Human Betacoronavirus 2c EMC/2012–related Viruses in Bats, Ghana and Europe

Abstract

We screened fecal specimens of 4,758 bats from Ghana and 272 bats from 4 European countries for betacoronaviruses.Viruses related to the novel human betacoronavirus EMC/2012 were detected in 46 (24.9%) of 185 Nycteris bats and 40 (14.7%) of 272 Pipistrellus bats.Their genetic relatedness indicated EMC/2012 originated from bats. C oronaviruses (CoVs) are enveloped viruses with a positive-sense, single-stranded RNA genome (1).CoVs are classified into 4 genera: Alphacoronavirus, Betacoronavirus (grouped further into clades 2a-2d), Gammacoronavirus, and Deltacoronavirus.Two human coronaviruses (hCoVs), termed hCoV-OC43 and -229E, have been known since the 1960s and cause chiefly mild respiratory disease (2).In 2002-2003, an outbreak of severe acute respiratory syndrome (SARS) leading to ≈850 deaths was caused by a novel group 2b betacoronavirus, SARS-CoV (3).A likely animal reservoir for SARS-CoV was identified in rhinolophid bats (4,5).In the aftermath of the SARS pandemic, 2 hCoVs, termed hCoV-NL63 and -HKU1, and numerous novel bat CoVs were described.In September 2012, health authorities worldwide were notified of 2 cases of severe respiratory disease caused by a novel hCoV (6,7).This virus, termed EMC/2012, was related to the 2c betacoronavirus clade, which had only been known to contain Tylonycteris bat coronavirus HKU4 and Pipistrellus bat coronavirus HKU5 (8).We previously identified highly diversified alphacoronaviruses and betacoronaviruses, but not clade 2c betacoronaviruses, in bats from Ghana (9).We also identified sequence fragments from a 2c betacoronavirus from 1 Pipistrellus bat in Europe (10).In this study, we analyzed an extended sample of 4,758 bats from Ghana and 272 bats from 4 European countries. The StudyFecal specimens were collected from 10 bat species in Ghana and 4 Pipistrellus species in Europe (Table 1).Bats were caught during 2009-2011 with mist nets, as described (9), in 7 locations across Ghana and 5 areas in Germany, the Netherlands, Romania, and Ukraine (Figure 1).The species, age, sex, reproductive status, and morphologic measurements of the bats were recorded.Fecal pellets were collected and suspended in RNAlater Stabilization Reagent (QIAGEN, Hilden, Germany).RNA was purified as described (11).CoV was detected by using nested reverse transcription PCR (RT-PCR) targeting the RNA-dependent RNA polymerase (RdRp) gene (12) (see Table 1 for assay oligonucleotides).A novel CoV was detected in insectivorous Nycteris cf.gambiensis specimens (online Technical Appendix wwwnc.cdc.gov/EID/pdfs/12-1503-Techapp.pdf;GenBank accession nos.JX899382-JX899384).A real-time RT-PCR was designed to permit sensitive and quantitative detection of this CoV (Table 1).Only Nycteris bats were positive for CoV (46 [24.9%] of 185 specimens) (Table 1).Demographic factors predictive of CoV in captured Nycteris bats were assessed.Juvenile bats and lactating females were significantly more likely to be CoV-infected than were adult