Coronavirus and Paramyxovirus Shedding by Bats in a Cave and Buildings in Ethiopia

Abstract

Bats are important hosts of zoonotic viruses with pandemic potential, including filoviruses, MERS-Coronavirus (CoV), SARS-CoV -1, and likely SARS-CoV-2. Viral infection and transmission among wildlife are dependent on a combination of factors that include host ecology and immunology, life history traits, roosting habitats, biogeography, and external stressors. Between 2016 and 2018, four species of insectivorous bats from a readily accessed roadside cave and buildings in Ethiopia were sampled and tested for viruses using consensus PCR assays for five viral families/genera. Previously identified and novel coronaviruses and paramyxoviruses were identified in 99 of the 589 sampled bats. Bats sampled from the cave site were more likely to test positive for a CoV than bats sampled from buildings; viral shedding was more common in the wet season; and rectal swabs were the most common sample type to test positive. A previously undescribed alphacoronavirus was detected in two bat species from different taxonomic families, sampling interfaces, geographic locations, and years. These findings expand knowledge of the range and diversity of coronaviruses and paramyxoviruses in insectivorous bats in Ethiopia and reinforce that an improved understanding of viral diversity and species-specific shedding dynamics is important for designing informed zoonotic disease surveillance and spillover risk reduction efforts.

Current and future environmental suitability for bats hosting potential zoonotic pathogens in rural Kenya

“…pumilus remains high at elevations greater than 1500 m. This finding is somewhat contradictory to earlier studies in which M . pumilus has not been captured at elevations above 1400 m (Benda et al., 2019; Katunzi et al., 2021; Lane et al., 2022).…”

Urban tolerance is phylogenetically constrained and mediated by pre‐adaptations in African bats

“…We then determined whether these species were present in urban (including suburban or peri‐urban) areas within their range (personal communication P. Webala, I. Tanshi and M.C. Schoeman; and Ancillotto et al, 2015; Andreani et al, 2019; Dekker et al, 2013; Fenton et al, 2002; Geldenhuys et al, 2013; Hoye & Spence, 2004; Jacobs & Barclay, 2009; Kurek et al, 2020; Lane et al, 2022; Legakis et al, 2000; O'Malley et al, 2020; Roswag et al, 2019; Schoeman, 2016; Schoeman & Waddington, 2011; Taylor et al, 1999; Wojtaszyn et al, 2013) and recorded this information as presence (1) or absence (0) in urban areas. We categorized roost specificity for each species as: utilizing 1 roost type = high, 2 roost types = medium, and ≥3 roost types = low.…”

Global Distribution and Molecular Evolution of Bat Coronaviruses

“…Several studies conducted in Africa showed that a large diversity of alpha and beta-CoVs was detected in different bat species [114][115][116][117][118][119][120][121]. In Kenya, detected bat CoVs were phylogenetically different from human and animal CoVs based on sequence analysis of ORFs of these viruses [122].…”