Fig. 4: Analysis of environmental samples in the HSM.

a, Schematic illustration of the experimental design. All 70 SARS-CoV-2-positive samples by RT-qPCR were included for RNA-seq. A total of 57 RNA-seq libraries were successfully constructed. Additionally, RNA-seq libraries of 115 SARS-CoV-2-negative samples passed library quality control. Kraken2 was used for genus classification. Kraken2 and the BOLD system were used for genus classification of Chordata. b, Heatmap showing the read distribution for four domains (Bacteria, Eukarya, viruses and Archaea), the Homo genus and the SARS-CoV-2 species, for SARS-CoV-2 RT-qPCR-positive or SARS-CoV-2 RT-qPCR-negative samples. c, Positive ratio of the illustrated genus in all tested samples. Top-ranked genera within the Chordata phylum are shown. d, Illustration of mammal genera in the market using the threshold of 100 reads per million based on Kraken2. The samples are grouped by SARS-CoV-2 RT-qPCR result and the NGS results analyzed with Bowie2. The blue bars indicate positively detected genera. e, Illustration of mammal genus distribution in samples with a high viral load. Data for Env_0020, Env_0313, Env_0354 and Env_0126 are shown. f, Distribution of the positively detected mammal genera in the market. Samples from four areas where multiple SARS-CoV-2 RT-qPCR-positive samples were detected are shown. The distribution of top mammal genera in each area is shown.