SARS-CoV-2, the causative agent of COVID-19, emerged in December 2019. Its origins remain uncertain. It has been reported that a number of the early human cases had a history of contact with the Huanan Seafood Market. Here we present the results of surveillance for SARS-CoV-2 within the market. From January 1st 2020, after closure of the market, 923 samples were collected from the environment. From 18th January, 457 samples were collected from 18 species of animals, comprising of unsold contents of refrigerators and freezers, swabs from stray animals, and the contents of a fish tank. Using RT-qPCR, SARS-CoV-2 was detected in 73 environmental samples, but none of the animal samples. Three live viruses were successfully isolated. The viruses from the market shared nucleotide identity of 99.99% to 100% with the human isolate HCoV-19/Wuhan/IVDC-HB-01/2019. SARS-CoV-2 lineage A (8782T and 28144C) was found in an environmental sample. RNA-seq analysis of SARS-CoV-2 positive and negative environmental samples showed an abundance of different vertebrate genera at the market. In summary, this study provides information about the distribution and prevalence of SARS-CoV-2 in the Huanan Seafood Market during the early stages of the COVID-19 outbreak.
Supplementary Fig. 1
Meta-information of the SARS-CoV-2 strains included in the phylogenetic analysis.
Supplementary Table 1
The information of the 1380 samples collected from or around the Huanan Seafood Market (HSM). Sample ID: Unique ID for each sample. Lab code: Temporary IDs used for sampling and laboratory testing. Sampling location: The relative location of the sampling site to the HSM, or the relationship of the site to the SHM, whether it is inside the HSM (east/west), near the HSM, or other. Type of vendor sold product including aquatic, seafood, poultry, livestock, wildlife, vegetable, and cold-chain product: Yes, means that the vendor where the sample was collected sells this type of product, and No means that the vendor where the sample was collected does not sell this type of product. These pieces of information together indicate the scope of business of the vendor where the sample was collected.
Supplementary Table 2
Information of the 73 positive environmental samples from the Huanan Seafood Marketa, including sample type, street No. Vendor No. and RT-PCR results.
Supplementary Table 3
Sample information and raw data link of the high-throughput sequencing data of 172 environmental samples from Huanan Seafood Market.
Supplementary Table 4
Seven complete or near complete SARS-CoV-2 genome sequences, including three SARS-CoV-2 sequences from environmental samples and the four sequence from cell supernatants.
Supplementary Table 5
Summary of number of reads mapped to positions 8782 and 28144 in different samples.
Supplementary Table 6
The distribution of different genera in 172 sequenced environmental samples. The abundance of each genera was analyzed using the Kranken2 method in metagenomic analyses. All genera, including those belonging to the domains Bacteria, Eukaryota, Viruses, and Archaea, were illustrated. The 172 samples included 60 SARS-CoV-2 PCR positive and 112 SARS-CoV-2 PCR negative samples, with detailed sample information listed in Extended Data Table 6.
Supplementary Table 7
The difference in genus between SARS-CoV-2 PCR-positive and -negative environmental samples was analyzed using statistical methods with DESeq2. The adjusted P values were reported.
Supplementary Table 8
Classification of genus within the Mammalia class using the barcode of life data (BOLD) system. The cytochrome c oxidase subunit I (COI) of genera in Chordata, as defined by the Barcode Index Number System, was used for sequence mapping.
Supplementary Table 9
Risk of co-existence with SARS-CoV-2 PCR-positive samples. Fisher’s exact test was used for statistical analysis.
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Liu, W.J., Liu, P., Lei, W. et al. Surveillance of SARS-CoV-2 at the Huanan Seafood Market. Nature (2023). https://doi.org/10.1038/s41586-023-06043-2
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