Molecular Detection and Characterization of Coronavirus Infection in Olive Baboons (Papio Anubis), Bats and Rodents in Laikipia County, Kenya

Abstract

Background: In the last few years, members of the subfamily coronavirinae of the family coronaviridae have been involved in human and animal epidemics causing high morbidity and mortality rates. The Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS) were linked to the alpha- and beta-coronaviruses with wildlife as sources of infections. Porcine epidemic diarrhea virus occurred and traced its origin from bats. The occurrence of these diseases has motivated interest to discover more zoonotic sources of coronaviruses and their transmission dynamics at the human-wildlife interfaces. Objective: The general objective of this study was to determine and characterize the presence of coronaviruses in olive baboons, bats and rodents using reverse transcription PCR (RT-PCR) in Laikipia, County Kenya. Methodology: 130 olive baboons (Papio anubis), 202 bats from 2 species (Chaerephon sp. and scotophilus sp.) and 161 rodents from eight species (Acomys kempis, Acomys percivalli, Elephantulus rufescens, Gerbilliscus robustus, Aethomys hindei, Myomyscus brodernani, Grammonys dolichorus, and Saccostomus meamsi) were humanely trapped and sampled in the dry season of September, 2017 and wet season of May, 2018. In total, 260 oral and rectal swabs were obtained from olive baboons, 404 from bats and 322 from rodents. These samples were screened for coronavirus (CoV) RNA using reverse transcription PCR. To increase the chances of viral detection, two cost-effective consensus PCR assays targeting RNA-dependent RNA polymerase gene to detect Coronaviruses (Watanabe assay targeting the polymerase gene at nucleotides 14,370-14,750 and Quan assay amplified at 17,480-17,820) were used. Results: Eight positive samples were obtained from bats in the rainy season constituting 8% (n=100) and 3.96% (n=202) by Quan assay. BLAST and phylogenetic analysis showed all

sequenced isolates belonged to unclassified alpha-coronavirus genus in the genbank. Five of the isolates are distant relatives of Kenyan bat coronaviruses and are new strains of the virus. Three clustered with reference bats coronavirus sequences from Kenya in the database. Elsewhere in the world, no cluster relationship was identified with other bat coronaviruses. Conclusion: This study demonstrated coronaviruses may be endemic in bat population in Kenya and with five new strains (384, 396, 383, 382, and 385) detected that require further genome analysis