While the novel Middle East respiratory syndrome coronavirus (MERS-CoV) is closely related to Tylonycteris bat CoV HKU4 (Ty-Bat. CoV HKU4) and Pipistrellus bat CoV HKU5 (Pi-Bat. CoV HKU5) in bats from Hong Kong, and other potential lineage C betacoronaviruses in bats from Africa, Europe, and America, its animal origin remains obscure. To better understand the role of bats in its origin, we examined the molecular epidemiology and evolution of lineage C betacoronaviruses among bats. Ty-Bat- CoV HKU4 and Pi-Bat. CoV HKU5 were detected in 29% and 25% of alimentary samples from lesser bamboo bat (Tylonycteris pachypus) and Japanese pipistrelle (Pipistrellus abramus), respectively. Sequencing of their RNA polymerase (Rd. Rp), spike (S), and nucleocapsid (N) genes revealed that MERS-CoV is more closely related to Pi-Bat. CoV HKU5 in Rd. Rp (92.1% to 92.3% amino acid [aa] identity) but is more closely related to Ty-Bat. CoV HKU4 in S (66.8% to 67.4% aa identity) and N (71.9% to 72.3% aa identity). Although both viruses were under purifying selection, the S of Pi-Bat. CoV HKU5 displayed marked sequence polymorphisms and more positively selected sites than that of Ty-Bat. CoV HKU4, suggesting that Pi-Bat. CoV HKU5 may generate variants to occupy new ecological niches along with its host in diverse habitats. Molecular clock analysis showed that they diverged from a common ancestor with MERS-CoV at least several centuries ago. Although MERS-CoV may have diverged from potential lineage C betacoronaviruses in European bats more recently, these bat viruses were unlikely to be the direct ancestor of MERS-CoV. Intensive surveillance for lineage C betaCo. Vs in Pipistrellus and related bats with diverse habitats and other animals in the Middle East may fill the evolutionary gap. © 2013, American Society for Microbiology.
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