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MeSH Disease

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SARS-CoV-2 proteins

ORF1ab (1)

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ORF10 (1)


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    Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

    Authors: Hong Zhou; Jingkai Ji; Xing Chen; Yuhai Bi; Juan Li; Tao Hu; Hao Song; Yanhua Chen; Mingxue Cui; Yanyan Zhang; Alice C. Hughes; Edward C. Holmes; Weifeng Shi

    doi:10.1101/2021.03.08.434390 Date: 2021-03-08 Source: bioRxiv

    Although a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV MESHD related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab PROTEIN, ORF7a PROTEIN, ORF8 PROTEIN, N, and ORF10 PROTEIN genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome MESHD virus and porcine epidemic diarrhea virus MESHD. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao HGNC and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.

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MeSH Disease
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