Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein
A canine coronavirus (CCoV) has now been reported from two independent human samples from Malaysia (respiratory, collected in 2017–2018; CCoV-HuPn-2018) and Haiti (urine, collected in 2017); these two viruses were nearly genetically identical. In an effort to identify any novel adaptations associate...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-04-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/5/853 |
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| author | Jordan D. Zehr Sergei L. Kosakovsky Pond Darren P. Martin Kristina Ceres Gary R. Whittaker Jean K. Millet Laura B. Goodman Michael J. Stanhope |
| author_facet | Jordan D. Zehr Sergei L. Kosakovsky Pond Darren P. Martin Kristina Ceres Gary R. Whittaker Jean K. Millet Laura B. Goodman Michael J. Stanhope |
| author_sort | Jordan D. Zehr |
| collection | DOAJ |
| description | A canine coronavirus (CCoV) has now been reported from two independent human samples from Malaysia (respiratory, collected in 2017–2018; CCoV-HuPn-2018) and Haiti (urine, collected in 2017); these two viruses were nearly genetically identical. In an effort to identify any novel adaptations associated with this apparent shift in tropism we carried out detailed evolutionary analyses of the spike gene of this virus in the context of related <i>Alphacoronavirus</i> 1 species. The spike 0-domain retains homology to CCoV2b (enteric infections) and Transmissible Gastroenteritis Virus (TGEV; enteric and respiratory). This domain is subject to relaxed selection pressure and an increased rate of molecular evolution. It contains unique amino acid substitutions, including within a region important for sialic acid binding and pathogenesis in TGEV. Overall, the spike gene is extensively recombinant, with a feline coronavirus type II strain serving a prominent role in the recombinant history of the virus. Molecular divergence time for a segment of the gene where temporal signal could be determined, was estimated at around 60 years ago. We hypothesize that the virus had an enteric origin, but that it may be losing that particular tropism, possibly because of mutations in the sialic acid binding region of the spike 0-domain. |
| first_indexed | 2024-03-10T01:38:17Z |
| format | Article |
| id | doaj.art-443b71ba1ca94b72877101f81f87a3c9 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T01:38:17Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-443b71ba1ca94b72877101f81f87a3c92023-11-23T13:29:10ZengMDPI AGViruses1999-49152022-04-0114585310.3390/v14050853Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike ProteinJordan D. Zehr0Sergei L. Kosakovsky Pond1Darren P. Martin2Kristina Ceres3Gary R. Whittaker4Jean K. Millet5Laura B. Goodman6Michael J. Stanhope7Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USAInstitute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USAComputational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7549, South AfricaDepartment of Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USADepartment of Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USAUnité de Virologie et Immunologie Moléculaires, UVSQ, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, FranceDepartment of Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USADepartment of Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USAA canine coronavirus (CCoV) has now been reported from two independent human samples from Malaysia (respiratory, collected in 2017–2018; CCoV-HuPn-2018) and Haiti (urine, collected in 2017); these two viruses were nearly genetically identical. In an effort to identify any novel adaptations associated with this apparent shift in tropism we carried out detailed evolutionary analyses of the spike gene of this virus in the context of related <i>Alphacoronavirus</i> 1 species. The spike 0-domain retains homology to CCoV2b (enteric infections) and Transmissible Gastroenteritis Virus (TGEV; enteric and respiratory). This domain is subject to relaxed selection pressure and an increased rate of molecular evolution. It contains unique amino acid substitutions, including within a region important for sialic acid binding and pathogenesis in TGEV. Overall, the spike gene is extensively recombinant, with a feline coronavirus type II strain serving a prominent role in the recombinant history of the virus. Molecular divergence time for a segment of the gene where temporal signal could be determined, was estimated at around 60 years ago. We hypothesize that the virus had an enteric origin, but that it may be losing that particular tropism, possibly because of mutations in the sialic acid binding region of the spike 0-domain.https://www.mdpi.com/1999-4915/14/5/853relaxed selectioncoronavirus tropism shiftcanine coronavirusfeline coronavirus |
| spellingShingle | Jordan D. Zehr Sergei L. Kosakovsky Pond Darren P. Martin Kristina Ceres Gary R. Whittaker Jean K. Millet Laura B. Goodman Michael J. Stanhope Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein Viruses relaxed selection coronavirus tropism shift canine coronavirus feline coronavirus |
| title | Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein |
| title_full | Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein |
| title_fullStr | Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein |
| title_full_unstemmed | Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein |
| title_short | Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein |
| title_sort | recent zoonotic spillover and tropism shift of a canine coronavirus is associated with relaxed selection and putative loss of function in ntd subdomain of spike protein |
| topic | relaxed selection coronavirus tropism shift canine coronavirus feline coronavirus |
| url | https://www.mdpi.com/1999-4915/14/5/853 |
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