE2 mice) were inoculated intranasally with
100,000 TCID
50
(~70,000 PFU), and all mice developed pathological symptoms consistent with COVID-19.
39
• Tr
ansgenic (hACE2) mice became infected after timed aerosol exposure (36 TCID
50
/minute) to between 900 and 1080
TCID
50
(~630-756 PFU). All mice (4/4) exposed for 25-30 minutes became infected, while no mice (0/8) became infected
after exposure for 0-20 minutes (up to 720 TCID
50
, ~504 PFU).
40
Key methodological details (e.g., particle size,
quantification of actual aerosol dose) are missing from the study’s report.
• Transgenic (hACE2) mice exposed intranasally to 400,000 PFU of SARS-CoV-2 develop typical human symptoms.
553
Other animal models
• Ferrets infected with 316,000 TCID
50
291
or 600,000 TCID
50
481
of SARS-CoV-2 by the intranasal route show similar symptoms
to human disease.
291, 481
Uninfected ferrets in direct contact with infected ferrets test positive and show disease as early
as 2 days post-contact.
291
In one study, direct contact was required to transfer infection between ferrets,
291
however,
transmission without direct contact was found in another study.
481
• In a ferret study, 1 in 6 individuals exposed to 10
2
PFU via the intranasal route became infected, while 12 out of 12
individuals exposed to >10
4
PFU became infected.
501
• Do
mestic cats exposed to 100,000 PFU of SARS-CoV-2 via the intranasal route developed severe pathological symptoms
including lesions in the nose, throat, and lungs.
530
In a separate study, infected cats showed no clinical signs, but were able
to shed virus and transmit to other cats.
59
Related Coronaviruses
• The infectious dose for severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) in mice is estimated to be between
67-540 PFU (average 240 PFU, intranasal route).
142, 144
• Genetically modified mice expressing DPP4 exposed intranasally to doses of Middle East respiratory syndrome
coronavirus (MERS-CoV) between 100 and 500,000 PFU show signs of infection. Infection with higher doses result in
severe syndromes.
15, 125, 330, 670
What do we need to know?
Identifying the infectious dose for humans by the various routes through which we become infected is critical to the
effective development of computational models to predict risk, develop diagnostics and countermeasures, and effective
decontamination strategies. Animal studies are a plausible surrogate.
• Human infectious dose by aerosol, surface contact (fomite), fecal-oral routes, and other potential routes of exposure
• Most appropriate animal model(s) to estimate the human infectious dose for SARS-CoV-2
• Does exposure dose determine disease severity?
REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
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Transmissibility – How does it spread from one host to another? How easily is it spread?
What do we know?
SARS-CoV-2 is passed easily between humans, likely through close contact with relatively large droplets and possibly
through smaller aerosolized particles.
• As of 8/4/2020, pandemic COVID-19 has caused at least 18,317,520 infections and 694,713 deaths
269
in 188 countries and
territories.
88, 520, 616
There are 4,718,249 confirmed COVID-19 cases across all 50 US states, with 155,478 deaths.
269
• Initial high-quality estimates of human transmissibility (R
0
) range from 2.2 to 3.1,
376, 445, 486, 634, 669
though recent estimates
suggest that early transmission rates were higher.
506
Transmission rates can vary substantially among neighboring
populations.
209, 597
The majority of new infections come from relatively few infectious individuals.
12, 167
• SARS-CoV-2 spreads through close contact and droplet transmission,
94
with fomite transmission
272
and aerosol
transmission likely.
22, 65, 219, 408
On 7/9/2020, the WHO acknowledged that aerosol transmission is plausible, and could not
be ruled out in all cases.
618
Both aerosolized viral RNA
222, 353
and infectious virus have been found in patient rooms.
508
• Modeling from the Diamond Princess Cruise Ship outbreak suggests that long-distance aerosol transmission (>2 m) was
more important than large droplet or fomite transmission, though results were highly dependent on assumptions
regarding the infectious dose in the upper vs. lower respiratory tract.
35
• SARS-CoV-2 replicates in the upper respiratory tract,
245
and infectious virus is detectable in throat and lung tissue for at
least 8 days.
621
Respiratory fluids from severely ill patients contained higher viral RNA loads than respiratory fluids from
mildly ill patients,
673
but similar viral RNA loads have been found in asymptomatic and symptomatic individuals.
319
• Children <5 years old have at least as much – and possibly much more – viral RNA in their upper respiratory tract as
children > 5 years old and adults.
238
Selection bias is a possible concern, though, as only symptomatic children were
tested, and younger children may have been symptomatic because of their high viral loads.
• In a Georgia summer camp, 260 of 344 tested attendees (campers and staff) tested positive for SARS-CoV-2 RNA, despite
all attendees having provided evidence of negative diagnostic tests within twelve days prior to attendance.
555
Children
below 10 had the highest rates of SARS-CoV-2 positivity, which decreased with increasing age.
555
In a separate study, older
children (>10 years old) transmitted SARS-CoV-2 as frequently as adults, while younger children (<10 years old)
transmitted infection less often.
447
These estimates, however, were generated during school closures, and may
underestimate the risk of infection from school-age children.
• SARS-CoV-2 may be spread by conversation and exhalation
8, 328, 509, 544
in indoor areas such as restaurants.
338
Clusters are
often associated with large gatherings indoors,
321, 446
including bars, restaurants, and music festivals.
656
• Experimentally infected ferrets were able to transmit SARS-CoV-2 to other ferrets through the air (ferrets in an adjacent
enclosure, separated by 10 cm).
482
Similar results have been documented in transgenic mice.
40
• Vertical transmission (mother to infant) has been confirmed
583
but appears rare.
107, 112, 115, 518, 563, 646, 652
• SARS-CoV-2 RNA has been found in semen from both clinically symptomatic and recovered cases,
329
but the potential for
sexual transmission is unknown. Infectious SARS-CoV-2 has also been cultured from patient feces
639
and urine.
551
Individuals can transmit SARS-CoV-2 to others before they have symptoms.
• Individuals may be infectious for 1-3 days prior to symptom onset.
30, 602
Pre-symptomatic
57, 298, 543, 550, 643, 672
or
asymptomatic
38, 251, 365
patients can transmit SARS-CoV-2.
356
At least 12% of all cases are estimated to be due to
asymptomatic transmission.
159
Between 23-56% of infections may be caused by pre-symptomatic transmission.
82, 237, 350
Individuals are most infectious before symptoms begin and within 5 days of symptom onset,
114
and pre-symptomatic
individuals contribute to environmental contamination.
270
• A
ttack rates of the virus are higher within households than casual contacts.
69, 527
The attack rate ranges from 11%,
50
16%,
334
and 38%
492
of household members, with rates increasing with age.
492
The attack rate for children is low in
households with an adult COVID-19 case.
541, 657
Individuals transmit infection to household members before they exhibit
symptoms at least as often as they do after symptoms develop.
273
Transmission rates are high in confined areas .
504
Undetected cases play a major role in transmission, and most cases are not reported.
661
• Models suggest up to 86% of early COVID-19 cases in China were undetected, and these infections were the source for
79% of reported cases.
333
Models estimate that the true number of cases may be approximately 11 times greater than the
reported number of cases in the UK,
648
and 5 to 10 times greater than the reported number of cases in the US.
274, 500, 534
Individuals who have recovered clinically, but test positive, appear unable to transmit COVID-19.
285
What do we need to know?
The relative contribution of different routes of transmission, such as close contact and droplet transmission versus
aerosol transmission and contaminated objects and surfaces (fomites), is unknown and requires additional research.
• Is sexual transmission possible?
• Is it possible to determine the route by which someone became infected by the clinical presentation or progression of
disease?
• How infectious are young children compared to adults?
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Host Range – How many species does it infect? Can it transfer from species to species?
What do we know?
SARS-CoV-2 is closely related to other coronaviruses circulating in bats in Southeast Asia. Previous coronaviruses have
passed through an intermediate mammal host before infecting humans, but the presence or identity of the SARS-CoV-2
intermediate host is unknown. Current evidence suggests a direct jump from bats to humans is plausible.
58
• Early genomic analysis indicates similarity to SARS-CoV-1,
677
with a suggested bat origin.
126, 677
• Positive samples from the South China Seafood Market strongly suggests a wildlife source,
96
though it is possible that the
virus was circulating in humans before the disease was associated with the seafood market.
43, 127, 641, 653
• Analysis of SARS-CoV-2 genomes suggests that a non-bat intermediate species is responsible for the beginning of the
outbreak.
489
The identity of the intermediate host remains unknown.
337, 344, 346
• Viruses similar to SARS-CoV-2 were present in pangolin samples collected several years ago,
312
and pangolins positive for
coronaviruses related to SARS-CoV-2 exhibited clinical symptoms such as cough and shortness of breath.
336
Additionally,
there is evidence of vertical transmission in pangolins, suggesting circulation in natural populations.
336
• However, a survey of 334 pangolins did not identify coronavirus nucleic acid in ‘upstream’ market chain samples,
suggesting that positive samples from pangolins may be the result of exposure to infected humans, wildlife or other
animals within the wildlife trade network. These data suggest that pangolins are incidental hosts of coronaviruses.
322
Additional research is needed to identify whether pangolins are a natural host of SARS-COV-2-related coronaviruses.
SARS-CoV-2 uses the same receptor for cell entry as the SARS-CoV-1 coronavirus that circulated in 2002/2003.
• Experiments show that SARS-CoV-2 Spike (S) receptor-binding domain binds the human cell receptor (ACE2) stronger than
SARS-CoV-1,
629
potentially explaining its high transmissibility. The same work suggests that differences between SARS-
CoV-2 and SARS-CoV-1 Spike proteins may limit the therapeutic ability of SARS antibody treatments.
629
• Modeling of SARS-CoV-2 Spike and ACE2 proteins suggests that SARS-CoV-2 can bind and infect human, bat, civet,
monkey and swine cells.
587
Host range predictions based on structural modeling, however, are difficult,
194
and additional
animal studies are needed to better define the host range.
• In vitro experiments suggest a broad host range for SARS-CoV-2, with more than 44 potential animal hosts, based on viral
binding to species-specific ACE2 orthologs.
351
The host range is predicted to be limited primarily to mammals.
• Genetic and protein analysis of primates suggests that African and Asian primates are likely more susceptible to SARS-
CoV-2, while South and Central American primates are likely less susceptible.
392
Identifying the SARS-CoV-2 host range is
important for identifying animal reservoirs.
• Changes in proteolytic cleavage of the Spike protein can also affect cell entry and animal host range, in addition to
receptor binding.
394
To date, ferrets, mink, hamsters, cats, deer mice, and primates have been shown to be susceptible to SARS-CoV-2
infection. It is unknown whether these animals can transmit infection to humans.
• Animal model studies suggest that Golden Syrian hamsters, primates, and ferrets may be susceptible to infection.
100, 291
In
the Netherlands, farmed mink developed breathing and gastrointestinal issues, which was diagnosed as SARS-CoV-2
infection.
1
It is thought that an infected mink has transmitted SARS-CoV-2 to a human.
307
Golden Syrian hamsters are able
to infect other hamsters via direct contact and close quarters aerosol transmission.
533
• Domestic cats are susceptible to infection with SARS-CoV-2 (100,000-520,000 PFU via the intranasal route
530
or a
combination of routes
224
), and can transmit the virus to other cats via droplet or short-distance aerosol.
530
Dogs exposed
to SARS-CoV-2 produced anti-SARS-CoV-2 antibodies
59
but exhibited no clinical symptoms.
530, 538
• Deer mice can be experimentally infected with SARS-CoV-2 via intranasal exposure to 10
5
TCID
50
of virus, and are able to
transmit the virus to uninfected deer mice through direct contact.
215
Their capacity as a reservoir species is unknown.
• Wild cats (tigers)
601
can be infected with SARS-CoV-2, although their ability to spread to humans is unknown.
377, 666
Two
cases of SARS-CoV-2 infection have been confirmed in pet domestic cats.
87
• Ducks, chickens, and pigs remained uninfected after experimental SARS-CoV-2 exposure (30,000 CFU for ducks and
chickens, 100,000 PFU for pigs, all via intranasal route).
530
There is currently no evidence that SARS-CoV-2 infects
livestock.
258
• Pigs and chickens were not susceptible to SARS-CoV-2 infection when exposed to an intranasal dose of 10
5
TCID
50
(~70,000 PFU).
515
Fruit bats and ferrets were susceptible to this same exposure.
515
•
Chicken, turkey, duck, quail, and geese were not susceptible to SARS-CoV-2 after experimental exposures.
549
What do we need to know?
The best animal model for replicating human infection by various routes is still unidentified.
• What is the intermediate host(s), if any?
• Can infected animals transmit to humans (e.g., pet cats to humans)?
• Can SARS-CoV-2 circulate in animal reservoir populations, potentially leading to future spillover events?
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Incubation Period – How long after infection do symptoms appear? Are people infectious during this time?
What do we know?
The majority of individuals develop symptoms within 14 days of exposure. For most people, it takes at least 2 days to
develop symptoms, and on average symptoms develop 5 days after exposure. Incubating individuals can transmit disease
for several days before symptom onset. Some individuals never develop symptoms but can still transmit disease.
• The incubation period of COVID-19 is between 5
318
and 6
603
days.
647
Fewer than 2.5% of infected individuals show
symptoms sooner than 2 days after exposure.
318
• There is evidence that younger (<14) and older (>75) individuals have longer COVID-19 incubation periods, creating a U-
shaped relationship between incubation period length and patient age.
299
• Individuals can test positive for COVID-19 even if they lack clinical symptoms.
38, 99, 220, 562, 672
• Individuals can be infectious while asymptomatic,
94, 494, 562, 672
and asymptomatic and pre-symptomatic individuals have
similar amounts of virus in the nose and throat compared to symptomatic patients.
30, 290, 681
• Peak infectiousness may be during the incubation period, one day before symptoms develop.
237
Infectious virus has been
cultured in patients up to 6 days before the development of symptoms.
30
• Infectious period is unknown, but possibly up to 10-14 days.
6, 333, 520
• Asymptomatic individuals are estimated to be infectious for a median of 9.5 days.
249
• On average, there are approximately 4
159
to 7.5
332
days between symptom onset in successive cases of a single
transmission chain (i.e., the serial interval). Based on data from 339 transmission chains in China, the mean serial interval
is between 4.6
647
and 5.29 days.
158
• The serial interval of COVID-19 has declined substantially over time as a result of increased case isolation,
18
meaning
individuals tend to transmit virus for less time.
• Children are estimated to shed virus for 15 days on average, with asymptomatic individuals shedding virus for less time
(11 days) than symptomatic individuals (17 days).
362
• Most hospitalized individuals are admitted within 8-14 days of symptom onset.
675
• Asymptomatic and mildly ill patients who test positive for SARS-CoV-2 take less time to test negative than severely ill
patients.
324
• Patients infected by asymptomatic or young (<20 years old) individuals may take longer to develop symptoms than those
infected by other groups of individuals.
603
• Viral RNA loads in the upper respiratory tract tend to peak within a few days of symptom onset and become undetectable
approximately two weeks after symptoms begin.
585
The duration of the infectious period is unknown,
585
though patients
can test positive for SARS-CoV-2 viral RNA for extended periods of time, particularly in stool samples.
What do we need to know?
While the incubation period is well-characterized overall, the duration of infectivity is poorly understood in different
patient populations (e.g., age, disease severity).
• What is the average infectious period during which individuals can transmit the disease?
• How infectious are asymptomatic and pre-symptomatic individuals compared to mildly, moderately, or severely ill
patients?
• How soon can asymptomatic patients transmit infection after exposure?
•
Does the incubation period correlate with disease severity or exposure dose?
REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
Updated 8/4/2020
CLEARED FOR PUBLIC RELEASE 7
Clinical Presentation – What are the signs and symptoms of an infected person?
What do we know?
Most symptomatic cases are mild, but severe disease can be found in any age group.
4
Older individuals and those with
underlying conditions are at higher risk of serious illness and death.
• Most symptomatic COVID-19 cases are mild (81%, n=44,000 cases).
562, 619
Initial COVID-19 symptoms include fever (87.9%
overall, but only 44-52% present with fever initially),
27, 220
cough (67.7%),
220
fatigue, shortness of breath, headache, and
reduced lymphocyte count.
95, 103, 250
Chills, muscle pain, headache, sore throat, and loss of taste or smell
453, 645
are also
possible COVID-19 symptoms.
95
GI symptoms are present in approximately 9% of patients,
491
but may be more common in
severe cases.
282
Neurological symptoms such as agitation,
239
loss of coordination,
378
and stroke
579
may present with
COVID-19,
451
may be more common in severe cases,
134
and neurological involvement (e.g., encephalitis) can be seen in
brain tissue on autopsy.
584
Ocular issues
636
and skin lesions
195
may also be symptoms of COVID-19.
60
There are concerns
that COVID-19 can lead to new-onset diabetes.
496
• Complications include acute respiratory distress syndrome (ARDS, 17-29% of hospitalized patients, leading to death in 4-
15% of cases),
111, 250, 589
pneumonia,
440
cardiac injury (20%),
531
secondary infection, kidney damage,
28, 547
arrhythmia,
sepsis, stroke (1.6% of hospitalized patients),
396
and shock.
220, 250, 589, 675
Most deaths are caused by respiratory failure or
respiratory failure combined with heart damage.
495
Half of hospitalized COVID-19 patients show abnormal heart scans.
161
• Approximately 15% of hospitalized patients are classified as severe,
220, 562
and approximately 5% of patients are admitted
to the ICU.
220, 562
Patient deterioration can be rapid.
214
The survival rate of patients requiring mechanical ventilation varies
widely (e.g., 35%,
257
70%,
33
75.5%
483
). Higher SARS-CoV-2 viral RNA load on admission (measured by RT-PCR cycle
threshold values) have been associated with greater risk of intubation and death.
370
Approximately 42% of ICU patients
die from COVID-19, though the rate is variable across studies.
29
• COVID-19 symptoms like fatigue and shortness of breath commonly persist for weeks
561
to months
80
after initial onset.
• US deaths due to COVID-19 have been underreported by up to 35% (March – April).
625
In New York City, up to 5,293 (22%)
of period-specific excess deaths are unexplained and could be related to the pandemic.
430
• Recent evidence suggests that SARS-CoV-2 may attack blood vessels in the lung, leading to clotting complications and
ARDS.
11, 580
Clotting may be associated with severely ill COVID-19 patients
293
and those with ARDS,
134
and affects multiple
human organ systems.
474
COVID-19 patients should be monitored for possible thrombosis.
327
In autopsies of several
COVID-19 patients, there was evidence of diffuse alveolar damage (DAD)
512
and increased blood clotting.
514
Approximately 40% of cases are asymptomatic.
433
• Between 16% and 58% of patients are asymptomatic throughout the course of their infection.
71, 319, 324, 404, 423, 556, 568
The case fatality rate is unknown, but individuals >60 and those with comorbidities are at elevated risk of death.
562, 675
• Cardiovascular disease, obesity,
13, 459
hypertension,
664
diabetes, and respiratory conditions all increase the CFR.
562, 675
Hypertension and obesity are common in the US
197
and contribute to mortality.
28, 443
• The CFR increases with age (data from China and Italy): 0-9 years < 0.1%, 10-19 years = 0-0.2%, 20-29 years = 0-0.2%, 30-
39 years = 0.2-0.3%, 40-49 years = 0.4%, 50-59 years = 1.0-1.3%, 60-69 years = 3.5-3.6%, 70-79 years = 8.0-12.8%, >80
years = 14.8-20.2%.
431
Minority populations are disproportionately affected by COVID-19.
• B
lack, Asian, and Minority Ethnic (BAME) populations acquire SARS-CoV-2 infection at higher rates than other groups
189, 439
and are hospitalized
197, 464
and die disproportionately.
241, 400
Hospitalization rates in Native American, Hispanic, and Black
populations are 4-5 times higher than those in non-Hispanic white populations.
90
In the US, Hispanic and Black patients
tend to die at younger ages than white patients.
628
• Pregnant women develop severe symptoms at similar
110, 280, 659
or slightly higher rates than the general population.
165
Severe symptoms in pregnant women may be associated with underlying conditions such as obesity.
354
There is some
evidence that rates of stillbirth and preterm delivery have increased during the COVID-19 pandemic,
393
though these
instances have not been conclusively linked to maternal COVID-19 infection.
289
More work is needed.
Children are susceptible to COVID-19,
155
though generally show milder
105, 361
or no symptoms.
• Between 21-28% of children (<19 years old) may be asymptomatic.
361, 448, 466
Most symptomatic children present with mild
or moderate symptoms,
213, 448
with few exhibiting severe or clinical illness.
633
• Severe symptoms in children are possible
349
and more likely in those with complex medical histories
525
or underlying
conditions such as obesity.
658
Infants are susceptible to illness,
156
and infant deaths have been recorded.
67, 361
• The WHO
615
and US CDC
268
have issued case definitions for a rare condition in children (termed Pediatric Multi-System
Inflammatory Syndrome)
207
linked to COVID-19 infection.
487
The prevalence of this condition is unknown.
What do we need to know?
Both the duration and prevalence of debilitating symptoms that inhibit an individual’s ability to function are not
understood. The true case-fatality rate is unknown.
• How does the asymptomatic fraction vary across age groups?
• How does COVID-19 contribute to pregnancy complications?
•
How long, on average, are affected individuals unable to perform normal jobs and responsibilities?
REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
Updated 8/4/2020
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Protective Immunity – How long does the immune response provide protection from reinfection?
What do we know?
Infected patients show productive immune responses, but the duration of any protection is unknown. Initial evidence
suggests that the neutralizing antibody response does not last more than a few months, though this varies by severity.
• In a small comparison series (n=74), both asymptomatic and mildly symptomatic individuals showed reductions in IgG
antibody levels 8 weeks after infection.
356
The half-life of one antibody (IgG) has been estimated at 36 days in COVID-19
patients.
256
The correlation to long-term immunity is unknown.
• In a larger study (n=175), most patients developed neutralizing antibodies within 10-15 days after disease onset. Elderly
patients had significantly higher neutralizing antibody titers than younger patients.
631
In a separate study, elderly patients
also showed higher viral loads than younger patients.
566
Approximately half of infected individuals on an aircraft carrier
developed detectable neutralizing antibody responses to SARS-CoV-2.
453
• In a study of 285 COVID-19 patients, 100% developed antiviral immunoglobulin-G within 19 days of symptom onset.
355
The
neutralizing ability of these antibodies was not tested.
355
In a smaller in vitro study (n=23 patients), levels of antibodies
(immunoglobulins M and G) were positively correlated with SARS-CoV-2 neutralizing ability.
566
In a smaller study of 44
patients, plasma from 91% demonstrated SARS-CoV-2 neutralizing ability, appearing ~8 days after symptom onset.
554
• A small subset of COVID-19 patients in China (8%) did not develop a serological response to infection, though the potential
for reinfection in these patients is unknown.
631
Similarly, between 16.7% (for IgG) and 51.7% (for IgM) of patients in a
separate study did not exhibit any immune response, in terms of production of those two types of antibodies.
558
• In a study of 221 COVID-19 patients, levels of two types of antibodies (IgM and IgG) were not associated with the severity
of symptoms.
248
However, in a smaller study, patients with severe disease showed stronger antibody responses than those
with non-severe symptoms.
566
Severely ill individuals develop higher levels of neutralizing antibodies
343
and greater T-cell
response frequencies
521
than mildly symptomatic or asymptomatic individuals.
• The early recovery phase of COVID-19 patients is characterized by inflammatory immune response.
607
• Two studies identified key components of the adaptive immune system (CD4
+
T cells) in the majority of recovered COVID-
19 patients, and these cells reacted to SARS-CoV-2 Spike protein.
62, 217
These studies also identified Spike protein
responses in CD4
+
T cells of ~30-40% of unexposed patients,
217
suggesting some cross-reactivity between other circulating
human coronaviruses and SARS-CoV-2.
62, 217
Long-lasting T-cell responses have been seen in SARS-CoV-1 patients, and T-
cell cross-reactivity reactivity between other coronaviruses and SARS-CoV-2 suggest additional immune protection.
320
The
strength and duration of any T-cell derived protection is currently unknown.
• Children do not appear to be protected from SARS-CoV-2 infection or severe COVID-19 symptoms by historical exposure
to seasonal coronaviruses.
523
Currently, there is no evidence that recovered patients can be reinfected with SARS-CoV-2.
• Two studies suggest limited reinfection potential in macaques. In the first, two experimentally infected macaques were
not capable of being reinfected 28 days after their primary infection resolved.
148
In the second, rhesus macaques exposed
to different doses of SARS-CoV-2 via the intranasal and intratracheal routes (10
4
– 10
6
PFU) developed pathological
infection and were protected upon secondary challenge 35 days after initial exposure.
102
• Ferrets infected with 10
2
-10
4
PFU were protected from acute lung injury following secondary challenge with SARS-CoV-2
28 days after initial exposure, but they did exhibit clinical symptoms such as lethargy and ruffled fur.
501
Cats exposed to
SARS-CoV-2 after initial recovery did not shed virus, suggesting some protective effect of primary infection.
59
• According to the WHO, there is no evidence of re-infection with SARS-CoV-2 after recovery.
317
• Patients can test positive via PCR for up to 37 days after symptoms appear,
675
and after recovery and hospital discharge.
313
The strength and duration of any immunity after initial COVID-19 infection is unknown.
19, 612
• In a small study (n=65), 95% of patients developed neutralizing antibodies within 8 days of symptom onset,
522
but
neutralizing antibody titers declined substantially when assayed after 60 days.
522
Individuals with more severe infections
developed higher neutralizing antibody levels that persisted longer than those with asymptomatic or mild infections.
522
Protective antibody immunity may depend on the severity of initial infection, and may not persist for more than a few
months, which is consistent with observations in other human coronaviruses.
• In a 35-year study of 10 men, immunity to seasonal coronaviruses waned after one year.
162
Reinfection was observed
between one and three years after initial infection.
162
•
Previous studies on coronavirus immunity suggest that neutralizing antibodies may wane after several years.
74, 635
What do we need to know?
As the pandemic continues, long-term monitoring of immune activity and reinfection status is needed.
• How long does the immune response last? Is there evidence of waning immunity?
• Can humans become reinfected, or are reports of reinfection vestiges from initial infection?
• How do different components of the immune response contribute to long-term protection?
•
How does initial disease severity affect the type, magnitude, and timing of any protective immune response?
REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
Updated 8/4/2020
CLEARED FOR PUBLIC RELEASE 9
Clinical Diagnosis – Are there tools to diagnose infected individuals? When during infection are they
effective?
What do we know?
Diagnosis of COVID-19 is based on symptoms consistent with COVID-19, PCR-based testing of active cases, and/or the
presence of SARS-CoV-2 antibodies in individuals. Confirmed cases are still underreported.
234
Testing is available to
individuals with or without a doctors referral based on state and local guidelines.
• The US CDC has expanded testing criteria, and recommends testing symptomatic individuals, asymptomatic individuals
with known exposures, and those necessary for public health surveillance.
92
• PCR protocols and primers have been widely shared internationally.
85, 129, 332, 529, 611, 617
• A combination of pharyngeal (throat) RT-PCR and chest tomography is recommended,
479
particularly when results from
either test are inconclusive.
303
A single throat swab detects 78.2% of infections, and duplicate tests identify 86.2% of
infections.
479
PCR tests using saliva are at least as effective as those using nasopharyngeal swabs.
108, 638
Evaluation of seven
RT-PCR diagnostic test kits in China showed high overall accuracy, but some variability among test kits.
588
• Nasal and pharyngeal swabs may be less effective as diagnostic specimens than sputum and bronchoalveolar lavage
fluid,
594
although evidence is mixed.
621
Combination RT-PCR and serology (antibody) testing may increase the ability to
diagnose patients with mild symptoms, or identify patients at higher risk of severe disease.
671
Assays targeting antibodies
against the nucleocapsid protein (N) instead of the Spike protein (S) of SARS-CoV-2 may improve detection.
68
• The timing of diagnostic PCR tests impacts results. The false-negative rate for RT-PCR tests is lowest between 7 and 9 days
after exposure, and PCR tests are more likely to give false-negative results before symptoms begin (within 4 days of
exposure) and more than 14 days after exposure.
310
The role of temporal changes in immunological response and variation
of diagnostic test results based on symptom severity warrants additional study.
300
• Diagnostic test results from at-home, mid-nasal swabs were comparable to clinician-conducted nasopharyngeal swabs,
though false-negatives were observed in individuals with low viral titer.
382
• Asymptomatic individuals have a higher likelihood of testing negative for a specific antibody (IgG) compared to
symptomatic patients, potentially due to lower viral loads (as measured by RT-PCR).
606
• The FDA issued an Emergency Use Authorization for an antigen-based diagnostic assay, limited to use in certified
laboratories (clinical laboratory improvement amendments, CLIA).
172
• The FDA released an Emergency Use Authorization enabling laboratories to develop and use tests in-house for patient
diagnosis.
177
Tests from the US CDC are available to states.
85, 94
Rapid test kits have been produced by universities and
industry.
48, 54, 137, 175, 582
Home tests are being developed, though they cannot be used for diagnosis and have not been
approved by the FDA.
416-417, 444
The US CDC is developing serological tests to assess SARS-CoV-2 exposure prevalence.
278
• The CRISPR-Cas12a system is being used to develop fluorescence-based COVID-19 diagnostic tests.
253
• Immunological indicators
36, 166, 236, 252, 461, 552, 590
and fasting blood glucose levels
593
may help differentiate between severe
and non-severe cases, and decision-support tools for diagnosing severe infections have been developed.
632
• Individuals who test positive again after hospital discharge were more likely to have had short hospital stays, be younger
than 18, and have had mild or moderate COVID-19 symptoms.
655
Validated serological (antibody) assays are being used to help determine who has been exposed to SARS-CoV-2.
Serological evidence of exposure does not indicate immunity.
• Repeated serological testing is necessary to identify asymptomatic
463
and other undetected patients.
507
Exclusively testing
symptomatic healthcare workers is likely to exclude a large fraction of COVID-19 positive personnel.
546
• Research has shown high variability in the ability of tests (ELISA
429
and lateral flow assays) by different manufacturers to
accurately detect positive and negative cases (sensitivity and specificity, respectively).
316, 608
The FDA has excluded several
dozen serological diagnostic assays based on failure to conform to updated regulatory requirements.
174
Researchers have
designed a standardized ELISA procedure for SARS-CoV-2 serology samples.
294
• Meta-analysis suggests that lateral flow assays (LFIA) are less accurate than ELISA or chemiluminescent methods (CLIA),
but that the target of serological studies (e.g., IgG or IgM) does not affect accuracy.
340
Most reported serological studies
suffer from bias related to selected patients, limiting their applicability to general populations.
340
• The false-positive rate of serological assays may account for a substantial portion of reported exposures,
46
particularly if
the true proportion of positive patients is low.
What do we need to know?
In general, PCR tests appear to be sensitive and specific, though confirmation via chest CT is recommended. The
sensitivity and specificity of serological testing methods is variable.
• How many serological tests need to be done to obtain an accurate picture of underlying exposure?
• What fraction of exposed individuals fail to develop antibody responses that are the target of serological assays?
• What is the relationship between disease severity and the timing of positive serological assays?
REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
Updated 8/4/2020
CLEARED FOR PUBLIC RELEASE 10
Medical Treatments – Are there effective treatments?
What do we know?
Treatment for COVID-19 is primarily supportive care,
220, 381
and no single standard of care exists. Drug trials are ongoing.
Remdesivir shows promise for reducing symptom duration
45
and mortality
205
in humans.
• Remdesivir can reduce the duration of symptoms in infected individuals, from 15 days to 11 days on average (compared to
controls).
45
Remdesivir received an Emergency Use Authorization from FDA
422
and is recommended for use in the EU.
620
• A press release reports that remdesivir reduced 14-day mortality in COVID-19 patients across racial and ethnic groups
when compared to standard of care alone, though concerns exist regarding the appropriate control group.
205
• A randomized clinical trial of remdesivir found no significant clinical benefits (n=237 patients), but the trial ended early.
599
Hydroxychloroquine is associated with risk of cardiac arrhythmias and provides limited to no clinical benefit.
120
• Hydroxychloroquine does not benefit mild-moderate COVID-19 cases,
84
was associated with adverse cardiac events in
severely ill patients,
287
and showed no efficacy as treatment or pre-exposure prophylaxis in non-human primates.
374
Several large clinical trials have stopped administering hydroxychloroquine due to lack of efficacy.
231, 242, 418
Other existing
studies have found no benefit of hydroxychloroquine (with or without azithromycin)
20, 104, 109, 200, 244, 296, 369, 371, 540, 559
as well
as cardiac side effects
47, 121, 203, 266, 372, 395, 511
and elevated risk of mortality.
369, 488
Hydroxychloroquine does not protect
individuals from infection either before
201
or after exposure.
61, 402
The FDA revoked its EUA for the drug on 6/15/20.
171
• Initial results purporting benefits of hydroxychloroquine and azithromycin
199
have been called into question. One small
clinical trial (n=62) suggests that hydroxychloroquine can reduce recovery time compared to control group,
113
but lacks key
methodological details.
113
A small retrospective study (n=48) found benefits to hydroxychloroquine, though details on
patient study population selection were limited.
651
A larger retrospective study (n=2,541) found that hydroxychloroquine
reduced mortality.
31
However, concerns still exist over the patient selection protocol and the time-course of the study.
323
Dexamethasone may significantly reduce mortality in severely ill and ventilated patients.
• Dexamethasone is associated with substantial reductions in mortality for patients receiving mechanical ventilation, and
smaller benefits for those receiving supplemental oxygen.
243
Dexamethasone did not reduce mortality in patients who did
not need oxygen or mechanical ventilation.
243
Other pharmaceutical interventions are being investigated.
• Several studies of methylprednisolone suggest clinical benefits in severely ill patients (e.g., reduction in ventilator use,
mortality), but have not been tested separately from other standard-of-care treatments.
130, 375, 497, 505, 510
Providing anti-
inflammatory treatments in the first few days of hospital admission may be beneficial.
399
Other corticosteroids are also
being studied and show some evidence of clinical improvement (ventilator-free days),
122
though the benefits of
glucocorticoids may depend heavily on patient inflammation (beneficial if high, detrimental if low).
286
• There is evidence for efficacy of several interferon-based treatments, including interferon beta-1b,
255
interferon beta-1a,
141
and interferon alpha-2b.
456
In these studies, interferons were generally administered with other treatments. A press
release suggests that an inhaled interferon beta reduced the need for mechanical ventilation.
462
• Observational studies have found benefits of tocilizumab
182, 233, 493, 542, 642
in severe COVID-19 patients,
76
and Phase II trial
results show limited reductions in mortality.
458
Tocilizumab efficacy may depend on C-reactive protein levels
192, 380
and may
be more beneficial when administered early.
212, 271, 288, 412
Tocilizumab has been associated with reduced risk of severe
illness
25, 295
and death,
412
but also an increased risk of secondary (non-COVID-19) infection.
221
Many studies of tocilizumab
suffer from non-random patient assignments and the confounding influence of concomitant treatments, despite showing
some clinical benefits.
208, 235, 409, 450, 472, 545, 567, 569
Randomized clinical trials are needed. Other trials have found benefits of
itolizumab
52
and bevacizumab
441
but no consistent benefits from sarilumab.
476
• Limited, preliminary evidence supports the efficacy of favipiravir,
106
intravenous immunoglobulin,
78
baricitinib,
75
ivermectin,
470
leflunomide,
247
pidotimod,
571
and colchicine.
513
Lenzilumab, a monoclonal antibody, showed benefits to
oxygenation levels in severely ill patients (n=12).
560
There is no clinical benefit from combination ritonavir/lopinavir.
77, 216,
339
The kinase inhibitor ruxolitinib may help to reduce symptom duration and mortality.
79
The anticoagulant heparin is
being used to mitigate risks of pulmonary embolism.
166
Systemic anticoagulant use was associated with reduced mortality
rates in severely ill patients.
442
Anakinra has showed some evidence of clinical benefit in small observational studies.
83
• T
rials are ongoing to evaluate the efficacy of a blood cleaning device used to reduce inflammatory neutrophils.
650
• Passive antibody therapy (convalescent serum)
81
is being given to patients,
176
appears safe,
279
and several small trials (<50
patients) suggest benefits from convalescent patient plasma for infected patients.
168, 348, 368, 379, 503, 526, 528
Some trial data
suggest benefits of plasma in terms of reduced hospitalization time,
10
though evidence is mixed.
153, 204, 331
What do we need to know?
Additional information on treatment efficacy is required, particularly from large randomized clinical trials.
• Do monoclonal antibodies exhibit any efficacy in human trials?
• Do androgen levels in males alter disease severity?
211, 407, 586
•
Can targeting the papain-like protease of SARS-CoV-2 reduce in vivo replication?
532
REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
Updated 8/4/2020
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Vaccines – Are there effective vaccines?
What do we know?
Work is ongoing to develop and produce a SARS-CoV-2 vaccine (e.g., Operation Warp Speed).
42, 225, 228-230, 421
Early results
are being released, but evidence should be considered preliminary until larger trials are completed.
Phase III Trials (testing for efficacy):
• Moderna has begun Phase III trials of its COVID-19 vaccine, which will target 30,000 participants.
406
• University of Oxford’s ChAdOx1 candidate (now called AZD1222) has begun Phase II/III human trials.
437
• Sinovac will begin Phase III trials of its CoronaVac candidate in healthcare professionals.
535
• Sinopharm will begin Phase III trials of its inactivated SARS-CoV-2 vaccine candidate.
41
Phase II Trials (initial testing for efficacy, continued testing for safety):
• CanSino’s Ad5-nCoV adenovirus vaccine candidate has undergone Phase II human trials.
341
China has given approval to
vaccinate members of its military with the product.
347
Phase II trial results showed positive immune responses in most
patients, but also indicated that prior infection with circulating adenoviruses may inhibit vaccine efficacy.
678
• Sinovac reported no severe adverse events among 600 Phase II participants given their CoronaVac candidate (inactivated
virus), and 90% of patients developed neutralizing antibodies 14 days after administration.
537
• Sinopharm reported neutralizing antibody development in all 1,120 participants given its inactivated virus vaccine (two
times, 14 days apart) with no severe adverse events.
342
• Inovio has registered for a Phase II trial of their INO-4800 DNA vaccine candidate.
262
Phase I Trials (initial testing for safety):
• mRNA vaccines developed by several groups are currently being tested in Phase I trials, including CureVac (candidate is
CVnCoV),
135
the Chinese Academy of Military Sciences (ARCoV),
146
BioNTech and Pfizer (BNT162 program),
460
Moderna
(mRNA-1273),
405
and Arcturus (ARCT-021).
26
Data from a Phase I trial of Moderna’s mRNA-1273 candidate suggest that the
vaccine is well-tolerated by human subjects, and induces an antibody response against SARS-CoV-2.
265
Preliminary Phase
I/II results for BioNTech’s BNT162b1 mRNA candidate show mild side effects in low dose groups, and patients generated
neutralizing antibodies at 21 days post vaccination.
414
• Adenovirus-based vaccines from several groups are being tested in Phase I trials, including CanSino (Ad5-nCoV),
679
Johnson and Johnson (Ad.26-COV2-S),
275
the University of Oxford (ChAdOx1, now called AZD1222),
577
and Gamaleya
Research Institute of Epidemiology and Microbiology (Gam-COVID-Vac Lyo).
614
Phase I trial results for the CanSino vaccine
(Ad5-nCoV) showed few severe adverse reactions in humans within 28 days of follow-up and appreciable antibody and T-
cell responses.
679
In Phase I/II trials, the ChAdOx-1 COVID-19 (AZD1222) vaccine showed a tolerable safety profile and
most recipients developed positive T-cell and neutralizing antibody responses.
191
• Several groups have developed heat-inactivated vaccine candidates, including the Chinese Academy of Medical
Sciences,
519
the Beijing Institute of Biological Products,
465
the Wuhan Institute of Biological Products,
637
Immunitor LLC (V-
Sars),
390
and Sinovac Biotech (CoronaVac).
536
Sinovac Biotech has reported that their inactivated virus vaccine (CoronaVac)
shows protective effects in rhesus macaques, particularly at high vaccine doses.
196
• Several groups are developing recombinant subunit vaccines, including Vaxine Pty (Covax-19),
581
Clover
Biopharmaceuticals (SCB-2019),
389
Novavax (NVX-CoV2373),
385
the Chinese Academy of Sciences (RBD-Dimer),
357
and
Medigen Vaccine Biologics (MVC-COV1901).
391
The University of Queensland has started Phase I trials of its UQ vaccine
candidate, which uses Spike protein subunits.
467
• Several groups are testing DNA vaccines in Phase I trials, including Inovio (INO-4800),
261
Genexine (GX-19)
202
and AnGes
(AG0301-COVID19).
24
Results from Inovio’s INO-4800 show no serious adverse side effects and high immunogenicity.
261
• Imperial College London is beginning Phase I/II trials of their RNA vaccine candidate, LNP-nCoVsnRNA.
427
• Shenzhen Geno-Immune Medical Institute is testing its aAPC
388
and lentiviral (LV-SMENP-DC)
386
vaccines.
• Symvivo Corporation (Canada) will begin a Phase I trial of its oral bacTRL-Spike vaccine candidate.
384
• A
ivita will begin a Phase Ib/II clinical trial of its DC-ATA candidate, comprised of dendritic cells and SARS-CoV-2 antigens.
387
• Medicago will begin the Phase I trials of their vaccine, a plant-derived virus-like-particle candidate.
383
• Phase I/II trials are beginning for vaccine candidates from Zydus Cadila (ZyCoV-D, DNA plasmid)
682
and Baharat (Covaxin,
inactivated rabies virus used as carrier for SARS-CoV-2 proteins).
170
• Kentucky BioProcessing will begin Phase I/II trials of their KBP-COVID-19 candidate based on a tobacco plant platform.
53
Non-target vaccines
•
The potential benefits of non-SARS-CoV-2 vaccines, such as Bacillus Calmette-Guerin (BCG), are under investigation.
169, 524
What do we need to know?
Published results from randomized clinical trials (Phase I – III) are needed.
• Safety and efficacy of vaccine candidates in humans, particularly from Phase III trials
• Length of any vaccine-derived immunity
• Evidence for vaccine-derived enhancement (immunopotentiation)
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Non-pharmaceutical Interventions – Are public health control measures effective at reducing spread?
What do we know?
Broad-scale control measures such as stay-at-home orders are effective at reducing transmission.
• Social distancing and other policies are estimated to have reduced COVID-19 spread by 44% in Hong Kong
133
and reduced
spread throughout China,
305, 309, 311, 358, 373, 592
Europe,
198, 284
and the US.
304
Restrictive lockdowns in China are estimated to
have reduced disease transmission within only a few days
680
by reducing contacts.
662
In China, modeling suggests that a
one-day delay in implementing control measures increased the time needed to curtail an outbreak by 2.4 days.
157
In the
US, each day of delay in emergency declarations and school closures was associated with a 5-6% increase in mortality.
649
• Modeling demonstrates that multifaceted restrictions and quarantines in China reduced the R
0
of SARS-CoV-2 from
greater than 3 to less than 1 between January 23 and February 5.
438, 663
Other studies identified large reductions in
transmission due to country lockdowns
190
and other social distancing measures,
246
but showed substantial variation.
190, 246
• A US county-level model found that shelter-in-place orders (SIPOs) and restaurant and bar closures were associated with
large reductions in exponential growth rate of cases.
131
School closures and cancellation of large gatherings had smaller
effects.
131
Similarly, researchers found that a larger number of public health interventions in place was strongly associated
with lower COVID-19 growth rates in the next week.
281
Individual behaviors such as wearing face coverings and practicing
social distancing have been associated with reduced risk of COVID-19 infection.
453
• Mobility
187, 315
and physical contact rates
267
decline after public health control measures are implemented. Mobility
reductions in the US have been associated with significant reductions in COVID-19 case growth.
37
Social distancing and
reductions in both non-essential visits to stores and overall movement distance led to lower transmission rates of SARS-
CoV-2.
411
Travel restrictions delay peak prevalence by only a few days but do not limit epidemic size.
17
• A combination of school closures, work restrictions, and other measures are likely required to effectively limit
transmission.
181, 301
School closures alone appear insufficient.
264, 311
Non-pharmaceutical interventions in China did not
reduce transmission equally across all populations.
438
• Contact tracing to identify infected individuals reduces the amount of time infectious individuals can transmit disease in a
population.
50
Robust contact tracing and case finding may be needed to control COVID-19 in the US, but requires
additional resources.
600
In South Korea, early implementation of rapid contact tracing, testing, and quarantine was able to
reduce the transmission rate of COVID-19.
550
Contact tracing combined with high levels of testing may limit COVID-19
resurgence once initial social distancing policies are relaxed.
16, 183
Contact tracing is likely to be more effective in
combination with measures such as expanded testing and physical distancing.
308
• The effectiveness of social distancing policies depends on income, as higher-income areas were associated with larger
reductions in mobility after stay-at-home orders than lower-income areas.
604
Research is needed to help plan for easing of restrictions. Testing is critical, and synchronized interventions may help.
• Relaxing public health interventions is projected to increase cases and deaths.
138, 574
As of 8/4/2020, 15 US states are
experiencing increases in the average daily rate of new confirmed cases, and 26 US states are experiencing increases in
the average daily rate of new COVID-19 deaths (for the prior 14 days).
426
• In the US, statistical modeling suggests that early school closures resulted in fewer deaths, though school closures were
often implemented in conjunction with other approaches and independent effects are difficult to assess.
32
• Modeling suggests that optimal control policies involve quickly quarantining infected individuals, and that periods of social
distancing or lock-down may be effective in reducing overall exposure from asymptomatic or unconfirmed cases.
570
Testing is critical to balancing public health and economic costs.
570
Rolling interventions, whereby social distancing
measures are put into place every few weeks, may keep healthcare demand below a critical point.
648
Undetected cases,
can lead to elevated risk of re-emergence after restrictions are lifted, highlighting the need for robust testing strategies.
226
• Synchronizing public health interventions and lockdowns across US state lines may reduce the total number of
interventions necessary to eliminate transmission as COVID-19 cases continue to resurge.
498
• Modeling indicates that COVID-19 is likely to become endemic in the US population, with regular, periodic outbreaks, and
that additional social or physical distancing measures may be required for several years to keep cases below critical care
capacity in absence of a vaccine or effective therapeutic.
292
Results depend on the duration of immunity after exposure.
292
• Balancing control measures to maintain R
0
below 1 may be more cost effective than allowing R
0
to increase above 1.
325
• Surveys indicate that the majority of Americans were complying with non-pharmaceutical interventions.
136
In the US,
mask use increased after recommendations from the White House Task force and CDC.
185
What do we need to know?
As different US states have implemented differing control measures at various times, a comprehensive analysis of social
distancing efficacy has not yet been conducted.
• What are plausible options for relaxing social distancing and other intervention measures without resulting in a resurgence
of COVID-19 cases?
• How will broad-scale school re-openings impact disease progression in the US?
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Environmental Stability – How long does the agent live in the environment?
What do we know?
SARS-CoV-2 can persist on surfaces for at least 3 days and on the surface of a surgical mask for up to 7 days depending on
conditions. If aerosolized intentionally, SARS-CoV-2 is stable for at least several hours. The seasonality of COVID-19
transmission is unknown. SARS-CoV-2 on surfaces is inactivated rapidly with sunlight.
SARS-CoV-2 Data
• In simulated saliva on stainless steel surfaces, SARS-CoV-2 exhibits negligible decay over 60 minutes in darkness, but loses
90% of infectivity every 6.8-12.8 minutes, depending on the intensity of simulated UVB radiation levels.
475
• The Department of Homeland Security (DHS) developed a data-based model for SARS-CoV-2 decay on inert surfaces
(stainless steel, ABS plastic and nitrile rubber) at varying temperature and relative humidity. This model estimates virus
decay in the absence of exposure to direct sunlight.
152
• SARS-CoV-2 can persist on plastic and metal surfaces between 3 days (21-23°C, 40% RH)
576
and 7 days (22°C, 65% RH).
Infectious virus can be recovered from a surgical mask after 7 days (22°C, 65% RH).
119
• At room temperature (22°C), SARS-CoV-2 remains detectable (via plaque assay) on paper currency for up to 24 hours, on
clothing for up to 4 hours, and on skin for up to 96 hours.
227
Persistence is reduced with warmer temperatures (37°C), and
enhanced at colder temperatures (4°C).
227
• SARS-CoV-2 persists for less than 3 days within the pages of library books, and for less than 1 day on the exterior of book
and DVD covers.
3
• Both temperature and humidity contribute to SARS-CoV-2 survival on nonporous surfaces, with cooler, less humid
environments facilitating survival (stainless steel, ABS plastic, and nitrile rubber; indoors only; simulated saliva matrix).
55
• Experimental studies using SARS-CoV-2 aerosols (1.78-1.96 μm mass median aerodynamic diameter in artificial saliva
matrix) found that simulated sunlight rapidly inactivates the virus, with 90% reductions in infectious concentration after 6
minutes in high-intensity sunlight (similar to mid-June) and 19 minutes in low-intensity sunlight (similar to early March or
October).
517
In dark conditions, the half-life of aerosolized SARS-CoV-2 is approximately 86 minutes in simulated saliva
matrix.
517
Humidity had no significant impact on aerosolized virus survival.
517
• DHS developed a tool for estimating the decay of airborne SARS-CoV-2 in different environmental conditions.
151
• SARS-CoV-2 has an aerosol half-life of 2.7 hours (without sunlight, particles <5 μm, tested at 21-23°C and 65% RH).
576
• Research suggests SARS-CoV-2 retains infectivity as an aerosol for up to 16 hours in appropriate conditions (23°C, 53% RH,
no sunlight).
179
• SARS-CoV-2 is susceptible to heat treatment (70°C) but can persist for at least two weeks at refrigerated temperatures
(4°C).
119, 473
• SARS-CoV-2 genetic material (RNA) was detected in symptomatic and asymptomatic cruise ship passenger rooms up to 17
days after cabins were vacated. The infectiousness of this material is not known.
410
• In a preliminary study, SARS-CoV-2 stability was enhanced when present with bovine serum albumin, which is commonly
used to represent sources of protein found in human sputum.
449
• No strong evidence exists showing a reduction in transmission with seasonal increase in temperature and humidity.
364
Modeling suggests that even accounting for potential reductions in transmission due to weather and behavioral changes,
public health interventions will still need to be in effect to limit COVID-19 transmission.
397
• A recent study determined that approximately 0.1-1% of initial SARS-CoV-2 inoculated on plastic, stainless steel, glass,
ceramics, wood, latex gloves, cotton, paper, and surgical masks remained after 48 hours.
352
Approximately 0.1% of SARS-
CoV-2 remains in fecal matter after 6 hours.
352
Approximately 0.1% of SARS-CoV-2 in human urine persists after 4-5
days.
352
• RNA in clinical samples collected in viral transport medium is stable at 18-25°C or 2-8°C for up to 21 days without
impacting real-time RT-PCR results.
539
RNA in clinical samples is also stable at 4°C for up for 4 weeks with regard to
quantitative RT-PCR testing (given that the sample contains 5,000 copies/mL). Separately, storage of RNA in phosphate
buffered saline (PBS) at room-temperature (18-25°C) resulted in unstable sample concentrations.
455
• SARS-CoV-2 was detectable on wooden chopsticks used by symptomatic and asymptomatic COVID-19 patients, though
sample sizes were small and no efforts were made to isolate infectious virus.
363
What do we need to know?
Additional testing on SARS-CoV-2, as opposed to surrogate viruses, is needed to support initial estimates of stability. Tests
quantifying infectivity, rather than the presence of viral RNA, are needed.
• Duration of SARS-CoV-2 infectivity via fomites and surfaces (contact hazard)
• Stability of SARS-CoV-2 on PPE (e.g., Tyvek)
•
Stability of SARS-CoV-2 in food (to date, no known infections from contaminated food).
609
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Decontamination – What are effective methods to kill the agent in the environment?
What do we know?
Soap and water, as well as common alcohol and chlorine-based cleaners, hand sanitizers, and disinfectants are effective
at inactivating SARS-CoV-2 on hands and surfaces.
SARS-CoV-2
• Alcohol-based hand rubs are effective at inactivating SARS-CoV-2.
306
• Chlorine bleach (1%, 2%), 70% ethanol and 0.05% chlorhexidine are effective against live virus in lab tests.
118
• Twice-daily cleaning with sodium dichloroisocyanurate decontaminated surfaces in COVID-19 patient hospital rooms.
432
• EPA has released a list of SARS-CoV-2 disinfectants, but most solutions were not tested on SARS-CoV-2.
14
Several solutions
have been tested against SARS-CoV-2 and found to be effective, including those based on para-chloro-meta-xylenol,
salicylic acid, and quaternary ammonium compounds.
260
Two of these products, Lysol Disinfectant Spray (EPA Reg No.
777-99) and Lysol Disinfectant Max Cover Mist (EPA Reg No. 777-127) have specifically been approved for SARS-CoV-2
decontamination.
366
• Oral antiseptic rinses used in pre-procedural rinses for dentistry containing povidone-iodine (PVP-I) are effective
decontaminants of SARS-CoV-2, with 15-sec and 30-sec contact times completely inactivating SARS-CoV-2 at
concentrations above 0.5% in lab tests.
51
• Holder pasteurization of donor breast milk spiked with SARS-CoV-2 rendered the virus inactive, demonstrating that
standard decontamination procedures are effective at reducing risk of COVID-19 risk in infants via donor breast milk.
573
• Efforts are ongoing to create paint-on surfaces that can rapidly inactivate SARS-CoV-2.
44
• Researchers have identified four methods capable of decontaminating N95 respirators while maintaining physical integrity
(fit factor): UV radiation, heating to 70°C, and vaporized hydrogen peroxide (VHP).
184
Ethanol (70%) was associated with
loss of physical integrity.
184
• Hydrogen peroxide vapor (VHP) can repeatedly decontaminate N95 respirators.
484
Devices capable of decontaminating
80,000 masks per day have been granted Emergency Use Authorization from the FDA.
172
• The FDA has issued an Emergency Use Authorization for a system capable of decontaminating ten N95 masks at a time
using devices already present in many US hospitals.
63
• Respirator decontamination methods such as VHP appear to maintain filtration efficiency after repeated decontamination
cycles.
454
Several decontamination methods, including VHP, moist heat, and UVC, are capable of decontaminating N95
respirators for 10-20 cycles without loss of fit or filtration efficiency.
7
Other Coronaviruses
• Chlorine-based
614
and ethanol-based
128
solutions are recommended.
• Heat treatment (56°C) is sufficient to kill coronaviruses,
469, 674
though effectiveness depends partly on protein in the
sample.
469
• 70% ethanol, 50% isopropanol, sodium hypochlorite (0.02% bleach), and UV radiation can inactivate several coronaviruses
(MHV and CCV).
502
• Ethanol-based biocides effectively disinfect coronaviruses dried on surfaces, including ethanol containing gels similar to
hand sanitizer.
254, 622
• Surface spray disinfectants such as Mikrobac, Dismozon, and Korsolex are effective at reducing infectivity of the closely
related SARS-CoV-1 after 30 minutes of contact.
468
• Coronaviruses may be resistant to heat inactivation for up to 7 days when stabilized in stool.
564-565
• Coronaviruses are more stable in matrixes such as respiratory sputum.
160
What do we need to know?
Additional decontamination studies, particularly with regard to PPE and other items in short supply, are needed.
• What is the minimal contact time for disinfectants?
• Does contamination with human fluids/waste alter disinfectant efficacy profiles?
• How effective is air filtration at reducing transmission in healthcare, airplanes, and public spaces?
• Are landfills and wastewater treatment plants effective at inactivating SARS-CoV-2?
•
Is heat or UV decontamination effective to clean N95 masks, respirators and other types of PPE for multi-use?
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PPE – What PPE is effective, and who should be using it?
What do we know?
The effectiveness of PPE for SARS-CoV-2 is currently unknown, and data from other related coronaviruses are used for
guidance. Healthcare workers are at high risk of acquiring COVID-19, even with recommended PPE.
• Healthcare worker illnesses
562
demonstrates human-to-human transmission despite isolation, PPE, and infection
control.
516
Risk of transmission to healthcare workers is high.
478
Contacts with healthcare workers tend to transmit COVID-
19 more often than other casual contacts.
596
Over 50% of US healthcare workers infected with COVID-19 report work in a
healthcare setting as their single source of exposure.
70
Hospital-acquired infection rates fell after introduction of
comprehensive infection control measures, including expanded testing and use of PPE for all patient contacts.
485
Universal
masking policies also reduced the rate of new healthcare worker infections.
595
• A modeling study suggests that healthcare workers are primarily at risk from droplet and inhalation exposure (compared
to contact with fomites), with greater risk while in closer proximity to patients.
277
• Even among healthcare personnel reporting adequate PPE early in the pandemic (March – April), rates of infection were
3.4 times higher in healthcare personnel than the general population.
420
• “Healthcare personnel entering the room [of SARS-CoV-2 patients] should use standard precautions, contact precautions,
airborne precautions, and use eye protection (e.g., goggles or a face shield).”
91
WHO indicates healthcare workers should
wear clean long-sleeve gowns as well as gloves.
613
PPE that covers all skin may reduce exposure to pathogens.
180, 605
• Respirators (NIOSH-certified N95, EUFFP2 or equivalent) are recommended for those dealing with possible aerosols.
614
Additional protection, such as a Powered Air Purifying Respirator (PAPR) with a full hood, should be considered for high-
risk procedures (i.e., intubation, ventilation).
66
• KN95 respirators are, under certain conditions, approved for use under FDA Emergency Use Authorization.
173
On May 7,
the FDA rescinded a number of KN95 models that no longer meet the EUA criteria and are no longer authorized.
178
• A study suggests that P100 respirators with removable filter cartridges have similar filtration efficiency compared to N95
respirators and could plausibly be used if N95 respirators were in short supply.
452
• Particular care should be taken with “duckbill” N95 respirators, which may fail fit tests after repeated doffing.
145
Dome-
shaped N95 respirators also failed fit tests after extended use.
145
Non-medical Masks may be effective at slowing transmission, though data are sparse.
2, 5
• On 4/3/2020, the US CDC recommended wearing cloth face masks in public where social distancing measures are difficult
to maintain.
93
The WHO recommends that the general population wear non-medical masks when in public settings and
when physical distancing is difficult, and that vulnerable populations (e.g., elderly) wear medical masks when close contact
is likely.
610
Infected individuals wearing facemasks in the home before the onset of symptoms was associated with a
reduction in household transmission.
598
• Modeling suggests that widespread use of facemasks is effective at reducing transmission
419
even when individual mask
efficiency is low,
163
though their benefits are maximized when most of the population wears masks.
186
• A meta-analysis of SARS-CoV-1, MERS, and COVID-19 transmission events found evidence that wearing face masks and eye
protection were each associated with lower risk of transmission.
123
N95 respirators were associated with a larger reduction
in transmission risk compared to surgical face masks.
123
Physical distance (>1 or 2 meters) was also associated with lower
transmission risk.
123
In a separate meta-analysis, N95 respirators were found to be beneficial for reducing the occurrence
of respiratory illness in health care professionals including influenza, though surgical masks were similarly effective for
influenza.
428
N95 respirators were associated with large reductions (up to 80%) in SARS-CoV-1 infections.
428
• Surgical face masks, respirators and homemade face masks may prevent transmission of coronaviruses from infectious
individuals (with or without symptoms) to other individuals.
140, 326, 575
Surgical masks were associated with a significant
reduction in the amount of seasonal coronavirus (not SARS-CoV-2) expressed as aerosol particles (<5 μm).
326
• The efficacy of homemade PPE, made with T-shirts, bandanas, or similar materials, is less than standard PPE, but may offer
some protection if no other options are available.
124, 139, 480
Some non-standard materials (e.g., cotton, cotton hybrids) may
be able to filter out >90% of simulant particles >0.3μm,
297
while other materials (e.g., T-shirt, vacuum cleaner bag, towels)
appear to have lower filtration efficacy (~35-62%).
591
Of 42 homemade materials tested, the three with the greatest
filtration efficiencies were layered cotton with raised visible fibers.
660
What do we need to know?
Most PPE recommendations have not been made on SARS-CoV-2 data, and comparative efficacy of different PPE for
different tasks (e.g., intubation) is unknown. Identification of efficacious PPE for healthcare workers is critical due to their
high rates of infection.
• Is COVID-19 transmitted by the aerosol/airborne route (in droplets and particles <5μm), and if so, what is the impact?
• When and how do N95 respirators and other face coverings fail?
• What is the appropriate PPE for first responders? Airport screeners?
• What are proper procedures for reducing spread and transmission rates in medical facilities?
• How effective are homemade masks at reducing SARS-CoV-2 transmission?
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Forensics – Natural vs intentional use? Tests to be used for attribution.
What do we know?
All current evidence supports the natural emergence of SARS-CoV-2 via a bat and possible intermediate mammal species.
• New analysis of SARS-CoV-2 and related SARS-like coronaviruses suggests that SARS-CoV-2 jumped directly from bats to
humans, without the influence of an intermediate 'mixing' host.
58
Pangolin coronaviruses were determined to be more
divergent and had split off from bat coronaviruses much earlier than SARS-CoV-2.
58
Current sampling of pangolin viruses
does not implicate them as a conduit to human adaptation of SARS-CoV-2.
58
These data suggest that SARS-CoV-2 emerged
from circulating bat coronaviruses in SE China/SE Asia and that additional zoonotic emergence of novel coronaviruses
could occur.
• Genomic analysis places SARS-CoV-2 into the beta-coronavirus clade, with close relationship to bat coronaviruses. The
SARS-CoV-2 virus is distinct from SARS-CoV-1 and MERS viruses.
154
• Genomic analysis suggests that SARS-CoV-2 is a natural variant and is unlikely to be human-derived or otherwise created
by “recombination” with other circulating strains of coronavirus.
21, 677
• Comparing genomes of multiple coronaviruses using machine-learning has identified key genomic signatures shared
among high case fatality rate coronaviruses (SARS-CoV-1, SARS-CoV-2, MERS) and animal counterparts.
223
These data
further suggest that SARS-CoV-2 emergence is the result of natural emergence and that there is a potential for future
zoonotic transmission of additional pathogenic strains to humans.
223
• Deletion mutants were identified at low levels in human clinical samples, suggesting that the PRRA furin cleavage site
alone is not fully responsible for human infection, but does confer a fitness advantage in the human host.
624
Additional
whole-genome sequencing in humans would help to confirm this finding.
• Genomic data support at least two plausible origins of SARS-CoV-2: “(i) natural selection in a non-human animal host prior
to zoonotic transfer, and (ii) natural selection in humans following zoonotic transfer.”
21
Both scenarios are consistent with
the observed genetic changes found in all known SARS-CoV-2 isolates.
• Some SARS-CoV-2 genomic evidence indicates a close relationship with pangolin coronaviruses,
623
and data suggest that
pangolins may be a natural host for beta-coronaviruses.
344, 346
Genomic evidence suggests a plausible recombination event
between a circulating coronavirus in pangolins and bats could be the source of SARS-CoV-2.
335, 640
Emerging studies are
showing that bats are not the only reservoir of SARS-like coronaviruses.
667
Additional research is needed.
• There are multiple studies showing that the SARS-CoV-2 S protein receptor binding domain, the portion of the protein
responsible for binding the human receptor ACE2, was acquired through recombination between coronaviruses from
pangolins and bats.
21, 335, 345, 667
These studies suggest that pangolins may have played an intermediate role in the
adaptation of SARS-CoV-2 to be able to bind to the human ACE2 receptor. Additional research is needed.
• A novel bat coronavirus (RmYN02) has been identified in China with an insertion between the S1/S2 cleavage site of the
Spike protein. While distinct from the furin cleavage site insertion in SARS-CoV-2, this evidence shows that such insertions
can occur naturally.
676
• Additionally, “[…] SARS-CoV-2 is not derived from any previously used virus backbone,” reducing the likelihood of
laboratory origination,
21
and “[…] genomic evidence does not support the idea that SARS-CoV-2 is a laboratory construct,
[though] it is currently impossible to prove or disprove the other theories of its origin.”
21
• Work with other coronaviruses has indicated that heparan sulfate dependence can be an indicator of prior cell passage,
due to a mutation in the previous furin enzyme recognition motif.
143
What do we need to know?
Identifying the intermediate species between bats and humans would aid in reducing potential spillover from a natural
source. Wide sampling of bats, other wild animals, and humans is needed to address the origin of SARS-CoV-2.
• What tests for attribution exist for coronavirus emergence?
• What is the identity of the intermediate species?
• Are there closely related circulating coronaviruses in bats or other animals with the novel PRRA cleavage site found in
SARS-CoV-2?
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Genomics – How does the disease agent compare to previous strains?
What do we know?
Current evidence suggests that SARS-CoV-2 accumulates substitutions and mutations at a similar rate as other
coronaviruses. Mutations and deletions in specific portions of the SARS-CoV-2 genome have not been linked to any
changes in transmission or disease severity, though modeling work is attempting to identify possible changes.
• There have been no documented cases of SARS-CoV-2 prior to December 2019. Preliminary genomic analyses, however,
suggest that the first human cases of SARS-CoV-2 emerged between 10/19/2019 – 12/17/2019.
23, 43, 471
• Analysis of more than 7,000 SARS-CoV-2 genome samples provides an estimated mutation rate of 6x10
-4
nucleotides per
genome per year.
578
The same analysis estimates the emergence of SARS-CoV-2 in humans between October and
December 2019.
578
This aligns with the first known human cases in China in early December 2019, in Europe in late
December 2019,
150
circulation in the US (Washington State) in February 2020,
627
and circulation in Mexico in March,
2020.
557
In both California
149
and New York City,
210
phylogenetic evidence supports multiple introductions of SARS-CoV-2
from both inside and outside the US.
• Despite evidence of variation in the genome
98
and areas under positive selection,
73
there are no known associations
between particular mutations and changes in transmission or virulence.
72
Thus, there is currently no evidence of distinct
SARS-CoV-2 phenotypes at this time.
367, 578
Research attempting to define clades or subgroups of SARS-CoV-2 based solely
on genomic features has suffered from limited data
654
and sampling bias.
193
In 94 COVID-19 patients, there was no
association between viral genotype and clinical severity.
668
• Phylogenetic and clinical analysis suggests the D614G mutation in the Spike protein is associated with higher rates of SARS-
CoV-2 transmission, but no change in clinical severity in infected patients.
302
However, it is difficult to determine whether
this mutation is overrepresented due to founder effects, or whether it truly spreads more rapidly than other isolates.
Preliminary experimental evidence suggests that this mutation increases infectivity in cell lines, but additional animal
model work is needed to confirm the effect of this mutation on transmission.
665
• Recent analysis of >16,000 genomes of SARS-CoV-2 suggests two major introductions in the US, one associated with the
West coast and one with the Eastern portion of the US.
413
• A genome-wide association study in humans identified two loci corresponding to higher risk of severe COVID-19 (3p.21.31
and 9q34.2), including one associated with blood type.
164
Individuals with type-O blood showed reduced risk of severe
disease, while individuals with type-A blood showed an increased risk.
164
• SARS-CoV-2 is acquiring nucleotide changes at a rate that suggests the virus is undergoing purifying selection (that the
genome is stabilizing toward a common genome).
630
Low genetic diversity early in the epidemic suggests that SARS-CoV-2
was capable of jumping to human and other mammalian hosts,
630
and that additional jumps into humans from reservoir
species may occur.
• Phylogenetics suggest that SARS-CoV-2 is of bat origin, but is closely related to coronaviruses found in pangolins.
344, 346
• The SARS-CoV-2 Spike protein, which mediates entry into host cells and is the major determinant of host range, is very
similar to the SARS-CoV-1 Spike protein.
359
The rest of the genome is more closely related to two separate bat
359
and
coronaviruses found in pangolins.
346
• An analysis of SARS-CoV-2 sequences from Singapore has identified a large nucleotide (382 bp) deletion in ORF-8.
548
In
Arizona, researchers identified an 81-base pair deletion (removing 27 amino acids) in the ORF-7a protein, indicating that
mutations can be detected by routine sentinel surveillance. The function of these deletions are unknown at this time.
240
• A recent report of virus mutations within patients needs more research.
283
Additional analysis of data suggests the results
may be due to experimental methods.
206, 644
• Structural modeling suggests that observed changes in the genetic sequence of the SARS-CoV-2 Spike protein may enhance
binding of the virus to human ACE2 receptors.
434
More specifically, changes to two residues (Q493 and N501) are linked
with improving the stability of the virus-receptor binding complex.
434
Additionally, structural modeling identified several
existing mutations that may enhance the stability of the receptor binding domain, potentially increasing binding
efficacy.
436
Infectivity assays are needed to validate the potential phenotypic results identified in these studies.
• A key difference between SARS-CoV-2 and other beta-coronaviruses is the presence of a polybasic furin cleavage site in the
Spike protein (insertion of a PRRA amino acid sequence between S1 and S2).
132
•
The US CDC is launching a national genomics consortium to assess SARS-CoV-2 genomic changes over time.
86
What do we need to know?
Research linking genetic changes to differences in phenotype (e.g., transmissibility, virulence, progression in patients) is
needed.
• Are there similar genomic differences in the progression of coronavirus strains from bat to intermediate species to human?
• Are there different strains or clades of circulating virus? If so, do they differ in virulence?
• What are the mutations in SARS-CoV-2 that allowed human infection and transmission?
•
How do viral mutations affect the long-term efficacy of specific vaccines?
REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
Updated 8/4/2020
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Forecasting – What forecasting models and methods exist?
What do we know?
There are many groups focused on forecasting cases, hospitalizations, or fatalities due to COVID-19. Each model has its
own methods and goals, summarized in this section. An evaluation of model performance is beyond the scope of this
document. Assumptions and limitations of each model are detailed at the linked reference.
US CDC forecasting
The US CDC is hosting an ongoing forecasting initiative, and provides ensemble forecasts based on the arithmetic mean of
participating groups.
89
• Columbia University Model: Spatially-explicit SEIR model incorporating contact rate reductions due to social distancing.
Estimates total cases and risk of healthcare overrun.
499
• Imperial College London: Week-ahead forecasts of cases, deaths, and transmissibility (R
0
) at the country-level.
Transmissibility estimates used to forecast incidence based on Poisson renewal process.
49
• Institute of Health Metrics and Evaluation (IHME): Mechanistic SEIR model combined with curve-fitting techniques to
forecast cases, hospital resource use, and deaths at the state and country level.
259
• Los Alamos National Laboratory: Forecasts of state-level cases and deaths based on statistical growth model fit to reported
data. Implicitly accounts for effects of social distancing and other control measures.
314
• Massachusetts Institute of Technology: Mechanistic SEIR model that forecasts cases, hospitalizations, and deaths. Also
includes estimates of intervention measures, allows users to project based on different intervention scenarios (e.g., social
distancing lasting for 3 vs. 4 weeks).
401
• Northeastern University: Spatially explicit, agent-based epidemic model used to forecast fatalities, hospital resource use,
and the cumulative attack rate (proportion of the population infected) for unmitigated and mitigated scenarios.
424
• Notre Dame University: Agent-based model forecasting cases and deaths for Midwest states. Includes effectiveness of
control measures like social distancing.
457
• University of California, Los Angeles: Mechanistic SIR model with statistical optimization to find best-fitting parameter
values. Estimates confirmed and active cases, fatalities, and transmission rates at the national and state levels.
572
• University of Chicago: Age-structured SEIR model that accounts for asymptomatic individuals and the effectiveness of
social distancing policies. Forecasts only for Illinois.
117
• University of Geneva: Country-level forecasts of cases, deaths, and transmissibility (R
0
). Uses statistical models fit to
reported data, not mechanistic models.
188
• University of Massachusetts, Amherst: Aggregation of state and national forecasts to create ensemble model.
477
• University of Texas, Austin: Machine learning model aimed at identifying links between social distancing measures and
changes in death rates. Forecasts fatalities at the state, metropolitan area, and national level. Cannot be used to make
projections beyond initial infection wave.
398
• Youyang Gu: Mechanistic SEIR model coupled with machine learning algorithms to minimize error between predicted and
observed values. Forecasts deaths and infections at the state and national level, including 60 non-US countries. Includes
effects of public health control efforts.
218
• Auquan: SEIR model used to forecast deaths and illnesses at the country and state level.
34
• CovidSim: SEIR model allowing users to simulate the effects of future intervention policies at the state and national level
(US only).
116
Other forecasting efforts:
• University of Georgia: Statistical models used to estimate the current number of symptomatic and incubating individuals,
beyond what is reported (e.g., “nowcasts”). Available at the state and national level for the US.
97
• Hospital IQ has a dashboard that forecasts hospital and ICU admissions for each county in the US. Relies in part on IHME
forecasts.
263
• COVID Act Now: State and county-level dashboard focused on re-opening strategies, showing trends in four metrics related
to COVID-19 risk (change in cases, total testing capacity, fraction of positive tests, and availability of ICU beds).
Fundamentally uses an SEIR model fit to observed data.
425
• Researchers use a rolling window analysis incorporating uncertainty in the generation time distribution to estimate time-
varying transmission rates in US states (the effective reproduction number, R
eff
or R
t
).
9
• Georgia Tech Applied Bioinformatics Laboratory: Tool providing probability of at least one infected individual attending an
event, accounting for event size and county/state COVID-19 prevalence.
101
• MITRE: Dashboards for COVID-19 forecasts and decision support tools, including regional comparisons and intervention
planning. Uses combinations of SEIR models and curve-fitting approaches.
403
What do we need to know?
Forecasts differ in how they handle public health interventions such as shelter-in-place orders and tracking how methods
change in the near future will be important for understanding limitations going forward.
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Table 1. Definitions of commonly-used acronyms
Acronym/Term Definition Description
ACE2 Angiotensin-converting enzyme 2
Acts as a receptor for SARS-CoV and SARS-CoV-2, allowing entry
into human cells
Airborne
transmission
Aerosolization of infectious
particles
Aerosolized particles can spread for long distances (e.g., between
hospital rooms via HVAC systems). Particles generally <5 μm.
ARDS
Acute respiratory distress
syndrome
Leakage of fluid into the lungs which inhibits respiration and leads
to death
Attack rate
Proportion of “at-risk” individuals
who develop infection
Defined in terms of “at-risk” population such as schools or
households, defines the proportion of individuals in those
populations who become infected after contact with an infectious
individual
CCV
Canine coronavirus
Canine coronavirus
CFR
Case Fatality Rate
Number of deaths divided by confirmed patients
CoV Coronavirus
Virus typified by crown-like structures when viewed under
electron microscope
COVID-19
Coronavirus disease 19
Official name for the disease caused by the SARS-CoV-2 virus.
Droplet
transmission
Sneezing, coughing
Transmission via droplets requires relatively close contact (e.g.,
within 6 feet)
ELISA
Enzyme-linked immunosorbent
assay
Method for serological testing of antibodies
Fomite Inanimate vector of disease
Surfaces such as hospital beds, doorknobs, healthcare worker
gowns, faucets, etc.
HCW
Healthcare worker
Doctors, nurses, technicians dealing with patients or samples
Incubation
period
Time between infection and
symptom onset
Time between infection and onset of symptoms typically
establishes guidelines for isolating patients before transmission is
possible
Infectious
period
Length of time an individual can
transmit infection to others
Reducing the infectious period is a key method of reducing overall
transmission; hospitalization, isolation, and quarantine are all
effective methods
Intranasal
Agent deposited into external
nares of subject
Simulates inhalation exposure by depositing liquid solution of
pathogen/virus into the nose of a test animal, where it is then
taken up by the respiratory system.
MERS
Middle-East Respiratory Syndrome
Coronavirus with over 2,000 cases in regional outbreak since 2012
MHV
Mouse hepatitis virus
Coronavirus surrogate
Nosocomial
Healthcare- or hospital-associated
infections
Characteristic of SARS and MERS outbreaks, lead to refinement of
infection control procedures
PCR Polymerase chain reaction
PCR (or real-time [RT] or quantitative [Q] PCR) is a method of
increasing the amount of genetic material in a sample, which is
then used for diagnostic testing to confirm the presence of SARS-
CoV-2
PFU Plaque forming unit
Measurement of the number of infectious virus particles as
determined by plaque forming assay. A measurement of sample
infectivity.
PPE Personal protective equipment
Gowns, masks, gloves, and any other measures used to prevent
spread between individuals
R
0
Basic reproduction number
A measure of transmissibility. Specifically, the average number of
new infections caused by a typical infectious individual in a wholly
susceptible population.
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Acronym/Term Definition Description
SARS
Severe Acute Respiratory
Syndrome
Coronavirus with over 8,000 cases in global 2002-2003 outbreak
SARS-CoV-2
Severe acute respiratory
syndrome coronavirus 2
Official name for the virus previously known as 2019-nCoV.
SEIR
Susceptible (S), exposed (E),
infected (I), and resistant (R)
A type of modeling that incorporates the flow of people between
the following states: susceptible (S), exposed (E), infected (I), and
resistant (R), and is being used for SARS-CoV-2 forecasting
Serial interval
Length of time between symptom
onset of successive cases in a
transmission chain
The serial interval can be used to estimate R
0
, and is useful for
estimating the rate of outbreak spread
SIR
Susceptible (S), infected (I), and
resistant (R)
A type of modeling that incorporates the flow of people between
the following states: susceptible (S), infected (I), and resistant (R),
and is being used for SARS-CoV-2 forecasting
TCID
50
50% Tissue Culture Infectious Dose
The number of infectious units which will infect 50% of tissue
culture monolayers. A measurement of sample infectivity.
Transgenic Genetically modified
In this case, animal models modified to be more susceptible to
MERS and/or SARS by adding proteins or receptors necessary for
infection
REQUIRED INFORMATION FOR EFFECTIVE INFECTIOUS DISEASE OUTBREAK RESPONSE SARS-CoV-2 (COVID-19)
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