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Through COVID-19 pandemic, Genome and Science (journal)

Research is ongoing as to whether SARS-CoV-2 came directly from bats or indirectly through an intermediate host, such as pangolins, civets, or raccoon dogs. Genomic sequence evidence indicates the spillover event introducing SARS-CoV-2 to humans likely occurred in late 2019. As with the 2002–2004 SARS-CoV-1 outbreak, efforts to trace the specific geographic and taxonomic origins of SARS-CoV-2 could take years, and results may be inconclusive.

In July 2022, two papers published in Science described novel epidemiological and genetic evidence that suggested the pandemic likely began at the Huanan Seafood Wholesale Market and did not come from a laboratory. In 2026, virologist Joel Wertheim and colleagues at UCSD published a study in Cell that compared evolutionary patterns of outbreaks of Ebola, influenza and other viruses. They found that the mutation pattern of SARS-CoV-2 matched five naturally occurring outbreaks, but did not resemble the 1977 Russian flu outbreak which was likely from a lab leak. Wertheim and other WHO-designated experts favor the origin of SARS-CoV-2 to have been in bats that passed it to animals sold in the Wuhan market.

Zoonosis

While there are multiple proposed explanations for how SARS-CoV-2 was introduced into and evolved adaptations suited to human populations, there is significant evidence and agreement that the most likely original viral reservoir for SARS-CoV-2 is horseshoe bats. The closest known viral relatives of SARS-CoV-2 are BANAL-52 and RaTG13, sampled from horseshoe bat droppings in Feuang, Laos, and Yunnan province in China respectively. The evolutionary distance between SARS-CoV-2 and RaTG13 is estimated to be about 50 years (between 38 and 72 years).

Bats are a significant reservoir species for a diverse range of coronaviruses, and humans have been found with antibodies for them suggesting that direct infection by bats is common. The zoonotic transmission of SARS-CoV-2 virus to humans took place in the context of exacerbating factors that could make such spillovers more likely. Human contact with bats has increased as human population centers encroach on bat habitats. Several social and environmental factors including climate change, natural ecosystem destruction and wildlife trade have also increased the likelihood for the emergences of zoonosis. One study made with the support of the European Union found climate change increased the likelihood of the pandemic by influencing distribution of bat species.

The earliest human cases of SARS-CoV-2 were identified in Wuhan, but the index case remains unknown. RaTG13 was sampled from bats in a mine in Mojiang County, Yunnan, located roughly 1,500 km (930 mi) away from Wuhan, and there are relatively few bat coronaviruses from Hubei province, where Wuhan is located.

Intermediate host

In addition to direct spillover, another pathway, considered highly likely by scientists, is that of transmission through an intermediate host. Specifically, this implies that a cross species transmission occurred prior to the human outbreak and that it had pathogenic results on the animal. This pathway has the potential to allow for greater adaptation to human transmission via animals with more similar protein shapes to humans, though this is not required for the scenario to occur. The evolutionary separation from bat viruses is explained in this case by the virus's presence in an unknown species with less viral surveillance than bats. The virus's ability to easily infect and adapt to additional species (including mink) provides evidence that such a route of transmission is possible.

A 2024 study of samples collected from Huanan Seafood Wholesale Market found genetic material of various possible intermediate hosts. The most likely were raccoon dogs. Additionally, the study suggests the raccoon dogs may have come from southern China, where the closest-known relatives to SARS-CoV-2 were found in bats.

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