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

Abstract

Understanding the circumstances that lead to pandemics is important for their prevention. Here, we analyze 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–8 December), while 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 prior to 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.

The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic

“…The sustained presence of a potential source of virus transmission into the human population in late 2019, plausibly from infected live mammals sold at the Huanan market, offers an explanation of our findings and the origins of SARS-CoV-2. The pattern of COVID-19 cases reported for the Huanan market, with the earliest cases in the same part of the market as the wildlife sales and evidence of at least two introductions ( 38 ), resembles the multiple cross-species transmissions of SARS-CoV-2 subsequently observed during the pandemic from animals to humans on mink farms ( 46 ) and from infected hamsters to humans in the pet trade ( 47 ). There was an extensive network of wildlife farms in western Hubei Province, including hundreds of thousands of raccoon dogs on farms in Enshi Prefecture, which supplied the Huanan market ( 48 ).…”

“…In a related study, we inferred separate introductions of SARS-CoV-2 lineages A and B into humans from likely infected animals at the Huanan market ( 38 ). We estimated the first COVID-19 case to have occurred in November 2019, with few human cases and hospitalizations occurring through mid-December ( 38 ).…”

“…In a related study, we inferred separate introductions of SARS-CoV-2 lineages A and B into humans from likely infected animals at the Huanan market ( 38 ). We estimated the first COVID-19 case to have occurred in November 2019, with few human cases and hospitalizations occurring through mid-December ( 38 ). A recent preprint ( 24 ) confirms the authenticity of the CCDC report (data S1) and records additional positive environmental samples in the southwestern area of the market selling live animals.…”

Ecological super‐spreaders drive host–range oscillations: Omicron and risk space for emerging infectious disease

“…Wherever humans established the virus, people were the primary reservoirs of infection in wildland, agricultural and urban environments (Rochman et al, 2021), serving as mediators of introduction and exposure among diverse mammalian hosts across terrestrial ecosystems Hale et al, 2022;Kuchipudi et al, 2022;Lytras et al, 2021;Oude Munnink et al, 2021;Pickering et al, 2022;Wei et al, 2021). The animal wet markets in Wuhan and other urban centres in China and Southeast Asia provided steppingstone opportunities for SARS-like viruses to colonize humans on at least two other recent occasions -SARS-CoV in 2003 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 (Huong et al, 2020;Lytras et al, 2021;Pekar et al, 2022;Worobey et al, 2022;Xia et al, 2021;.…”

Tens of thousands of people exposed to bat coronaviruses each year

“…The virus almost certainly emerged in bats, but how it came to infect people has been the subject of intensive research and multiple international investigations. Two studies published in Science last month 2,3 suggest that the virus probably jumped from animals -bats or other intermediate species -to people on two separate occasions at a live-animal market in Wuhan, China, sparking the COVID-19 pandemic.…”