Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in Gabon

Abstract

Little research on coronaviruses has been conducted on wild animals inAfrica. 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.open Scientific RepoRtS | (2020) 10:7314 | https://doi.org/10.1038/s41598-020-64159-1www.nature.com/scientificreports www.nature.com/scientificreports/ play an important role in the chain of transmission and the emergence of these viruses in humans, namely palm civets 5 and wild rodents, in which infections by an alphacoronavirus and a betacoronavirus have been recently identified 16 .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. ruber 17 , to our knowledge, there is no information on the carriage of other mammalian species. CoVs are prone to host switching 18 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.

Wide Diversity of Coronaviruses in Frugivorous and Insectivorous Bat Species: A Pilot Study in Guinea, West Africa

“…It also confirms the observations from the large study on CoVs in more than 12,000 bats across Africa and Asia from Anthony et al (2017) who demonstrated that increasing sampling efforts leads to increased identification of new lineages. Although we studied only very few samples from Hipposideros bats, we did not only find a high infection rate (7/21, 33%), but observed also a high genetic diversity among their CoVs in accordance with most previous studies on Hipposideros species in Africa [ 15 , 34 , 35 , 39 , 40 , 41 , 42 ]. The human 229E α-CoV falls in a clade of bat CoVs that is widely present in Hipposideros bats from Kenya, Zimbabwe, Mozambique, Gabon, Ghana and also in our study in Guinea.…”

“…and two frugivorous species (4/9 Eidolon helvum and 1/1 Nanonycteris sp.). However, it cannot be excluded that this could be related to the season when samples were collected, for example several studies have shown temporal variations of CoV infections associated with parturition [ 37 , 41 , 53 , 54 , 55 ]. Longer follow-up should be done on these bat species in Guinea to assess temporal dynamics of CoV infection.…”

“…Moreover, the β-CoVs observed in Hipposideros bats belong to the SarbeCoV subgenus where they form a sister-clade to the clade of human and animal CoVs related to SARS-CoV-1 and -2. Within this viral clade, the genetic diversity is also very high, and viruses from this clade are present in Hipposideros species across Africa [ 15 , 35 , 39 , 41 , 59 ]. CoVs have also been described in Hipposideros bats in China and Thailand, suggesting a potential new clade [ 55 , 60 , 61 ].…”

“…Several studies have shown a large diversity of CoVs in bats across Africa, but limited data are currently available on bat CoVs in Sub-Saharan Africa and especially from West Africa, where we have currently only information on bats from Ghana and Nigeria [ 15 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 ]. Nevertheless, new alpha (α-CoVs) and betacoronaviruses (β-CoVs) have been described in Africa, including some closely related to human CoVs such as HCoV-229E, or SARS-CoVs [ 15 , 34 , 35 ].…”

Viral Evolution of Multiple Coronavirus Genomes on Genomic Index Maps

“…They may cause wider diseases with different levels of severity in a variety of hosts. It is essential to investigate proximal origin [1], probable intermediate hosts [2], evolutionary conservation [3,4], genetic diversity of Bat [5][6][7], genome-based classification/phylogenies [8,9], genetic evolution analysis [10] and coronavirus mutations affecting deadliness of strains [11] for medical treatments of COVID-19 patients.…”