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      Novel Canine Coronavirus Isolated from a Hospitalized Pneumonia Patient, East Malaysia

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          Abstract

          Background

          During the validation of a highly sensitive pan-species coronavirus (CoV) semi-nested RT-PCR assay, we found canine CoV (CCoV) RNA in nasopharyngeal swabs from eight (2.5%) of 301 patients hospitalized with pneumonia during 2017-18 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 one-step RT-PCR assays, and viral isolation was performed in A72 canine cells. Complete genome sequencing was conducted using Sanger method.

          Results

          Two of eight specimens contained sufficient amounts of CCoVs as confirmed by less-sensitive single-step RT-PCR assays, and one specimen demonstrated cytopathic effects (CPE) in A72 cells. Complete genome sequencing of the virus causing CPE identified it as a novel canine-feline recombinant alphacoronavirus (genotype II) that we named CCoV-HuPn-2018. Most of 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 nt (12-aa) deletion in the N protein and the presence of full-length and truncated 7b non-structural protein which may have clinical relevance.

          Conclusions

          This is the first report of a novel canine-feline recombinant alphacoronavirus isolated from a human pneumonia patient. 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.

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          Author and article information

          Journal
          Clin Infect Dis
          Clin Infect Dis
          cid
          Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
          Oxford University Press (US )
          1058-4838
          1537-6591
          20 May 2021
          Affiliations
          [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
          Author notes

          These two authors contributed equally.

          Corresponding author: Gregory C. Gray, MD, MPH, FIDSA, Professor, Division of Infectious Diseases DUMC Box 102359, Duke University, Durham, NC 27710, gregory.gray@ 123456duke.edu , +1 (919) 684-1032
          Article
          ciab456
          10.1093/cid/ciab456
          8194511
          34013321
          © The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

          This article is made available via the PMC Open Access Subset for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing. Upon expiration of these permissions, PMC is granted a perpetual license to make this article available via PMC and Europe PMC, consistent with existing copyright protections.

          This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model ( https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

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