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Origin and Spread of the Dengue Virus Type 1, Genotype V in Senegal, 2015–2019

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Origin and Spread of the Dengue Virus Type 1, Genotype V in Senegal, 2015–2019 viruses Article Origin and Spread of the Dengue Virus Type 1, Genotype V in Senegal, 2015–2019 Idrissa Dieng 1,2 , Marielton dos Passos Cunha 3 , Moussa Moïse Diagne 1 , Pape Mbacké Sembène 2,4, Paolo Marinho de Andrade Zanotto 3, Ousmane Faye 1, Oumar Faye 1,* and Amadou Alpha Sall 1 1 Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal; [email protected] (I.D.); [email protected] (M.M.D.); [email protected] (O.F.); [email protected] (A.A.S.) 2 Department of Animal Biology, Faculty of Science et Technics, Université Cheikh Anta Diop de Dakar(UCAD), Fann BP 5005, Dakar, Senegal; [email protected] 3 Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo 05508-000, Brazil; [email protected] (M.d.P.C.); [email protected] (P.M.d.A.Z.) 4 BIOPASS (IRD-CBGP, ISRA, UCAD), Campus de Bel-Air, BP 1386, Dakar CP 18524, Senegal * Correspondence: [email protected]; Tel.: +221-77-655-59-16/+221 Abstract: Dengue virus (DENV) is the most widespread arthropod-borne virus, with the number and severity of outbreaks increasing worldwide in recent decades. Dengue is caused by genetically distinct serotypes, DENV-1–4. Here, we present data on DENV-1, isolated from patients with dengue fever during an outbreak in Senegal and Mali (Western Africa) in 2015–2019, that were analyzed by sequencing the envelope (E) gene. The emergence and the dynamics of DENV-1 in Western Africa were inferred by using maximum likelihood and Bayesian methods. The DENV-1 grouped into a monophyletic cluster that was closely related to those from Southeast Asia. The virus appears to have been introduced directly into Medina Gounass (Suburb of Dakar), Senegal (location probability Citation: Dieng, I.; dos Passos Cunha, = 0.301, posterior = 0.76). The introduction of the virus in Senegal occurred around 2014 (95% HPD M.; Diagne, M.M.; Sembène, P.M.; de = 2012.88–2014.84), and subsequently, the virus moved to regions within Senegal (e.g., Louga and Andrade Zanotto, P.M.; Faye, O.; Fatick), causing intense outbreaks in the subsequent years. The virus appears to have been introduced Faye, O.; Sall, A.A. Origin and Spread in Mali (a neighboring country) after its introduction in Senegal. In conclusion, we present evidence of the Dengue Virus Type 1, Genotype V in Senegal, 2015–2019. that the outbreak caused by DENV-1 in urban environments in Senegal and Mali after 2015 was Viruses 2021, 13, 57. https://doi.org/ caused by a single viral introduction from Asia. 10.3390/v13010057 Keywords: dengue virus type 1; phylogeny; phylogeography; origin; Senegal Academic Editor: Hye Kwon Kim Received: 6 November 2020 Accepted: 16 December 2020 Published: 4 January 2021 1. Introduction The dengue virus (DENV-1–4) is the world’s most important arbovirus transmitted by Publisher’s Note: MDPI stays neu- infected Aedes mosquitoes. It is endemic in more than 100 countries, and it is estimated tral with regard to jurisdictional clai- that 50 million cases occur annually worldwide [1,2]. Its vector, the Aedes aegypti mosquito, ms in published maps and institutio- is widely distributed in tropical and subtropical areas around the world [3]. DENV is an nal affiliations. enveloped, positive-sense, single-stranded RNA virus that belongs to the genus Flavivirus, family Flaviviridae [4,5]. Its genome has a single open reading frame encoding for three structural proteins (capsid (C), membrane (M) and envelope (E)) and seven non-structural Copyright: © 2021 by the authors. Li- (NS) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5) [6]. Dengue viruses have censee MDPI, Basel, Switzerland. four antigenically and genetically distinct serotypes, sharing around 65% of genome simi- This article is an open access article larity [7], subsequently subdivided into distinct genotypes [8–10]. Dengue virus infection distributed under the terms and con- has diverse clinical manifestations, which range from asymptomatic illness to hemorrhagic ditions of the Creative Commons At- fever that can culminate in death [11]. tribution (CC BY) license (https:// Since the first half of the 20th century, all serotypes experienced an increase in genetic creativecommons.org/licenses/by/ diversity [12], causing variations leading to new genotypes with distinct lineages [13,14]. 4.0/). Viruses 2021, 13, 57. https://doi.org/10.3390/v13010057 https://www.mdpi.com/journal/viruses Viruses 2021, 13, 57 2 of 12 Some studies have revealed associations between genetic diversity and features such as clinical manifestations, virulence and epidemic potential [8,15]. DENV-1 exists in five distinct genotypes (genotypes I–V) [16,17]. Recently, a basal group of DENV-1 with highly divergent sequences was reported, possibly constituting a new genotype (genotype VI) [16]. In Africa, the landscape of DENV circulation was historically dominated by the occurrence of sylvatic DENV-2 [18]. Over the past two decades, a drastic change in epidemiological patterns has been observed in Africa, with urban outbreaks of DENV reported in Senegal [19] and several cases exported to Europe [20]. In Senegal, DENV-1 was first isolated from two cases in 1979 (Digoutte J.P., personal communication). Since then, no studies reported isolation of this serotype. In 2015, a study on malaria in children less than 10 years old allowed for the detection of three DENV-1 cases in Guediawaye (Medina Gounass), in the suburb of Dakar [21]. This was followed two years later by an outbreak, mainly of DENV-1, in Louga city with 131 confirmed cases (submitted paper). In 2018, another outbreak associated with DENV-1 occurred in Fatick city, Senegal. Since the notification of the first confirmed cases in the Fatick region on 21 September 2018, and as of 27 October 2018, a total of 1740 suspected cases were reported. Among them, 145 were confirmed, and the remaining 1595 were not characterized as DENV-1. Seven districts from four regions have continued to report confirmed cases: Touba (Diourbel region, 105 cases), Diourbel (Diourbel region, 1 case), Mbacke (Diourbel region, 1 case), Fatick (Fatick region, 33 cases), Gossas (Fatick region, 1 case), Coki (Louga region, 1 case) and Richard-Toll (Saint Louis region, 3 cases) [22]. Despite the increased number of sporadic cases and outbreaks in Senegal during the last 10 years, the origin and spread pattern of circulating DENV-1 strains remain unknown. At present, no phylodynamics studies of dengue virus (DENV-1–4) in Senegal have been reported. The present study describes the origin and phylogeographic profile of the DENV-1 epidemiologic spread in Senegal from 2015 to 2019. 2. Materials and Methods 2.1. Ethics Committee Samples used in this study are part of the Institut Pasteur in Dakar collection (WHO Collaborating Centre for Arboviruses and/or Hemorrhagic Fever Reference and Research). None of the data were directly derived from human samples, but rather from a cell culture supernatant. Therefore, all the samples were anonymous and only isolation IDs were used during the analysis. 2.2. Sample Collection The strains analyzed during this study were obtained from a cell culture supernatant derived from sporadic DENV cases from 2015 to 2019 and epidemic strains sampled be- tween 2017 and 2018 (Figure1). Throughout the study, 189 samples were subjected to quantitative reverse transcription PCR (RT-qPCR) to determine serotypes using a TibMol- Biol Modular Dx Dengue typing kit (Cat-No. 40-0700-24) (TibMolBiol, Berlin, Germany). Forty-seven were positive for DENV-1, and, of these, a total of 36 isolates from 6 different localities across Senegal and Mali were selected (Table1) and included in the present study. All other samples belonged to the other serotypes (DENV-2 and DENV-3). No co-infections were detected. Viruses 2021, 13, 57 3 of 12 Viruses 2020, 12, x FOR PEER REVIEW 3 of 12 . Figure 1. A map showing the locations where DENV−1 positive samples were sampled. The red dots correspond to Figure 1. A map showing the locations where DENV−1 positive samples were sampled. The red dots correspond to out- outbreak samples and the blue dots to sporadic samples. break samples and the blue dots to sporadic samples. Table 1. Sequenced strains during this study. Table 1. Sequenced strains during this study. Sequence ID City Country Year EpidemiologicalEpidemiological Context Sequence ID City Country Year 307339 Louga Senegal 2017 OutbreakContext 307424307339 LougaLouga SenegalSenegal 20172017 Outbreak Outbreak 307424 Louga Senegal 2017 Outbreak 303165 Louga Senegal 2017 Outbreak 303165 Louga Senegal 2017 Outbreak 302883302883 LougaLouga SenegalSenegal 20172017 Outbreak Outbreak 307419307419 LougaLouga SenegalSenegal 20172017 Outbreak Outbreak 273756273756 DakarDakar SenegalSenegal 20152015 Sporadic Sporadic 297855 NA Mali 2017 Outbreak 297855 NA Mali 2017 Outbreak 310386 Saint Louis Senegal 2018 Sporadic 310386310460 Saint LouisDakar SenegalSenegal 20182018 Sporadic Sporadic 310460313165 DakarFatick SenegalSenegal 20182018 Outbreak Sporadic 313165313167 FatickFatick SenegalSenegal 20182018 Outbreak Outbreak 313169 Fatick Senegal 2018 Outbreak 313167 Fatick Senegal 2018 Outbreak 313639 Fatick Senegal 2018 Outbreak 313169313644 FatickFatick SenegalSenegal 20182018 Outbreak Outbreak 313639313718 FatickFatick SenegalSenegal 20182018 Outbreak Outbreak 313644313852 FatickFatick SenegalSenegal 20182018 Outbreak Outbreak 313943 Fatick Senegal 2018 Outbreak 313718
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