A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China
At the end of 2019, A new type of beta-CoV, SARS-CoV-2 emerged and triggered the COVID-19 pandemic, which spread overwhelmingly around the world in less than a year. However, the origin and direct ancestral viruses of SARS-CoV-2 remain unknown. RaTG13, a novel coronavirus found in bats in China’s Yu...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2021-01-01
|
| Series: | Emerging Microbes and Infections |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/22221751.2021.1964925 |
| _version_ | 1818987874763145216 |
|---|---|
| author | Li-li Li Jing-lin Wang Xiao-hua Ma Xiao-man Sun Jin-song Li Xiao-fei Yang Wei-feng Shi Zhao-jun Duan |
| author_facet | Li-li Li Jing-lin Wang Xiao-hua Ma Xiao-man Sun Jin-song Li Xiao-fei Yang Wei-feng Shi Zhao-jun Duan |
| author_sort | Li-li Li |
| collection | DOAJ |
| description | At the end of 2019, A new type of beta-CoV, SARS-CoV-2 emerged and triggered the COVID-19 pandemic, which spread overwhelmingly around the world in less than a year. However, the origin and direct ancestral viruses of SARS-CoV-2 remain unknown. RaTG13, a novel coronavirus found in bats in China’s Yunnan Province, is the closest relative virus of the SARS-CoV-2 identified so far. In this study, a new SARS-CoV-2 related virus, provisionally named PrC31, was discovered in Yunnan province by retrospectively analyse bat next generation sequencing (NGS) data of intestinal samples collected in 2018. PrC31 shared 90.7% and 92.0% nucleotide identities to the genomes of SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment of PrC31 showed that several genomic regions, especially orf1a and orf8 had the highest homology with those corresponding genomic regions of SARS-CoV-2 than any other related viruses. Phylogenetic analysis indicated that PrC31 shared a common ancestor with SARS-CoV-2 in evolutionary history. The differences between the PrC31 and SARS-CoV-2 genomes were mainly manifested in the spike genes. The amino acid homology between the receptor binding domains of PrC31 and SARS-CoV-2 was only 64.2%. Importantly, recombination analysis revealed that PrC31 underwent multiple complex recombination events (including three recombination breakpoints) involving the SARS-CoV and SARS-CoV-2 sub-lineages, indicating that PrC31 evolved from yet-to-be-identified intermediate recombination strains. Combined with previous studies, it is revealed that the beta-CoVs may possess a more complex recombination mechanism than we thought. |
| first_indexed | 2024-12-20T19:13:37Z |
| format | Article |
| id | doaj.art-95e2ac51f99f4a6fa06b0e4a52191519 |
| institution | Directory Open Access Journal |
| issn | 2222-1751 |
| language | English |
| last_indexed | 2024-12-20T19:13:37Z |
| publishDate | 2021-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj.art-95e2ac51f99f4a6fa06b0e4a521915192022-12-21T19:29:10ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512021-01-011011683169010.1080/22221751.2021.1964925A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, ChinaLi-li Li0Jing-lin Wang1Xiao-hua Ma2Xiao-man Sun3Jin-song Li4Xiao-fei Yang5Wei-feng Shi6Zhao-jun Duan7National Institute for Viral Disease Control and Prevention, China CDC, Beijing, People’s Republic of ChinaYunnan Tropical and Subtropical Animal Viral Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, People’s Republic of ChinaNational Institute for Viral Disease Control and Prevention, China CDC, Beijing, People’s Republic of ChinaNational Institute for Viral Disease Control and Prevention, China CDC, Beijing, People’s Republic of ChinaNational Institute for Viral Disease Control and Prevention, China CDC, Beijing, People’s Republic of ChinaNational Engineering Research Center of Freshwater Fisheries, Beijing Fisheries Research Institute, Beijing, People’s Republic of ChinaKey Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Taian, People’s Republic of ChinaNational Institute for Viral Disease Control and Prevention, China CDC, Beijing, People’s Republic of ChinaAt the end of 2019, A new type of beta-CoV, SARS-CoV-2 emerged and triggered the COVID-19 pandemic, which spread overwhelmingly around the world in less than a year. However, the origin and direct ancestral viruses of SARS-CoV-2 remain unknown. RaTG13, a novel coronavirus found in bats in China’s Yunnan Province, is the closest relative virus of the SARS-CoV-2 identified so far. In this study, a new SARS-CoV-2 related virus, provisionally named PrC31, was discovered in Yunnan province by retrospectively analyse bat next generation sequencing (NGS) data of intestinal samples collected in 2018. PrC31 shared 90.7% and 92.0% nucleotide identities to the genomes of SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment of PrC31 showed that several genomic regions, especially orf1a and orf8 had the highest homology with those corresponding genomic regions of SARS-CoV-2 than any other related viruses. Phylogenetic analysis indicated that PrC31 shared a common ancestor with SARS-CoV-2 in evolutionary history. The differences between the PrC31 and SARS-CoV-2 genomes were mainly manifested in the spike genes. The amino acid homology between the receptor binding domains of PrC31 and SARS-CoV-2 was only 64.2%. Importantly, recombination analysis revealed that PrC31 underwent multiple complex recombination events (including three recombination breakpoints) involving the SARS-CoV and SARS-CoV-2 sub-lineages, indicating that PrC31 evolved from yet-to-be-identified intermediate recombination strains. Combined with previous studies, it is revealed that the beta-CoVs may possess a more complex recombination mechanism than we thought.https://www.tandfonline.com/doi/10.1080/22221751.2021.1964925SARS-CoV-2batscoronavirusesrecombinationevolution |
| spellingShingle | Li-li Li Jing-lin Wang Xiao-hua Ma Xiao-man Sun Jin-song Li Xiao-fei Yang Wei-feng Shi Zhao-jun Duan A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China Emerging Microbes and Infections SARS-CoV-2 bats coronaviruses recombination evolution |
| title | A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China |
| title_full | A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China |
| title_fullStr | A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China |
| title_full_unstemmed | A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China |
| title_short | A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China |
| title_sort | novel sars cov 2 related coronavirus with complex recombination isolated from bats in yunnan province china |
| topic | SARS-CoV-2 bats coronaviruses recombination evolution |
| url | https://www.tandfonline.com/doi/10.1080/22221751.2021.1964925 |
| work_keys_str_mv | AT lilili anovelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT jinglinwang anovelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT xiaohuama anovelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT xiaomansun anovelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT jinsongli anovelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT xiaofeiyang anovelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT weifengshi anovelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT zhaojunduan anovelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT lilili novelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT jinglinwang novelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT xiaohuama novelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT xiaomansun novelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT jinsongli novelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT xiaofeiyang novelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT weifengshi novelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina AT zhaojunduan novelsarscov2relatedcoronaviruswithcomplexrecombinationisolatedfrombatsinyunnanprovincechina |