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, including 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 interspecies transmission of viruses, we surveyed gastrointestinal tissue obtained from bats collected in caves in Nigeria that are frequented by humans. Coronavirus consensus PCR and unbiased high-throughput pyrosequencing revealed the presence of coronavirus 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 the M 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.

Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS

“…3 branch deeply in the phylogenetic tree and likely represent not only new species, but even new genetic clades. This is exemplified by the unclassified African Hipposideros betacoronaviruses (Pfefferle et al, 2009;Quan et al, 2010;Tong et al, 2009), which putatively represent a yet to be defined Betacoronavirus clade e and unclassified neotropical Carollia and Pteronotus viruses (Corman et al, 2013b) putatively corresponding to additional Betacoronavirus clades. Fig.…”

“…Most other CoVs have been confined to single host genera, exemplified by the detection of SARS-related CoVs and several alphacoronaviruses in Rhinolophus, Myotis, Miniopterus, Nyctalus and Carollia bat hosts, including detections of closely related viruses in individual bats separated by thousands of miles (Corman et al, 2013b;Drexler et al, 2010;Tang et al, 2006). Similarly, Hipposideros betacoronaviruses from Thailand, Kenya, Nigeria and Ghana are closely related (Gouilh et al, 2011;Pfefferle et al, 2009;Quan et al, 2010;Tong et al, 2009) and the betacoronavirus HKU9 has been detected in different species of flying foxes in Africa and Asia (Anthony et al, 2013b;Lau et al, 2010b;Tao et al, 2012;Watanabe et al, 2010;Woo et al, 2007). Of note, the detection of both host-specific and -nonspecific mammalian CoVs parallels what can be observed in the avian Coronavirinae genera.…”

Middle East Respiratory Syndrome Coronavirus Antibodies in Dromedary Camels, Bangladesh, 2015

“…We extracted total nucleic acid by using EasyMag (bioMérieux) and performed cDNA synthesis by using SuperScript III first-strand synthesis supermix (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. We performed pancoronavirus PCR targeting the RdRp gene ( 5 ) and MERS-CoV real-time PCR targeting the upstream envelope protein gene and nucleocapsid protein genes N2 and N3 ( 6 ). We screened serum samples by using a MERS-CoV ELISA ( 7 ) and confirmed the results by using a MERS-CoV pseudoparticle neutralization test ( 8 ).…”

Severe acute respiratory syndrome coronavirus accessory proteins 6 and 9b interact in vivo

“…The etiological agent of this disease was found to be a previously unknown coronavirus (SARS-CoV) Fouchier et al, 2003;Ksiazek et al, 2003;Lee et al, 2003;Peiris et al, 2003;Rota et al, 2003). In the last years SARS-CoV like viruses have been found circulating in bats from several continents (Drexler et al, 2010;Lau et al, 2005;Quan et al, 2010;Rihtaric et al, 2010) and bats have been described as putative reservoirs of SARS-CoV (Calisher et al, 2006;Li et al, 2005). Thus, the possibility of SARS reoccurrence remains.…”