Novel Canine Coronavirus Isolated from a Hospitalized Patient With Pneumonia in East Malaysia

• Published in: Clinical infectious diseases 2022-02, Vol.74 (3), p.446-454
• Main Authors: Vlasova, Anastasia N, Diaz, Annika, Damtie, Debasu, Xiu, Leshan, Toh, Teck-Hock, Lee, Jeffrey Soon-Yit, Saif, Linda J, Gray, Gregory C
• Format: Article
• Language: English
• Subjects: Animals; Cats; Coronavirus Infections - veterinary; Coronavirus, Canine - genetics; Dog Diseases; Dogs; Humans; Malaysia; Phylogeny; Pneumonia
• ISSN: 1058-4838; 1537-6591
• DOI: 10.1093/cid/ciab456

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. 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.