Prevalence and genetic diversity analysis of human coronaviruses among cross-border children

Liu, Peilin; Shi, Lei; Zhang, Wei; He, Jianan; Liu, Chunxiao; Zhao, Chunzhong; Kong, Siu Kai; Loo, Jacky Fong Chuen; Gu, Dayong; Hu, Longfei

The coronaviruses detected from SZ-HK ports had a high homology with the published strains indicated a stable gene sequences in S and RdRp. However, there were great genetic diversity among these circulating strains. OC43 detected in this report cluster with genotype B, D and E strains, while none of genotypes A and C were detected, probably because genotype A strains had disappeared and genotype C strains were not included in this study [9] . We observed six OC43 coronaviruses were closely related to the genotype B detected from Beijing based on S genes. It possessed 99% nt identities and showed an incongruent phylogenetic relationship between RdRp and S genes. New Recombination genotypes led by high intra-specific diversity have been reported in studying OC43 coronaviruses circulating in France, where eight different recombinants were discovered and confirmed with in silico analysis of complete genomes available using partial genome sequencing [10] . At present, the base substitution and insertion in OC43 and HKU1 is novel and could not find any matches in either OC43 or HKU1 strains in Genbank library. More importantly, these amino acid sites are located in one of the putative regions of HKU1 receptor binding domain [26] . The protein structure and its related function, especially on the efficiency on human infection, need to be investigated in the future.