Coronaviruses Are Abundant and Genetically Diverse in West and Central African Bats, including Viruses Closely Related to Human Coronaviruses

Viruses. 2023 Jan 25;15(2):337. doi: 10.3390/v15020337.


Bats are at the origin of human coronaviruses, either directly or via an intermediate host. We tested swabs from 4597 bats (897 from the Democratic Republic of Congo (DRC), 2191 from Cameroon and 1509 from Guinea) with a broadly reactive PCR in the RdRp region. Coronaviruses were detected in 903 (19.6%) bats and in all species, with more than 25 individuals tested. The highest prevalence was observed in Eidolon helvum (239/733; 39.9%) and Rhinolophus sp. (306/899; 34.1%), followed by Hipposideros sp. (61/291; 20.9%). Frugivorous bats were predominantly infected with beta coronaviruses from the Nobecovirus subgenus (93.8%), in which at least 6 species/genus-specific subclades were observed. In contrast, insectivorous bats were infected with beta-coronaviruses from different subgenera (Nobecovirus (8.5%), Hibecovirus (32.8%), Merbecovirus (0.5%) and Sarbecovirus (57.6%)) and with a high diversity of alpha-coronaviruses. Overall, our study shows a high prevalence and genetic diversity of coronaviruses in bats and illustrates that Rhinolophus bats in Africa are infected at high levels with the Sarbecovirus subgenus, to which SARS-CoV-2 belongs. It is important to characterize in more detail the different coronavirus lineages from bats for their potential to infect human cells, their evolution and to study frequency and modes of contact between humans and bats in Africa.

Keywords: Africa; Rhinolophus; Sarbecovirus; bat; coronavirus; diversity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Behavior Therapy
  • COVID-19*
  • Cameroon
  • Chiroptera*
  • Humans
  • SARS-CoV-2
  • Severe acute respiratory syndrome-related coronavirus*

Grant support

This work was supported by grants of the Agence Nationale de Recherche sur le SIDA et les Maladies Infectieuses (ANRS-COV10), EBO-SURSY project funded by the European Union (FOOD/2016/379-660), and BIODIV-AFREID project (BiodivERsA ERA-Net COFUND programme), 2018–2019 joint call for proposals (grant number ANR-19-EBI3-0004). Eddy Lusamaki was supported by a doctoral fellowship from the French foreign office.