Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies.
Viruses
; 15(2)2023 01 31.
Article
in English
| MEDLINE | ID: covidwho-2225680
ABSTRACT
Phylogenetic trees of coronaviruses are difficult to interpret because they undergo frequent genomic recombination. Here, we propose a new method, coloured genomic bootstrap (CGB) barcodes, to highlight the polyphyletic origins of human sarbecoviruses and understand their host and geographic origins. The results indicate that SARS-CoV and SARS-CoV-2 contain genomic regions of mixed ancestry originating from horseshoe bat (Rhinolophus) viruses. First, different regions of SARS-CoV share exclusive ancestry with five Rhinolophus viruses from Southwest China (RfYNLF/31C 17.9%; RpF46 3.3%; RspSC2018 2.0%; Rpe3 1.3%; RaLYRa11 1.0%) and 97% of its genome can be related to bat viruses from Yunnan (China), supporting its emergence in the Rhinolophus species of this province. Second, different regions of SARS-CoV-2 share exclusive ancestry with eight Rhinolophus viruses from Yunnan (RpYN06 5.8%; RaTG13 4.8%; RmYN02 3.8%), Laos (RpBANAL103 3.3%; RmarBANAL236 1.7%; RmBANAL52 1.0%; RmBANAL247 0.7%), and Cambodia (RshSTT200 2.3%), and 98% of its genome can be related to bat viruses from northern Laos and Yunnan, supporting its emergence in the Rhinolophus species of this region. Although CGB barcodes are very useful in retracing the origins of human sarbecoviruses, further investigations are needed to better take into account the diversity of coronaviruses in bats from Cambodia, Laos, Myanmar, Thailand and Vietnam.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Chiroptera
/
Severe acute respiratory syndrome-related coronavirus
/
COVID-19
Type of study:
Case report
/
Observational study
/
Randomized controlled trials
Limits:
Animals
/
Humans
Country/Region as subject:
Asia
Language:
English
Year:
2023
Document Type:
Article
Affiliation country:
V15020406
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