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

Vlasova, Anastasia N; Diaz, Annika; Damtie, Debasu; Xiu, Leshan; Toh, Teck-Hock; Lee, Jeffrey Soon-Yit; Saif, Linda J; Gray, Gregory C

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.