Molecular epidemiology of lineage C betacoronaviruses in bats in Hong Kong

Abstract

Nine years after the Severe Acute Respiratory Syndrome (SARS) pandemic in 2003, a novel human coronavirus, Middle East Respiratory Syndrome coronavirus (MERS-CoV), emerged in the Middle East in 2012 and was believed to be of animal origin. Molecular study on the genome of MERS-CoV showed that it belongs to lineage C betacoronavirus and is closely related to the previously described Tylonycteris bat coronavirus HKU4 (Ty-BatCoV HKU4) and Pipistrellus bat coronavirus HKU5 (Pi-BatCoV HKU5) identified in Tylonycteris pachypus and Pipistrellus abramus respectively. In this study, 597 respiratory and 934 alimentary specimens from 1174 bats of 12 different species were collected in 20 sampling sites of Hong Kong over seven years from November 2005 to November 2012. Degenerate primers designed from alignment of RdRp genes of lineage C betacoronaviruses were able to amplify partial RdRp sequences in two bat species only in this study, including 8 lesser bamboo bats and 34 Japanese pipistrelle, with 200-bp sequences shared 99-100% and 96-100% nucleotide identities to Ty-BatCoV HKU4 and Pi-BatCoV HKU5 respectively. Phylogenetic analysis showed that Ty-BatCoV HKU4 and Pi-BatCoV HKU5 were closely related to but still distinct from MERS-CoV, implying that the two bat coronaviruses are probably not the direct ancestor virus of MERS-CoV. The infection of Pi-BatCoV HKU5 is independent of sex (P = 0.494) but juvenile Japanese pipistrelles were more susceptible to the infection (P = 0.000101) while the infection of Ty-BatCoV HKU4 is independent of both sex (P = 0.464) and age (P = 0.193). Additionally, the mean body weight of the adult lesser bamboo bats positive for Ty-BatCoV HKU4 was significantly lower than that of the negative ones (P = 0.03). On the other hand, there was no significant difference in the mean body weights between the positive and negative bats for Pi-BatCoV HKU5 among the juvenile Japanese pipistrelles (P = 0.06). Continuous surveillance study of coronaviruses on different bat species as well as other potential intermediate animal hosts should be carried on the evolution study of the lineage C betacoronaviruses.