Identification of a Severe Acute Respiratory Syndrome Coronavirus- Like Virus in a Leaf-Nosed Bat in Nigeria

ABSTRACT Bats are reservoirs for emerging zoonotic viruses that can have a profound impact on human and animal health, in-cluding lyssaviruses, filoviruses, paramyxoviruses, and severe acute respiratory syndrome coronaviruses (SARS-CoVs). In the course of a project focused on pathogen discovery in contexts where human-bat contact might facilitate more efficient interspe-cies transmission of viruses, we surveyed gastrointestinal tissue obtained from bats collected in caves in Nigeria that are fre-quented by humans. Coronavirus consensus PCR and unbiased high-throughput pyrosequencing revealed the presence of coro-navirus sequences related to those of SARS-CoV in a Commerson’s leaf-nosed bat (Hipposideros commersoni). Additional genomic sequencing indicated that this virus, unlike subgroup 2b CoVs, which includes SARS-CoV, is unique, comprising three overlapping open reading frames between theM and N genes and two conserved stem-loop II motifs. Phylogenetic analyses in conjunction with these features suggest that this virus represents a new subgroup within group 2 CoVs. IMPORTANCE Bats (order Chiroptera, suborders Megachiroptera andMicrochiroptera) are reservoirs for a wide range of viruses that cause diseases in humans and livestock, including the severe acute respiratory syndrome coronavirus (SARS-CoV), respon-sible for the global SARS outbreak in 2003. The diversity of viruses harbored by bats is only just beginning to be understood be-cause of expanded wildlife surveillance and the development and application of new tools for pathogen discovery. This paper describes a new coronavirus, one with a distinctive genomic organization that may provide insights into coronavirus evolutio