Novel Canine Coronavirus Isolated from a Hospitalized Patient With Pneumonia in East Malaysia. (20th May 2021)

• Record Type: Journal Article
• Authors: Vlasova, Anastasia N; Diaz, Annika; Damtie, Debasu; Xiu, Leshan; Toh, Teck-Hock; Lee, Jeffrey Soon-Yit; Saif, Linda J; Gray, Gregory C
• Is Part Of: Clinical infectious diseases. Volume 74:Number 3(2022)
• Page Start: 446
• Page End: 454
• Publication Date: 2021-05-20
• Subjects: canine coronavirus -- novel alphacoronavirus -- pneumonia: zoonotic disease -- East Malaysia; Communicable diseases -- Periodicals; 616.905
• DOI: 10.1093/cid/ciab456
• Languages: English
• ISSNs: 1058-4838

Abstract

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. Abstract : This is the first complete genome characterization of a novel canine-feline recombinant alphacoronavirus isolated from a child with pneumonia. Similar to severe acute respiratory syndrome coronavirus, this novel virus possesses some unique genetic features suggestive of recent zoonotic transmission.