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https://s3.us-west-1.wasabisys.com/virusreports/2020/05/cropped-virus-favicon-32x32.png SARS-CoV- Archives - Virus Reports http://virusreports.net/tag/sars-cov/ 32 32 Alleged US case of SARS-CoV-2 reinfection raises questions http://virusreports.net/alleged-us-case-of-sars-cov-2-reinfection-raises-questions/ http://virusreports.net/alleged-us-case-of-sars-cov-2-reinfection-raises-questions/#respond Fri, 04 Sep 2020 12:21:54 +0000 https://virusreports.net/alleged-us-case-of-sars-cov-2-reinfection-raises-questions/ A 25-year-old male seems to have the United States’ first case of reinfection with SARS-CoV-2, the virus that causes COVID-19.Share on PinterestResearchers wonder under which circumstances reinfection is possible and what it might imply.The resident of Reno, Nevada tested positive for infection with SARS-CoV-2 in mid-April 2020 after the onset of mild symptoms, such as…

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A 25-year-old male seems to have the United States’ first case of reinfection with SARS-CoV-2, the virus that causes COVID-19.

A photo of drive-through COVID-19 testing to accompany the article, Share on Pinterest
Researchers wonder under which circumstances reinfection is possible and what it might imply.

The resident of Reno, Nevada tested positive for infection with SARS-CoV-2 in mid-April 2020 after the onset of mild symptoms, such as a sore throat, a cough, headaches, nausea, and diarrhea.

After recovering, he twice tested negative for the virus in May. But at the end of that month, just 48 days after the first positive test, he tested positive again, this time with more severe symptoms, including a fever.

He was later admitted to a hospital after developing difficulties breathing and received supplemental oxygen.

Stay informed with live updates on the current COVID-19 outbreak and visit our coronavirus hub for more advice on prevention and treatment.

When researchers, led by the Nevada State Public Health Laboratory (NSPHL), sequenced the virus particles in each of the positive test samples, they found substantial differences.

For the virus that caused the first infection to mutate from one sequence to the other within 48 days would require a very fast mutation rate — one considerably faster than any previously observed in this virus.

The scientists therefore believe that the second case was a new infection, not a resurgence of the original infection after persisting without symptoms in the intervening period.

They also note that the male did not appear to have a suppressed immune system, tested negative for HIV, and was not taking immunosuppressant drugs.

To rule out the possibility that the two samples came from different individuals, as a result of mishandling or mislabeling, the researchers called on the services of the Washoe County Sheriff’s Office. Forensic testing by its scientists confirmed that the specimens were indeed from the same person.

The findings have not yet been peer-reviewed or published in a journal, but the researchers have posted them as a preprint on the server SSRN.

“If reinfection is possible on such a short timeline, there may be implications for the efficacy of vaccines developed to fight the disease. It may also have implications for herd immunity,” says Mark Pandori, Ph.D., director of the NSPHL and senior author of the research.

If reinfection were widespread, it would suggest that a vaccine may not produce sufficiently long-lasting immunity against the virus. By the same token, long-term herd immunity — the point at which so many people in a population have immunity that it halts the spread of the infection — would be unattainable.

However, there is currently no evidence that reinfection is anything more than a rare occurrence. In their paper, the authors write:

“An implication of this finding is that initial exposure to the SARS-CoV-2 virus may not result in a level of immunity that is 100% protective for all individuals. […] It is crucial to note that the frequency of such a phenomenon is not defined by a singular case study. This may represent a rare event.”

In late August 2020, scientists in Hong Kong reported the world’s first confirmed reinfection with SARS-CoV-2.

In this case, reported in Clinical Infectious Diseases, the person experienced no symptoms of the second infection, which occurred 142 days after the first.

This provides evidence for a more optimistic scenario, in which individuals who have had the infection once are able to mount faster, more robust immune responses to a second infection. As a result, they may experience few, if any, symptoms.

In this scenario, either vaccinations or herd immunity could still potentially protect populations from severe infections.

Overall, there remains considerable uncertainty about the degree of protection provided by an initial infection.

Medical News Today recently reported on research indicating that even people who have had mild or asymptomatic COVID-19 — and who have no antibodies capable of neutralizing the virus — may be protected against future infection.

The researchers behind this study found that immune cells called memory T cells appeared to provide long-lasting defenses against the virus.

For live updates on the latest developments regarding the novel coronavirus and COVID-19, click here.

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Experimental SARS-CoV-2 test works in 45 minutes http://virusreports.net/experimental-sars-cov-2-test-works-in-45-minutes/ http://virusreports.net/experimental-sars-cov-2-test-works-in-45-minutes/#respond Tue, 04 Aug 2020 13:21:35 +0000 https://virusreports.net/experimental-sars-cov-2-test-works-in-45-minutes/ Researchers have developed a new SARS-CoV-2 test that works in 45 minutes and only requires simple equipment, according to a preprint version of the research.Share on PinterestOlder COVID-19 tests can have turnaround times of up to 9 days.Image credit: Amilcar Orfali/Getty Images.The researchers, from the University of Colorado Boulder, report their development in a preprint…

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Researchers have developed a new SARS-CoV-2 test that works in 45 minutes and only requires simple equipment, according to a preprint version of the research.

Biochemist Daniela Beatriz Ori manipulates swab samples to make a real time polymerase chain reaction (RT-PCR) analysis for COVID-19 testing at the biochemistry lab of Central Navy Hospital Dr. Pedro Malloon April 28, 2020 in Buenos Aires, Argentina. The hospital, which is treating COVID-19 patients, has capacity to process up to 36 swab samples a day.Share on Pinterest
Older COVID-19 tests can have turnaround times of up to 9 days.

Image credit: Amilcar Orfali/Getty Images.

The researchers, from the University of Colorado Boulder, report their development in a preprint article that has yet to be peer reviewed.

While scientists are working to develop vaccines for SARS-CoV-2 and treatments for the disease that it causes, COVID-19, they are also trying to develop more effective testing procedures.

Until an effective vaccine and treatment protocol are developed, emergency measures will likely continue, in order to counter reoccurring waves of the pandemic. In addition to social distancing and good hygiene, widespread testing can help limit the spread of the virus.

Preprint research has suggested that up to 70% of people with SARS-CoV-2 who are younger than 60 could be asymptomatic. Testing as many people in a community as possible can identify asymptomatic people, who can then self-isolate to curb the virus’ spread.

When it comes to testing, time is of the essence. Findings of a different preprint study suggest that the speed of results is crucial: The longer a person does not know that they have the virus, the longer they can infect other people.

In the United States, the current turnaround time for results is slow. According to the researchers behind the present study:

“Many SARS-CoV-2 tests require that biospecimens be collected, transported to centralized labs, logged, queued, processed, analyzed, and then [the] results [are] communicated back to the agency that sent the sample for testing and finally delivered to the person who had the test.”

Now, however, the University of Colorado Boulder team has developed a SARS-CoV-2 test that can produce a result in 45 minutes.

Moreover, it requires no expensive, complicated equipment, meaning that it could be deployed widely in communities, not only in laboratories and hospitals.

According to Prof. Sara Sawyer, senior author of the research and a virologist at the university’s Department of Molecular, Cellular, and Developmental Biology, “Every test that has been approved to date requires that the sample, even if it’s saliva, be processed in a clinical diagnostic lab or at a doctor’s office, using sophisticated equipment. That can take up to 9 days right now.”

Nicholas Meyerson, Ph.D., the lead author of the research, adds:

“We are facing a serious testing shortage in this country right now, as more people want to get tested and diagnostics labs are overwhelmed. We’ve developed a test that could get results to people much faster.”

This experimental test requires a person to spit into a tube, add a solution, seal the tube, and return it for analysis.

Testing staff then run the test using pipettes, a heating source, and an enzyme mixture — all of which are readily available and easy to transport.

The aim is to identify specific regions of the SARS-CoV-2 genome. If the test is positive, the reaction tubes turn from pink to yellow. If the test is negative, the tubes stay pink.

To check the effectiveness of the test, the researchers added an inactive form of SARS-CoV-2 at various concentrations to 30 out of 60 saliva samples, randomized the samples, then gave them to colleagues to test.

“The test predicted with 100% accuracy all of the negative samples, and 29 of [the] 30 positive samples were predicted accurately,” says Meyerson.

A second party are currently validating the researchers’ findings.

Although the test appears to be slightly less sensitive than current COVID-19 tests, the researchers argue that its ability to produce rapid results is more important, when it comes to restricting the spread of the virus.

According to Prof. Roy Parker, director of the university’s BioFrontiers Institute:

“Our modeling showed that whether a test is sensitive or supersensitive is not that important. What is important is frequent testing, with the test results returned as fast as possible, which identifies more infected people faster and can limit new infections.”

Dr. Parker and colleagues have demonstrated this in a preprint article, which is also awaiting peer review.

Nonetheless, if the findings are verified following peer review then they will be valuable in helping to significantly increase both the number of SARS-CoV-2 tests available to a country and the speed with which their results can be returned.

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Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing http://virusreports.net/discovery-of-sars-cov-2-antiviral-drugs-through-large-scale-compound-repurposing/ http://virusreports.net/discovery-of-sars-cov-2-antiviral-drugs-through-large-scale-compound-repurposing/#respond Fri, 24 Jul 2020 15:21:18 +0000 https://virusreports.net/discovery-of-sars-cov-2-antiviral-drugs-through-large-scale-compound-repurposing/ AbstractThe emergence of the novel SARS coronavirus 2 (SARS-CoV-2) in 2019 has triggered an ongoing global pandemic of severe pneumonia-like disease designated as coronavirus disease 2019 (COVID-19)1. The development of a vaccine is likely to require at least 12-18 months, and the typical timeline for approval of a novel antiviral therapeutic can exceed 10 years. Thus, repurposing…

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Abstract

The emergence of the novel SARS coronavirus 2 (SARS-CoV-2) in 2019 has triggered an ongoing global pandemic of severe pneumonia-like disease designated as coronavirus disease 2019 (COVID-19)1. The development of a vaccine is likely to require at least 12-18 months, and the typical timeline for approval of a novel antiviral therapeutic can exceed 10 years. Thus, repurposing of known drugs could significantly accelerate the deployment of novel therapies for COVID-19. Towards this end, we profiled a library of known drugs encompassing approximately 12,000 clinical-stage or FDA-approved small molecules. We report the identification of 100 molecules that inhibit viral replication, including 21 known drugs that exhibit dose response relationships. Of these, thirteen were found to harbor effective concentrations likely commensurate with achievable therapeutic doses in patients, including the PIKfyve kinase inhibitor apilimod2–4, and the cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825, and ONO 5334. Notably, MDL-28170, ONO 5334, and apilimod were found to antagonize viral replication in human iPSC-derived pneumocyte-like cells, and the PIKfyve inhibitor also demonstrated antiviral efficacy in a primary human lung explant model. Since most of the molecules identified in this study have already advanced into the clinic, the known pharmacological and human safety profiles of these compounds will enable accelerated preclinical and clinical evaluation of these drugs for the treatment of COVID-19.

Author information

Author notes

  1. These authors contributed equally: Laura Riva, Shuofeng Yuan

Affiliations

  1. Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA

    Laura Riva, Xin Yin, Laura Martin-Sancho, Naoko Matsunaga, Lars Pache, Paul D. De Jesus, Peter Teriete, Kristina M. Herbert, Andrey Rubanov, Yuan Pu, Courtney Nguyen & Sumit K. Chanda

  2. State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, Hong Kong, China

    Shuofeng Yuan, Jasper Fuk-Woo Chan, Jianli Cao, Vincent Kwok-Man Poon & Kwok-Yung Yuen

  3. Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria

    Sebastian Burgstaller-Muehlbacher

  4. Calibr at Scripps Research, La Jolla, CA, 92037, USA

    Mitchell V. Hull, Tu-Trinh H. Nguyen, Peter G. Schultz & Arnab K. Chatterjee

  5. Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA

    Max W. Chang & Christopher Benner

  6. Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA

    Kuoyuan Cheng & Eytan Ruppin

  7. Biological Sciences Graduate Program, University of Maryland, College Park, MD, 20742, USA

    Kuoyuan Cheng

  8. Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA

    Angela Choi, Raveen Rathnasinghe, Michael Schotsaert, Lisa Miorin, Wen-Chun Liu, Kris M. White, Randy Albrecht, Jeffrey R. Johnson & Adolfo García-Sastre

  9. Global Health and Emerging pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA

    Angela Choi, Raveen Rathnasinghe, Michael Schotsaert, Lisa Miorin, Wen-Chun Liu, Kris M. White, Randy Albrecht & Adolfo García-Sastre

  10. Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA

    Angela Choi & Raveen Rathnasinghe

  11. Huffington Foundation Center for Cell-based Research in Parkinson‘s Disease, Department for Cell, Regenerative and Developmental Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Marion Dejosez & Thomas P. Zwaka

  12. Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, Hong Kong, China

    Ko-Yung Sit

  13. Texas Biomedical Research Institute, San Antonio, TX, USA

    Luis Martinez-Sobrido

  14. Department of Biological Sciences, Purdue University, West Lafayette, IN, USA

    Mackenzie E. Chapman & Andrew D. Mesecar

  15. Department of Biochemistry, Purdue University, West Lafayette, IN, USA

    Emma K. Lendy & Andrew D. Mesecar

  16. Inception Therapeutics, 6175 Nancy Ridge Dr, San Diego, 92121, USA

    Richard J. Glynne

  17. Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA

    Ren Sun

  18. Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA

    Andrew I. Su

  19. Department of Medicine – Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA

    Adolfo García-Sastre

  20. The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA

    Adolfo García-Sastre

Corresponding authors

Correspondence to
Arnab K. Chatterjee or Kwok-Yung Yuen or Sumit K. Chanda.

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion of the limitations and bias associated with the CPE-based primary screen performed in Vero E6 cells and its IF-based orthogonal validation. It also contains Supplementary Figure 1, a depiction of the gating strategy for flow cytometry analyses of iPSC-derived pneumocyte-like cells.

Enriched drug targets

Supplementary Table 1 . A list of drug targets enriched in GSEA analysis of HTS data.

RNAseq and GSEA analyses

Supplementary Table 2 . Processed RNAseq data from mock-infected and SARS-CoV-2 infected Vero E6 cells (MOI=0.3) collected 24 hpi (“RNAseq_Vero E6”). GSEA analysis of these RNAseq dataset (“GSEA_Vero E6”) and GSAE analysis of publicly available RNA-seq dataset of nasopharyngeal swab specimens collected from COVID-19 patients (“GSEA_Mason’s paper”). P-values were calculated as described in the materials and methods.

List of validated antiviral compounds

Supplementary Table 3 . A list of compounds confirmed to inhibit infection by 40 % or more at a single dose (1 or 2.5 µM) in Vero E6 cells.

List of the 21 most potent compounds validated in dose response across multiple cell lines

Supplementary Table 4 . Activities, reported mechanism of action (MOA), and clinical profiles of the most potent 21 compounds with dose-activity relationships listed in Figure 3. The target class and the likely antiviral mechanism are also indicated. NA- not available; QD- once daily; BID-twice daily. Information retrieved from CortellisTM (Clarivate Analytics) and drugbank.com.

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Cite this article

Riva, L., Yuan, S., Yin, X. et al. Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing.
Nature (2020). https://doi.org/10.1038/s41586-020-2577-1

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SC dog confirmed with SARS-CoV-2 virus that causes COVID-19, vet says http://virusreports.net/sc-dog-confirmed-with-sars-cov-2-virus-that-causes-covid-19-vet-says/ http://virusreports.net/sc-dog-confirmed-with-sars-cov-2-virus-that-causes-covid-19-vet-says/#respond Thu, 16 Jul 2020 17:21:02 +0000 https://virusreports.net/sc-dog-confirmed-with-sars-cov-2-virus-that-causes-covid-19-vet-says/ this dog is being trained to detect prostate cancer. She's presented with urine samples on Rewarded. When she identifies the correct one, This'll Dog is able to identify the odor off malaria sufferers. Their next mission here is to train dogs to sniff out people infected with Cove in 19. The way we're gonna do…

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this dog is being trained to detect prostate cancer. She’s presented with urine samples on Rewarded. When she identifies the correct one, This’ll Dog is able to identify the odor off malaria sufferers. Their next mission here is to train dogs to sniff out people infected with Cove in 19. The way we’re gonna do that is by collecting using face masks, and we’re asking people to wear these face smiles for a few hours. Then we can feed collect those, and the other thing we’re going to do is get people to wear nylon socks. That sounds a bit strange, but we know from previous experience that this is a really good way of collecting odors from people, and it’s such an easy way to do it. If the training is successful, one of their first deployments is likely to be airports where dogs are already used to sniff out drugs and other contraband. If they help reopen the travel industry. That could be the boost to international trade that governments everywhere have been looking for. Max Foster, CNN outside London,

SC dog confirmed with SARS-CoV-2 virus that causes COVID-19, vet says

The dog had to be euthanized due to his chronic condition

A Charleston County dog has been confirmed positive for SARS-CoV-2, the virus that causes COVID-19 in humans, according to Clemson University. Dr. Boyd Parr, state veterinarian and director of Clemson Livestock Poultry Health (LPH), said a private veterinarian decided to test the dog – an 8- or 9-year-old shepherd mix – for SARS-CoV-2 after one of its owners was confirmed to have COVID-19.Veterinary findings indicated the dog had a chronic health condition.(Video above: Airport dogs could sniff out coronavirus)The U.S. Department of Agriculture (USDA) National Veterinary Services Laboratories confirmed the virus in the dog on July 9. Clemson LPH and the S.C. Department of Health and Environmental Control (DHEC) continue to investigate this case with the USDA and the U.S. Centers for Disease Control and Prevention (CDC) to assure any information relevant to COVID-19 is documented.“Based on current knowledge, there continues to be no evidence that pets play a significant role in spreading SARS-CoV-2 to people,” Parr said. “It remains a good idea to restrict contact with your pets and other animals, just like you do with other people if you are infected with COVID-19 in order to protect them from exposure to the virus as recommended by the CDC.”The dog had to be euthanized due to his chronic condition, Parr said.This is the first confirmed animal detection of SARS-CoV-2 in South Carolina. A list of all confirmed cases in the United States, tracked by USDA, can be viewed here.Routine testing of animals is not recommended at this time. The CDC includes more information about testing animals on its website here.The decision to test an animal, including companion animals, livestock, and wild or zoo animals, should be made in consultation with and the approval of both appropriate state animal health and public health officials, according to the CDC.For more information about the virus in animals and recommendations for pet owners, click here. If you have questions about COVID-19, click here.

CLEMSON, S.C. —

A Charleston County dog has been confirmed positive for SARS-CoV-2, the virus that causes COVID-19 in humans, according to Clemson University.

Dr. Boyd Parr, state veterinarian and director of Clemson Livestock Poultry Health (LPH), said a private veterinarian decided to test the dog – an 8- or 9-year-old shepherd mix – for SARS-CoV-2 after one of its owners was confirmed to have COVID-19.

Veterinary findings indicated the dog had a chronic health condition.

(Video above: Airport dogs could sniff out coronavirus)

The U.S. Department of Agriculture (USDA) National Veterinary Services Laboratories confirmed the virus in the dog on July 9.

Clemson LPH and the S.C. Department of Health and Environmental Control (DHEC) continue to investigate this case with the USDA and the U.S. Centers for Disease Control and Prevention (CDC) to assure any information relevant to COVID-19 is documented.

“Based on current knowledge, there continues to be no evidence that pets play a significant role in spreading SARS-CoV-2 to people,” Parr said. “It remains a good idea to restrict contact with your pets and other animals, just like you do with other people if you are infected with COVID-19 in order to protect them from exposure to the virus as recommended by the CDC.”

The dog had to be euthanized due to his chronic condition, Parr said.

This is the first confirmed animal detection of SARS-CoV-2 in South Carolina.

A list of all confirmed cases in the United States, tracked by USDA, can be viewed here.

Routine testing of animals is not recommended at this time.

The CDC includes more information about testing animals on its website here.

The decision to test an animal, including companion animals, livestock, and wild or zoo animals, should be made in consultation with and the approval of both appropriate state animal health and public health officials, according to the CDC.

For more information about the virus in animals and recommendations for pet owners, click here.

If you have questions about COVID-19, click here.

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SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls http://virusreports.net/sars-cov-2-specific-t-cell-immunity-in-cases-of-covid-19-and-sars-and-uninfected-controls/ http://virusreports.net/sars-cov-2-specific-t-cell-immunity-in-cases-of-covid-19-and-sars-and-uninfected-controls/#respond Wed, 15 Jul 2020 15:21:00 +0000 https://virusreports.net/sars-cov-2-specific-t-cell-immunity-in-cases-of-covid-19-and-sars-and-uninfected-controls/ AbstractMemory T cells induced by previous pathogens can shape the susceptibility to, and clinical severity of, subsequent infections1. Little is known about the presence of pre-existing memory T cells in humans with the potential to recognize SARS-CoV-2. Here, we first studied T cell responses to structural (nucleocapsid protein, NP) and non-structural (NSP-7 and NSP13 of…

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Abstract

Memory T cells induced by previous pathogens can shape the susceptibility to, and clinical severity of, subsequent infections1. Little is known about the presence of pre-existing memory T cells in humans with the potential to recognize SARS-CoV-2. Here, we first studied T cell responses to structural (nucleocapsid protein, NP) and non-structural (NSP-7 and NSP13 of ORF1) regions of SARS-CoV-2 in COVID-19 convalescents (n=36). In all of them we demonstrated the presence of CD4 and CD8 T cells recognizing multiple regions of the NP protein. We then showed that SARS-recovered patients (n=23) still possess long-lasting memory T cells reactive to SARS-NP 17 years after the 2003 outbreak, which displayed robust cross-reactivity to SARS-CoV-2 NP. Surprisingly, we also frequently detected SARS-CoV-2 specific T cells in individuals with no history of SARS, COVID-19 or contact with SARS/COVID-19 patients (n=37). SARS-CoV-2 T cells in uninfected donors exhibited a different pattern of immunodominance, frequently targeting the ORF-1-coded proteins NSP7 and 13 as well as the NP structural protein. Epitope characterization of NSP7-specific T cells showed recognition of protein fragments with low homology to “common cold” human coronaviruses but conserved amongst animal betacoranaviruses. Thus, infection with betacoronaviruses induces multispecific and long-lasting T cell immunity to the structural protein NP. Understanding how pre-existing NP- and ORF-1-specific T cells present in the general population impact susceptibility and pathogenesis of SARS-CoV-2 infection is of paramount importance for the management of the current COVID-19 pandemic.

Author information

Author notes

  1. These authors contributed equally: Nina Le Bert, Anthony T. Tan

Affiliations

  1. Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore

    Nina Le Bert, Anthony T. Tan, Kamini Kunasegaran, Christine Y. L. Tham, Morteza Hafezi, Adeline Chia, Melissa Hui Yen Chng, Meiyin Lin, Nicole Tan, Martin Linster, Wan Ni Chia, Lin-Fa Wang, Eng Eong Ooi, Jenny Guek-Hong Low & Antonio Bertoletti

  2. Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore

    Meiyin Lin & Yee-Joo Tan

  3. National Center of Infectious Diseases, Singapore, Singapore

    Mark I-Cheng Chen

  4. Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore

    Shirin Kalimuddin & Jenny Guek-Hong Low

  5. Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore

    Paul Anantharajal Tambyah

  6. Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore

    Paul Anantharajal Tambyah

  7. Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore

    Yee-Joo Tan

  8. Singapore Immunology Network, A*STAR, Singapore, Singapore

    Antonio Bertoletti

Corresponding author

Correspondence to
Antonio Bertoletti.

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Le Bert, N., Tan, A.T., Kunasegaran, K. et al. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls.
Nature (2020). https://doi.org/10.1038/s41586-020-2550-z

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Is SARS-CoV-2 airborne? Questions abound—but here’s what we know http://virusreports.net/is-sars-cov-2-airborne-questions-abound-but-heres-what-we-know/ http://virusreports.net/is-sars-cov-2-airborne-questions-abound-but-heres-what-we-know/#respond Thu, 09 Jul 2020 13:21:04 +0000 https://virusreports.net/is-sars-cov-2-airborne-questions-abound-but-heres-what-we-know/ Cloudy with a chance of COVID — A look at the data on aerosol transmission. Beth Mole - Jul 9, 2020 11:30 am UTC Enlarge / A doctor wears a hood as he tests the seal of an N95 respiratory mask during a training at the La Clinica San Antonio Neighborhood Health Center in California.…

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Cloudy with a chance of COVID —

A look at the data on aerosol transmission.


A doctor wears a hood as he tests the seal of an N95 respiratory mask during a training at the La Clinica San Antonio Neighborhood Health Center in California.

Enlarge / A doctor wears a hood as he tests the seal of an N95 respiratory mask during a training at the La Clinica San Antonio Neighborhood Health Center in California.

A debate has erupted among researchers over the potential for the pandemic coronavirus, SARS-CoV-2, to spread through the air and—if it does so often enough—what to do about it.

Though talk of airborne transmission has been simmering since the beginning of the pandemic, it reached a boiling point this week following a letter penned by two researchers and addressed to “national and international bodies.” The letter, eventually signed by 239 researchers, urged those bodies to acknowledge the potential for airborne spread and to recommend control measures aimed at preventing it.

“Most public health organizations, including the World Health Organization, do not recognize airborne transmission except for aerosol-generating procedures [AGPs] performed in healthcare settings,” the letter stated. The evidence on airborne transmission is “admittedly incomplete,” the letter went on, but “[f]ollowing the precautionary principle, we must address every potentially important pathway to slow the spread of COVID-19.”

The letter was published Monday as a commentary piece titled “It is Time to Address Airborne Transmission of COVID-19” in the journal Clinical Infectious Diseases. But by then, it had already created a dustup, making headlines in The New York Times, The Washington Post, the Los Angeles Times, and others.

Most of the media coverage has homed in on the conflict with the WHO, casting the researchers’ letter as yet another ding against the organization’s pandemic response. In the past months, many researchers and public health experts have criticized the WHO, saying it stumbled in the wake of fast-paced research relating to mask use and garbled messaging on the risks of virus transmission from people who show no symptoms of COVID-19, among other things. The WHO’s stance on aerosols is yet another example of the organization being overly cautious at interpreting data and sluggish at recommending life-saving precautions, critics say.

Meanwhile, researchers have erupted in debate of their own regarding airborne transmission. There are disputes over the data—and what it means—as well as definitions of airborne droplets and how the current data should translate to precautions and protective measures.

Splitting spittle

At the crux of the debate is how, exactly, different research groups classify the throng of teeny globs that spew from our mouths and noses as we breathe, talk, sing, laugh, shout, sneeze, and cough.

At one end of the spectrum, there are relatively large droplets, launched often from coughs and sneezes, that have the trajectory of ballistic missiles. These tiny droplets of respiratory secretions can be loaded with infectious virus, cozy in their moist bubbles. But as they are relatively heavy, these droplets tend to fall rapidly to the ground and often don’t make it farther than a meter or two from their launch site.

On the other end of the spectrum, there are aerosols. These are often defined as being less than 5 micrometers in diameter (a micrometer is one-millionth of a meter. For reference, the width of a human hair can range from around 20 micrometers to nearly 200 micrometers.) Aerosols—which are sometimes called droplet nuclei—are lighter than respiratory droplets and can hang in the air, potentially for hours. They can also travel much farther from their launch site, easily traversing and swirling around a large room.

But unlike the plump ballistic droplets, aerosols don’t provide such a cushy environment for viruses. In aerosols, viral particles are more exposed to the elements and may have shorter survival times depending on temperature and humidity levels of a room. And because aerosols are much smaller, they pack in fewer viral particles. A person may have to suck in a high number of aerosol particles to get sufficient dose of virus to trigger an infection.

When relating this to the spread of germs and disease, many epidemiologists try to keep things simple and categorize transmission as being either largely from the ballistic respiratory droplet route or the aerosol route. The mumps virus is in the respiratory droplet category, for instance, which is spread from contact with saliva or close-range sneezes and coughs. The measles virus, which can linger in the air for hours and infect someone well after a sick person has left the room, spreads by aerosols.

These uncomplicated disease transmission bins have been useful and sufficient—up until now, it seems.

Swirling simplicity

The transmission of respiratory infections is, of course, far more complicated. Not all large respiratory droplets fall within one or two meters, and not all aerosols travel far with infectious virus. We don’t only produce large droplets while sneezing and coughing, and we don’t only produce aerosols while breathing or talking.

We produce a jet stream of respiratory particles—of varying intensities, with droplets of an entire range of sizes, from big, middling, to small—all the time. We do it while breathing, talking, singing, chanting, yelling, laughing, sneezing, coughing, whistling, etc.

WHO recommends avoiding the three Cs.

Enlarge / WHO recommends avoiding the three Cs.

For now, we do not know the range of droplet sizes that SARS-CoV-2 virus particles use to get around. And we do not know how many SARS-CoV-2 virus particles a person has to inhale to get infected and come down with COVID-19.

That said, there is a growing pile of information on people who have been infected and how their infections likely happened. The bulk of it points to close contact—being within two meters of an infected person where they could be exposed to respiratory droplets of any size, whether they’re plump ballistic ones or aerosolized. There is little data so far suggesting people get infected at long distances or that people are infected from being in rooms long after COVID-19 patients have passed through, like measles. This knocks back the idea of classical aerosol spread. Clinical data, meanwhile, has clearly found SARS-CoV-2 lurking in people’s throats and noses.

With that combination of data, epidemiologists at the WHO and other health agencies placed SARS-CoV-2 in the respiratory droplet bin and acted accordingly. They recommended that health care providers take precautions against infectious respiratory droplets. They recommended the public stay two meters away from each other, cover their coughs, and wash their hands. They recommended that sick people wear masks at all times, and—eventually—they recommended that the healthy public wear masks when physical distancing isn’t possible.

Though epidemiologists—including those at the WHO—understand that reality is far more complex, they’ve stuck to the straightforward droplet approach, given data that suggests the bulk of infections align with the short-range droplet category. But other researchers, many of whom are engineers and environmental health experts, are now pushing back, noting that SARS-CoV-2 may be aerosolized.

Debated data

In a study published in March in the New England Journal of Medicine, researchers at the US National Institutes of Health found that when they put SARS-CoV-2 into a three-jet Collison nebulizer, they could create SARS-CoV-2 aerosols that held viable virus aloft for up to three hours.

Further, some researchers argue that aerosols best explain some so-called “super-spreading events” when many people become infected at once. In the letter to health bodies—written by Lidia Morawska, an air quality engineer at Queensland University of Technology, and Donald Milton, an environmental health researcher at the University of Maryland—the authors note a study of a super-spreading event in a Chinese restaurant. The study found that SARS-CoV-2 spread from one infected person to people at their table plus unrelated people at two nearby tables that happened to be in the stream of an air conditioning unit. The authors of the study concluded that “aerosol transmission of SARS-CoV-2 due to poor ventilation may explain the community spread of COVID-19.”

But epidemiologists and infectious disease experts have pushed back on this line of thinking.

In a press conference Tuesday, WHO chief scientist Soumya Swaminathan noted that data like the NIH’s nebulizer experiment is not necessarily useful for understanding what happens in real life. She explained:

So you have bioengineers and experts in physics who do experiments in laboratories and come out with that kind of data. Now, whether that exactly reflects what happens in day-to-day settings and clinical settings, we cannot extrapolate. Right? So, then you have to take ecological, descriptive data—sometimes from outbreaks that happen in different settings—which may point in a certain direction. But then you cannot always rule out [other possibilities]. For example, it may point to the fact that there could have been limited airborne transmission, but it could also be through fomites [contaminated objects] or other means.

Swaminathan added that the WHO is continually reviewing the data—reading 500 and up to 1,000 COVID-19 studies each day. The WHO technical lead on COVID-19, Maria Van Kerkhove, said that the WHO is working on a scientific brief about transmission, potentially updating the group’s thinking on aerosols. The organization has been working with researchers for weeks now and plans to release the document in the coming days.

Other experts have been more sharply critical of the aerosol argument. In a statement, infectious disease expert Babak Javid of Tsinghua University School of Medicine, Beijing, went further in knocking back the hypothesis of airborne spread in the Chinese restaurant. As he wrote (emphasis his):

In this opinion piece, the authors cite one well-documented transmission cluster in a restaurant in China as evidence for airborne transmission. The source patient was at one table, and diners at several other tables were infected: all of them downstream of an air-conditioner that was positioned in the room. There was no physical contact between the parties. This certainly supports transmission via the air conditioner airflow, be they small or large droplets. However, it should be noted that diners on adjacent tables to the source patient, but who were not in the direction of airflow were not infected. This argues strongly against airborne particles that can distribute throughout a room over a period of time being a source of infection. Furthermore, we know from numerous studies of clearly documented transmission events that physical distance is protective, even indoors. For example, in the well described cluster of the first European outbreak in Munich, one diner transmitted to another, and their only contact was a brief conversation to pass the salt. No other diners in the room were infected. Studying transmission among Beijing households (i.e. necessarily indoors, and for prolonged periods), physical distance of >1m from the source patient was the most consistent and protective factor.

Moreover, air sampling in hospitals has been inconsistent in detecting virus—sometimes turning up with genetic material from SARS-CoV-2 and sometimes not. Even so, experts at WHO and elsewhere note that genetic material alone in air samples does not necessarily mean that there are whole, infectious viruses floating around.

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New, more infectious SARS-CoV-2 variant does not cause worse symptoms http://virusreports.net/new-more-infectious-sars-cov-2-variant-does-not-cause-worse-symptoms/ http://virusreports.net/new-more-infectious-sars-cov-2-variant-does-not-cause-worse-symptoms/#respond Wed, 08 Jul 2020 15:22:17 +0000 https://virusreports.net/new-more-infectious-sars-cov-2-variant-does-not-cause-worse-symptoms/ Research shows that a new variant of SARS-CoV-2, which is now the dominant form of the virus, is more infectious in cell cultures. However, clinical data suggest that the variant does not cause more severe illness.Share on PinterestA new, widespread variant of SARS-CoV-2 is more infectious but does not cause more serious symptoms, recent research…

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Research shows that a new variant of SARS-CoV-2, which is now the dominant form of the virus, is more infectious in cell cultures. However, clinical data suggest that the variant does not cause more severe illness.

coronavirus concept illustrationShare on Pinterest
A new, widespread variant of SARS-CoV-2 is more infectious but does not cause more serious symptoms, recent research suggests.

All viruses mutate, and the new coronavirus, SARS-CoV-2, is no exception. As an RNA virus, the new coronavirus is highly prone to mutation, partly because the replication enzymes of RNA viruses make more mistakes when copying genetic material.

Although the virus is mutating slowly, scientists had raised concerns that some of the mutations could make the virus more infectious.

One mutation in particular – D614G – has been a focus of concern, as it occurs in the spike protein of the virus. This site is important because it is the spike protein that attaches to host cells and eventually leads to their infection.

Stay informed with live updates on the current COVID-19 outbreak and visit our coronavirus hub for more advice on prevention and treatment.

D614G refers to a change in the amino acid (from D to G) in position 614, and people may also refer to it as the G614 variant.

Over a month, the G614 variant became the dominant form of SARS-CoV-2 around the world. There is evidence of G614 mainly in Europe in February, and by April, it had overtaken the original D614 form worldwide.

The rapid domination of this variant suggests that it may give the virus an advantage, increasing its infectiousness. To evaluate this, a team of researchers led by Los Alamos National Laboratory (LANL) near Santa Fe, NM, tracked global patterns of the G614 variant and performed experiments in cells.

Their results confirmed that the G614 variant is more infectious but, fortunately, is not associated with a more severe form of COVID-19.

The team’s findings appear in the journal Cell.

The G614 variant first piqued the study team’s interest in April, when they noticed a repeated pattern across the globe.

Bette Korber, a theoretical biologist at LANL and lead author of the study, explains, “All over the world, even when local epidemics had many cases of the original form circulating, soon after the D614G variant was introduced into a region, it became the prevalent form.”

Korber’s team developed a bioinformatics tool to identify mutations in the spike protein that were becoming more common, using the SARS-CoV-2 sequence database hosted by GISAID. Tens of thousands of SARS-CoV-2 genetic sequences are available on GISAID, which has become the standard for sharing sequences among COVID-19 researchers.

Their analysis showed that before March 1, the G614 variant was present in 10% of sequences. By the end of the month, it represented almost 70% of sequences in the database.

The shift to G614 forms of the virus occurred across the world, first in Europe and then in North America and Asia. It occurred at the national, subnational, county, and city levels.

The geographical data clearly indicate that the G614 variant is more infectious. To confirm this in vitro, the researchers performed cell studies using forms of viruses with either the original (D614) or new (G614) variant of the spike protein.

They found that viruses with the D614G mutation were significantly more infectious — in some cases, by more than nine times.

By analyzing real-life data from almost 1,000 COVID-19 patients, they also showed that the G614 variant is associated with a higher viral load.

This finding is based on the fact that less viral genetic material was necessary to perform a diagnostic test in people with the G614 form of the virus.

However, there is some good news here. Despite its association with a higher viral load, the new variant of SARS-CoV-2 does not appear to be associated with worse outcomes.

“[E]ven though patients with the new G virus carried more copies of the virus than patients infected with D, there wasn’t a corresponding increase in the severity of illness,” explains co-author of the study Prof. Erica Ollmann Saphire, from the La Jolla Institute for Immunology, CA.

The researchers found no link between the new G614 variant and disease severity, which they assessed using data on hospitalization for COVID-19.

Although the new variant of the virus does not appear to cause more severe symptoms, it is more infectious, and the authors recommend continued measures for protection, including mask wearing.

“These findings suggest that the newer form of the virus may be even more readily transmitted than the original form — whether or not that conclusion is ultimately confirmed, it highlights the value of what were already good ideas: to wear masks and to maintain social distancing.”

– Bette Korber

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Serology for SARS-CoV-2: Apprehensions, opportunities, and the path forward http://virusreports.net/serology-for-sars-cov-2-apprehensions-opportunities-and-the-path-forward/ http://virusreports.net/serology-for-sars-cov-2-apprehensions-opportunities-and-the-path-forward/#respond Tue, 19 May 2020 17:21:19 +0000 https://virusreports.net/serology-for-sars-cov-2-apprehensions-opportunities-and-the-path-forward/ AbstractSerological testing for SARS-CoV-2 has enormous potential to contribute to COVID-19 pandemic response efforts. However, the required performance characteristics of antibody tests will critically depend on the use case (individual-level vs. population-level).Making data-driven decisions on how to fight the COVID-19 pandemic without completely shutting down economies will require better tools to understand the extent of…

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Abstract

Serological testing for SARS-CoV-2 has enormous potential to contribute to COVID-19 pandemic response efforts. However, the required performance characteristics of antibody tests will critically depend on the use case (individual-level vs. population-level).

Making data-driven decisions on how to fight the COVID-19 pandemic without completely shutting down economies will require better tools to understand the extent of transmission. The current crisis presents an opportunity to rethink how health systems generate and use surveillance data, and how to harness the power of serological tests and seroepidemiology. The world’s health systems are rushing to develop and implement testing for clinical use, evaluations of social policy, and quantification of population-level risk, which has brought into sharp focus the challenges facing surveillance programs throughout the world. There is an urgent need to monitor variations in disease transmission across populations and geographies in near real-time. Rapid detection of active cases and contact tracing – using direct tests for presence of the virus (acute phase diagnosis) – is the cornerstone of containment strategies. For later phases of pandemic control – when the key questions involve when, where, and how to lift confinement measures, and relax social distancing constraints – serological testing to measure antibody responses to the virus becomes paramount to refine understanding of transmission intensity and population susceptibility.

Antibody tests to detect exposure to SARS-CoV-2, the virus responsible for COVID-19, are rapidly becoming available (a list is maintained by FIND at https://www.finddx.org/covid-19/pipeline/), with the majority configured for detection of IgG antibodies to the Spike (S) protein of the virus, though other isotypes and antigens are being explored. Testing platforms under development include classical solid phase immunoassays (mostly ELISA formats, ranging from manual or semi-automated to high flow automatons capable of handling several thousands of samples per day); methods based on bead-based flow cytometry and chemiluminescence (capable of high throughput as well as multiplexing); and lateral flow immunochromatographic assays (that have attracted the most attention, due to potential point of care (POC) usage and suitability for home self-testing). Assessing performance characteristics of these new tests is extremely important and challenging, raising issues regarding thresholds for sensitivity/specificity, potential cross-reactivity with other coronaviruses (particularly other subgroup B coronaviruses), the use of neutralization assays as a gold standard reference, difficulties harmonizing results reporting across different platforms, concerns for quality control in manufacturing, and most importantly, a lack of baseline data required for test interpretation. (1) The performance of different test platforms is likely to vary considerably; for instance, point of care lateral flow assays are likely to be fraught with more problems of sensitivity/specificity than ELISA formats, however their low cost and ease of use will facilitate more rapid scale-up and widespread adoption.

Despite enormous and ongoing efforts to study immune responses to COVID-19 in different clinical settings, to date there is insufficient data and poor understanding of the magnitude and duration of antibody responses (IgM, IgG, and IgA) following asymptomatic, mild, and severe infections. We do not yet understand how antibody responses vary across diverse populations with different genetic backgrounds, comorbidities, or infection histories. In this article, we discuss the use case for individual- versus population-level serological testing, with a focus on IgG testing applications. We emphasize the dangers of using current serologic tests for individual-level risk assessments, but highlight the potential power of deploying population-level serological testing (i.e., serosurveillance or seroepidemiology) – even with assays of moderate sensitivity/specificity.

Use cases for SARS-CoV-2 serology

At the individual level, serologic tests are frequently used to support clinical diagnosis by determining recent or prior infection (to supplement PCR detection), or to determine vaccination status and requirements for boosting. In vaccine trials, individual assessments of antibody endpoints may be used to determine serostatus prior to enrollment, as a tool to reduce bias, simplify analyses, and minimize required sample sizes. (2) Specific to SARS-CoV-2, a widely discussed idea in the media has been the issuance of “immune passports” – the proposed use of serology to infer immunity and thus enable a person to work on the front lines or return to daily work routines. Such an application must be predicated on an established surrogate of protection – a given antibody endpoint associated with clinical protection from infection – and a test with sufficient specificity to ensure people are not unintentionally put in harm’s way. (3) Serology tests with relatively high but imperfect specificity may lead to substantial false-positive results when used in low incidence settings (Fig. 1A). For example, in a setting where 5% of the population has been infected, a test with 96% specificity and 90% sensitivity would lead to just 54% of positive results indicating a true infection (i.e., positive predictive value). In addition to the risks of false positives, false negatives may occur in some previously-infected persons who fail to produce antibodies specific to the antigens/epitopes in a given assay, or whose antibodies have already quickly waned, or, when used during an on-going epidemic, among those who have not yet mounted a specific antibody response. (4, 5) For these individuals that don’t mount a measurable antibody response despite having been infected, obtaining permission to return to work could be onerous. Further considerations that may undermine the individual use-case is that even with a true positive antibody result we do not know how well that translates to protection or immunity, nor whether those positive by an antibody test could still shed virus and infect others.

Fig. 1 Interpretation of serological assays within the context of individual-use versus population-level studies.

(A) Individual-use: proportion of positive test results expected to be true positives (Positive Predictive Value) is a function of true seroprevalence in the population. (B) Population-level studies: the adjusted seroprevalence estimate is obtained after correcting the measured seroprevalence for the imperfect sensitivity and specificity of the assay. Estimated seroprevalence is therefore a function of test performance, and is defined as (proportion of positive tests + (spec – 1)) / (sens + spec -1). (9, 10) Source code for figure posted at: https://github.com/HopkinsIDD/covid-science-immuno

Credit: A. Kitterman/Science Immunology

” data-hide-link-title=”0″ data-icon-position=”” href=”https://immunology.sciencemag.org/content/immunology/5/47/eabc6347/F1.large.jpg?width=800&height=600&carousel=1″ rel=”gallery-fragment-images-808785728″ title=”Interpretation of serological assays within the context of individual-use versus population-level studies. (A) Individual-use: proportion of positive test results expected to be true positives (Positive Predictive Value) is a function of true seroprevalence in the population. (B) Population-level studies: the adjusted seroprevalence estimate is obtained after correcting the measured seroprevalence for the imperfect sensitivity and specificity of the assay. Estimated seroprevalence is therefore a function of test performance, and is defined as (proportion of positive tests + (spec – 1)) / (sens + spec -1). (9, 10) Source code for figure posted at: https://github.com/HopkinsIDD/covid-science-immuno”>

Fig. 1 Interpretation of serological assays within the context of individual-use versus population-level studies.

(A) Individual-use: proportion of positive test results expected to be true positives (Positive Predictive Value) is a function of true seroprevalence in the population. (B) Population-level studies: the adjusted seroprevalence estimate is obtained after correcting the measured seroprevalence for the imperfect sensitivity and specificity of the assay. Estimated seroprevalence is therefore a function of test performance, and is defined as (proportion of positive tests + (spec – 1)) / (sens + spec -1). (9, 10) Source code for figure posted at: https://github.com/HopkinsIDD/covid-science-immuno

Credit: A. Kitterman/Science Immunology

At the population level, representative cross-sectional serosurveys can provide aggregate ‘snapshots’ of infection history and immunity of a population. Understanding the proportion of the population infected by SARS-CoV-2 cannot be assessed based on PCR confirmed cases alone, due to variations in testing practices, timing of sampling, and the clinical spectrum of disease (e.g., asymptomatic infections). In contrast to case data, seroepidemiological datasets provide a less biased picture of risk of death (infection fatality rate), the amplitude of transmission in different populations, and can highlight disparities in infection rates without typical health-seeking behavior biases. Understanding age-specific or spatial distribution of susceptibility could guide policymakers about where to intervene and to what degree, by helping to answer questions such as: What IgG seroprevalence in children is acceptable to allow schools to open? Do infection attack rates differ between children and adults? Population-level surveys could also help estimate the probability and timing of future waves of disease, which will critically depend upon duration of immunity, (6) measure the impact of interventions such as physical distancing or vaccination, and in later stages, confirm the absence of transmission.

Here we underscore key differences between individual- and population-level use cases and emphasize that different use cases will require tests with different performance characteristics: while assays that “certify” an individual’s immunity need to be correlated with protection and have near-perfect specificity (to limit the number of false positives, when seroprevalence is low), assays to ascertain population-level exposure would have utility as long as the sensitivity and specificity are well-defined for the target population allowing for adjustment of seroprevalence estimates (Fig. 1B). Optimal thresholds for sensitivity/specificity can be “tuned” depending on local prevalence and intended use of the assay. For example, when conducting a serosurvey in low-prevalence settings, to achieve better precision of point estimates of disease burden, the assay specificity should be prioritized, typically at the cost of sensitivity. This can be achieved by raising the cutoff value for the assay used, for example by setting higher optical density readings as the threshold for positivity in an ELISA. Similarly, in a high-prevalence setting, test sensitivity should be prioritized at the cost of specificity. Thus, we recommend the consideration of multiple threshold values (cutoffs) for assays that can be flexibly used in different contexts.

Foundational studies to enhance the utility and interpretation of SARS-CoV-2 serology.

While many SARS-CoV-2 serological assays may have insufficient performance characteristics (sensitivity/specificity) to warrant use at the individual level, and the WHO currently recommends restricting antibody testing to research use only, we argue that these imperfect tests may nevertheless provide highly valuable tools to address critical public health questions, such as the safety of relaxing stay-at-home orders or school closures, or evaluations of alternative intervention measures. To fully realize the benefits of population-level seroepidemiological studies, a number of fundamental questions must be addressed, relating to test performance, the dynamics of antibody responses in relation to infection, and the link between antibody responses and immunity (Table 1). Answering these questions across different populations and epidemiologic contexts will require various study designs, which we view as key for optimal interpretation of the growing number of population-based, cross-sectional serological surveys.

Table 1 Overview of foundational studies to inform the interpretation and design of serological surveillance systems.

Governance

Serosurveillance for SARS-CoV-2 will only be capable of contributing to actionable public health information if serology measurements flow into efficient data pipelines. Scale-up of serological testing for pandemic response must therefore be accompanied by a governance model at the sub-national, national and international levels, and by an operational research agenda that evaluates the utility of assays within specific contexts. With the plethora of new tests in development and diverse testing strategies, there is an urgent need for national-level strategies to enable pooling of results generated from different methods and sources. National-level governance will be required to provide oversight for sample collection and processing, linkage to personal data, and to coordinate results analysis to the appropriate scale for policy relevance. Much like a national census is translated into infrastructure appropriations, serosurveillance could be used for resource allocations (and future vaccination efforts) to target transmission hotspots.

Data from carefully designed serostudies are urgently needed prior to widespread adoption or implementation of antibody testing programs. To ensure comparison across studies, there is a need for harmonization of assay protocols, sharing of reference standards, and a set of best-practices for reporting results. Because seroepidemiological studies will require measurement of healthy individuals, various strategies for opportunistic sampling of individuals in community settings should be explored, as described in a proposed Global Serum Bank. (7) A host of ethical and privacy issues will need to be addressed; we suggest that serosurveillance platforms should incorporate broad consent, enabling future screening of serum collections for multiple biomarkers of public health concern beyond SARS-CoV-2 alone. The SARS-CoV-2 pandemic has highlighted the value of transparency in disease surveillance for all nations. We see a role for international coordination of national seroepidemiology programs to facilitate standardizing methods and dissemination of results among national public health laboratories.

In summary, seroepidemiological studies and integrated serosurveillance platforms are urgently needed to guide and tailor SARS-CoV-2 response efforts, and will continue to be critical for mitigating post-pandemic resurgence. Coordinated serosurveillance provides opportunities to combine control efforts for different diseases into one coordinated program; this may be particularly valuable to assess impact of the COVID-19 crisis on routine immunization programs. (8) Platforms should be designed with a longer term vision beyond COVID-19, to generate capacity for ‘precision public health’ to monitor additional major diseases, and provide insights into how disease occurrence is interrelated with other health risk factors. Finally, we stress that investing now in a fundamental and operational research agenda will allow us to rapidly develop serosurveillance as a powerful tool for population-level public health; however, the complexity of using serological assays within low prevalence settings to inform individual-based risk assessments – i.e., to inform decisions regarding return to work – is dangerously premature.

References and Notes

  1. Wu F, Wang A, Liu M, et al. Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. medRxiv 2020; posted April 6, 2020. DOI: https://doi.org/. 10.1101/2020.03.30.20047365

  2. Tan W, Lu Y, Zhang J, et al. Viral Kinetics and Antibody Responses in Patients with COVID-19. medRxiv 2020; posted April 20, 2020. DOI: https://doi.org/. 10.1101/2020.03.24.20042382

Acknowledgments: Funding: JTW was supported by a commissioned grant from the Health and Medical Research Fund from the Government of the Hong Kong Special Administrative Region. Author contributions: JEB, ASA, MF, GV, DW, and DTL contributed to the initial draft of the manuscript. All authors provided critical feedback and contributed to the final manuscript. Competing interests: The authors declare that they have no competing interests.

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Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility http://virusreports.net/presymptomatic-sars-cov-2-infections-and-transmission-in-a-skilled-nursing-facility/ http://virusreports.net/presymptomatic-sars-cov-2-infections-and-transmission-in-a-skilled-nursing-facility/#respond Fri, 24 Apr 2020 19:27:47 +0000 https://virusreports.net/presymptomatic-sars-cov-2-infections-and-transmission-in-a-skilled-nursing-facility/ 22 References1 Citing ArticleAbstract BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can spread rapidly within skilled nursing facilities. After identification of a case of Covid-19 in a skilled nursing facility, we assessed transmission and evaluated the adequacy of symptom-based screening to identify infections in residents. MethodsWe conducted two serial point-prevalence surveys, 1 week apart,…

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Abstract

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can spread rapidly within skilled nursing facilities. After identification of a case of Covid-19 in a skilled nursing facility, we assessed transmission and evaluated the adequacy of symptom-based screening to identify infections in residents.

Methods

We conducted two serial point-prevalence surveys, 1 week apart, in which assenting residents of the facility underwent nasopharyngeal and oropharyngeal testing for SARS-CoV-2, including real-time reverse-transcriptase polymerase chain reaction (rRT-PCR), viral culture, and sequencing. Symptoms that had been present during the preceding 14 days were recorded. Asymptomatic residents who tested positive were reassessed 7 days later. Residents with SARS-CoV-2 infection were categorized as symptomatic with typical symptoms (fever, cough, or shortness of breath), symptomatic with only atypical symptoms, presymptomatic, or asymptomatic.

Results

Twenty-three days after the first positive test result in a resident at this skilled nursing facility, 57 of 89 residents (64%) tested positive for SARS-CoV-2. Among 76 residents who participated in point-prevalence surveys, 48 (63%) tested positive. Of these 48 residents, 27 (56%) were asymptomatic at the time of testing; 24 subsequently developed symptoms (median time to onset, 4 days). Samples from these 24 presymptomatic residents had a median rRT-PCR cycle threshold value of 23.1, and viable virus was recovered from 17 residents. As of April 3, of the 57 residents with SARS-CoV-2 infection, 11 had been hospitalized (3 in the intensive care unit) and 15 had died (mortality, 26%). Of the 34 residents whose specimens were sequenced, 27 (79%) had sequences that fit into two clusters with a difference of one nucleotide.

Conclusions

Rapid and widespread transmission of SARS-CoV-2 was demonstrated in this skilled nursing facility. More than half of residents with positive test results were asymptomatic at the time of testing and most likely contributed to transmission. Infection-control strategies focused solely on symptomatic residents were not sufficient to prevent transmission after SARS-CoV-2 introduction into this facility.

Introduction

The first reported case of coronavirus disease 2019 (Covid-19) in the United States was diagnosed in a resident of Snohomish County, Washington, on January 20, 2020.1 In late February, an outbreak was identified in a skilled nursing facility in neighboring King County; morbidity and mortality among residents were high, straining the regional health care system.2,3

We report another outbreak of Covid-19 in a separate skilled nursing facility in the same county. In the course of this outbreak investigation, Public Health–Seattle and King County (PHSKC) and the Centers for Disease Control and Prevention (CDC) identified residents with asymptomatic SARS-CoV-2 infection, which prompted further investigation. We performed serial point-prevalence surveys to assess the extent of transmission and to evaluate the adequacy of symptom-based screening of residents to identify infections. Initial findings of this investigation were previously reported.4

Description of the Outbreak

On February 29, 2020, in response to increased local awareness of Covid-19 in King County, Washington, administrative leadership at Facility A instituted enhanced infection-control measures. Nursing staff assessed residents twice daily for possible signs and symptoms of Covid-19, including fever (oral or temporal temperature measurement), cough, shortness of breath, and other symptoms. Health care personnel were assessed at the start of each shift with oral temperature measurement and screening for symptoms, including cough, shortness of breath, sore throat, or any other respiratory symptoms.

On March 1, one member of the health care staff tested positive for SARS-CoV-2 after having worked in a single unit (Unit 1) while symptomatic on February 26, the first day of symptoms, and on February 28. On March 5, the facility was informed that a hospitalized resident of Unit 1 (in whom symptoms had developed on March 2 and testing was done on March 3) had been diagnosed with Covid-19. Subsequently, all visitors were restricted and communal activities were canceled. PHSKC and the CDC initiated an outbreak investigation, and on March 6, provided on-site infection prevention and control recommendations, including the recommendation that all health care staff entering symptomatic residents’ rooms wear eye protection, a gown, gloves, and a face mask (N95 respirators were not routinely available).5 On March 8, the CDC and PHSKC offered testing to all residents in Unit 1; 13 of 15 residents present were tested for SARS-CoV-2 (2 residents declined). A total of 6 residents tested positive; of these, 4 had symptoms (e.g., fever, cough, shortness of breath, or sore throat) and 2 had been asymptomatic during the preceding 14 days. On March 9, the facility implemented Covid-19 transmission-based precautions for all residents of Unit 1, regardless of symptoms or infection status.

Methods

Study Population

Facility A is a 116-bed skilled nursing facility divided into four separate units with an equal mix of short- and long-term residents in each unit. There were 89 residents present at Facility A on March 3, the date of the first positive test in a resident. Facility A provided a list of full-time health care personnel by occupation. Results of positive SARS-CoV-2 tests obtained during postmortem examination or by outside health care providers during clinical evaluation of symptomatic residents and staff were provided to the CDC and PHSKC through March 26. All symptomatic health care personnel were advised to be tested by their health care provider; asymptomatic staff members were not tested as part of this investigation.

Point-Prevalence Surveys

On two occasions, residents in the facility were offered SARS-CoV-2 testing as part of a facility-wide point-prevalence survey. The first survey was performed for all assenting residents, including those who had previously tested positive, on March 13 (10 days after the first resident had tested positive for SARS-CoV-2). Nasopharyngeal and oropharyngeal swabs were collected in accordance with CDC guidelines.6 A second survey was conducted 7 days later (March 19–20) for residents who had had either a negative test result or a positive result with atypical or no symptoms reported in the first survey.

Symptom Assessment

On the day of point-prevalence surveys, a standardized symptom-assessment form was completed by nurses for each resident tested. Symptoms present during the preceding 14 days were recorded on the basis of interview and review of medical records. Asymptomatic residents with a positive test result were reassessed for symptoms 7 days later. For additional details on symptom assessment, see the Supplementary Appendix, available with the full text of this article at NEJM.org.

Residents were classified as symptomatic if they had had at least one new or worsened typical or atypical symptom of Covid-19 in the preceding 14 days. Residents with subjective fever or temperature greater than 100.0°F (37.8°C), cough, or shortness of breath were classified as symptomatic with typical symptoms.7 Residents were classified as symptomatic with atypical symptoms if their symptoms included only chills, malaise, increased confusion, rhinorrhea, nasal congestion, sore throat, myalgia, dizziness, headache, nausea, or diarrhea.

Asymptomatic residents were those who had no symptoms or only stable chronic symptoms (e.g., chronic cough without worsening). Presymptomatic residents were those who were asymptomatic at the time of testing but developed symptoms within 7 days after testing. Residents who did not develop symptoms in the 7 days after testing remained classified as asymptomatic.

Laboratory Testing

The Washington State Public Health Laboratory performed one-step real-time reverse transcriptase–polymerase chain reaction (rRT-PCR) on all samples, using the SARS-CoV-2 CDC assay protocol; cycle threshold (Ct) values were reported for two genetic markers: the N1 and N2 viral nucleocapsid protein gene regions.8,9 Values below 40 cycles indicate a positive result for SARS-CoV-2.

All rRT-PCR–positive specimens from point-prevalence surveys were shipped to the CDC for viral culture using Vero-CCL-81 cells. Cells showing cytopathic effect were used for SARS-CoV-2 rRT-PCR to confirm isolation and viral growth in culture. Nucleic acid was extracted from rRT-PCR–positive specimens and amplified for subsequent sequencing (Oxford Nanopore MinION), with phylogenetic trees inferred with the neighbor-joining method.10 Additional details on culture and sequencing methods are provided in the Supplementary Appendix.

Analyses

The daily proportions of residents with any known positive test for SARS-CoV-2 (including those tested as part of clinical management) were described according to their unit in the facility. The daily growth rate for the facility was estimated through regression analysis, using the log-transformed daily cumulative counts of all residents who were positive for SARS-CoV-2 from March 3 through March 20; doubling time was estimated by dividing the natural logarithm of 2 by the growth rate. Similarly, doubling time was estimated for all residents of King County, using case count data reported through the PHSKC Covid-19 data dashboard.11

All analyses were completed with SAS software, version 9.4 (SAS Institute). Data were collected as part of public health response and were deemed non–human subjects research by the CDC.

Results

Residents

Figure 1. Figure 1. Residents in Facility A on March 3 through Two Point-Prevalence Surveys.

Shown are all 89 residents who lived in skilled nursing facility A from March 3, when the first resident tested positive for SARS-CoV-2. By March 13, the date of the first point-prevalence survey, 82 residents remained in the facility, and 76 were tested. By the second point-prevalence survey, 48 of the 76 residents tested in the point-prevalence surveys had been identified as positive. Overall, 57 residents were positive as of March 26. Cycle threshold values were available for 47 residents who tested positive in the point-prevalence surveys on March 13 and March 19–20.

Table 1. Table 1. Demographic Characteristics and Reported Symptoms in Residents of Facility A at the Time of Testing.

Of the 89 residents who lived in Facility A when the first resident with confirmed Covid-19 was tested, 57 (64%) had tested positive for SARS-CoV-2 either during the point-prevalence surveys, clinical evaluation, or postmortem examination as of March 26. Seventy-six residents participated in the first point-prevalence survey on March 13 (Figure 1). Of these 76 residents, 48 (63%) tested positive in either the initial or subsequent point-prevalence surveys. Demographic characteristics, coexisting conditions, and symptoms of surveyed residents were similar, regardless of test result (Table 1).

Of the 48 residents who tested positive from the surveys, 17 (35%) reported typical symptoms, 4 (8%) reported only atypical symptoms, and 27 (56%) reported no new symptoms or changes in chronic symptoms at the time of testing (Table 1 and Table S1). Among the 27 residents classified as asymptomatic, 15 reported no symptoms and 12 reported only stable chronic symptoms. Fifteen (56%) residents who were asymptomatic at the time of testing had documented cognitive impairment; similar proportions were reported in symptomatic residents (Table S2).

In the 7 days after their positive test, 24 of the 27 asymptomatic residents (89%) had onset of symptoms and were recategorized as presymptomatic. The median time to symptom onset was 4 days (interquartile range, 3 to 5). The most common new symptoms were fever (71%), cough (54%), and malaise (42%) (Table S3).

Cycle Threshold and Viral Culture

Figure 2. Figure 2. Cycle Threshold Values and Results of Viral Culture for Residents with Positive SARS-CoV-2 Tests According to Their Symptom Status.

Shown are N1 target cycle threshold values and viral culture results for 47 residents’ first positive test for SARS-CoV-2 stratified by the resident’s symptom status at the time of the test. One positive test was not assessed for culture growth. Typical symptoms include fever, cough, and shortness of breath; atypical symptoms include chills, malaise, increased confusion, rhinorrhea or nasal congestion, myalgia, dizziness, headache, nausea, and diarrhea.

rRT-PCR Ct values for the N1 genetic markers for 47 residents ranged from 13.7 to 37.9; median Ct values for the four symptom status groups were similar (asymptomatic residents, 25.5; presymptomatic residents, 23.1; residents with atypical symptoms, 24.2; and residents with typical symptoms, 24.8) (Figure 2). SARS-CoV-2 growth was identified from 31 of 46 rRT-PCR–positive specimens (Figure 2). Viral growth was observed for specimens obtained from 10 of 16 residents with typical symptoms, 3 of 4 with atypical symptoms, 17 of 24 who were presymptomatic, and 1 of 3 who remained asymptomatic.

Figure 3. Figure 3. Cycle Threshold Values Relative to First Evidence of Fever, Cough, or Shortness of Breath.

Shown are N1 target cycle threshold values and viral culture results for each resident’s positive tests for SARS-CoV-2 shown by day since the first evidence of fever, cough, or shortness of breath (N=55). Dates of onset of typical symptoms were known for 43 residents; 12 residents with two specimens that were positive for SARS-CoV-2 are also included. One positive test was not assessed for culture growth. The relationship between the first test and the second test for residents who had two positive tests is shown in Figure S2.

We observed no correlation between Ct values and the number of days from the first evidence of typical symptoms. Ct values consistent with a high viral load were identified among residents who tested positive before typical symptom onset (median Ct value among 26 observations, 24.0; interquartile range, 20.4 to 28.5) and those who tested positive 7 or more days after typical symptom onset (median Ct value among 8 observations, 25.0; interquartile range, 21.3 to 28.2) (Figure 3, and Fig. S1). Viable virus was isolated from specimens collected 6 days before to 9 days after the first evidence of typical symptoms.

Prevalence and Transmission in the Facility

Figure 4. Figure 4. Timeline Showing Prevalence, Notable Events, and Implementation of Infection Prevention and Control Measures at Facility A.

Dashed lines indicate the prevalence of Covid-19 based on test results obtained during clinical evaluation of symptomatic residents before a unit-wide or facility-wide point-prevalence survey (PPS); the dotted line indicates the prevalence based on results from a unit-specific point-prevalence survey; and solid lines indicate the prevalence based on results from clinical evaluation and a facility-wide point-prevalence survey. PPE denotes personal protective equipment.

We estimated the doubling time among residents to be 3.4 days (95% confidence interval [CI], 2.5 to 5.3) (Table S4). The doubling time for the surrounding King County was 5.5 days (95% CI, 4.8 to 6.7). As of April 3, a total of 11 of the 57 residents with SARS-CoV-2 infection identified by March 26 had been admitted to the hospital (including 3 in intensive care) and 15 had died (mortality, 26%). The unit where presumed introduction of infection took place and where the first resident with SARS-CoV-2 infection lived (Unit 1) had the highest prevalence in the facility at the end of the first point-prevalence survey. Although other units identified SARS-CoV-2 infection in residents later, their prevalence also continued to increase (Figure 4, and Fig. S4).

By the time of the first point-prevalence survey, 11 of 138 full-time staff members (8%) had had a positive test for SARS-CoV-2. By March 26, a total of 55 of the 138 (40%) had reported symptoms, 51 (37%) had been tested, and 26 (19%) had received a positive test result. Of the 26 staff members with positive tests, 17 were nursing staff and 9 had occupations that provided services across multiple units during their shift (therapists, environmental services, dietary services). No staff members with Covid-19 were hospitalized.

Thirty-nine specimens from 34 residents were sequenced. All sequences were identical or highly similar to sequences reported in previous analyses of Covid-19 cases in Washington (Fig. S3). Of the 34 residents whose specimens were sequenced, 27 (79%) had sequences that fit into two clusters with one nucleotide difference (Fig. S4 and Table S5).

Discussion

Twenty-three days after identifying the first resident with SARS-CoV-2 infection, Facility A had a 64% prevalence of Covid-19 among residents, with a case fatality rate of 26% despite early adoption of infection-control measures. In addition, Covid-19 was diagnosed in 26 members of the staff (19%). These findings are strikingly similar to descriptions of the first Covid-19 outbreak in a U.S. skilled nursing facility, which occurred in the same county at nearly the same time.2 In the investigation reported here, more than half of the residents with positive tests were asymptomatic at the time of testing. Transmission from asymptomatic residents infected with SARS-CoV-2 most likely contributed to the rapid and extensive spread of infection to other residents and staff. Symptom-based infection-control strategies were not sufficient to prevent transmission after the introduction of SARS-CoV-2 into this skilled nursing facility.

Although we are unable to quantify the contributions of asymptomatic and presymptomatic residents to transmission of SARS-CoV-2 in this facility, evidence suggests that these residents had the potential for substantial viral shedding. Ct values indicating large quantities of viral RNA were identified, and viable SARS-CoV-2 was isolated from specimens of asymptomatic and presymptomatic residents. Evidence of transmission from presymptomatic persons has been shown in epidemiologic investigations of SARS-CoV-2.12-14

We estimated that the doubling time in this facility was 3.4 days, which is faster than that of the surrounding community, 5.5 days. The accelerated doubling time was likely to have been due to inadequately controlled intrafacility transmission, which sequencing and spatiotemporal data suggest was the primary driver of new infections. Shedding of high viral titers from the respiratory tract, including shedding before the onset of symptoms, might have led to droplet and possibly aerosol transmission. Residents and staff members with undetected SARS-CoV-2 infection are likely to have contributed to transmission through interactions between and among residents and staff. The contribution of indirect contact transmission in this outbreak is not known. However, contaminated environmental surfaces and shared medical devices could also have played a role. Most of the early transmission appeared to have occurred in Unit 1, where the initial introduction of SARS-CoV-2 took place, several days before other units were involved. Early recognition of initial SARS-CoV-2 introduction combined with early interventions in all units might prevent spread within a facility.

The CDC and PHSKC confirmed Covid-19 infection in 26 symptomatic staff members associated with this skilled nursing facility as of March 26; these staff members most likely contributed to intrafacility transmission. A concurrent study of King County health care personnel with Covid-19 showed that 65% worked while symptomatic and that 17% of symptomatic health care personnel initially had mild, nonspecific symptoms and no fever, cough, shortness of breath, or sore throat.15 The potential for viral shedding from staff members with SARS-CoV-2 infection during either the presymptomatic or the mildly symptomatic phase of the illness reinforces current recommendations for expanded symptom screening for health care personnel and universal use of face masks for all health care staff in long-term care facilities.5

Current interventions for preventing SARS-CoV-2 transmission in health care settings rely primarily on the presence of signs and symptoms to identify and isolate residents and staff who might have Covid-19. The data presented here suggest that sole reliance on symptom-based strategies may not be effective to prevent introduction of SARS-CoV-2 and further transmission in skilled nursing facilities. Impaired immune responses associated with aging and the high prevalence of underlying conditions, such as cognitive impairment and chronic cough, make it difficult to recognize early signs and symptoms of respiratory viral infections in this population.16 Studies have shown that in the elderly, including those living in skilled nursing facilities, influenza often manifests with few or atypical symptoms, delaying diagnosis and contributing to transmission.17,18 Furthermore, symptom-based cohorting strategies could inadvertently increase the risk of SARS-CoV-2 exposure for uninfected residents, given that typical symptoms were common in those who tested negative.

Our investigation demonstrated a poor correlation between symptom onset and viral shedding that was potentially due to the difficulty of ascertaining precise dates of symptom onset or to differences in viral shedding in this population. Studies in other populations show that SARS-CoV-2 shedding is highest early in the illness.19,20 Our investigation shows that some facility residents shed virus for more than 7 days after symptom onset, a finding seen in some other populations.21 These data support current recommendations preferring a test-based strategy to discontinue transmission-based precautions for residents of skilled nursing facilities.22 If a non–test-based strategy is used, these data support extending the duration of transmission-based precautions.22

Because asymptomatic or presymptomatic residents might play an important role in transmission in this high-risk population, additional prevention measures merit consideration, including using testing to guide the use of transmission-based precautions, isolation, and cohorting strategies. The ability to test large numbers of residents and staff with rapid turn-around times may expedite cohorting of residents and staff in locations designated for the care of those with SARS-CoV-2 infection either in different locations within individual facilities or in separate facilities.

This investigation has several limitations. First, challenges in symptom ascertainment may have resulted in misclassification of symptom grouping for some residents. However, multiple sources of symptom data were used to minimize such misclassification. The accuracy of symptom ascertainment for this investigation is likely to be equivalent to, if not exceed, symptom screening in most skilled nursing facilities, and thus, these findings should be generalizable to this setting. Second, because this analysis was conducted among residents of a skilled nursing facility, it is not known whether the findings apply to the general population, including younger persons, those without underlying medical conditions, or similarly aged populations in the general community or in other long-term care settings. Third, asymptomatic staff members were not tested; therefore, we are unable to document their role in transmission in this facility.

SARS-CoV-2 can spread rapidly after introduction into skilled nursing facilities, resulting in substantial morbidity and mortality and increasing the burden on regional health care systems. Unrecognized asymptomatic and presymptomatic infections most likely contribute to transmission in these settings. During the current Covid-19 pandemic, skilled nursing facilities and all long-term care facilities should take proactive steps to prevent introduction of SARS-CoV-2. These steps include restricting visitors and nonessential personnel from entering the building, requiring universal use of face masks by all staff for source control while in the facility, and implementing strict screening of staff. Our data suggest that symptom-based strategies for identifying residents with SARS-CoV-2 are insufficient for preventing transmission in skilled nursing facilities. Once SARS-CoV-2 has been introduced, additional strategies should be implemented to prevent further transmission, including use of recommended personal protective equipment, when available, during all resident care activities regardless of symptoms.5 Consideration should be given to test-based strategies for identifying residents and staff with SARS-CoV-2 infection for the purpose of excluding infected staff and cohorting residents, either in designated units within a facility or in a separate facility designated for residents with Covid-19.

Funding and Disclosures

Disclosure forms provided by the authors are available with the full text of this article at NEJM.org.

Ms. Arons and Ms. Hatfield contributed equally to this article.

The findings and conclusion in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.

This article was published on April 24, 2020, at NEJM.org.

We thank the facility residents; the staff of Facility A for their ongoing efforts to provide care in the face of these challenges; staff at the local and state health departments responding to this public health emergency; staff at the Washington State Department of Health Public Health Laboratories; CDC staff at the Emergency Operations Center; and members of the Covid-19 response teams at the local, state, and national levels for their unwavering commitment in the face of this global public health emergency.

Author Affiliations

From the Centers for Disease Control and Prevention COVID-19 Emergency Response (M.M.A., K.M.H., S.C.R., A.K., A.J., J.R.J., J.T., K.S., A.C.B., L.P.O., S. Tanwar, J.W.D., J. Harney, Z.C., J.M.B., M.M., P.P., C.M.C., H.P.M.L., N.T., S. Tong, A.T., Y.T., A.U., J. Harcourt, N.D.S., T.A.C., M.A.H., J.A.J.), and the Epidemic Intelligence Service (M.M.A., A.K., A.J., J.T., A.C.B., L.P.O., S. Tanwar, J.W.D.) and the Laboratory Leadership Service (J.R.J., C.M.C.), Centers for Disease Control and Prevention — all in Atlanta; and Public Health — Seattle & King County (S.C., C.B.-S., L.C.P., M.K., J.L., J.S.D.) and the University of Washington, Department of Medicine (J.S.D.), Seattle, the Washington State Public Health Laboratory, Shoreline (J.S.D.), and the Washington State Department of Health, Tumwater (P.M.) — all in Washington.

Address reprint requests to Dr. Jernigan at the Centers for Disease Control and Prevention, 1600 Clifton Rd., Mailstop A-31, Atlanta, GA 30333, or at [email protected].

A complete list of the investigators is included in the Supplementary Appendix, available at NEJM.org.

Supplementary Material

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SARS-CoV-2 may be exploiting our immune system’s ‘first responder’ cells http://virusreports.net/sars-cov-2-may-be-exploiting-our-immune-systems-first-responder-cells/ http://virusreports.net/sars-cov-2-may-be-exploiting-our-immune-systems-first-responder-cells/#respond Fri, 24 Apr 2020 15:21:39 +0000 https://virusreports.net/sars-cov-2-may-be-exploiting-our-immune-systems-first-responder-cells/ Home News An illustration showing the SARS-CoV-2 virus binding to an ACE2 receptor on a human cell. (Image: © Shutterstock) The new coronavirus, known as SARS-CoV-2, may be using part of the human body's own immune response against us, a new study suggests.The novel coronavirus is known to use a keyhole called the ACE2 receptor…

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An illustration showing the SARS-CoV-2 virus binding to an ACE2 receptor on a human cell.

An illustration showing the SARS-CoV-2 virus binding to an ACE2 receptor on a human cell.

(Image: © Shutterstock)

The new coronavirus, known as SARS-CoV-2, may be using part of the human body’s own immune response against us, a new study suggests.

The novel coronavirus is known to use a keyhole called the ACE2 receptor to “unlock” a cell and get inside, where it replicates and wreaks havoc. Now, researchers have found that the gene that encodes the ACE2 receptor may be stimulated by interferons, one of the body’s main defenses against viruses. When a foreign pathogen invades, interferons act like “first responders”; the immune system releases these proteins to alert other cells that there’s a pathogen in the body.

But when interferons rush to alert the body to the coronavirus, they’re actually stimulating the gene that ramps up expression of ACE2 receptors, which may lead to more ACE2 production and allow SARS-CoV-2 to infect even more cells.

Related: 20 of the worst epidemics and pandemics in history 

What is ACE2?

ACE2 is much more than just a portal for a virus; it plays a critical role in normal lung function and in the circulatory system, said study co-senior researcher Jose Ordovas-Montanes, a principal investigator in the Division of Gastroenterology at Boston Children’s Hospital. 

Normally, the ACE2 receptor puts the brakes on a circuit that could cause high blood pressure, said Ordovas-Montanes, who is also an assistant professor of pediatrics at Harvard Medical School. The receptor also helps to stop blood vessels from becoming leaky.

“Here we have a situation where a virus targets ACE2 as a principal entry route into cells, and at the same time can disable its normal function,” Ordovas-Montanes told Live Science. By targeting ACE2, SARS-CoV-2 “could be exploiting our own antiviral defenses and tissue-protective responses simultaneously,” he said. However, “more research needs to be done to understand if this is the case.” 

Related: The 12 deadliest viruses on Earth

This finding is important, given that interferons are being tested as a possible treatment for the new coronavirus. However, it’s still unclear whether an interferon treatment would help or harm patients.

“It might be that in some patients, because of the timing or the dose, interferon can contain the virus, while in others, interferon promotes more infection,” Ordovas-Montanes said in a statement. “We want to better understand where the balance lies and how we can maintain a productive antiviral response without producing more target cells for the virus to infect.”

Timing is everything

The researchers had a head start, of sorts, against SARS-CoV-2. Ordovas-Montanes and study co-senior researcher Alex Shalek, Pfizer-Laubach Career Development associate professor of chemistry at MIT, were already studying the different types of cells in the respiratory system and intestine when COVID-19 hit the world. They had previously collected data on humans, other primates and mice.

“We were perfectly primed to identify which cells may be primary targets for viral infection in human nasal, lung and intestinal samples,” Ordovas-Montanes told Live Science. 

Earlier research had revealed that SARS-CoV-2 docks onto cells with ACE2 receptors with the help of an enzyme known as TMPRSS2. This enzyme slices the spike protein of the virus to activate it and allow the virus to enter the cell, Ordovas-Montanes said. 

Related: 11 surprising facts about the respiratory system

“Without this docking and activation on a cell, the virus is not as effective at gaining entry,” he said. “These two factors appear almost essential.”

This led Ordovas-Montanes, Shalek and their colleagues to ask the question: Which cells in the respiratory tract and intestine express both ACE2 and TMPRSS2?

Cell treasure hunt

To investigate, the team used a technique known as single-cell RNA-sequencing, which looks at each cell as an individual, rather than as an “average” mixture of cells, Ordovas-Montanes said.

“If you consider each cell to be a unique person within a room of people, the best way to get to know everyone is by having a conversation with them individually, rather than assuming any averages, which could be misleading,” he explained. 

This experiment showed that less than 10% of human respiratory and intestinal cells make both ACE2 and TMPRSS2. These cells fall into three categories: goblet cells in the nose that make mucus in the upper airway; type II pneumocytes, which provide support for oxygen exchange in the lungs; and ileal absorptive enterocytes, a type of cell that lines the intestine and helps with nutrient absorption.

Another experiment in non-human primate cells showed similar results.

“All three [are] essential for tissue function,” Ordovas-Montanes said. “We are now collaborating with groups at the Broad Institute and worldwide through the Human Cell Atlas community to understand the true viral targets from COVID-19 samples.”

The interferon connection

After identifying these cells, the researchers realized that all three cell types had something in common: There was a recurrent pattern of genes being turned on by interferons in these cells. The team wondered whether some of those genes included those for ACE2, which could lead to more of the receptor on the cells.

“We could find nothing in the literature to support this idea,” Ordovas-Montanes said. 

Undeterred, they pushed on. Surprisingly, the team found that in primary epithelial cells in the human airway, interferon did lead to more ACE2 gene expression in a dose-dependent fashion. “That is, as you add more interferon, you get more ACE2 expression,” he said. 

However, increased gene expression doesn’t always mean that the protein (that is, the receptor) gets made. That’s an experiment for another study, he said. 

Related: Wuhan lab says there’s no way coronavirus originated there. Here’s the science.

Now, the team wants to explore what SARS-CoV-2 is doing in the cells it infects. They plan to study tissue samples from children and adults, so they can figure out why youngsters are generally less affected by the virus than adults. 

The study is part of a large collaboration that included Boston Children’s, MIT, Harvard, Africa Health Research Institute, the Human Cell Atlas (HCA) and the Lung Biological Network group. 

A preprint of study was published online April 21 in the journal Cell

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Originally published on Live Science.

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