Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies
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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/2/406 |
| _version_ | 1827755187925680128 |
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| author | Alexandre Hassanin Opale Rambaud |
| author_facet | Alexandre Hassanin Opale Rambaud |
| author_sort | Alexandre Hassanin |
| collection | DOAJ |
| description | 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 (<i>Rhinolophus</i>) viruses. First, different regions of SARS-CoV share exclusive ancestry with five <i>Rhinolophus</i> 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 <i>Rhinolophus</i> species of this province. Second, different regions of SARS-CoV-2 share exclusive ancestry with eight <i>Rhinolophus</i> 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 <i>Rhinolophus</i> 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. |
| first_indexed | 2024-03-11T08:00:50Z |
| format | Article |
| id | doaj.art-7e6a57af462a4a619f9a27c3841a09f6 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-11T08:00:50Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-7e6a57af462a4a619f9a27c3841a09f62023-11-16T23:48:35ZengMDPI AGViruses1999-49152023-01-0115240610.3390/v15020406Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case StudiesAlexandre Hassanin0Opale Rambaud1Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, EPHE, MNHN, UA, 75231 Paris, FranceInstitut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, EPHE, MNHN, UA, 75231 Paris, FrancePhylogenetic 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 (<i>Rhinolophus</i>) viruses. First, different regions of SARS-CoV share exclusive ancestry with five <i>Rhinolophus</i> 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 <i>Rhinolophus</i> species of this province. Second, different regions of SARS-CoV-2 share exclusive ancestry with eight <i>Rhinolophus</i> 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 <i>Rhinolophus</i> 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.https://www.mdpi.com/1999-4915/15/2/406coronavirusgenomerecombinationCOVID-19reservoir hostsecondary host |
| spellingShingle | Alexandre Hassanin Opale Rambaud Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies Viruses coronavirus genome recombination COVID-19 reservoir host secondary host |
| title | Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies |
| title_full | Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies |
| title_fullStr | Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies |
| title_full_unstemmed | Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies |
| title_short | Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies |
| title_sort | retracing phylogenetic host and geographic origins of coronaviruses with coloured genomic bootstrap barcodes sars cov and sars cov 2 as case studies |
| topic | coronavirus genome recombination COVID-19 reservoir host secondary host |
| url | https://www.mdpi.com/1999-4915/15/2/406 |
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