A comprehensive survey of bat sarbecoviruses across China for the origin tracing of SARS-CoV and SARS-CoV-2
2021
Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 have been
thought to originate from bat, but whether the cross-species transmission occurred
directly from bat to human or through an intermediate host remains elusive. In this
study, we performed CoV screening of 102 samples collected from animal-selling stalls
of Wuhan Huanan Market (WHM) and pharyngeal and anal swabs from13,064 bats collected
at 703 locations across China, covering almost all known southern hotspots for sarbecovirus,
between 2016 and 2021. This is the first systematic survey of bat CoV in China during
the outbreak of Corona Virus Disease 2019. We found four non-sarbeco CoVs in samples
of WHM, and 142 SARS-CoV related CoVs (SARSr-CoV) and 4 recombinant CoVs in bats,
of which YN2020B-G share the highest sequence identity with SARS-CoV among all known
bat CoVs, suggesting endemic SARSr-CoVs in bats in China. However, we did not find
any SARS-CoV-2 related CoVs (SC2r-CoV) in any samples, including specimens collected
from the only two domestic places where RaTG13 and RmYN02 were previously reported
(the Tongguan caves and the karst caves around the Xishuangbanna Tropical Botanical
Garden), indicating that SC2r-CoVs might not actively circulate among bats in China.
Phylogenetic analysis showed that there are three different lineages of sarbecoviruses,
L1 (SARSr-CoV), L2 (SC2r-CoV), and L-R (a novel CoV lineage from L1 and L2 recombination),
in China. Of note, L-R CoVs are only found in R. pusillus. Further macroscopical analysis
of the genetic diversity, host specificity for colonization and accidental infection,
and geographical characteristics of available CoVs in database revealed the presence
of a general geographical distribution pattern for bat sarbecoviruses, with the highest
genetic diversity and sequence homology to SARS-CoV or SARS-CoV-2 along the southwest
border of China, the least in the northwest of China. Considering the receptor binding
motifs for spike gene of sarbecoviruses in Indochina Peninsula show the greatest diversity,
our data provide the rationale that extensive surveys in further south and southwest
to or of China might be needed for finding closer ancestors of SARS-CoV and SARS-CoV-2.
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