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

Abstract

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.

SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression

“…Generally, Alphacoronavirus and Betacoronavirus infect mammals while Gammacoronavirus , and Deltacoronavirus infect both birds and mammals [ 6 ]. Interestingly, CoVs infection in human is only associated with Alphacoronaviruses and Betacoronaviruses genera [ 7 ]. CoVs that are able to infect human include: Human coronavirus NL63 (HCoV-NL63), Human coronavirus 229E (HCoV-229E), Human coronavirus OC43 (HCoV-OC43), Human coronavirus HKU1 (HCoV-HKU1), SARS-CoV, MERS-CoV, and SARS-CoV-2.…”

“…CoVs that are able to infect human include: Human coronavirus NL63 (HCoV-NL63), Human coronavirus 229E (HCoV-229E), Human coronavirus OC43 (HCoV-OC43), Human coronavirus HKU1 (HCoV-HKU1), SARS-CoV, MERS-CoV, and SARS-CoV-2. HCoV-NL63 and HCoV-229E belong to Alphacoronaviruses , while HCoV-OC43, HCoV-HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2 belong to the Betacoronavirus [ 7 , 8 ].…”

“…Human coronaviruses are commonly transmitted via the respiratory tract and most of them cause a mild infection like respiratory distress and diarrhea. Based on their pathogenicity, two alpha-CoVs (HCoV-229E and HCoV-NL63) and two beta-CoVs (HCoV-OC43 and HCoV-HKU1) cause a mild infection, while SARS-CoV, MERS-CoV, and SARS-CoV-2 are highly pathogenic to humans and cause severe infection in the lower respiratory system with the high potentiality of fatal respiratory diseases [ 7 , 9 – 12 ].…”

Sarbecovirus RBD indels and specific residues dictating ACE2 multi-species adaptiveness

“…The Severe Acute Respiratory Syndrome (SARS) outbreak and COVID-19 pandemic significantly raised awareness of the zoonotic risks posed by sarbecoviruses 12,13 . The Sarbecovirus subgenus, also known as lineage B β-coronaviruses, encompasses hundreds of SARS-related viruses exhibiting varying RBM sequences 1,[3][4][5][6][7][8][9][14][15][16] . Most sarbecoviruses naturally infect rhinolophus bats, the primary natural reservoir for these viruses 2,[17][18][19] .…”

Extensive Survey and Analysis of Factors Associated with Presence of Antibodies to Orthoebolaviruses in Bats from West and Central Africa

“…The low number of bats in which viral RNA was detected can be partially explained by the fact that orthoebolaviruses are most likely cleared from their hosts and can only be detected for a limited time period. Bats are infected with a wide diversity of potential pathogenic RNA viruses for humans [ 27 ] and seasonal variations in infection and immunological status have also been documented for other viral infections like henipaviruses, lyssaviruses, and coronaviruses in bats [ 5 , 28 , 29 , 30 , 31 , 32 ]. Temporal dynamics in viral shedding and seroprevalence have also been shown for Marburg virus [ 33 ].…”