The source of human infection with Middle East respiratory syndrome coronavirus remains unknown, but molecular investigation indicated that bats in Saudi Arabia are infected with several alphacoronaviruses and betacoronaviruses. Virus from one bat showed 100% nucleotide identity to virus from the human index case-patient. Bats might play a role in human infections . Since Middle East respiratory syndrome (MERS) was described in September 2012, over 90 cases have been reported worldwide, 70 from Saudi Arabia.The incidence on infection with the causative agent, betacoronavirus, has not been determined; however the mortality rate among those who received clinical care is about 65%. Although instances of human-to-human transmission have been documented between case-patients and others in close contact, the sources of infection for most patients remain unknown . In October 2012 and April 2013, three agencies collected samples from bats in regions where MERS cases had been identified. The agencies are the Ministry of Health of Saudi Arabia, the Center for Infections and Immunity of Columbia University, and EcoHealth Alliance.During the October investigation, the team interviewed the family of an index case-patient in Bisha and collected samples from bats <12 km from his home, in an abandoned date palm orchard, and <1 km from his place of employment, a hardware store that fronted a garden and date palm orchard. Although neither family members nor employees recalled seeing bats, the team observed roosting bats and guano in abandoned wells and ruins within 12 km of his home and insectivorous bats at dusk in the garden behind his store.During the 3 week April investigation, fecal samples were collected on tarps laid out at bat roosting sites in and around Bisha, Unaizah, and Riyadh. Representative animals at each roosting site were captured, identified morphologically, and released after wing punch biopsy samples were collected for speciation by DNA analysis. Samples were collected into cryovials. All samples were stored in liquid nitrogen and conveyed to Riyadh for storage at -80 degrees Celsius before being transported to Columbia University in New York in dry nitrogen.Total nucleic acid was extracted from samples by using the NucliSENS easyMAG system and subjected to 8 PCRs with primers and protocols designed to amplify regions within the helicase, RNA polymerase and nucleocapsid or envelop proteins of CoVs. Products were sequenced and analyzed for similarity to GenBank database. However, because the closest reference sequence was from T. nudiventris bats, at 84% identity they presume that the product represents bona fide T. perforates bat cytochrome B gene sequence. A wide range of CoV species are circulating among bats in Saudi Arabia.Although the prevalence of CoV was high, MERS CoV was found in only 1 bat. Furthermore, the sensitivity for viral nucleic acid detection in samples collected in October 2012 was probably reduced because of failure in cold chain transport. Whereas 219 of 675 of fecal pellets collected in April revealed a CoV sequence by PCR, only 8 of 148 of rectal swab samples or fecal pellets collected in October were positive by the same assays.