Detection of Rift Valley Fever Virus Lineage H From South Africa Through the Syndromic Sentinel Surveillance Network in Senegal

Abstract

Background Rift Valley fever virus (RVFV) is an arbovirus that causes epizootics and epidemics among livestock population and humans. Our surveillance system has revealed multiple emergences and re-emergences of RVFV in West Africa over the last decade. Methods In Senegal a sentinel syndromic surveillance network (4S) has been implemented since 2011. Samples from human suspected arbovirus infection in 4S sentinel sites were sent to Institut Pasteur de Dakar (IPD) where arbovirus diagnosis by enzyme-linked immunosorbent assay (ELISA), real-time reverse transcription polymerase chain reaction (RT-PCR), and virus isolation were performed. Overall, IPD has received a total of 1,149 samples from arboviral suspected patients through the 4S network from January to December 2020. These samples were screened for seven arboviruses including RVFV. Whole genome sequencing of positive RVFV samples by RT-PCR were performed using Illumina Miseq platform followed by genome assembly. Phylogenetic analysis were performed using MEGA X. Results Out of the 1,149 arbovirus suspected cases, four RVFV positive samples were detected with RT-PCR while five RVFV positive samples were detected by ELISA. Complete genome sequences were obtained for three strains among the four positive samples by RT-PCR. Phylogenetic analyses indicated an emergence of a virus first described in South Africa during a major outbreak. Conclusion Strong surveillance system allowed the detection of RVFV outbreak in Senegal in 2020. The obtained genomes clustered with strains from South Africa belonging to lineage H. This calls for an implementation of a strong surveillance system in wild animals, humans, and livestock simultaneously in all African Countrries.

Re-Introduction of West Nile Virus Lineage 1 in Senegal from Europe and Subsequent Circulation in Human and Mosquito Populations between 2012 and 2021

“…Here we describe for the first time the detection of several WNV human cases in Senegal, associated with a strong detection of the virus in the mosquito vector. Indeed, the improvement of arbovirus surveillance in Senegal with the implementation of the 4S system and new diagnostic tools made it possible to highlight the circulation of many arboviruses including dengue, Crimean-Congo hemorrhagic fever, Rift Valley fever and WNV viruses in humans as well as in arthropods [43,44,65,66]. Before the implementation of the 4S network for arboviruses surveillance, WNV detection in humans was limited to two cases detected in Dakar in 1970 and 1991 [41].…”

“…For each arboviral disease suspected case, a dry tube venous sample is taken and sent to the arbovirus reference laboratory at IPD. All collected samples were tested by differential arboviral RT-PCR and ELISA for the detection of viral genome and IgM antibodies for WNV and other arboviruses [43].…”

“…Indeed, since 2011, the Institut Pasteur de Dakar (IPD) has set up in collaboration with the Ministry of Health a countrywide surveillance network named "4S" (Syndromic Sentinel Surveillance in Senegal) focused on influenza viruses and other respiratory viruses [42]. Since 2015, because of an increasing number of febrile cases not related to respiratory viruses, arbovirus and bacteria detection have been included in this surveillance system [43]. Furthermore, this human surveillance is coupled with a mosquito-based arbovirus surveillance system, which has also been in place for a long time and permitted the isolation and identification of many viruses including WNV, from mosquitoes in Barkedji and Kedougou areas [44].…”

Contemporary epidemiological data of Rift Valley fever virus in humans, mosquitoes and other animal species in Africa: A systematic review and meta‐analysis

“…Of the 388 eligible articles, 183 were excluded for multiple reasons described in Figure 1. Finally, a total of 205 articles (629 data on prevalence and/or CFR) met the inclusion criteria for this systematic review (Abakar et al., 2014; Abdallah et al., 2016; Adamu, 2020; Adamu et al., 2021; Adesiyun et al., 2020; Ahmed et al., 2018, 2020; Alhaji, 2020; Andayi et al., 2014; Andriamandimby et al., 2010; Andriamandimby et al., 2018; Aradaib et al., 2013; Archer et al., 2011, 2013; Atuman et al., 2022; Ayari‐Fakhfakh et al., 2011; Ba et al., 2012; Baudin et al., 2016; Beechler et al., 2015; van den Bergh et al., 2022; Bett et al., 2019; Bird et al., 2008; Bisimwa et al., 2016; Bloland et al., 2010; Blomstrom et al., 2016; Bob et al., 2017, 2022; Bonney et al., 2013; Bosworth et al., 2016; Boushab et al., 2015, 2016; Boussini et al., 2013, 2014; Breiman et al., 2010; Budasha et al., 2018; Budodo et al., 2020; Bukbuk et al., 2014; Centers for Disease Control and Prevention 2007; Chambaro et al., 2022; Chengula et al., 2014; Chevalier et al., 2005, 2011; Cichon et al., 2021; Clements et al., 2019; Cook et al., 2017; Cosseddu et al., 2021; Di Nardo et al., 2014; Diallo et al., 2005; Dione et al., 2022; Dondona et al., 2016; Durand et al., 2003, 2020; Dutuze et al., 2020; Ebogo‐Belobo et al., 2022; Eckstein et al., 2022; El Bahgy et al., 2018; El Mamy et al., …”

Human and Livestock Surveillance Revealed the Circulation of Rift Valley Fever Virus in Agnam, Northern Senegal, 2021

“…Due to the high risk of RVF introduction by livestock trade with neighboring Mauritania, Senegal’s northern regions are the most exposed. In Senegal, serological and molecular evidence of RVFV circulation has been reported in humans, livestock, and mosquitoes [ 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 ]. Aedes vexans , Culex quinquefasciatus, and Culex poicilipes can transmit the disease [ 12 ].…”