Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environ-mental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that mar-ket-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistentwith market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identifywildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboorats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal virusesthat infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches,we recover genotypes of market animals and compare them with those from farms and other markets. Thisanalysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritizefor serological and viral sampling.