Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in Miniopterus bats

Abstract

We previously reported the detection of bat coronaviruses (bat CoVs 1A, 1B, HKU7, HKU8 and bat-severe acute respiratory syndrome coronavirus) in Miniopterus spp. that cohabit a cave in Hong Kong. Here, we report the full genomic sequences of bat CoVs 1A, 1B and HKU8. Bat CoVs 1A and 1B, which are commonly found in the Miniopterus, are phylogenetically closely related. Using species-specific RT-PCR assays, bat CoVs 1A and 1B were confirmed to have distinct host specificities to Miniopterus magnater and Miniopterus pusillus, respectively. Interestingly, co-infections of bat CoVs 1B and HKU8 in M. pusillus are detected in seven of 38 virus-positive specimens collected from 2004 to 2006. These findings highlight that co-infections of some coronaviruses might be common events in nature. The biological basis for the host restriction of bat coronaviruses, however, is yet to be determined. Coronavirus (CoV) is a genus of viruses in the familyCoronaviridae under the order Nidovirales. Based on antigenic and genetic analyses, CoVs are divided into three major groups. The viruses have positive-sense, singlestranded RNA genomes with sizes ranging from 27000 to 32000 nt (Gorbalenya et al., 2006). Their genomes are polycistronic and contain at least five major open reading frames (ORFs) with the characteristic gene order [59-replicase (rep), spike (S), envelope (E), membrane (M) and nucleocapsid (N)-39]. The severe acute respiratory syndrome (SARS) outbreak in 2003 highlighted the potential health threat of coronaviruses to humans (Peiris et al., 2003). This prompted an intensive search for the precursor of SARS CoV in wildlife and the discovery of several novel CoVs in bats in China, including the viruses that are closely related to SARS CoV (Dong et al., 2007;Lau et al., 2005;Poon et al., 2005;Tang et al., 2006;Woo et al., 2006). Recently, the biological importance of bats for the ecology of coronaviruses was further reiterated by the discovery of novel bat CoVs (BtCoVs) in other continents (Dominguez et al., 2007;Muller et al., 2007).We previously reported the discovery of the first BtCoV (Poon et al., 2005). In addition, we also performed a longitudinal study on Miniopterus magnater and Miniopterus pusillus bats that cohabit an abandoned cave in Hong Kong (Chu et al., 2006). BtCoV HKU7 and bat-SARS-CoV were detected only once in our specimens, while BtCoVs 1A, 1B and HKU8 were detected repeatedly in these bats. A clear host species restriction was observed with BtCoV 1A being found in M. magnater and BtCoV 1B in M. pusillus even though these two CoVs are genetically very similar and the two bat species co-inhabit the same cave. Thus, these virus surveillance studies might allow unique opportunities to understand better the dynamics and prevalence of coronaviruses within a single geographical location. To understand better the genetic relationships of the BtCoVs that are repeatedly found in the local Miniopterus spp, representative faecal samples positive for BtCoVs 1A, 1B and HKU8 in our previous investigations were selec...

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