A metagenomics-based survey of the virus diversity in mosquito vectors allows the first detection of Sindbis virus in Burkina Faso

Mosquito-borne viruses represent a threat to human health worldwide. This taxonomically-diverse group includes numerous viruses that recurrently spread into new regions. Thus, periodic surveillance of the arbovirus diversity in a given region can help optimizing the diagnosis of arboviral infections. Nevertheless, such screenings are rarely carried out, especially in low-income countries. Consequently, case investigation is often limited to a fraction of the arbovirus diversity. This situation probably results in undiagnosed cases. Here, we have explored the diversity of mosquito-borne viruses in two regions of Burkina Faso. To this end, we have screened mosquitoes collected along three years in six urban and rural areas using untargeted metagenomics. The analysis focused on two mosquito species, Aedes aegypti and Culex quinquefasciatus, considered among the main vectors of arboviruses worldwide. The screening detected Sindbis virus (SINV, Togaviridae) for the first time in Burkina Faso. This zoonotic arbovirus has spread from Africa into Europe. SINV causes periodic outbreaks in Europe but its distribution and epidemiology in Africa remains largely unstudied. SINV was detected in one of the six areas of the study, and at a single year. Detection was validated with isolation in cell culture. SINV was only detected in Cx. quinquefasciatus, thus extending the list of potential vectors of SINV in nature. SINV infection rate in mosquitoes was similar to those observed in European regions that experience SINV outbreaks. A phylogenetic analysis placed the nearly-full genome within a cluster of Central African strains of lineage I. This cluster is supposedly at the origin of the SINV strains introduced into Europe. Thus, West Africa should also be considered as a potential source of the European SINV strains. Our results call for studies on the prevalence of SINV infections in the region to estimate disease burden and the interest of SINV diagnostic in case investigation. Author summaryMosquito-borne viruses are responsible for millions of cases worldwide every year. Moreover, they have repeatedly shown an ability to spread over large distances. Thus, periodic surveys of the arbovirus diversity in a given region can help to define the diagnostic tests to use during case investigation. However, comprehensive surveys are rarely carried out, especially in low-income countries. Here, the arbovirus diversity was assessed in two main mosquito vectors in Burkina Faso using untargeted metagenomics. This screening identified Sindbis virus (SINV), a zoonotic arbovirus, for the first time in Burkina Faso. Moreover, SINV was found in nature for the first time in Culex quinquefasciatus, a main mosquito vector of several pathogens and with a cosmopolitan distribution. SINV leads to periodic outbreaks mainly in Europe. Despite a likely African origin, its distribution and epidemiology in Africa remains largely unstudied. The SINV sequence from Burkina Faso felt within the cluster of Central African strains thought to be at the origin of the European SINV strains. Thus, our results indicate that West Africa should be considered as another potential source of the SINV introductions in Europe. Further studies are required to characterize SINV epidemiology in Burkina Faso and the West African region.