Discordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronaviruses
Abstract Four distinct species of human coronaviruses (HCoVs) circulate in humans. Despite the recent attention due to SARS-CoV-2, a comprehensive understanding of the molecular epidemiology and genomic evolution of HCoVs remains unclear. Here, we employed primary differentiated human nasal epitheli...
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| Format: | Article |
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Nature Portfolio
2024-10-01
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| Series: | npj Viruses |
| Online Access: | https://doi.org/10.1038/s44298-024-00058-w |
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| _version_ | 1850182647312023552 |
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| author | Marcus G. Mah Michael A. Zeller Rong Zhang Yan Zhuang Venance P. Maro John A. Crump Matthew P. Rubach Eng Eong Ooi Jenny G. Low De Yun Wang Gavin J. D. Smith Yvonne C. F. Su |
| author_facet | Marcus G. Mah Michael A. Zeller Rong Zhang Yan Zhuang Venance P. Maro John A. Crump Matthew P. Rubach Eng Eong Ooi Jenny G. Low De Yun Wang Gavin J. D. Smith Yvonne C. F. Su |
| author_sort | Marcus G. Mah |
| collection | DOAJ |
| description | Abstract Four distinct species of human coronaviruses (HCoVs) circulate in humans. Despite the recent attention due to SARS-CoV-2, a comprehensive understanding of the molecular epidemiology and genomic evolution of HCoVs remains unclear. Here, we employed primary differentiated human nasal epithelial cells for the successful isolation and genome sequencing of HCoVs derived from two retrospective cohorts in Singapore and Tanzania. Phylodynamic inference shows that HCoV-229E and HCoV-OC43 were subject to stronger genetic drift and reduced purifying selection from the early 2000s onwards, primarily targeting spike Domain A and B. This resulted in increased lineage diversification, coinciding with a higher effective reproductive number (Re>1.0). However, HCoV-NL63 and HCoV-HKU1 experienced weaker genetic drift and selective pressure with prolonged regional persistence. Our findings suggest that HCoV-229E and HCoV-OC43 viruses are adept at generating new variants and achieving widespread intercontinental dissemination driven by continuous genetic drift, recombination, and complex migration patterns. |
| format | Article |
| id | doaj-art-ed670ac84052412681d9be5fda103202 |
| institution | OA Journals |
| issn | 2948-1767 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Viruses |
| spelling | doaj-art-ed670ac84052412681d9be5fda1032022025-08-20T02:17:34ZengNature Portfolionpj Viruses2948-17672024-10-012111610.1038/s44298-024-00058-wDiscordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronavirusesMarcus G. Mah0Michael A. Zeller1Rong Zhang2Yan Zhuang3Venance P. Maro4John A. Crump5Matthew P. Rubach6Eng Eong Ooi7Jenny G. Low8De Yun Wang9Gavin J. D. Smith10Yvonne C. F. Su11Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College RoadProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College RoadProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College RoadProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College RoadKilimanjaro Christian Medical CentreKilimanjaro Christian Medical CentreProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College RoadProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College RoadProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College RoadDepartment of Otolaryngology, Yong Loo Lin School of Medicine, National University of SingaporeProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College RoadProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College RoadAbstract Four distinct species of human coronaviruses (HCoVs) circulate in humans. Despite the recent attention due to SARS-CoV-2, a comprehensive understanding of the molecular epidemiology and genomic evolution of HCoVs remains unclear. Here, we employed primary differentiated human nasal epithelial cells for the successful isolation and genome sequencing of HCoVs derived from two retrospective cohorts in Singapore and Tanzania. Phylodynamic inference shows that HCoV-229E and HCoV-OC43 were subject to stronger genetic drift and reduced purifying selection from the early 2000s onwards, primarily targeting spike Domain A and B. This resulted in increased lineage diversification, coinciding with a higher effective reproductive number (Re>1.0). However, HCoV-NL63 and HCoV-HKU1 experienced weaker genetic drift and selective pressure with prolonged regional persistence. Our findings suggest that HCoV-229E and HCoV-OC43 viruses are adept at generating new variants and achieving widespread intercontinental dissemination driven by continuous genetic drift, recombination, and complex migration patterns.https://doi.org/10.1038/s44298-024-00058-w |
| spellingShingle | Marcus G. Mah Michael A. Zeller Rong Zhang Yan Zhuang Venance P. Maro John A. Crump Matthew P. Rubach Eng Eong Ooi Jenny G. Low De Yun Wang Gavin J. D. Smith Yvonne C. F. Su Discordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronaviruses npj Viruses |
| title | Discordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronaviruses |
| title_full | Discordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronaviruses |
| title_fullStr | Discordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronaviruses |
| title_full_unstemmed | Discordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronaviruses |
| title_short | Discordant phylodynamic and spatiotemporal transmission patterns driving the long-term persistence and evolution of human coronaviruses |
| title_sort | discordant phylodynamic and spatiotemporal transmission patterns driving the long term persistence and evolution of human coronaviruses |
| url | https://doi.org/10.1038/s44298-024-00058-w |
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