Anastasia N Vlasova1, Annika Diaz1, Debasu Damtie2,3, Leshan Xiu4,5,6, Teck-Hock Toh7,8, Jeffrey Soon-Yit Lee7,8, Linda J Saif1, Gregory C Gray4,5,9,10. 1. Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA. 2. Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia. 3. The Ohio State University Global One Health LLC, Eastern Africa Regional Office, Addis Ababa, Ethiopia. 4. Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA. 5. Duke Global Health Institute, Duke University, Durham, North Carolina, USA. 6. NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. 7. Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia. 8. Faculty of Medicine, SEGi University, Kota Damansara, Selangor, Malaysia. 9. Global Health Research Center, Duke Kunshan University, Kunshan, China. 10. Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.
Abstract
BACKGROUND: During the validation of a highly sensitive panspecies coronavirus (CoV) seminested reverse-transcription polymerase chain reaction (RT-PCR) assay, we found canine CoV (CCoV) RNA in nasopharyngeal swab samples from 8 of 301 patients (2.5%) hospitalized with pneumonia during 2017-2018 in Sarawak, Malaysia. Most patients were children living in rural areas with frequent exposure to domesticated animals and wildlife. METHODS: Specimens were further studied with universal and species-specific CoV and CCoV 1-step RT-PCR assays, and viral isolation was performed in A72 canine cells. Complete genome sequencing was conducted using the Sanger method. RESULTS: Two of 8 specimens contained sufficient amounts of CCoVs as confirmed by less-sensitive single-step RT-PCR assays, and 1 specimen demonstrated cytopathic effects in A72 cells. Complete genome sequencing of the virus causing cytopathic effects identified it as a novel canine-feline recombinant alphacoronavirus (genotype II) that we named CCoV-human pneumonia (HuPn)-2018. Most of the CCoV-HuPn-2018 genome is more closely related to a CCoV TN-449, while its S gene shared significantly higher sequence identity with CCoV-UCD-1 (S1 domain) and a feline CoV WSU 79-1683 (S2 domain). CCoV-HuPn-2018 is unique for a 36-nucleotide (12-amino acid) deletion in the N protein and the presence of full-length and truncated 7b nonstructural protein, which may have clinical relevance. CONCLUSIONS: This is the first report of a novel canine-feline recombinant alphacoronavirus isolated from a human patient with pneumonia. If confirmed as a pathogen, it may represent the eighth unique coronavirus known to cause disease in humans. Our findings underscore the public health threat of animal CoVs and a need to conduct better surveillance for them.
BACKGROUND: During the validation of a highly sensitive panspecies coronavirus (CoV) seminested reverse-transcription polymerase chain reaction (RT-PCR) assay, we found canine CoV (CCoV) RNA in nasopharyngeal swab samples from 8 of 301 patients (2.5%) hospitalized with pneumonia during 2017-2018 in Sarawak, Malaysia. Most patients were children living in rural areas with frequent exposure to domesticated animals and wildlife. METHODS: Specimens were further studied with universal and species-specific CoV and CCoV 1-step RT-PCR assays, and viral isolation was performed in A72 canine cells. Complete genome sequencing was conducted using the Sanger method. RESULTS: Two of 8 specimens contained sufficient amounts of CCoVs as confirmed by less-sensitive single-step RT-PCR assays, and 1 specimen demonstrated cytopathic effects in A72 cells. Complete genome sequencing of the virus causing cytopathic effects identified it as a novel canine-feline recombinant alphacoronavirus (genotype II) that we named CCoV-human pneumonia (HuPn)-2018. Most of the CCoV-HuPn-2018 genome is more closely related to a CCoV TN-449, while its S gene shared significantly higher sequence identity with CCoV-UCD-1 (S1 domain) and a feline CoV WSU 79-1683 (S2 domain). CCoV-HuPn-2018 is unique for a 36-nucleotide (12-amino acid) deletion in the N protein and the presence of full-length and truncated 7b nonstructural protein, which may have clinical relevance. CONCLUSIONS: This is the first report of a novel canine-feline recombinant alphacoronavirus isolated from a human patient with pneumonia. If confirmed as a pathogen, it may represent the eighth unique coronavirus known to cause disease in humans. Our findings underscore the public health threat of animal CoVs and a need to conduct better surveillance for them.
Authors: Arné de Klerk; Phillip Swanepoel; Rentia Lourens; Mpumelelo Zondo; Isaac Abodunran; Spyros Lytras; Oscar A MacLean; David Robertson; Sergei L Kosakovsky Pond; Jordan D Zehr; Venkatesh Kumar; Michael J Stanhope; Gordon Harkins; Ben Murrell; Darren P Martin Journal: Virus Evol Date: 2022-06-14
Authors: Yaozong Chen; Lulu Sun; Irfan Ullah; Guillaume Beaudoin-Bussières; Sai Priya Anand; Andrew P Hederman; William D Tolbert; Rebekah Sherburn; Dung N Nguyen; Lorie Marchitto; Shilei Ding; Di Wu; Yuhong Luo; Suneetha Gottumukkala; Sean Moran; Priti Kumar; Grzegorz Piszczek; Walther Mothes; Margaret E Ackerman; Andrés Finzi; Pradeep D Uchil; Frank J Gonzalez; Marzena Pazgier Journal: Sci Adv Date: 2022-07-13 Impact factor: 14.957
Authors: Ben Jackson; Maciej F Boni; Matthew J Bull; Amy Colleran; Rachel M Colquhoun; Alistair C Darby; Sam Haldenby; Verity Hill; Anita Lucaci; John T McCrone; Samuel M Nicholls; Áine O'Toole; Nicole Pacchiarini; Radoslaw Poplawski; Emily Scher; Flora Todd; Hermione J Webster; Mark Whitehead; Claudia Wierzbicki; Nicholas J Loman; Thomas R Connor; David L Robertson; Oliver G Pybus; Andrew Rambaut Journal: Cell Date: 2021-08-17 Impact factor: 41.582
Authors: Edward C Holmes; Stephen A Goldstein; Angela L Rasmussen; David L Robertson; Alexander Crits-Christoph; Joel O Wertheim; Simon J Anthony; Wendy S Barclay; Maciej F Boni; Peter C Doherty; Jeremy Farrar; Jemma L Geoghegan; Xiaowei Jiang; Julian L Leibowitz; Stuart J D Neil; Tim Skern; Susan R Weiss; Michael Worobey; Kristian G Andersen; Robert F Garry; Andrew Rambaut Journal: Cell Date: 2021-08-19 Impact factor: 41.582
Authors: Francisco Rodríguez-Frías; Josep Quer; David Tabernero; Maria Francesca Cortese; Selene Garcia-Garcia; Ariadna Rando-Segura; Tomas Pumarola Journal: Microorganisms Date: 2021-12-06