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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
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