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.

Here we review the existing evidence of animal alphacoronaviruses ( Alphacoronavirus 1 species ) circulating in human patients with acute respiratory illness. Thus far, the viruses similar to canine, feline and porcine alphacoronaviruses (including the most recent CCoV-HuPn-2018 and HuCCoV_Z19) have been detected in humans in Haiti, Malaysia, Thailand, and USA. The available data suggest that these viruses emerged in different geographic locations independently and have circulated in humans for at least 20 years. Additional studies are needed to investigate their prevalence and disease impact.