4.8 Article

The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

期刊

SCIENCE
卷 377, 期 6609, 页码 960-966

出版社

AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/science.abp8337

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资金

  1. National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Department of Health and Human Services [75N93021C00015]
  2. NIH [T15LM011271, 5T32AI007244-38, R01AI135992, R01AI136056, R01AI132223, R01AI132244, U19AI142790, U54CA260581, U54HG007480, OT2HL158260, R01AI153044, U19AI135995, U01AI151812, UL1TR002550]
  3. National Science Foundation (NSF) [NSF-2028040]
  4. Coalition for Epidemic Preparedness Innovation
  5. Wellcome Trust Foundation
  6. Gilead Sciences
  7. European and Developing Countries Clinical Trials Partnership Programme
  8. Wellcome Trust [206298/Z/17/Z-ARTIC]
  9. European Research Council [725422-ReservoirDOCS]
  10. Australian Research Council Laureate Fellowship [FL170100022]
  11. National Research Foundation of Korea - Ministry of Science and Information and Communication Technologies, Republic of Korea [NRF2017M3A9E4061995, NRF-2019R1A2C2084206]
  12. Branco Weiss Fellowship
  13. Epidemiology and Laboratory Capacity (ELC) - Centers for Disease Control and Prevention (CDC) [6NU50CK000517-01-07]

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Understanding the circumstances that lead to pandemics is crucial for their prevention. In this study, the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic was analyzed. The results suggest that before February 2020, SARS-CoV-2 likely consisted of two distinct viral lineages, labeled A and B. Through phylodynamic rooting methods and epidemic simulations, it was revealed that these lineages were the result of at least two separate cross-species transmission events into humans. The findings indicate that widespread circulation of SARS-CoV-2 in humans before November 2019 is unlikely, and define the narrow time window between the first jump of SARS-CoV-2 into humans and the first reported cases of COVID-19.
Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted A and B. Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.

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