Molecular Detection of Alpha- and Betacoronaviruses in Bats from Afar Region, Ethiopia

Bats are critical reservoirs of coronaviruses, including zoonotic strains, yet gaps remain in understanding coronavirus diversity within Ethiopia's understudied bat populations. This study investigated coronavirus prevalence and genetic diversity in bats from Afar and Dire Dawa, Eastern Ethiopia.

A cross-sectional study was conducted from November 2015 to June 2016 in purposively selected sites of Afar and Dire Dawa, Ethiopia, where bats were captured using 12 × 3-m mist nets. Ribonucleic acid (RNA) was screened by real-time polymerase chain reaction (RT-PCR) targeting the RNA-dependent RNA polymerase (RdRp) gene, with confirmatory PCR for the open reading frame 1a (ORF1a) region.

A total of 141 bats were captured, including 129 Chaerephon pumilus, 11 Epomophorus labiatus and 1 Mops condylurus, from which 278 oropharyngeal swabs, rectal swabs, and urine specimens were collected. Coronaviruses were detected in eight bats (5.7%): five C. pumilus, two E. labiatus and one M. condylurus. Of these, three were detected from rectal swabs, three from oral swabs and two from urine samples. A higher proportion of adult bats (6.7%, 6/89) carried the virus compared to juveniles, with similar proportions of males (5.5%, 3/55) and females (5.8%, 5/86) testing positive. Sequencing revealed six Alphacoronaviruses (75%) and two Betacoronaviruses (25%; lineage D).

The study contributes important baseline data on coronavirus diversity in the area. Continued genomic surveillance, including full-genome sequencing and broader ecological sampling, is essential to advance understanding of coronavirus evolution and maintenance within bat populations.