Coronavirus surveillance in wildlife from two Congo basin countries detects RNA of multiple species circulating in bats and rodents

Charles Kumakamba, Fabien R. Niama, Francisca Muyembe, Jean Vivien Mombouli, Placide Mbala Kingebeni, Rock Aime Nina, Ipos Ngay Lukusa, Gerard Bounga, Frida N'Kawa, Cynthia Goma Nkoua, Joseph Atibu Losoma, Prime Mulembakani, Maria Makuwa, Ubald Tamufe, Amethyst Gillis, Matthew Lebreton, Sarah H. Olson, Kenneth Cameron, Patricia Reed, Alain OndzieAlex Tremeau-Bravard, Brett R. Smith, Jasmine Pante, Bradley S. Schneideri, David J. McIver, James A. Ayukekbong, Nicole A. Hoff, Anne W. Rimoin, Anne Laudisoit, Corina Monagin, Tracey Goldstein, Damien O. Joly, Karen Saylors, Nathan D. Wolfe, Edward M. Rubin, Romain Bagamboula Mpassi, Jean J.Muyembe Tamfum, Christian E. Lange

Research output: Contribution to journalArticlepeer-review

Abstract

Coronaviruses play an important role as pathogens of humans and animals, and the emergence of epidemics like SARS, MERS and COVID-19 is closely linked to zoonotic transmission events primarily from wild animals. Bats have been found to be an important source of coronaviruses with some of them having the potential to infect humans, with other animals serving as intermediate or alternate hosts or reservoirs. Host diversity may be an important contributor to viral diversity and thus the potential for zoonotic events. To date, limited research has been done in Africa on this topic, in particular in the Congo Basin despite frequent contact between humans and wildlife in this region. We sampled and, using consensus coronavirus PCR-primers, tested 3,561 wild animals for coronavirus RNA. The focus was on bats (38%), rodents (38%), and primates (23%) that posed an elevated risk for contact with people, and we found coronavirus RNA in 121 animals, of which all but two were bats. Depending on the taxonomic family, bats were significantly more likely to be coronavirus RNA-positive when sampled either in the wet (Pteropodidae and Rhinolophidae) or dry season (Hipposideridae, Miniopteridae, Molossidae, and Vespertilionidae). The detected RNA sequences correspond to 15 alpha- A nd 6 betacoronaviruses, with some of them being very similar (>95% nucleotide identities) to known coronaviruses and others being more unique and potentially representing novel viruses. In seven of the bats, we detected RNA most closely related to sequences of the human common cold coronaviruses 229E or NL63 (>80% nucleotide identities). The findings highlight the potential for coronavirus spillover, especially in regions with a high diversity of bats and close human contact, and reinforces the need for ongoing surveillance.

Original languageEnglish (US)
Article numbere0236971
JournalPloS one
Volume16
Issue number6 June
DOIs
StatePublished - Jun 2021

ASJC Scopus subject areas

  • General

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