Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in Gabon
Abstract
Little research on coronaviruses has been conducted on wild animals in Africa. Here, we screened a wide range of wild animals collected in six provinces and five caves of Gabon between 2009 and 2015. We collected a total of 1867 animal samples (cave-dwelling bats, rodents, non-human primates and other wild animals). We explored the diversity of CoVs and determined the factors driving the infection of CoVs in wild animals. Based on a nested reverse transcription-polymerase chain reaction, only bats, belonging to the Hipposideros gigas (4/156), Hipposideros cf. ruber (13/262) and Miniopterus inflatus (1/249) species, were found infected with CoVs. We identified alphacoronaviruses in H. gigas and H. cf. ruber and betacoronaviruses in H. gigas. All Alphacoronavirus sequences grouped with Human coronavirus 229E (HCoV-229E). Ecological analyses revealed that CoV infection was significantly found in July and October in H. gigas and in October and November in H. cf ruber. The prevalence in the Faucon cave was significantly higher. Our findings suggest that insectivorous bats harbor potentially zoonotic CoVs; highlight a probable seasonality of the infection in cave-dwelling bats from the North-East of Gabon and pointed to an association between the disturbance of the bats’ habitat by human activities and CoV infection.
Introduction
Coronaviruses (CoVs) belonging to the Coronaviridae family are viruses known to infect a wide range of animals and humans. In humans, CoVs are responsible for mild to severe respiratory illnesses such as the Severe Acute Respiratory Syndrome (SARS) and the Middle-East Respiratory Syndrome (MERS). The epidemic of SARS which started in 2002 in China, and spread on various other continents such as North America and Europe, reached a mortality rate of 9%1. The other severe epidemic illness (MERS) appeared more recently in the Middle East, and like the SARS, it also spread in other countries in Africa, America and Europe with case fatality rates of 35% (reviewed by de Wit et al.2). Currently the world is facing an ongoing pandemic caused by a new coronavirus (SARS-CoV-2) that emerged in China in December 2019 and caused disease (COVID-19) resulting in 118 326 confirmed cases and 4292 deaths as of March 11, 20203. Since the emergence of these respiratory diseases, CoVs have been considered a real public health problem because of their ability to become epidemic and pandemic4. Even though human to human transmission of SARS-CoV and MERS-CoV occurs mainly through nosocomial transmission, some human cases recorded were occasionally the results of a zoonotic transmission5. This raised an interest in the identification of animal reservoirs. Indeed, it appears that almost each human CoV have zoonotic origins or otherwise have a close relative that circulate in wild animals (bats)6,7,8 and domestic animals (camels and cattle)9,10. Besides SARS-CoVs and MERS-CoVs, numerous other CoVs have been detected in bats in Africa, Asia, Europe and America and are classified into the genera Alphacoronavirus and Betacoronavirus11,12. For SARS-CoV-2, a recent study revealed that the whole genome sequence of SARS-CoV-2 was most closely related with a bat coronavirus detected in bats from Yunnan Province in China13. Consequently, bats were defined as reservoirs of ancestral coronaviruses which were transmitted to humans14,15. Other wildlife species appear to play an important role in the chain of transmission and the emergence of these viruses in humans, namely palm civets5 and wild rodents, in which infections by an alphacoronavirus and a betacoronavirus have been recently identified16.
Gabon, a country located in Central Africa, displays a large diversity of wildlife species. Aside from bats in which CoVs have been detected in the cave-dwelling species Hipposideros cf. ruber17, to our knowledge, there is no information on the carriage of other mammalian species. CoVs are prone to host switching18 and could be a current and future threat to public health.
The aim of this study was to explore the genetic diversity and the ecology of CoVs circulating among several wild mammals in Gabon in order to determine the potential reservoir species of these viruses and the risk for zoonotic emergence, and identify the factors driving CoVs infection in bats.
