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1.
Science ; 377(6609): 951-959, 2022 08 26.
Article in English | MEDLINE | ID: covidwho-1962061

ABSTRACT

Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2-susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.


Subject(s)
COVID-19 , Pandemics , SARS-CoV-2 , Seafood , Viral Zoonoses , Animals , COVID-19/epidemiology , COVID-19/transmission , COVID-19/virology , China/epidemiology , Humans , SARS-CoV-2/isolation & purification , Seafood/virology , Viral Zoonoses/epidemiology , Viral Zoonoses/transmission , Viral Zoonoses/virology
2.
Science ; 377(6609): 960-966, 2022 08 26.
Article in English | MEDLINE | ID: covidwho-1962060

ABSTRACT

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.


Subject(s)
COVID-19 , Pandemics , SARS-CoV-2 , Viral Zoonoses , Animals , COVID-19/epidemiology , COVID-19/transmission , COVID-19/virology , Computer Simulation , Genetic Variation , Genomics/methods , Humans , Molecular Epidemiology , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Viral Zoonoses/epidemiology , Viral Zoonoses/virology
3.
Nat Commun ; 13(1): 3645, 2022 Jun 25.
Article in English | MEDLINE | ID: covidwho-1908172

ABSTRACT

Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts reveals that Alpha variant alleles comprise around 75% of the genomes, whereas the Epsilon variant alleles comprise around 20% of the sample. Further investigation reveals the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.


Subject(s)
COVID-19 , Superinfection , Genome, Viral/genetics , Humans , New York City/epidemiology , Recombination, Genetic , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
4.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-296564

ABSTRACT

Within a year of the shutdowns caused by the COVID-19 pandemic, virtual meetings transformed from an auxiliary service to an essential work platform for hundreds of millions of people worldwide. Universities rapidly accelerated adoption of virtual platforms for remote conferences, classes, and seminars amidst a second crisis testing institutional commitment to the principles of equity, diversity, and inclusion. Here we present thorough guidelines for drawing out hope from the Pandora's box of virtual programming now open to the world. We review milestones from our first year organizing the Diversity and Science Lecture series (DASL) and explore insights into equity, diversity, and inclusion in STEM gleaned from hosted speakers' talk content. Nearly every speaker highlighted the importance of social or interpersonal support to their career progression, and three-fifths of speakers commented on race or ethnicity. Other recurring topics each received attention from a minority of speakers: immigrant identity, gender identity, mental health, sexual minorities, disability, and rural or agricultural background. We conclude with generalizable advice on creating new remote lecture series that benefit executive team members, speakers, and attendees. Our success with DASL demonstrates that community building and knowledge sharing can flourish under a remote lecture framework.

5.
Science ; 372(6540): 412-417, 2021 04 23.
Article in English | MEDLINE | ID: covidwho-1199748

ABSTRACT

Understanding when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We used a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated before the time of the most recent common ancestor of all sequenced SARS-CoV-2 genomes. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province, China. By characterizing the likely dynamics of the virus before it was discovered, we show that more than two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Genome, Viral , Pandemics , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Animals , COVID-19/transmission , China/epidemiology , Computer Simulation , Evolution, Molecular , Genetic Fitness , Humans , Models, Theoretical , Phylogeny , Retrospective Studies , Viral Zoonoses
6.
bioRxiv ; 2020 Nov 24.
Article in English | MEDLINE | ID: covidwho-955722

ABSTRACT

Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province. By characterizing the likely dynamics of the virus before it was discovered, we show that over two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.

7.
Science ; 370(6516): 564-570, 2020 10 30.
Article in English | MEDLINE | ID: covidwho-760215

ABSTRACT

Accurate understanding of the global spread of emerging viruses is critical for public health responses and for anticipating and preventing future outbreaks. Here we elucidate when, where, and how the earliest sustained severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission networks became established in Europe and North America. Our results suggest that rapid early interventions successfully prevented early introductions of the virus from taking hold in Germany and the United States. Other, later introductions of the virus from China to both Italy and Washington state, United States, founded the earliest sustained European and North America transmission networks. Our analyses demonstrate the effectiveness of public health measures in preventing onward transmission and show that intensive testing and contact tracing could have prevented SARS-CoV-2 outbreaks from becoming established in these regions.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Phylogeny , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Air Travel , COVID-19 , China/epidemiology , Computer Simulation , Contact Tracing , Coronavirus Infections/prevention & control , Evolution, Molecular , Genome, Viral , Germany/epidemiology , Humans , Italy/epidemiology , Mass Screening , Mutation , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , SARS-CoV-2 , Washington/epidemiology
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