Genetic diversity of alpha-coronavirus in bats from China

Abstract

Background: Human coronaviruses are distributed across 2 genera of Coronavirinae, Alphacoronavirus and Betacoronavirus, both of which are hypothesized to draw their gene pool from bats. Two recently emerged human coronaviruses, SARS coronavirus (SARS-CoV) and MERS coronavirus (MERS-CoV) have caused deadly epidemics in different parts of the world. Both of these coronaviruses belong to the genus Betacoronavirus which includes 2 more classified human coronaviruses, OC43 (HCoV OC43) and HKU1(HCoV HKU1), causing respiratory symptoms in humans. Another 2 known human coronaviruses, NL63 (HCoV NL63) and 229E (HCoV 229E) belong to the genus Alphacoronavirus. For improved understanding of the molecular epidemiology and diversity of alphacoronaviruses, we surveyed bats of from Yunnan province in China. Material/methods: We studied the presence of diverse alphacoronaviruses in alimentary samples of 348 bats belonging to 5 genera from Yunnan province in China by amplifying a 440-bp fragment of RNA dependent RNA polymerase (RdRp) gene using reverse-transcription (RT) PCR. Results: 35 of 348 alimentary samples tested positive for diverse alphacoronaviruses. A sequence from lesser brown horseshoe bat (Rhinolophus stheno) and a sequence from Daubenton’s bats (Myotis daubentonii) of Mojiang district possessed 92-93% similarity to Rhinolophus bat CoV HKU2 (Rh-BatCoV HKU2). Another 4 sequences from M. daubentonii from a different district possessed a lower nucleotide identity of 81% to Rh-BatCoV HKU2. Twenty four M. daubentonii bats from this district were also found to be carrying RdRp sequences possessing 78-99% nucleotide identity to Myotis bat CoV HKU6 (My-BatCoV HKU6). Two RdRp sequences from M. daubentonii bats of Mojiang district possessed 96% nucleotide identity to Miniopterus bat CoV HKU7 (Mi-BatCoV HKU7) while another sequence from the same host species possessed 96% identity to Miniopterus bat CoV HKU8 (Mi-BatCoV HKU8). Two sequences from Pomona roundleaf bats (Hipposideros pomona) possessed 81-87% nucleotide identity to Hipposideros bat CoV HKU10 (Hi-BatCoV HKU10). Conclusions: Two samples which possessed 92-93% nucleotide identities to Rh-BatCoV HKU2 were detected from R. stheno and M. daubentonii instead of Chinese horseshoe bats (R. sinicus), suggesting interspecies transmission of alphacoronaviruses among different bat species. Further, another 4 samples from M. daubentonii possessed only 80% nucleotide identity to Rh-BatCoV HKU2, which may represent a novel species. M. daubentonii bats may harbour a large Alphacoronavirus diversity as 2 of the RdRp sequences obtained were closely related to Mi-BatCoV HKU7 and Mi- BatCoV HKU8 and another 24 sequences had 78-99% identity to My-BatCoV HKU6. Two samples with 81-87% nucleotide identity to Hi-BatCoV HKU10 may represent novel CoVs or possibly interspecies transmission variants of BatCoV HKU10 that we described previously to have recently been transmitted between Leschenault’s rousettes (Rousettus leschenaultii) and H. pomona bats. The results and data suggest there to be a rich diversity of alphacoronaviruses and presently uncharacterised Coronavirinae species circulating in bats from China.