Molecular epidemiology and characterization of bat coronaviruses in Southern China

Abstract

Coronavirus was under extensive research since the emergence of Severe Acute Respiratory Syndrome caused by SARS coronavirus in 2003. Before the SARS outbreak, human coronaviruses were found to be correlated to mild respiratory tract infections. However, the emergence of highly virulent coronaviruses including SARS-CoV and MERS-CoV arose the research value on these viruses. With the improvement in our understanding towards coronaviruses recently, it is found that bats were the animal hosts of over 100 coronaviruses. It is hypothesized that bat coronaviruses may serve as the gene pool of Alphacoronaviruses and Betacoronaviruses. There is a possibility that novel coronavirus species with high virulence towards human could be emerged due to random recombination events. Therefore, regular surveillance and studies of coronaviruses can assist us to understand more towards coronaviruses in biodiversity.

In this study, molecular surveillance of coronaviruses was carried out for local bats and bats from mainland China. 1419 samples from local bats including anal swab, fecal sample and mouth swab were collected and 360 anal swab samples were collected from bats in mainland China. Molecular screening results of coronaviruses using the partial region of RNA-dependent RNA polymerase (RdRp) gene showed that 2 local bat samples with 99% nucleotides identity to Hi-BatCoV HKU10. Myotis daubentonii coronavirus was found in 1 sample from local bats with 96% identity. 7 local bat samples were found to contain potential novel Alphacoronavirus shared 81% nucleotides identity towards the partial region of RdRp gene of Hi-BatCoV HKU10. For the bat samples from China, 22 positive samples were detected including 18 Ty-BatCoV HKU4, 3 SARSr-Rh-BatCoV HKU3 and 1 potential novel Alphacoronavirus sharing 81% nucleotides identity towards BtNv-AlphaCoV/SC2013.

Phylogenetic analysis of the spike gene of Ty-BatCoV HKU4 and SARSr-Rh-BatCoV HKU3 from mainland bat samples was performed to examine the mutation characteristic of the receptor binding domain of spike protein. Results indicated that non-synonymous substitutions occurred at the receptor binding domain of spike protein of Ty-BatCoV HKU4 but not in SARSr-Rh-BatCoV HKU3. Continuous molecular surveillance and genomic study of different bat coronaviruses should be carried on. Further researches on novel coronaviruses should be conducted such as bioinformatics analysis, virulence study and serological study.