Phylogeography of horseshoe bat sarbecoviruses in Vietnam and
neighbouring countries. Implications for the origins of SARS-CoV and
SARS-CoV-2
Abstract
Previous studies on horseshoe bats (Rhinolophus spp.) have described
many coronaviruses related to SARS-CoV (SARSCoVr) in China and only a
few coronaviruses related to SARS-CoV-2 (SARSCoV2r) in Yunnan (southern
China), Cambodia, Laos and Thailand. Here, we report the results of
several field missions carried out in 2017, 2021 and 2022 across Vietnam
during which 1,218 horseshoe bats were sampled from 19 locations.
Sarbecoviruses were detected in 11% of faecal RNA extracts, with much
more positives for Rhinolophus thomasi (46%). We assembled 38
Sarbecovirus genomes, including 32 SARSCoVr, four SARSCoV2r; and two
recombinants of SARSCoVr and SARSCoV2r (RecSar), one showing a Spike
protein very similar to SARS-CoV-2. We detected a bat co-infected with
four coronaviruses, including two sarbecoviruses. Our analyses revealed
that Sarbecovirus genomes evolve in Vietnam under strong geographic and
host constraints. First, we found evidence for a deep separation between
viruses from northern Vietnam and those from central and southern
Vietnam. Second, we detected only SARSCoVr in Rhinolophus thomasi, both
SARSCoVr and SARSCoV2r in Rhinolophus affinis, and only RecSar in
Rhinolophus pusillus captured close to the border with China. Third, the
bias in favour of Uracil in synonymous third codon-positions of SARSCoVr
viruses showed a negative correlation with latitudes. Our results also
provided support for an emergence of SARS-CoV in horseshoe bats from
northern Yunnan and emergence of SARS-CoV-2 in horseshoe bats from
northern Indochina subtropical forests (southern Yunnan, northern Laos
and north-western Vietnam).