The detection of diverse coronaviruses, including MERS-related coronaviruses, in South African bat populations and their associated ecology in Neoromica capensis

  • Cronjé N
  • Ithete N
  • Schoeman M
  • et al.
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Purpose: Coronaviruses are RNA viruses encompassing four genera. The alpha- and betacoronaviruses commonly cause mild disease in humans. However, outbreaks of severe respiratory disease in 2002 and 2012 led to the identification of highly pathogenic human betacoronaviruses, SARS- and MERS-CoV, respectively. Bats are believed to be the reservoir host from which all mammalian coronaviruses emerged. Few studies have been published on South African bat coronaviruses; only 16 bat alphacoronavirus and two betacoronavirus sequences have been reported. Phylogenetic inference shows that the betacoronavirus sequences belong to the same viral species as MERS-CoV. Through a One Health approach, this study aimed to describe coronavirus diversity within South African bat populations as well as factors that might influence bat-coronavirus ecology. Methods & Materials: During a general surveillance effort, 404 bat faecal pellets were screened using PCR assays targeting conserved regions of the coronavirus genome. An additional 183 faecal pellets, collected from Neoromicia capensis bats, were screened as part of a species-specific surveillance study. Using mixed effects logistic regression analyses, collected ecological sampling data were collated with screening results to identify possible predictors of coronavirus infection in N. capensis bats. Results: Based on putative coronavirus species classification criteria, the general surveillance effort detected nine coronavirus species, eight alphacoronaviruses and one MERS-related betacoronavirus, from eight different bat species. The species-specific surveillance detected three coronavirus species, including MERS-related betacoronaviruses, and identified several instances of coinfection with two different coronaviruses. The mixed effects logistic regression analyses indicated that female N. capensis bats and bats trapped at low altitude sites with low body condition scores were most likely to be coronavirus positive. Conclusion: This study demonstrates that diverse coronaviruses are present in different South African bat species and lends additional support to an ongoing circulation of MERS-related betacoronaviruses in this region. The observed cases of coinfection indicate the potential for recombination that could lead to the emergence of a new coronavirus that might have zoonotic potential. The collation of ecological data with screening results revealed that both host and environmental factors may influence coronavirus ecology. These findings could assist the development of improved wildlife surveillance sampling strategies for better detection of novel bat coronaviruses.




Cronjé, N., Ithete, N. L., Schoeman, M. C., & Preiser, W. (2019). The detection of diverse coronaviruses, including MERS-related coronaviruses, in South African bat populations and their associated ecology in Neoromica capensis. International Journal of Infectious Diseases, 79, 2–3.

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