Prevalence and genetic diversity of Coronaviruses circulating in insectivorous bat colonies in Mashonaland West Province, Zimbabwe

Introduction: This study aims to establish prevalence and genetic diversity of Coronaviruses circulating in two insectivorous bat colonies in Zimbabwe. More than 60 bat species have been recorded in Zimbabwe. The country is thus a potential at risk area for the emergence of zoonotic infections from bats. Previous studies carried out in Zimbabwe included the characterisation of Dicistrovirus, Coronavirus and Paramyxovirus in insectivorous bats (Hipposideros Caffer) at one of the sites. Coronaviruses belong to the order Nidoviridae, divided into 4 genera where Alpha and Beta coronaviruses cause pathogenesis in mammals whereas the Gamma and Delta infect avian species. To date studies have linked bats to the seven human related coronaviruses including SARS-CoV-1 and -2 and MERS-CoV. The study sites represent an anthropogenic interface where human populations are directly or indirectly exposed to viral pathogens hosted by bats, thus it is of importance, to know the prevalence and genetic diversity and of coronaviruses in these sites to better monitor and establish surveillance tools that can be used to predict and eventually prevent future emergences. Materials and Methods The study was carried out in Hurungwe district, Mashonaland West province in Zimbabwe at two different sites : Magweto cave (1034 bat fecal samples collected) and Chirundu Safari (852 bat faecal samples collected). The sites were chosen due to their large bat communities and species diversity and due to the existence of bat-human interfaces. At least 4 species per site were discovered after capture and release. The two sites were sampled once a month for 6 consecutive months on an average of 3 days per site. Non-invasive sampling was carried out, individual bat faeces were collected and placed in RNAlater before laboratory analysis. After DNA/RNA extraction from the faeces, Reverse transcription was carried out on the nucleic acids using Random Primers following by classical nested PCR PCR that amplifies a 440bp fragment in the polymerase gene of coronaviruses. Positive samples were sequenced by sanger method and partial nucleic acid sequences were then compared to existing CoV sequences. Phylogenetic analyses were done by using Maximum likelihood method (PhyML). Results and Discussion: Preliminary results from the Chirundu bat community showed a prevalence of 5-10 % (obtained from 25 % of our sampling) in two prominent insectivorous bat species, Hipposideros caffer and Rhinolophus spp. Preliminary results for the Magweto cave showed a prevalence of 2-7 % (obtained from 40 % of our sampling) in the bat community of small sized Hipposideridae and Rhinolophidae, which is low compared to the other site. For the larger Hipposideros gigas from Magweto cave, prevalence of coronaviruses was between 40-50 %. The sequencing of the positive samples showed a high genetic diversity of coronaviruses with both Alpha and Beta coronaviruses represented in both sites. The positive samples were closely related to HKU2, HKU4, HKU10 and 229-E, SARS-CoV and MERS-CoV coronaviruses.