Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS-CoV and SARS-CoV-2.
Chiroptera
Southeast Asia
coronavirus genome
molecular evolution
phylogeny
recombination
Journal
Molecular ecology
ISSN: 1365-294X
Titre abrégé: Mol Ecol
Pays: England
ID NLM: 9214478
Informations de publication
Date de publication:
19 Aug 2024
19 Aug 2024
Historique:
revised:
16
07
2024
received:
13
03
2024
accepted:
19
07
2024
medline:
20
8
2024
pubmed:
20
8
2024
entrez:
20
8
2024
Statut:
aheadofprint
Résumé
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 1218 horseshoe bats were sampled from 19 locations. Sarbecoviruses were detected in 11% of faecal RNA extracts, with much more positives among 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 geographical 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 extracted from R. thomasi 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).
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e17486Subventions
Organisme : Agence Nationale de la Recherche
ID : ANR-21-CO12-0002
Organisme : Vietnam Academy of Science and Technology
ID : KHCBTĐ.02/22-24
Organisme : Vietnam Academy of Science and Technology
ID : QTHU01.01/22-23
Organisme : National Research, Development, and Innovation Fund of Hungary
ID : NKFIH FK137778
Organisme : National Research, Development, and Innovation Fund of Hungary
ID : RRF-2.3.1-21-2022-00010
Organisme : János Bolyai Research Scholarship of the Hungarian Academy of Sciences
ID : BO/00825/21
Informations de copyright
© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.
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