Molecular epidemiology of coronaviruses in animals

Abstract

As the animals are an ongoing source of the coronaviruses, more and more bird coronaviruses were found as Deltacoronavirus recently, their abilities to fly over a long distances from place to place increase the potential of spreading the CoVs to other animals. Therefore it is a need to study and investigate the CoVs circulating in different animals. In this study, a total of 2792 samples from 103 cats, 96 dogs, 19 dolphins, 20 sea lions, 6 seals, 4 red pandas, 4 giant pandas, 4 Asian small-clawed otters, 9 tortoises, 7 monkeys, 2 bears, 2 capybaras, 231 Horses, 94China rodents were screened for the presence of coronaviruses using pan-CoVs PCR primers targeting the partial RdRp gene of coronaviruses. We also particularly looked for Deltacoronaviruses (Group 4 coronaviruses), using Group 4 CoVs consensus primers. Thirteen stray cat samples, including samples 01-03 and 05-14, one stray dog sample (sample 04) and one rodent sample (sample 15) were found to be positive for CoVs. However, none of the samples were found to be positive using Group 4 CoVs consensus primers. The DNA sequence of partial RdRp of sample 05-14 were identical and sample 02-03 also had a sequence identity of 100% while sample 01 had slightly different in the RdRp DNA sequence with the others. Phylogenetic analysis based on the DNA sequence of partial RdRp revealed that sample 01-14 belonged to Alphaconoavirus, sample 02-03 formed a cluster with FCoV-UU31 (95% nucleotide identities), sample 01 clustered together with FCoV-black (98% nucleotide identities), sample 04 and 05-14 being more closely-related to CCoV-S378 (96% nucleotide identities) and FCoV-UU7(98% nucleotide identities) respectively. However, sample 15 formed a distinct cluster with MHV-1(89% nucleotide identities) within Betacoronavirus. All the thirteen isolates (sample 01-03, 05-14) within Alphaconoavirus were identical in terms of their partial RdRp amino acid sequence while sample 04 had 100% identity to CCoV-S378 and sample 015 had 90% identity to MHV-1.The phylogenetic analysis of the partial RdRp amino acid sequence also revealed similar result as the DNA sequence. To sum up, coronavirus is more common in cats rather than in dogs, rodents, horses and other mammals examined in this study. However, none of the Detacoronavirus was found from all the animal samples.