Challenging the notion of Aedes aegypti as the primary chikungunya virus vector: insights from Kédougou, Southeastern Senegal

Challenging the notion of Aedes aegypti as the primary chikungunya virus vector: insights from Kédougou, Southeastern Senegal | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Challenging the notion of Aedes aegypti as the primary chikungunya virus vector: insights from Kédougou, Southeastern Senegal Alioune Gaye, Moussa Moïse Diagne, Diawo Diallo, El Hadji Ndiaye, and 12 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6865029/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 03 Sep, 2025 Read the published version in BMC Infectious Diseases → Version 1 posted 12 You are reading this latest preprint version Abstract Background Chikungunya fever (CHIK) caused by the mosquito-borne chikungunya virus (CHIKV) and transmitted by Aedes mosquitoes, remains a public health burden throughout the tropics. During the CHIK outbreak in the southeastern Senegal in August 2023, an entomologic investigation was conducted to identify the vector(s) and characterize the virus strains. Methods Adult mosquitoes were collected indoors and outdoors from houses of confirmed CHIK cases and their immediate neighborhoods using Prokopack aspirators and double-net traps and all water containers were inspected for aquatic stages. Mosquito pools were tested for CHIKV by RT-qPCR and positive samples were subjected to whole genome sequencing using Illumina iSeq system. Results Animal watering points; bricks and tree holes were the most common sites for Aedes aegypti larvae and pupae. While immature Ae. aegypti were found in all affected villages, with Breteau and Container indices exceeded the WHO epidemic thresholds, Ae. furcifer emerged as the most abundant host-seeking species in domestic areas. CHIKV was detected in 31 mosquito pools, primarily in Ae. furcifer (22 pools) and only one pool of Ae. aegypti . Other Aedes species accounted for 8 positive pools and Anopheles gambiae , the primary malaria vector, one pool. Phylogenetic analysis confirmed the close relationship between 2023 CHIKV strains circulating in humans and mosquitoes, and those responsible for the 2015 outbreak. Conclusions Our study highlights the urgent need to include sylvatic mosquitoes in surveillance and control programs that until now have mainly focused on Ae. aegypti . Moreover, the potential role of Anopheles gambiae in the CHIKV transmission in Senegal warrants further investigation. Chikungunya outbreak epidemic chikungunya vector wild Aedes vectors chikungunya amplification Aedes furcifer Figures Figure 1 Figure 2 Background Chikungunya virus (CHIKV) is a mosquito-borne alphavirus of the family Togaviridae , that causes a febrile illness, often accompanied by severe joint pain as well as other common signs and symptoms including muscle pain, headache, nausea, fatigue and rash [ 1 ]. The joint pain associated with chikungunya can be debilitating and may persist for weeks or months [ 2 ]. Known to be endemic for at least decades in Africa and Asia [ 3 ], CHIKV has spread in recent years to other parts of the world, including Europe [ 4 ] and the Americas [ 5 ]. CHIKV is transmitted to humans by mosquitoes, with Aedes aegypti recognized as the principal epidemic vector in most locations worldwide, and Ae. albopictus as a secondary vector. In Africa sylvatic Aedes mosquitoes are considered to play an important role only in CHIKV maintenance in the enzootic cycle involving non-human primates living in the forest canopies [ 6 , 7 ]. In West Africa, sylvatic CHIK amplification tends to occur cyclically, approximately every 4 years [ 8 ]. As reported in previous publications, an outbreak was detected in 2006 in southeastern Senegal with only 6 confirmed cases [ 9 ], coinciding with an outbreak in Nigeria and Cameroon [ 10 , 11 ]. Subsequently in 2009, another outbreak affected Ghana, Ivory Coast and Burkina Faso, as well as southeastern Senegal, where 20 human cases were confirmed [ 12 , 13 ]. More recently in 2015, another CHIK outbreak occurred in the Kédougou region of Senegal with 40 confirmed cases reported across its three administrative subdivisions: Kédougou, Salemata and Saraya [ 14 ]. Various factors are suspected to influence the cyclic emergence of CHIKV including climatic conditions such as temperature, rainfall and humidity, which impact the vectorial capacity of mosquitoes. Additionally, the herd immunity acquired during previous outbreaks may temporarily reduce the transmission intensity. Over time, CHIKV undergoes genetic changes that can affect its ability to replicate, be transmitted, or evade the host immune response. Moreover, human activities and movement can contribute to virus spread and its introduction into new areas with young, susceptible populations. In August 2023, Senegal experienced a CHIK outbreak, with over 200 confirmed cases reported in the Kédougou region [ 15 ]. An entomological investigation was undertaken with the objective to identify the mosquito vectors involved and genetically characterize the virus responsible of the epidemic. Materials and Methods Study site Mosquito collections were carried out during August to September, 2023, across ten geographic sites in southeastern Senegal, encompassing five predominant land cover classes: village, agriculture, barren, savanna, forest as previously described [ 6 ]. In addition, 13 villages (Laminya, Nathia, Boundoucondi, Ibel, Badian, Fodé Binia, Lafia, Bembou, Faraba, Badioula, Kolia and Kondokho) where human chikungunya were confirmed, were investigated. Figure 1 shows villages with human cases (in red) and surveillance sites (in blue) where mosquitoes were sampled, Southeastern Senegal, August 2023. Adult mosquitoes were sampled across all biotopes and localities, while immature stages were sampled exclusively in villages where human cases were detected. Mosquito sampling Immature stages sampling was performed indoor and outdoor of randomly selected human habitations. All artificial and natural water-holding containers were inspected, using a flashlight if necessary, and considered as positive when harboring at least one larva or pupa of Ae. aegypti . From each positive container, a sample of larvae and/or pupae was collected, reared to adulthood, and identified morphologically. Resting and host-seeking adult mosquitoes were collected indoors and outdoors in each locality using a Prokopack aspirator [ 16 ]. Additionally, host-seeking mosquitoes were collected in the other landcover classes by aspiration in a double net baited by humans. Sample processing . Immature mosquitoes sampled from water container were reared to adulthood, while adults collected in nature were processed directly. Morphological identification of mosquitoes was performed on a chill table using appropriate keys [ 17 – 21 ]. Mosquitoes were pooled by species, sex, physiological status (engorged or unengorged), collection method, location, and date. Pools were then tested in the field laboratory for virus detection. Field-based Next Generation sequencing was also used for whole genome sequencing of positive samples. Molecular detection. Mosquito pools were homogenized in 1.5-ml Eppendorf tubes containing 500 µl of L-15 medium (Gibco BRL, Grand Island, NY, USA) using sterile pestles in a biosafety level 2 laboratory. The homogenates were centrifuged at 8,000 rpm for 10 min at 4°C. The supernatant was retained for further analyses, while mosquito debris was discarded. For CHIKV detection, RNA was extracted from 140 µl of supernatant using the QiaAmp Viral RNA Extraction Kit (Qiagen, Heiden, Germany) following the manufacturer’s protocol. RNA was amplified using a one-step real-time RT-qPCR assay with the TIB Molbiol LightMix® (Berlin, Germany). The 20 µL reaction volume consisted of 5 µL of extracted RNA, 2× Master Mix, 10 µM of specific primers (Forward: AAg CTY CgC gTC CTT TAC CAAg, Reverse: CCA AAT TgT CCY ggT CTT CCT) and probe (6FAM/CCA Atg TCY TCM gCC Tgg ACA CCTTT/TMR) targeting CHIKV in singleplex. Whole Genome Sequencing and phylogenetic analysis . Confirmed CHIKV-positive samples were processed for field-based Next Generation sequencing using the Twist Biosciences Comprehensive Viral Research Panel (CVRP) to obtain the whole viral genome. Enriched sample libraries were loaded onto an Illumina iSeq 100 sequencing system, and genome assembly was performed using the Chan Zuckerberg ID (CZ-ID; formerly IDSeq) platform [ 22 ]. All generated sequences were aligned using MAFFT with a representative CHIKV dataset covering the West African (WA), East-Central-South African (ECSA) and Asian genotypes. Maximum likelihood trees were generated using IQ-TREE [ 23 ] with a 1,000 bootstrap iterations, utilizing the best-fit substitution model determined by ModelFinder and 1,000 bootstrap replicates for statistical reliability and visualization was made with FigTree V1.4.4 [ 24 ]. Data analysis Data from larval surveys were used to estimate three key entomological indices: the Breteau Index (BI) defined as the number of containers positive for immature stages of Ae. aegypti per 100 housing units [ 25 ], the Container Index (CI) representing the number of containers positive for immature Ae. aegypti per 100 inspected water containers [ 26 ] and the Breeding Preference (BP) defined as the ratio of the percentage of positive containers (Y) to the percentage of that type of inspected container (X). The highest Y/X ratio indicated the preferred type of breeding site for mosquitoes. Epidemic thresholds for BI and CI were set at 5% and 3%, respectively, based on WHO standards [ 27 ]. The minimum field infection rates for CHIKV were calculated, including 95% confidence intervals (lower and upper limits), using the PooledInfRate software, version 4.0 [ 28 ]. Statistical differences were determined with a significance level set at p < 0.05. Results Collection of immature stages and adult mosquitoes . A total of 742 water containers was inspected across the surveyed sites, showing significant variations in Ae. aegypti breeding preferences between administrative departments. In Saraya tree holes emerged as the most preferred sites, followed by bricks. In contrast, in Kédougou department, animal watering troughs and bricks were the sites most commonly inhabited by mosquito immatures (Table 1 ). At the village level, animal watering troughs were identified as the most commonly occupied containers in 9 out of 12 villages. Other notable immature habitats included tree-holes, bricks, water storage containers and tires. In all the villages investigated, the epidemic risk indices consistently exceeded the thresholds defined by the WHO across all surveyed villages (see additional file). Table 1 Aedes aegypti immature habitats at the department level, Kédougou region, August 2023 Departments Container type Containers inspected (X%) * Positive containers (Y%) ψ Immature site Preference (Y%/X%) SARAYA Clay jars 85 (14.10) 6 (3.11) 0.22 Water storage containers 152 (25.21) 11 (5.70) 0.23 Tires 62 (10.28) 24 (12.44) 1.21 Bricks 106 (17.58) 88 (45.60) 2.59 Animal watering 13 (2.16) 9 (4.66) 2.16 Abandoned containers 181 (30.02) 52 (26.94) 0.90 Basins 2 (0.33) 1 (0.52) 1.56 Tree holes 2 (0.33) 2 (1.04) 3.12 TOTAL 603 193 KEDOUGOU Clay jars 32 (24.06) 4 (5.97) 0.25 Water storage containers 26 (19.55) 5 (7.46) 0.38 Tires 14 (10.53) 8 (11.94) 1.13 Bricks 29 (21.80) 29 (43.28) 1.99 Animal watering 6 (4.51) 6 (8.96) 1.99 Abandoned containers 26 (19.55) 15 (22.39) 1.15 TOTAL 133 67 * X% = Containers inspected /Total examined ψ Y% = Positive containers /Total Positives A total of 6209 adult mosquitoes belonging to 49 species and 8 genera were collected during the period of the CHIK outbreak. Of these, 31 mosquito pools comprising 8 species (7 Aedes and 1 Anopheles species) were found infected by CHIKV (Table 2 ). Ae. furcifer was the only species found infected across all biotopes. In the forest biotope, Ae. taylori was the most frequently infected species (p = 0.03, statistically significantly higher than Ae. vittatus ,) followed by Ae. furcifer . In the savanna, Ae. dalzieli showed the highest infection rate (p = 0.02, statistically significantly higher than Ae. vittatus ,) followed by Ae. furcifer . In village settings, An. gambiae was the most frequently infected species followed by Ae. furcifer , while in Barren and Agriculture environments, Ae. furcifer was the only infected species. Table 2 Infection rates of mosquito species associated with CHIKV in different biotopes, Kédougou, 2023. Biotope Species Total Pos Total mosquitoes Total negative pools Infection rate Lower confidence Upper confidence Forest Ae. africanus 1 179 85 5.586 0.001 0.031 Forest Ae. furcifer 8 941 144 0.008 0.004 0.017 Forest Ae. luteocephalus 1 190 85 0.005 0.001 0.029 Forest Ae. taylori 3 129 30 0.023 0.008 0.066 Savanna Ae. dalzieli 1 5 3 0.2 0.036 0.624 Savanna Ae. furcifer 3 273 45 0.011 0.004 0.032 Savanna Ae. vittatus 1 380 46 0.002 0.0005 0.015 Village Ae. aegypti 1 149 65 0.007 0.001 0.037 Village Ae. furcifer 7 508 70 0.014 0.007 0.028 Village An. gambiae 1 68 22 0.015 0.003 0.079 Barren Ae. furcifer 3 320 36 0.009 0.003 0.027 Agriculture Ae. furcifer 1 259 41 0.004 0.001 0.022 Phylogenetic analysis The phylogenetic analysis revealed that the 2023 CHIKV outbreak strain in Kedougou belongs to the WA genotype, forming a highly supported monophyletic group (bootstrap ≥ 95) with strains from the 2015 and 2005 outbreaks in the same region [ 29 ]. These sequences share 98.80–98.96% nucleotide identity with the reference strain HM045817 (2005), underscoring their close genetic relationship. Furthermore, the clustering of mosquito and human sequences confirmed that the same viral strain circulated between these hosts during the outbreak. Figure 2 provides results of the phylogenetic analysis of CHIKV sequences obtained from mosquitoes (labeled with red identifier numbers) and humans (labeled with blue identifier numbers) during the 2023 outbreak in southeastern Senegal. The sequences are grouped according to their genetic lineage, including those belonging to the West African, East/Central/South African (ECSA), and Asian genotypes. Discussion Nearly worldwide, Aedes aegypti along with Ae. albopictus is considered the primary epidemic vector of several common, human-amplified arboviruses such as dengue, yellow fever, Zika and CHIKV [ 6 , 30 – 33 ]. In fact, Ae. aegypti has been several times found associated with CHIKV in central [ 34 ], southern [ 35 ] and eastern parts of Africa [ 36 ], and also identified elsewhere in Africa as the main epidemic vector [ 37 , 38 ]. Furthermore, populations of Ae. aegypti from South Africa [ 39 ], Cameroon [ 40 ], Senegal and Cape Verde [ 41 , 42 ] have been shown to be experimentally competent for CHIKV transmission. Moreover, vertical transmission of CHIKV in Ae. aegypti has been demonstrated experimentally in India [ 37 ]. All of these results support a major CHIKV vector role for Ae. aegypti . For many decades, Ae. aegypti formosus , the ancestral, sylvatic form that evolved into the domesticated Ae. aegypti aegypti , was considered as the only subspecies present in southern Senegal [ 43 ]. However, recent studies have shown the presence of both subspecies in Kédougou department [ 44 ] with larval development sites found in both forest and, more recently, in domestic environments. These changing distribution patterns are likely linked to deforestation driven by agriculture, gold mining and other human activities, leading to the domestication of wild Ae. aegypti populations in response to urbanization. Such adaptation to the domestic environment has also been observed in Nigeria [ 45 ] and Gabon [ 46 ]. In our study, Ae. aegypti was abundant in immature stages in all potential aquatic sites and the epidemic risk indices were above the thresholds defined by the WHO [ 25 , 26 ]. In other words, the indices were sufficiently high for this species to ensure CHIK transmission. Also, at the adult stage Ae. aegypti were found during our investigation in all affected localities. However, CHIKV infection in Ae. aegypti was surprisingly low, with only one positive pool, representing just 3.2% of positives. Therefore, the main epidemic vector worldwide apparently did not play a major role in CHIKV transmission to humans during this outbreak. The zoophilic tendency of Ae. aegypti generally observed in West Africa [ 47 ] may explain this finding. The Ae. aegypti formosus form is significantly more abundant in the Kédougou area. However, it has been previously shown to be less endophilic and anthropophilic than the Ae. aegypti aegypti and thus less involved in human-amplified arbovirus transmission [ 48 ]. Therefore, Ae. aegypti formosus probably plays no major role in either maintenance of the sylvatic cycle or the spillover of CHIKV to humans in this region [ 6 ]. Our findings highlight a significant involvement of wild mosquitoes in CHIKV transmission during this epidemic, suggesting epizootic amplification of the sylvatic cycle. CHIKV was detected in 29 pools of wild Aedes mosquitoes, predominantly Ae. furcifer (22 pools), which accounted for 71% of positives. Historically, Ae. furcifer has been found most frequently infected with CHIKV [ 49 , 50 ] and is competent to transmit the virus [ 51 , 52 ]. The same profile of infected mosquitoes was previously observed in 2009–2010, when among the 42 CHIKV-positive pools, most were wild mosquitoes. Only one pool of Ae. aegypti was found positive [ 6 ]. The same trend was observed during the 2015 amplification with the sylvatic vectors recording 93.7% of the CHIKV detections and only 6.25% (2/32 pools) for Ae. aegypti [ 53 ]. These findings corroborated our results and support the conclusion that Ae. aegypti does not play a significant role in CHIKV outbreaks in the Kédougou region. The higher number of human cases (over 200 persons) recorded among men and young people over 15 years of age [ 15 ] supports the hypothesis that transmission occurred mainly outside of human dwellings. Sustained domestic transmission would be expected to affect age groups, including children under 15 years of age, who generally stay at home and spend more time indoors. Ae. furcifer , known to have great ecological plasticity [ 6 ], was frequently found infected and biting humans in villages at high density in Senegal [ 6 , 43 , 54 ] and elsewhere in Africa [ 55 ], indicating its major role in CHIKV transmission. We also found during our investigation one PCR-positive pool of male An. gambiae . Other species within the Anopheles genus such as An. funestus , An. coustani and An. domicola have been found naturally infected with CHIKV in the Kédougou region during a previous study in 2009–2010 [ 6 ]. Subsequently in 2015, 3 pools of female An. gambiae were found positive for CHIKV in the same area during a co-amplification with YFV and ZIKV [ 53 ], suggesting sustained CHIKV transmission by An. gambiae . Vector competence studies of An. gambiae showed a CHIKV infection rate of 43% at day 7 post-bloodmeal, although viral titers in the mosquitoe hemocoel were low and CHIKV-positive saliva was not detected [ 56 ]. Moreover An. gambiae and An. funestus , both present in the Kédougou region and transmitting malaria parasites, are the only known vectors of o’nyong-nyong virus (ONNV), a close relative of CHIKV [ 57 , 58 ]. Also, An. stephensi was recently shown to be a competent ONNV vector [ 59 ]. All of these findings suggested that malaria vectors should be monitored for their potential role in CHIKV transmission in Senegal and elsewhere in Africa. Phylogenetic analysis confirmed that the same CHIKV strain circulated between humans and mosquitoes during 2023, harboring shared mutations compared to CHIKV strains that circulated in 2005 and 2015 [ 15 ]. These mutations deserve further study as CHIKV mutations can greatly affect vector host range [ 60 ]. Conclusions This study highlights the persistence of an endemic CHIKV strain in a sylvatic transmission cycle primarily, emphasizing the significant role of wild, sylvatic Aedes species in CHIKV amplification and transmission to humans. Our findings underscore the urgent need to assess the insecticide resistance status of these species and integrate them into vector control programs. Further studies are required to better understand the many factors that contribute to the amplifications of arboviruses like CHIKV at the interface of humans and both sylvatic and urban environments, which can facilitate virus re-emergence and transmission. Abbreviations Ae. Aedes An. Anopheles BI Breteau index BP Breeding Preference CHIK Chikungunya fever CHIKV Chikungunya virus CI Container index CVRP Comprehensive Viral Research Panel CZ-ID Chan Zuckerberg ID ECSA East-Central-South African MAFFT Multiple Alignment using Fast Fourier Transform NY New York ONNV o’nyong-nyong virus RNA Ribonucleic Acid RT-qPCR Real time quantitative polymerase chain reaction USA United State of America WA West African WHO World Health Organization YFV Yellow fever virus ZIKV Zika virus Declarations Ethics approval and consent to participate Not applicable Consent for publication The included institutions do not explicitly require/give formal approval for presentations or publication of authored works related to collaborative or individual research. Competing interests The authors declare no competing interests. Funding This work was entirely supported by the West African Center for Emerging Infectious Diseases (NIH/NIAID) under Grant Number U01 AI151801. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author Contribution A.G., M.D. (Mawlouth Diallo), D.D. and M.M.D. conceived and designed the study. A.G., D.D., E.N., M.G. and M.D. (Mawlouth Diallo) collected the mosquito samples on field. A.G., D.D., E.N., M.G., M.D. (Madeleine Dieng), M.K., M.H.D.N., I.D. (Idrissa Dieng) and S.S. performed the laboratory experiments. A.G., I.D. (Ibrahima Dia), D.D., B.D., E.N., F.A.S., C.W., S.C.W. and M.D. (Mawlouth Diallo) analyzed the data. A.G., M.D. (Mawlouth Diallo) and M.M.D. drafted the manuscript. A.G., M.M.D., D.D., E.N., M.H.D.N., M.G., I.D. (Idrissa Dieng), M.D. (Madeleine Dieng), M.K., S.S., B.D., F.A.S., C.W., I.D. (Ibrahima Dia), S.C.W. and M.D. (Mawlouth Diallo) critically revised, read and approved the final manuscript. Acknowledgement We would like to thank the Medical Officer of Kédougou and Saraya districts, the Regional Hygiene Brigade Officer of Kédougou, the community health workers and the local populations for their collaboration. We also thank Maimouna Mbanne, Seynabou Mbaye Ba Souna Diop and Serge Freddy Moukaha Doukanda for their technical assistance Data availability Not applicable. References Pialoux G, Gaüzère B-A, Jauréguiberry S, Strobel M. Chikungunya, an epidemic arbovirosis. Lancet Infect Dis. 2007;7:319–27. Kularatne SAM, Gihan MC, Weerasinghe SC, Gunasena S. Concurrent outbreaks of Chikungunya and Dengue fever in Kandy, Sri Lanka, 2006–07: a comparative analysis of clinical and laboratory features. Postgrad Med J. 2009;85:342–6. Volk SM, Chen R, Tsetsarkin KA, Adams AP, Garcia TI, Sall AA, et al. Genome-Scale Phylogenetic Analyses of Chikungunya Virus Reveal Independent Emergences of Recent Epidemics and Various Evolutionary Rates. J Virol. 2010;84:6497–504. Delisle E, Rousseau C, Broche B, Leparc-Goffart I, L’Ambert G, Cochet A, et al. Chikungunya outbreak in Montpellier, France, September to October 2014. Eurosurveillance. 2015;20. Leparc-Goffart I, Nougairede A, Cassadou S, Prat C, De Lamballerie X. Chikungunya in the Americas. The Lancet. 2014;383:514. Diallo D, Sall AA, Buenemann M, Chen R, Faye O, Diagne CT, et al. Landscape ecology of sylvatic chikungunya virus and mosquito vectors in southeastern Senegal. PLoS Negl Trop Dis. 2012;6:e1649. Russo G, Subissi L, Rezza G. Chikungunya fever in Africa: a systematic review. Pathog Glob Health. 2020;114:136–44. Althouse BM, Hanley KA, Diallo M, Sall AA, Ba Y, Faye O, et al. Impact of climate and mosquito vector abundance on sylvatic arbovirus circulation dynamics in Senegal. Am J Trop Med Hyg. 2015;92:88. Sow A, Loucoubar C, Diallo D, Faye O, Ndiaye Y, Senghor CS, et al. Concurrent malaria and arbovirus infections in Kedougou, southeastern Senegal. Malar J. 2016;15:47. Peyrefitte CN, Rousset D, Pastorino BAM, Pouillot R, Bessaud M, Tock F, et al. Chikungunya Virus, Cameroon, 2006. Emerg Infect Dis. 2007;13:768–71. Leroy EM, Nkoghe D, Ollomo B, Nze-Nkogue C, Becquart P, Grard G, et al. Concurrent Chikungunya and Dengue Virus Infections during Simultaneous Outbreaks, Gabon, 2007. Emerg Infect Dis. 2009;15:591–3. Sow A, Nikolay B, Faye O, Cauchemez S, Cano J, Diallo M, et al. Changes in the Transmission Dynamic of Chikungunya Virus in Southeastern Senegal. Viruses. 2020;12:196. Lim JK, Ridde V, Agnandji ST, Lell B, Yaro S, Yang JS, et al. Seroepidemiological Reconstruction of Long-term Chikungunya Virus Circulation in Burkina Faso and Gabon. J Infect Dis. 2023;227:261–7. Senegal: Elevated chikungunya activity reported in the Kedougou Region through August /update 1. Senegal: Elevated chikungunya activity reported in the Kedougou Region through August /update 1 | Crisis24. https://crisis24.garda.com/alerts/2023/08/senegal-elevated-chikungunya-activity-reported-in-the-kedougou-region-through-august-update-1. Accessed 15 Feb 2024. Dieng I, Sadio BD, Gaye A, Sagne SN, Ndione MHD, Kane M, et al. Genomic characterization of a reemerging Chikungunya outbreak in Kedougou, Southeastern Senegal, 2023. Emerg Microbes Infect. 2024;13:2373308. Vazquez-Prokopec GM, Galvin WA, Kelly R, Kitron U. A New, Cost-Effective, Battery-Powered Aspirator for Adult Mosquito Collections. J Med Entomol. 2009;46:1256–9. Edwards FW. Mosquitoes of the Ethiopian Region. HI.-Culicine Adults and Pupae. 1941. Ferrara L, Germain M, Hervy J-P. Aedes (Diceromyia) furcifer (Edwards, 1913) et Aedes (Diceromyia) taylori Edwards, 1936: le point sur la différenciation des adultes. Cah ORSTOM Sér Ent Méd Parasitol. 1984;22:179–83. Huang Y-M, Ward RA. A pictorial key for the identification of the mosquitoes associated with yellow fever in Africa. Mosq Syst. 1981;13:138–49. Diagne N, Fontenille D, Konate L, Faye O, Lamizana MT, Legros F. Les anophèles du Sénégal: liste commentée et illustrée. Bull Société Pathol Exot. 1994;87:267–77. Robert V, Ndiaye EH, Rahola N, Le Goff G, Boussès P, Diallo D, et al. Clés dichotomiques illustrées d’identification des femelles et des larves de moustiques (Diptera : Culicidae) du Burkina Faso, Cap-Vert, Gambie, Mali, Mauritanie, Niger, Sénégal et Tchad. 2022;:181 p. Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, et al. IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. GigaScience. 2020;9:giaa111. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74. Rambault A. FigTree [http://tree. bio. ed. ac. uk/software/figtree/]. 2017. Taufflieb R, Simonkovich E, Dieng PY. Enquête sur le vecteur urbain de fièvre jaune Aedes aegypti dans l’ouest du Sénégal. Multigraph Doc ORSTOM Dakar. 1972;20941. Asia WHORO for S-E. Comprehensive Guideline for Prevention and Control of Dengue and Dengue Haemorrhagic Fever. Revised and expanded edition. WHO Regional Office for South-East Asia; 2011. Chang F-S, Tseng Y-T, Hsu P-S, Chen C-D, Lian I-B, Chao D-Y. Re-assess Vector Indices Threshold as an Early Warning Tool for Predicting Dengue Epidemic in a Dengue Non-endemic Country. PLoS Negl Trop Dis. 2015;9:e0004043. Biggerstaff B. PooledInRate, version 4.0: An Excel® add-in to compute infection rates from pooled data. Fort Collins CO Cent Dis Control Prev. 2016. Dieng I, Ndiaye M, Kane M, Balde D, Mbanne M, Diop SMBS, et al. An amplicon-based Illumina and nanopore sequencing workflow for Chikungunya virus West Africa genotype. 2023;:2023.12.07.23299611. Madewell ZJ. Arboviruses and Their Vectors. South Med J. 2020;113:520–3. Diallo M, Tall A, Dia I, Ba Y, Sarr FD, Ly AB, et al. Yellow fever outbreak in central part of Senegal 2002: epidemiological findings. J Public Health Epidemiol. 2013;5:291–6. Diouf B, Gaye A, Dieng I, Diagne CT, Ndiaye EH, Mhamadi M, et al. Dengue 1 outbreak in Rosso, northern Senegal, October 2021: entomologic investigations. J Med Entomol. 2024;61:222–32. Powers AM. Chikungunya. Clin Lab Med. 2010;30:209–19. Mombouli J-V, Bitsindou P, Elion DOA, Grolla A, Feldmann H, Niama FR, et al. Chikungunya Virus Infection, Brazzaville, Republic of Congo, 2011. Emerg Infect Dis. 2013;19:1542–3. Gudo ES, Pinto G, Vene S, Mandlaze A, Muianga AF, Cliff J, et al. Serological Evidence of Chikungunya Virus among Acute Febrile Patients in Southern Mozambique. PLoS Negl Trop Dis. 2015;9:e0004146. Sang RC, Ahmed O, Faye O, Kelly CLH, Yahaya AA, Mmadi I, et al. Entomologic investigations of a chikungunya virus epidemic in the Union of the Comoros, 2005. Am J Trop Med Hyg. 2008;78:77–82. Agarwal A, Dash PK, Singh AK, Sharma S, Gopalan N, Rao PVL, et al. Evidence of Experimental Vertical Transmission of Emerging Novel ECSA Genotype of Chikungunya Virus in Aedes aegypti. PLoS Negl Trop Dis. 2014;8:e2990. Monath: The arboviruses: epidemiology and ecology - Google Scholar. https://scholar.google.com/scholar_lookup?title=The%20arboviruses%3A%20epidemiology%20and% 20ecology&author=P%20Jupp&author=B%20McIntosh&author=T%20Monath&publication_year=1988 &book=The%20arboviruses%3A%20epidemiology%20and%20ecology. Accessed 13 Oct 2024. Jupp PG, McIntosh BM. Aedes furcifer and other mosquitoes as vectors of chikungunya virus at Mica, northeastern Transvaal, South Africa. J Am Mosq Control Assoc. 1990;6:415–20. Paupy C, Ollomo B, Kamgang B, Moutailler S, Rousset D, Demanou M, et al. Comparative Role of Aedes albopictus and Aedes aegypti in the Emergence of Dengue and Chikungunya in Central Africa. Vector-Borne Zoonotic Dis. 2010;10:259–66. Diagne CT, Faye O, Guerbois M, Knight R, Diallo D, Faye O, et al. Vector Competence of Aedes aegypti and Aedes vittatus (Diptera: Culicidae) from Senegal and Cape Verde Archipelago for West African Lineages of Chikungunya Virus. Am J Trop Med Hyg. 2014;91:635–41. Vazeille M, Yébakima A, Lourenço-de-Oliveira R, Andriamahefazafy B, Correira A, Rodrigues JM, et al. Oral receptivity of Aedes aegypti from Cape Verde for yellow fever, dengue, and chikungunya viruses. Vector Borne Zoonotic Dis Larchmt N. 2013;13:37–40. Cornet M, Chateau R, Valade M, Dieng P, Raymond H, Lorand A. Données bio-écologiques sur les vecteurs potentiels du. Virus amaril au Sénégal oriental. Rôle des différentes espéces dans la transmission du virus. Cah Orstom Entomol Méd Parasitol. 1978;16:315–41. Diouf B, Dia I, Sene NM, Ndiaye EH, Diallo M, Diallo D. Morphology and taxonomic status of Aedes aegypti populations across Senegal. PLoS One. 2020;15:e0242576. Nasidi A, Monath TP, DeCock K, Tomori O, Cordellier R, Olaleye OD, et al. Urban yellow fever epidemic in western Nigeria, 1987. Trans R Soc Trop Med Hyg. 1989;83:401–6. Vazeille-Falcoz M, Failloux AB, Mousson L, Elissa N, Rodhain F. Oral receptivity of Aedes aegypti formosus from Franceville (Gabon, central Africa) for type 2 dengue virus. Bull Soc Pathol Exot 1990. 1999;92:341–2. Boorman JP, Service MW. Some records of mosquitoes (Culicidae, Diptera) from the Niger delta area, southern Nigeria. West Afr Med J. 1960;9:67–72. Diouf B, Sene NM, Ndiaye EH, Gaye A, Ngom EHM, Gueye A, et al. Resting Behavior of Blood-Fed Females and Host Feeding Preferences of Aedes aegypti (Diptera: Culicidae) Morphological Forms in Senegal. J Med Entomol. 2021;58:2467–73. Jupp PG. Mosquitoes as vectors of human disease in South Africa. South Afr Fam Pract. 2005;47:68–72. Diallo M, Thonnon J, Traore-Lamizana M, Fontenille D. Vectors of Chikungunya virus in Senegal: current data and transmission cycles. Am J Trop Med Hyg. 1999;60:281–6. Paterson HE, McIntosh BM. Further Studies on the Chikungunya Outbreak in Southern Rhodesia in 1962. Ann Trop Med Parasitol. 1964. Jupp PG, McIntosh BM, dos Santos I, de Moor P. Laboratory vector studies on six mosquito and one tick species with chikungunya virus. Trans R Soc Trop Med Hyg. 1981;75:15–9. Diallo D, Fall G, Diagne CT, Gaye A, Ba Y, Dia I, et al. Concurrent amplification of Zika, chikungunya, and yellow fever virus in a sylvatic focus of arboviruses in Southeastern Senegal, 2015. BMC Microbiol. 2020;20:181. Diallo M, Ba Y, Sall AA, Diop OM, Ndione JA, Mondo M, et al. Amplification of the sylvatic cycle of dengue virus type 2, Senegal, 1999–2000: entomologic findings and epidemiologic considerations. Emerg Infect Dis. 2003;9:362. Mondet B. Importance d’Aedes (Diceromyia) Furcifer Edwards, 1913 (Diptera: Culicidae) Parmi Les Vecteurs Potentiels d’Arboviroses, dans l’Épidémiologie de la Fièvre Jaune en Savane Sub-Soudanienne de Côte-d’Ivoire. Ann Société Entomol Fr NS. 1997;33:47–54. Vanlandingham D, Hong C, Klingler K, Tsetsarkin K, Horne K, Powers A, et al. Differential Infectivities of O’Nyong-Nyong and Chikungunya Virus Isolates in Anopheles Gambiae and Aedes Aegypti Mosquitoes. Am J Trop Med Hyg. 2005;72:616–21. Williams MC, Woodall JP. O’nyong-nyong fever: an epidemic virus disease in East Africa. II. Isolation and some properties of the virus. Trans R Soc Trop Med Hyg. 1961;55. Williams MC, Woodall JP, Corbet PS, Gillett JD. O’nyong-nyong fever: an epidemic virus disease in East Africa. VIII. Virus isolations from Anopheles mosquitoes. Trans R Soc Trop Med Hyg. 1965;59. Mutsaers M, Engdahl CS, Wilkman L, Ahlm C, Evander M, Lwande OW. Vector competence of Anopheles stephensi for O’nyong-nyong virus: a risk for global virus spread. Parasit Vectors. 2023;16:133. Tsetsarkin KA, Chen R, Weaver SC. Interspecies transmission and chikungunya virus emergence. Curr Opin Virol. 2016;16:143–50. Additional Declarations No competing interests reported. Supplementary Files AdditionalFile.docx Cite Share Download PDF Status: Published Journal Publication published 03 Sep, 2025 Read the published version in BMC Infectious Diseases → Version 1 posted Editorial decision: Revision requested 07 Jul, 2025 Reviews received at journal 06 Jul, 2025 Reviews received at journal 04 Jul, 2025 Reviews received at journal 03 Jul, 2025 Reviewers agreed at journal 26 Jun, 2025 Reviewers agreed at journal 25 Jun, 2025 Reviewers agreed at journal 25 Jun, 2025 Reviewers invited by journal 25 Jun, 2025 Editor invited by journal 24 Jun, 2025 Editor assigned by journal 23 Jun, 2025 Submission checks completed at journal 23 Jun, 2025 First submitted to journal 10 Jun, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6865029","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":477429514,"identity":"5f94e8a9-820e-4d14-8f3c-21e74d05bae4","order_by":0,"name":"Alioune Gaye","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABAElEQVRIie3RMUsDMRTA8RcCvSXHrSmCfoWUg4pQm6/ScHCTnRwdrBy8W+J+Sz+Fy42FQG/JB3AQtBScFLIKBT3tVVyadnTIf3rLj/fgAYRC/7BeRGY/Q1Kwc+eOIQntCG/0kFTtwA6RftENgi1zyo4hwtC7dVyPQPBsSS/rsZSRHjrYPHkIKdLY5i1R5XpqM6WZTSuCrz6CJzEaGDwqpFOkE8avUiAzs5fILfkE8bxCeoG3kp29pQCb/aTbsgDxvYWgIZqzlvS8pBjMMWO8JeTeNkrb/BoUekhTrl7ecXyaVKp0H/WNjErzAM5z2K7tN7q3AkwOgl2/JBQKhUJ/+gIW3FKqOktHJwAAAABJRU5ErkJggg==","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":true,"prefix":"","firstName":"Alioune","middleName":"","lastName":"Gaye","suffix":""},{"id":477429515,"identity":"c829a980-20df-44dc-bd49-1a5f872e750e","order_by":1,"name":"Moussa Moïse Diagne","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Moussa","middleName":"Moïse","lastName":"Diagne","suffix":""},{"id":477429517,"identity":"a0aff944-ce9f-4fe4-bb9e-237203bc3f64","order_by":2,"name":"Diawo Diallo","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Diawo","middleName":"","lastName":"Diallo","suffix":""},{"id":477429520,"identity":"9037dd84-d32c-467a-b6c1-89b39be1a0c6","order_by":3,"name":"El Hadji Ndiaye","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"El","middleName":"Hadji","lastName":"Ndiaye","suffix":""},{"id":477429521,"identity":"c908fd19-55ca-40ef-9d29-496f60174dfc","order_by":4,"name":"Marie Henriette Dior Ndione","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Marie","middleName":"Henriette Dior","lastName":"Ndione","suffix":""},{"id":477429524,"identity":"cc2de059-bd58-438d-a403-8693107ee74d","order_by":5,"name":"Moussa Gaye","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Moussa","middleName":"","lastName":"Gaye","suffix":""},{"id":477429525,"identity":"7b17d6dd-3740-4567-a02d-a2990da33ba1","order_by":6,"name":"Idrissa Dieng","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Idrissa","middleName":"","lastName":"Dieng","suffix":""},{"id":477429526,"identity":"b7233568-95bf-40bf-8809-86c7b8fe9ff1","order_by":7,"name":"Madeleine Dieng","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Madeleine","middleName":"","lastName":"Dieng","suffix":""},{"id":477429527,"identity":"9d2d5989-c749-4d1c-9f86-b2ed3936d696","order_by":8,"name":"Mouhamed Kane","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Mouhamed","middleName":"","lastName":"Kane","suffix":""},{"id":477429528,"identity":"9ca5b7dd-5006-4fa3-9e1d-efce615d4fc0","order_by":9,"name":"Safietou Sankhe","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Safietou","middleName":"","lastName":"Sankhe","suffix":""},{"id":477429529,"identity":"602f30ed-a332-4e0d-94d2-4f59fd6e3c18","order_by":10,"name":"Babacar Diouf","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Babacar","middleName":"","lastName":"Diouf","suffix":""},{"id":477429530,"identity":"61debbb0-076b-40d8-8208-4401a15bead4","order_by":11,"name":"Faty Amadou Sy","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Faty","middleName":"Amadou","lastName":"Sy","suffix":""},{"id":477429531,"identity":"2c17907e-ac44-4d2e-9ec9-e3dcc0a16d66","order_by":12,"name":"Caroline Weldon","email":"","orcid":"","institution":"University of Texas Medical Branch","correspondingAuthor":false,"prefix":"","firstName":"Caroline","middleName":"","lastName":"Weldon","suffix":""},{"id":477429532,"identity":"988d906f-994c-453a-8e11-54624327aab1","order_by":13,"name":"Ibrahima Dia","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Ibrahima","middleName":"","lastName":"Dia","suffix":""},{"id":477429533,"identity":"2beb004d-68d9-4d66-b215-8f0d48b29b90","order_by":14,"name":"Scott C. Weaver","email":"","orcid":"","institution":"University of Texas Medical Branch","correspondingAuthor":false,"prefix":"","firstName":"Scott","middleName":"C.","lastName":"Weaver","suffix":""},{"id":477429534,"identity":"3c47cb14-6944-44eb-8b22-d1eb30b8eb20","order_by":15,"name":"Mawlouth Diallo","email":"","orcid":"","institution":"Institut Pasteur de Dakar","correspondingAuthor":false,"prefix":"","firstName":"Mawlouth","middleName":"","lastName":"Diallo","suffix":""}],"badges":[],"createdAt":"2025-06-10 16:23:20","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6865029/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6865029/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12879-025-11402-7","type":"published","date":"2025-09-03T15:57:36+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":85757811,"identity":"abb565c2-6290-4fcd-8ce4-801896860722","added_by":"auto","created_at":"2025-07-01 10:59:20","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":876319,"visible":true,"origin":"","legend":"\u003cp\u003eMosquito sampling sites\u003c/p\u003e","description":"","filename":"Figure1BMC.tiff.jpg","url":"https://assets-eu.researchsquare.com/files/rs-6865029/v1/9ab7ffa32d67f61631d6b55b.jpg"},{"id":85755277,"identity":"2f9adc71-28be-4d4c-b459-f8973b0386eb","added_by":"auto","created_at":"2025-07-01 10:43:20","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":297127,"visible":true,"origin":"","legend":"\u003cp\u003eCHIKV sequences obtained from mosquitoes and humans during 2023 outbreak in southeastern Senegal\u003c/p\u003e","description":"","filename":"Figure2BMC.jpg","url":"https://assets-eu.researchsquare.com/files/rs-6865029/v1/aee5edc986b1a8484b055288.jpg"},{"id":90828187,"identity":"22fe8a1e-200a-402b-961f-f62450f51ced","added_by":"auto","created_at":"2025-09-08 16:06:02","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2110239,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6865029/v1/ea5cb399-34f7-48c1-ae3f-8dc030ff4e8a.pdf"},{"id":85755275,"identity":"835988d1-be4d-4798-baf6-35659177cbf7","added_by":"auto","created_at":"2025-07-01 10:43:20","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":19813,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile.docx","url":"https://assets-eu.researchsquare.com/files/rs-6865029/v1/f7a89847a20d42d5636753dd.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Challenging the notion of Aedes aegypti as the primary chikungunya virus vector: insights from Kédougou, Southeastern Senegal","fulltext":[{"header":"Background","content":"\u003cp\u003eChikungunya virus (CHIKV) is a mosquito-borne alphavirus of the family \u003cem\u003eTogaviridae\u003c/em\u003e, that causes a febrile illness, often accompanied by severe joint pain as well as other common signs and symptoms including muscle pain, headache, nausea, fatigue and rash [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. The joint pain associated with chikungunya can be debilitating and may persist for weeks or months [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. Known to be endemic for at least decades in Africa and Asia [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e], CHIKV has spread in recent years to other parts of the world, including Europe [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e] and the Americas [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. CHIKV is transmitted to humans by mosquitoes, with \u003cem\u003eAedes aegypti\u003c/em\u003e recognized as the principal epidemic vector in most locations worldwide, and \u003cem\u003eAe. albopictus\u003c/em\u003e as a secondary vector. In Africa sylvatic \u003cem\u003eAedes\u003c/em\u003e mosquitoes are considered to play an important role only in CHIKV maintenance in the enzootic cycle involving non-human primates living in the forest canopies [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn West Africa, sylvatic CHIK amplification tends to occur cyclically, approximately every 4 years [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. As reported in previous publications, an outbreak was detected in 2006 in southeastern Senegal with only 6 confirmed cases [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e], coinciding with an outbreak in Nigeria and Cameroon [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e, \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. Subsequently in 2009, another outbreak affected Ghana, Ivory Coast and Burkina Faso, as well as southeastern Senegal, where 20 human cases were confirmed [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e, \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. More recently in 2015, another CHIK outbreak occurred in the K\u0026eacute;dougou region of Senegal with 40 confirmed cases reported across its three administrative subdivisions: K\u0026eacute;dougou, Salemata and Saraya [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eVarious factors are suspected to influence the cyclic emergence of CHIKV including climatic conditions such as temperature, rainfall and humidity, which impact the vectorial capacity of mosquitoes. Additionally, the herd immunity acquired during previous outbreaks may temporarily reduce the transmission intensity. Over time, CHIKV undergoes genetic changes that can affect its ability to replicate, be transmitted, or evade the host immune response. Moreover, human activities and movement can contribute to virus spread and its introduction into new areas with young, susceptible populations.\u003c/p\u003e \u003cp\u003eIn August 2023, Senegal experienced a CHIK outbreak, with over 200 confirmed cases reported in the K\u0026eacute;dougou region [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. An entomological investigation was undertaken with the objective to identify the mosquito vectors involved and genetically characterize the virus responsible of the epidemic.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eStudy site\u003c/h2\u003e \u003cp\u003eMosquito collections were carried out during August to September, 2023, across ten geographic sites in southeastern Senegal, encompassing five predominant land cover classes: village, agriculture, barren, savanna, forest as previously described [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. In addition, 13 villages (Laminya, Nathia, Boundoucondi, Ibel, Badian, Fod\u0026eacute; Binia, Lafia, Bembou, Faraba, Badioula, Kolia and Kondokho) where human chikungunya were confirmed, were investigated. Figure\u0026nbsp;1 shows villages with human cases (in red) and surveillance sites (in blue) where mosquitoes were sampled, Southeastern Senegal, August 2023. Adult mosquitoes were sampled across all biotopes and localities, while immature stages were sampled exclusively in villages where human cases were detected.\u003c/p\u003e\n\u003ch3\u003eMosquito sampling\u003c/h3\u003e\n\u003cp\u003e \u003cem\u003eImmature stages\u003c/em\u003e sampling was performed indoor and outdoor of randomly selected human habitations. All artificial and natural water-holding containers were inspected, using a flashlight if necessary, and considered as positive when harboring at least one larva or pupa of \u003cem\u003eAe. aegypti\u003c/em\u003e. From each positive container, a sample of larvae and/or pupae was collected, reared to adulthood, and identified morphologically.\u003c/p\u003e \u003cp\u003e \u003cem\u003eResting and host-seeking adult mosquitoes\u003c/em\u003e were collected indoors and outdoors in each locality using a Prokopack aspirator [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. Additionally, host-seeking mosquitoes were collected in the other landcover classes by aspiration in a double net baited by humans.\u003c/p\u003e \u003cp\u003e \u003cb\u003eSample processing\u003c/b\u003e. Immature mosquitoes sampled from water container were reared to adulthood, while adults collected in nature were processed directly. Morphological identification of mosquitoes was performed on a chill table using appropriate keys [\u003cspan additionalcitationids=\"CR18 CR19 CR20\" citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. Mosquitoes were pooled by species, sex, physiological status (engorged or unengorged), collection method, location, and date. Pools were then tested in the field laboratory for virus detection. Field-based Next Generation sequencing was also used for whole genome sequencing of positive samples.\u003c/p\u003e \u003cp\u003e \u003cb\u003eMolecular detection.\u003c/b\u003e Mosquito pools were homogenized in 1.5-ml Eppendorf tubes containing 500 \u0026micro;l of L-15 medium (Gibco BRL, Grand Island, NY, USA) using sterile pestles in a biosafety level 2 laboratory. The homogenates were centrifuged at 8,000 rpm for 10 min at 4\u0026deg;C. The supernatant was retained for further analyses, while mosquito debris was discarded.\u003c/p\u003e \u003cp\u003eFor CHIKV detection, RNA was extracted from 140 \u0026micro;l of supernatant using the QiaAmp Viral RNA Extraction Kit (Qiagen, Heiden, Germany) following the manufacturer\u0026rsquo;s protocol. RNA was amplified using a one-step real-time RT-qPCR assay with the TIB Molbiol LightMix\u0026reg; (Berlin, Germany). The 20 \u0026micro;L reaction volume consisted of 5 \u0026micro;L of extracted RNA, 2\u0026times; Master Mix, 10 \u0026micro;M of specific primers (Forward: AAg CTY CgC gTC CTT TAC CAAg, Reverse: CCA AAT TgT CCY ggT CTT CCT) and probe (6FAM/CCA Atg TCY TCM gCC Tgg ACA CCTTT/TMR) targeting CHIKV in singleplex.\u003c/p\u003e \u003cp\u003e \u003cb\u003eWhole Genome Sequencing and phylogenetic analysis\u003c/b\u003e. Confirmed CHIKV-positive samples were processed for field-based Next Generation sequencing using the Twist Biosciences Comprehensive Viral Research Panel (CVRP) to obtain the whole viral genome. Enriched sample libraries were loaded onto an Illumina iSeq 100 sequencing system, and genome assembly was performed using the Chan Zuckerberg ID (CZ-ID; formerly IDSeq) platform [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eAll generated sequences were aligned using MAFFT with a representative CHIKV dataset covering the West African (WA), East-Central-South African (ECSA) and Asian genotypes. Maximum likelihood trees were generated using IQ-TREE [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e] with a 1,000 bootstrap iterations, utilizing the best-fit substitution model determined by ModelFinder and 1,000 bootstrap replicates for statistical reliability and visualization was made with FigTree V1.4.4 [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e].\u003c/p\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003eData analysis\u003c/h2\u003e \u003cp\u003eData from larval surveys were used to estimate three key entomological indices: the Breteau Index (BI) defined as the number of containers positive for immature stages of \u003cem\u003eAe. aegypti\u003c/em\u003e per 100 housing units [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e], the Container Index (CI) representing the number of containers positive for immature \u003cem\u003eAe. aegypti\u003c/em\u003e per 100 inspected water containers [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e] and the Breeding Preference (BP) defined as the ratio of the percentage of positive containers (Y) to the percentage of that type of inspected container (X). The highest Y/X ratio indicated the preferred type of breeding site for mosquitoes. Epidemic thresholds for BI and CI were set at 5% and 3%, respectively, based on WHO standards [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. The minimum field infection rates for CHIKV were calculated, including 95% confidence intervals (lower and upper limits), using the PooledInfRate software, version 4.0 [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. Statistical differences were determined with a significance level set at p\u0026thinsp;\u0026lt;\u0026thinsp;0.05.\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cp\u003e \u003cb\u003eCollection of immature stages and adult mosquitoes\u003c/b\u003e. A total of 742 water containers was inspected across the surveyed sites, showing significant variations in \u003cem\u003eAe. aegypti\u003c/em\u003e breeding preferences between administrative departments. In Saraya tree holes emerged as the most preferred sites, followed by bricks. In contrast, in K\u0026eacute;dougou department, animal watering troughs and bricks were the sites most commonly inhabited by mosquito immatures (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). At the village level, animal watering troughs were identified as the most commonly occupied containers in 9 out of 12 villages. Other notable immature habitats included tree-holes, bricks, water storage containers and tires. In all the villages investigated, the epidemic risk indices consistently exceeded the thresholds defined by the WHO across all surveyed villages (see additional file).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003e\u003cem\u003eAedes aegypti\u003c/em\u003e immature habitats at the department level, K\u0026eacute;dougou region, August 2023\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"5\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eDepartments\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eContainer type\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eContainers inspected (X%) *\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003ePositive containers (Y%) \u003csup\u003eψ\u003c/sup\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eImmature site Preference (Y%/X%)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"8\" rowspan=\"9\"\u003e \u003cp\u003eSARAYA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eClay jars\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e85 (14.10)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e6 (3.11)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.22\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eWater storage containers\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e152 (25.21)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e11 (5.70)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.23\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTires\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e62 (10.28)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e24 (12.44)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1.21\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eBricks\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e106 (17.58)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e88 (45.60)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e2.59\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAnimal watering\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e13 (2.16)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e9 (4.66)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2.16\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAbandoned containers\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e181 (30.02)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e52 (26.94)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.90\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eBasins\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2 (0.33)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1 (0.52)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1.56\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eTree holes\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2 (0.33)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2 (1.04)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e3.12\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTOTAL\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e603\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e193\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"6\" rowspan=\"7\"\u003e \u003cp\u003eKEDOUGOU\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eClay jars\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e32 (24.06)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4 (5.97)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.25\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eWater storage containers\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e26 (19.55)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5 (7.46)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e0.38\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTires\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e14 (10.53)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8 (11.94)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1.13\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eBricks\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e29 (21.80)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e29 (43.28)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e1.99\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cb\u003eAnimal watering\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e6 (4.51)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e6 (8.96)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e1.99\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAbandoned containers\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e26 (19.55)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e15 (22.39)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1.15\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTOTAL\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e133\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e67\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"5\"\u003e\u003cb\u003e*\u003c/b\u003e X% = Containers inspected /Total examined\u003c/td\u003e\u003c/tr\u003e \u003ctr\u003e\u003ctd colspan=\"5\"\u003e\u003csup\u003e\u003cb\u003eψ\u003c/b\u003e\u003c/sup\u003e Y% = Positive containers /Total Positives\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eA total of 6209 adult mosquitoes belonging to 49 species and 8 genera were collected during the period of the CHIK outbreak. Of these, 31 mosquito pools comprising 8 species (7 \u003cem\u003eAedes\u003c/em\u003e and 1 \u003cem\u003eAnopheles\u003c/em\u003e species) were found infected by CHIKV (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). \u003cem\u003eAe. furcifer\u003c/em\u003e was the only species found infected across all biotopes. In the forest biotope, \u003cem\u003eAe. taylori\u003c/em\u003e was the most frequently infected species (p\u0026thinsp;=\u0026thinsp;0.03, statistically significantly higher than \u003cem\u003eAe. vittatus\u003c/em\u003e,) followed by \u003cem\u003eAe. furcifer\u003c/em\u003e. In the savanna, \u003cem\u003eAe. dalzieli\u003c/em\u003e showed the highest infection rate (p\u0026thinsp;=\u0026thinsp;0.02, statistically significantly higher than \u003cem\u003eAe. vittatus\u003c/em\u003e,) followed by \u003cem\u003eAe. furcifer\u003c/em\u003e. In village settings, \u003cem\u003eAn. gambiae\u003c/em\u003e was the most frequently infected species followed by \u003cem\u003eAe. furcifer\u003c/em\u003e, while in Barren and Agriculture environments, \u003cem\u003eAe. furcifer\u003c/em\u003e was the only infected species.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eInfection rates of mosquito species associated with CHIKV in different biotopes, K\u0026eacute;dougou, 2023.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBiotope\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSpecies\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eTotal Pos\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTotal mosquitoes\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eTotal negative pools\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eInfection rate\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLower confidence\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eUpper confidence\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eForest\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. africanus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e179\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e85\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e5.586\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.001\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.031\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eForest\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. furcifer\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e941\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e144\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.008\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.004\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.017\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eForest\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. luteocephalus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e190\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e85\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.005\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.001\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.029\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eForest\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. taylori\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e129\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.023\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.008\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.066\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSavanna\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. dalzieli\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.036\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.624\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSavanna\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. furcifer\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e273\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e45\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.011\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.004\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.032\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSavanna\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. vittatus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e380\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e46\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.002\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.0005\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.015\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVillage\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. aegypti\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e149\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e65\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.007\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.001\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.037\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVillage\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. furcifer\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e508\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.014\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.007\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.028\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eVillage\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAn. gambiae\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e68\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.015\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.003\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.079\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBarren\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. furcifer\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e320\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e36\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.009\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.003\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.027\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAgriculture\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAe. furcifer\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e259\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e41\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e0.004\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e \u003cp\u003e0.001\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c8\"\u003e \u003cp\u003e0.022\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e\n\u003ch3\u003ePhylogenetic analysis\u003c/h3\u003e\n\u003cp\u003eThe phylogenetic analysis revealed that the 2023 CHIKV outbreak strain in Kedougou belongs to the WA genotype, forming a highly supported monophyletic group (bootstrap\u0026thinsp;\u0026ge;\u0026thinsp;95) with strains from the 2015 and 2005 outbreaks in the same region [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. These sequences share 98.80\u0026ndash;98.96% nucleotide identity with the reference strain HM045817 (2005), underscoring their close genetic relationship. Furthermore, the clustering of mosquito and human sequences confirmed that the same viral strain circulated between these hosts during the outbreak.\u003c/p\u003e \u003cp\u003eFigure 2 provides results of the phylogenetic analysis of CHIKV sequences obtained from mosquitoes (labeled with red identifier numbers) and humans (labeled with blue identifier numbers) during the 2023 outbreak in southeastern Senegal. The sequences are grouped according to their genetic lineage, including those belonging to the West African, East/Central/South African (ECSA), and Asian genotypes.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eNearly worldwide, \u003cem\u003eAedes aegypti\u003c/em\u003e along with \u003cem\u003eAe. albopictus\u003c/em\u003e is considered the primary epidemic vector of several common, human-amplified arboviruses such as dengue, yellow fever, Zika and CHIKV [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan additionalcitationids=\"CR31 CR32\" citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. In fact, \u003cem\u003eAe. aegypti\u003c/em\u003e has been several times found associated with CHIKV in central [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e], southern [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e] and eastern parts of Africa [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e], and also identified elsewhere in Africa as the main epidemic vector [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e, \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. Furthermore, populations of \u003cem\u003eAe. aegypti\u003c/em\u003e from South Africa [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e], Cameroon [\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e], Senegal and Cape Verde [\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e, \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e] have been shown to be experimentally competent for CHIKV transmission. Moreover, vertical transmission of CHIKV in \u003cem\u003eAe. aegypti\u003c/em\u003e has been demonstrated experimentally in India [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e]. All of these results support a major CHIKV vector role for \u003cem\u003eAe. aegypti\u003c/em\u003e.\u003c/p\u003e \u003cp\u003eFor many decades, \u003cem\u003eAe. aegypti formosus\u003c/em\u003e, the ancestral, sylvatic form that evolved into the domesticated \u003cem\u003eAe. aegypti aegypti\u003c/em\u003e, was considered as the only subspecies present in southern Senegal [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e]. However, recent studies have shown the presence of both subspecies in K\u0026eacute;dougou department [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e] with larval development sites found in both forest and, more recently, in domestic environments. These changing distribution patterns are likely linked to deforestation driven by agriculture, gold mining and other human activities, leading to the domestication of wild \u003cem\u003eAe. aegypti\u003c/em\u003e populations in response to urbanization. Such adaptation to the domestic environment has also been observed in Nigeria [\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e] and Gabon [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn our study, \u003cem\u003eAe. aegypti\u003c/em\u003e was abundant in immature stages in all potential aquatic sites and the epidemic risk indices were above the thresholds defined by the WHO [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. In other words, the indices were sufficiently high for this species to ensure CHIK transmission. Also, at the adult stage \u003cem\u003eAe. aegypti\u003c/em\u003e were found during our investigation in all affected localities. However, CHIKV infection in \u003cem\u003eAe. aegypti\u003c/em\u003e was surprisingly low, with only one positive pool, representing just 3.2% of positives. Therefore, the main epidemic vector worldwide apparently did not play a major role in CHIKV transmission to humans during this outbreak. The zoophilic tendency of \u003cem\u003eAe. aegypti\u003c/em\u003e generally observed in West Africa [\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e] may explain this finding. The \u003cem\u003eAe. aegypti formosus\u003c/em\u003e form is significantly more abundant in the K\u0026eacute;dougou area. However, it has been previously shown to be less endophilic and anthropophilic than the \u003cem\u003eAe. aegypti aegypti\u003c/em\u003e and thus less involved in human-amplified arbovirus transmission [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e]. Therefore, \u003cem\u003eAe. aegypti formosus\u003c/em\u003e probably plays no major role in either maintenance of the sylvatic cycle or the spillover of CHIKV to humans in this region [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eOur findings highlight a significant involvement of wild mosquitoes in CHIKV transmission during this epidemic, suggesting epizootic amplification of the sylvatic cycle. CHIKV was detected in 29 pools of wild \u003cem\u003eAedes\u003c/em\u003e mosquitoes, predominantly \u003cem\u003eAe. furcifer\u003c/em\u003e (22 pools), which accounted for 71% of positives. Historically, \u003cem\u003eAe. furcifer\u003c/em\u003e has been found most frequently infected with CHIKV [\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e, \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e] and is competent to transmit the virus [\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e, \u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThe same profile of infected mosquitoes was previously observed in 2009\u0026ndash;2010, when among the 42 CHIKV-positive pools, most were wild mosquitoes. Only one pool of \u003cem\u003eAe. aegypti\u003c/em\u003e was found positive [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. The same trend was observed during the 2015 amplification with the sylvatic vectors recording 93.7% of the CHIKV detections and only 6.25% (2/32 pools) for \u003cem\u003eAe. aegypti\u003c/em\u003e [\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e]. These findings corroborated our results and support the conclusion that \u003cem\u003eAe. aegypti\u003c/em\u003e does not play a significant role in CHIKV outbreaks in the K\u0026eacute;dougou region.\u003c/p\u003e \u003cp\u003eThe higher number of human cases (over 200 persons) recorded among men and young people over 15 years of age [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e] supports the hypothesis that transmission occurred mainly outside of human dwellings. Sustained domestic transmission would be expected to affect age groups, including children under 15 years of age, who generally stay at home and spend more time indoors. \u003cem\u003eAe. furcifer\u003c/em\u003e, known to have great ecological plasticity [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e], was frequently found infected and biting humans in villages at high density in Senegal [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e, \u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e] and elsewhere in Africa [\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e], indicating its major role in CHIKV transmission.\u003c/p\u003e \u003cp\u003eWe also found during our investigation one PCR-positive pool of male \u003cem\u003eAn. gambiae\u003c/em\u003e. Other species within the \u003cem\u003eAnopheles\u003c/em\u003e genus such as \u003cem\u003eAn. funestus\u003c/em\u003e, \u003cem\u003eAn. coustani\u003c/em\u003e and \u003cem\u003eAn. domicola\u003c/em\u003e have been found naturally infected with CHIKV in the K\u0026eacute;dougou region during a previous study in 2009\u0026ndash;2010 [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. Subsequently in 2015, 3 pools of female \u003cem\u003eAn. gambiae\u003c/em\u003e were found positive for CHIKV in the same area during a co-amplification with YFV and ZIKV [\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e], suggesting sustained CHIKV transmission by \u003cem\u003eAn. gambiae\u003c/em\u003e. Vector competence studies of \u003cem\u003eAn. gambiae\u003c/em\u003e showed a CHIKV infection rate of 43% at day 7 post-bloodmeal, although viral titers in the mosquitoe hemocoel were low and CHIKV-positive saliva was not detected [\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e]. Moreover \u003cem\u003eAn. gambiae\u003c/em\u003e and \u003cem\u003eAn. funestus\u003c/em\u003e, both present in the K\u0026eacute;dougou region and transmitting malaria parasites, are the only known vectors of o\u0026rsquo;nyong-nyong virus (ONNV), a close relative of CHIKV [\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e, \u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e]. Also, \u003cem\u003eAn. stephensi\u003c/em\u003e was recently shown to be a competent ONNV vector [\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e]. All of these findings suggested that malaria vectors should be monitored for their potential role in CHIKV transmission in Senegal and elsewhere in Africa.\u003c/p\u003e \u003cp\u003ePhylogenetic analysis confirmed that the same CHIKV strain circulated between humans and mosquitoes during 2023, harboring shared mutations compared to CHIKV strains that circulated in 2005 and 2015 [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. These mutations deserve further study as CHIKV mutations can greatly affect vector host range [\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e].\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eThis study highlights the persistence of an endemic CHIKV strain in a sylvatic transmission cycle primarily, emphasizing the significant role of wild, sylvatic \u003cem\u003eAedes\u003c/em\u003e species in CHIKV amplification and transmission to humans. Our findings underscore the urgent need to assess the insecticide resistance status of these species and integrate them into vector control programs. Further studies are required to better understand the many factors that contribute to the amplifications of arboviruses like CHIKV at the interface of humans and both sylvatic and urban environments, which can facilitate virus re-emergence and transmission.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cdiv class=\"DefinitionList\"\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003e\u003cem\u003eAe.\u003c/em\u003e\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003e \u003cem\u003eAedes\u003c/em\u003e \u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003e\u003cem\u003eAn.\u003c/em\u003e\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003e \u003cem\u003eAnopheles\u003c/em\u003e \u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eBI\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eBreteau index\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eBP\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eBreeding Preference\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eCHIK\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eChikungunya fever\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eCHIKV\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eChikungunya virus\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eCI\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eContainer index\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eCVRP\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eComprehensive Viral Research Panel\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eCZ-ID\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eChan Zuckerberg ID\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eECSA\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eEast-Central-South African\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eMAFFT\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eMultiple Alignment using Fast Fourier Transform\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eNY\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eNew York\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eONNV\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eo\u0026rsquo;nyong-nyong virus\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eRNA\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eRibonucleic Acid\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eRT-qPCR\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eReal time quantitative polymerase chain reaction\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eUSA\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eUnited State of America\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eWA\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eWest African\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eWHO\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eWorld Health Organization\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eYFV\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eYellow fever virus\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eZIKV\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eZika virus\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003c/div\u003e"},{"header":"Declarations","content":"\u003cp\u003e \u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e \u003cp\u003eNot applicable\u003c/p\u003e \u003c/p\u003e \u003cp\u003e \u003cstrong\u003eConsent for publication\u003c/strong\u003e \u003cp\u003eThe included institutions do not explicitly require/give formal approval for presentations or publication of authored works related to collaborative or individual research.\u003c/p\u003e \u003c/p\u003e \u003cp\u003e \u003cstrong\u003eCompeting interests\u003c/strong\u003e \u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e \u003c/p\u003e\u003ch2\u003eFunding\u003c/h2\u003e \u003cp\u003eThis work was entirely supported by the West African Center for Emerging Infectious Diseases (NIH/NIAID) under Grant Number U01 AI151801. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\u003c/p\u003e\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eA.G., M.D. (Mawlouth Diallo), D.D. and M.M.D. conceived and designed the study. A.G., D.D., E.N., M.G. and M.D. (Mawlouth Diallo) collected the mosquito samples on field. A.G., D.D., E.N., M.G., M.D. (Madeleine Dieng), M.K., M.H.D.N., I.D. (Idrissa Dieng) and S.S. performed the laboratory experiments. A.G., I.D. (Ibrahima Dia), D.D., B.D., E.N., F.A.S., C.W., S.C.W. and M.D. (Mawlouth Diallo) analyzed the data. A.G., M.D. (Mawlouth Diallo) and M.M.D. drafted the manuscript. A.G., M.M.D., D.D., E.N., M.H.D.N., M.G., I.D. (Idrissa Dieng), M.D. (Madeleine Dieng), M.K., S.S., B.D., F.A.S., C.W., I.D. (Ibrahima Dia), S.C.W. and M.D. (Mawlouth Diallo) critically revised, read and approved the final manuscript.\u003c/p\u003e\u003ch2\u003eAcknowledgement\u003c/h2\u003e\u003cp\u003eWe would like to thank the Medical Officer of K\u0026eacute;dougou and Saraya districts, the Regional Hygiene Brigade Officer of K\u0026eacute;dougou, the community health workers and the local populations for their collaboration. We also thank Maimouna Mbanne, Seynabou Mbaye Ba Souna Diop and Serge Freddy Moukaha Doukanda for their technical assistance\u003c/p\u003e\u003ch2\u003eData availability\u003c/h2\u003e \u003cp\u003eNot applicable.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003ePialoux G, Ga\u0026uuml;z\u0026egrave;re B-A, Jaur\u0026eacute;guiberry S, Strobel M. Chikungunya, an epidemic arbovirosis. Lancet Infect Dis. 2007;7:319\u0026ndash;27.\u003c/li\u003e\n\u003cli\u003eKularatne SAM, Gihan MC, Weerasinghe SC, Gunasena S. Concurrent outbreaks of Chikungunya and Dengue fever in Kandy, Sri Lanka, 2006\u0026ndash;07: a comparative analysis of clinical and laboratory features. Postgrad Med J. 2009;85:342\u0026ndash;6.\u003c/li\u003e\n\u003cli\u003eVolk SM, Chen R, Tsetsarkin KA, Adams AP, Garcia TI, Sall AA, et al. Genome-Scale Phylogenetic Analyses of Chikungunya Virus Reveal Independent Emergences of Recent Epidemics and Various Evolutionary Rates. J Virol. 2010;84:6497\u0026ndash;504.\u003c/li\u003e\n\u003cli\u003eDelisle E, Rousseau C, Broche B, Leparc-Goffart I, L\u0026rsquo;Ambert G, Cochet A, et al. Chikungunya outbreak in Montpellier, France, September to October 2014. Eurosurveillance. 2015;20.\u003c/li\u003e\n\u003cli\u003eLeparc-Goffart I, Nougairede A, Cassadou S, Prat C, De Lamballerie X. Chikungunya in the Americas. The Lancet. 2014;383:514.\u003c/li\u003e\n\u003cli\u003eDiallo D, Sall AA, Buenemann M, Chen R, Faye O, Diagne CT, et al. Landscape ecology of sylvatic chikungunya virus and mosquito vectors in southeastern Senegal. PLoS Negl Trop Dis. 2012;6:e1649.\u003c/li\u003e\n\u003cli\u003eRusso G, Subissi L, Rezza G. Chikungunya fever in Africa: a systematic review. Pathog Glob Health. 2020;114:136\u0026ndash;44.\u003c/li\u003e\n\u003cli\u003eAlthouse BM, Hanley KA, Diallo M, Sall AA, Ba Y, Faye O, et al. Impact of climate and mosquito vector abundance on sylvatic arbovirus circulation dynamics in Senegal. Am J Trop Med Hyg. 2015;92:88.\u003c/li\u003e\n\u003cli\u003eSow A, Loucoubar C, Diallo D, Faye O, Ndiaye Y, Senghor CS, et al. Concurrent malaria and arbovirus infections in Kedougou, southeastern Senegal. Malar J. 2016;15:47.\u003c/li\u003e\n\u003cli\u003ePeyrefitte CN, Rousset D, Pastorino BAM, Pouillot R, Bessaud M, Tock F, et al. Chikungunya Virus, Cameroon, 2006. Emerg Infect Dis. 2007;13:768\u0026ndash;71.\u003c/li\u003e\n\u003cli\u003eLeroy EM, Nkoghe D, Ollomo B, Nze-Nkogue C, Becquart P, Grard G, et al. Concurrent Chikungunya and Dengue Virus Infections during Simultaneous Outbreaks, Gabon, 2007. Emerg Infect Dis. 2009;15:591\u0026ndash;3.\u003c/li\u003e\n\u003cli\u003eSow A, Nikolay B, Faye O, Cauchemez S, Cano J, Diallo M, et al. Changes in the Transmission Dynamic of Chikungunya Virus in Southeastern Senegal. Viruses. 2020;12:196.\u003c/li\u003e\n\u003cli\u003eLim JK, Ridde V, Agnandji ST, Lell B, Yaro S, Yang JS, et al. Seroepidemiological Reconstruction of Long-term Chikungunya Virus Circulation in Burkina Faso and Gabon. J Infect Dis. 2023;227:261\u0026ndash;7.\u003c/li\u003e\n\u003cli\u003eSenegal: Elevated chikungunya activity reported in the Kedougou Region through August /update 1. Senegal: Elevated chikungunya activity reported in the Kedougou Region through August /update 1 | Crisis24. https://crisis24.garda.com/alerts/2023/08/senegal-elevated-chikungunya-activity-reported-in-the-kedougou-region-through-august-update-1. Accessed 15 Feb 2024.\u003c/li\u003e\n\u003cli\u003eDieng I, Sadio BD, Gaye A, Sagne SN, Ndione MHD, Kane M, et al. Genomic characterization of a reemerging Chikungunya outbreak in Kedougou, Southeastern Senegal, 2023. Emerg Microbes Infect. 2024;13:2373308.\u003c/li\u003e\n\u003cli\u003eVazquez-Prokopec GM, Galvin WA, Kelly R, Kitron U. A New, Cost-Effective, Battery-Powered Aspirator for Adult Mosquito Collections. J Med Entomol. 2009;46:1256\u0026ndash;9.\u003c/li\u003e\n\u003cli\u003eEdwards FW. Mosquitoes of the Ethiopian Region. HI.-Culicine Adults and Pupae. 1941.\u003c/li\u003e\n\u003cli\u003eFerrara L, Germain M, Hervy J-P. Aedes (Diceromyia) furcifer (Edwards, 1913) et Aedes (Diceromyia) taylori Edwards, 1936: le point sur la diff\u0026eacute;renciation des adultes. Cah ORSTOM S\u0026eacute;r Ent M\u0026eacute;d Parasitol. 1984;22:179\u0026ndash;83.\u003c/li\u003e\n\u003cli\u003eHuang Y-M, Ward RA. A pictorial key for the identification of the mosquitoes associated with yellow fever in Africa. Mosq Syst. 1981;13:138\u0026ndash;49.\u003c/li\u003e\n\u003cli\u003eDiagne N, Fontenille D, Konate L, Faye O, Lamizana MT, Legros F. Les anoph\u0026egrave;les du S\u0026eacute;n\u0026eacute;gal: liste comment\u0026eacute;e et illustr\u0026eacute;e. Bull Soci\u0026eacute;t\u0026eacute; Pathol Exot. 1994;87:267\u0026ndash;77.\u003c/li\u003e\n\u003cli\u003eRobert V, Ndiaye EH, Rahola N, Le Goff G, Bouss\u0026egrave;s P, Diallo D, et al. Cl\u0026eacute;s dichotomiques illustr\u0026eacute;es d\u0026rsquo;identification des femelles et des larves de moustiques (Diptera : Culicidae) du Burkina Faso, Cap-Vert, Gambie, Mali, Mauritanie, Niger, S\u0026eacute;n\u0026eacute;gal et Tchad. 2022;:181 p.\u003c/li\u003e\n\u003cli\u003eKalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, et al. IDseq\u0026mdash;An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. GigaScience. 2020;9:giaa111.\u003c/li\u003e\n\u003cli\u003eNguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268\u0026ndash;74.\u003c/li\u003e\n\u003cli\u003eRambault A. FigTree [http://tree. bio. ed. ac. uk/software/figtree/]. 2017.\u003c/li\u003e\n\u003cli\u003eTaufflieb R, Simonkovich E, Dieng PY. Enqu\u0026ecirc;te sur le vecteur urbain de fi\u0026egrave;vre jaune Aedes aegypti dans l\u0026rsquo;ouest du S\u0026eacute;n\u0026eacute;gal. Multigraph Doc ORSTOM Dakar. 1972;20941.\u003c/li\u003e\n\u003cli\u003eAsia WHORO for S-E. Comprehensive Guideline for Prevention and Control of Dengue and Dengue Haemorrhagic Fever. Revised and expanded edition. WHO Regional Office for South-East Asia; 2011.\u003c/li\u003e\n\u003cli\u003eChang F-S, Tseng Y-T, Hsu P-S, Chen C-D, Lian I-B, Chao D-Y. Re-assess Vector Indices Threshold as an Early Warning Tool for Predicting Dengue Epidemic in a Dengue Non-endemic Country. PLoS Negl Trop Dis. 2015;9:e0004043.\u003c/li\u003e\n\u003cli\u003eBiggerstaff B. PooledInRate, version 4.0: An Excel\u0026reg; add-in to compute infection rates from pooled data. Fort Collins CO Cent Dis Control Prev. 2016.\u003c/li\u003e\n\u003cli\u003eDieng I, Ndiaye M, Kane M, Balde D, Mbanne M, Diop SMBS, et al. An amplicon-based Illumina and nanopore sequencing workflow for Chikungunya virus West Africa genotype. 2023;:2023.12.07.23299611.\u003c/li\u003e\n\u003cli\u003eMadewell ZJ. Arboviruses and Their Vectors. South Med J. 2020;113:520\u0026ndash;3.\u003c/li\u003e\n\u003cli\u003eDiallo M, Tall A, Dia I, Ba Y, Sarr FD, Ly AB, et al. Yellow fever outbreak in central part of Senegal 2002: epidemiological findings. J Public Health Epidemiol. 2013;5:291\u0026ndash;6.\u003c/li\u003e\n\u003cli\u003eDiouf B, Gaye A, Dieng I, Diagne CT, Ndiaye EH, Mhamadi M, et al. Dengue 1 outbreak in Rosso, northern Senegal, October 2021: entomologic investigations. J Med Entomol. 2024;61:222\u0026ndash;32.\u003c/li\u003e\n\u003cli\u003ePowers AM. Chikungunya. Clin Lab Med. 2010;30:209\u0026ndash;19.\u003c/li\u003e\n\u003cli\u003eMombouli J-V, Bitsindou P, Elion DOA, Grolla A, Feldmann H, Niama FR, et al. Chikungunya Virus Infection, Brazzaville, Republic of Congo, 2011. Emerg Infect Dis. 2013;19:1542\u0026ndash;3.\u003c/li\u003e\n\u003cli\u003eGudo ES, Pinto G, Vene S, Mandlaze A, Muianga AF, Cliff J, et al. Serological Evidence of Chikungunya Virus among Acute Febrile Patients in Southern Mozambique. PLoS Negl Trop Dis. 2015;9:e0004146.\u003c/li\u003e\n\u003cli\u003eSang RC, Ahmed O, Faye O, Kelly CLH, Yahaya AA, Mmadi I, et al. Entomologic investigations of a chikungunya virus epidemic in the Union of the Comoros, 2005. Am J Trop Med Hyg. 2008;78:77\u0026ndash;82.\u003c/li\u003e\n\u003cli\u003eAgarwal A, Dash PK, Singh AK, Sharma S, Gopalan N, Rao PVL, et al. Evidence of Experimental Vertical Transmission of Emerging Novel ECSA Genotype of Chikungunya Virus in Aedes aegypti. PLoS Negl Trop Dis. 2014;8:e2990.\u003c/li\u003e\n\u003cli\u003eMonath: The arboviruses: epidemiology and ecology - Google Scholar. https://scholar.google.com/scholar_lookup?title=The%20arboviruses%3A%20epidemiology%20and%\u003cbr\u003e20ecology\u0026amp;author=P%20Jupp\u0026amp;author=B%20McIntosh\u0026amp;author=T%20Monath\u0026amp;publication_year=1988\u003cbr\u003e\u0026amp;book=The%20arboviruses%3A%20epidemiology%20and%20ecology. Accessed 13 Oct 2024.\u003c/li\u003e\n\u003cli\u003eJupp PG, McIntosh BM. Aedes furcifer and other mosquitoes as vectors of chikungunya virus at Mica, northeastern Transvaal, South Africa. J Am Mosq Control Assoc. 1990;6:415\u0026ndash;20.\u003c/li\u003e\n\u003cli\u003ePaupy C, Ollomo B, Kamgang B, Moutailler S, Rousset D, Demanou M, et al. Comparative Role of Aedes albopictus and Aedes aegypti in the Emergence of Dengue and Chikungunya in Central Africa. Vector-Borne Zoonotic Dis. 2010;10:259\u0026ndash;66.\u003c/li\u003e\n\u003cli\u003eDiagne CT, Faye O, Guerbois M, Knight R, Diallo D, Faye O, et al. Vector Competence of Aedes aegypti and Aedes vittatus (Diptera: Culicidae) from Senegal and Cape Verde Archipelago for West African Lineages of Chikungunya Virus. Am J Trop Med Hyg. 2014;91:635\u0026ndash;41.\u003c/li\u003e\n\u003cli\u003eVazeille M, Y\u0026eacute;bakima A, Louren\u0026ccedil;o-de-Oliveira R, Andriamahefazafy B, Correira A, Rodrigues JM, et al. Oral receptivity of Aedes aegypti from Cape Verde for yellow fever, dengue, and chikungunya viruses. Vector Borne Zoonotic Dis Larchmt N. 2013;13:37\u0026ndash;40.\u003c/li\u003e\n\u003cli\u003eCornet M, Chateau R, Valade M, Dieng P, Raymond H, Lorand A. Donn\u0026eacute;es bio-\u0026eacute;cologiques sur les vecteurs potentiels du. Virus amaril au S\u0026eacute;n\u0026eacute;gal oriental. R\u0026ocirc;le des diff\u0026eacute;rentes esp\u0026eacute;ces dans la transmission du virus. Cah Orstom Entomol M\u0026eacute;d Parasitol. 1978;16:315\u0026ndash;41.\u003c/li\u003e\n\u003cli\u003eDiouf B, Dia I, Sene NM, Ndiaye EH, Diallo M, Diallo D. Morphology and taxonomic status of Aedes aegypti populations across Senegal. PLoS One. 2020;15:e0242576.\u003c/li\u003e\n\u003cli\u003eNasidi A, Monath TP, DeCock K, Tomori O, Cordellier R, Olaleye OD, et al. Urban yellow fever epidemic in western Nigeria, 1987. Trans R Soc Trop Med Hyg. 1989;83:401\u0026ndash;6.\u003c/li\u003e\n\u003cli\u003eVazeille-Falcoz M, Failloux AB, Mousson L, Elissa N, Rodhain F. Oral receptivity of Aedes aegypti formosus from Franceville (Gabon, central Africa) for type 2 dengue virus. Bull Soc Pathol Exot 1990. 1999;92:341\u0026ndash;2.\u003c/li\u003e\n\u003cli\u003eBoorman JP, Service MW. Some records of mosquitoes (Culicidae, Diptera) from the Niger delta area, southern Nigeria. West Afr Med J. 1960;9:67\u0026ndash;72.\u003c/li\u003e\n\u003cli\u003eDiouf B, Sene NM, Ndiaye EH, Gaye A, Ngom EHM, Gueye A, et al. Resting Behavior of Blood-Fed Females and Host Feeding Preferences of Aedes aegypti (Diptera: Culicidae) Morphological Forms in Senegal. J Med Entomol. 2021;58:2467\u0026ndash;73.\u003c/li\u003e\n\u003cli\u003eJupp PG. Mosquitoes as vectors of human disease in South Africa. South Afr Fam Pract. 2005;47:68\u0026ndash;72.\u003c/li\u003e\n\u003cli\u003eDiallo M, Thonnon J, Traore-Lamizana M, Fontenille D. Vectors of Chikungunya virus in Senegal: current data and transmission cycles. Am J Trop Med Hyg. 1999;60:281\u0026ndash;6.\u003c/li\u003e\n\u003cli\u003ePaterson HE, McIntosh BM. Further Studies on the Chikungunya Outbreak in Southern Rhodesia in 1962. Ann Trop Med Parasitol. 1964.\u003c/li\u003e\n\u003cli\u003eJupp PG, McIntosh BM, dos Santos I, de Moor P. Laboratory vector studies on six mosquito and one tick species with chikungunya virus. Trans R Soc Trop Med Hyg. 1981;75:15\u0026ndash;9.\u003c/li\u003e\n\u003cli\u003eDiallo D, Fall G, Diagne CT, Gaye A, Ba Y, Dia I, et al. Concurrent amplification of Zika, chikungunya, and yellow fever virus in a sylvatic focus of arboviruses in Southeastern Senegal, 2015. BMC Microbiol. 2020;20:181.\u003c/li\u003e\n\u003cli\u003eDiallo M, Ba Y, Sall AA, Diop OM, Ndione JA, Mondo M, et al. Amplification of the sylvatic cycle of dengue virus type 2, Senegal, 1999\u0026ndash;2000: entomologic findings and epidemiologic considerations. Emerg Infect Dis. 2003;9:362.\u003c/li\u003e\n\u003cli\u003eMondet B. Importance d\u0026rsquo;Aedes (Diceromyia) Furcifer Edwards, 1913 (Diptera: Culicidae) Parmi Les Vecteurs Potentiels d\u0026rsquo;Arboviroses, dans l\u0026rsquo;\u0026Eacute;pid\u0026eacute;miologie de la Fi\u0026egrave;vre Jaune en Savane Sub-Soudanienne de C\u0026ocirc;te-d\u0026rsquo;Ivoire. Ann Soci\u0026eacute;t\u0026eacute; Entomol Fr NS. 1997;33:47\u0026ndash;54.\u003c/li\u003e\n\u003cli\u003eVanlandingham D, Hong C, Klingler K, Tsetsarkin K, Horne K, Powers A, et al. Differential Infectivities of O\u0026rsquo;Nyong-Nyong and Chikungunya Virus Isolates in Anopheles Gambiae and Aedes Aegypti Mosquitoes. Am J Trop Med Hyg. 2005;72:616\u0026ndash;21.\u003c/li\u003e\n\u003cli\u003eWilliams MC, Woodall JP. O\u0026rsquo;nyong-nyong fever: an epidemic virus disease in East Africa. II. Isolation and some properties of the virus. Trans R Soc Trop Med Hyg. 1961;55.\u003c/li\u003e\n\u003cli\u003eWilliams MC, Woodall JP, Corbet PS, Gillett JD. O\u0026rsquo;nyong-nyong fever: an epidemic virus disease in East Africa. VIII. Virus isolations from Anopheles mosquitoes. Trans R Soc Trop Med Hyg. 1965;59.\u003c/li\u003e\n\u003cli\u003eMutsaers M, Engdahl CS, Wilkman L, Ahlm C, Evander M, Lwande OW. Vector competence of Anopheles stephensi for O\u0026rsquo;nyong-nyong virus: a risk for global virus spread. Parasit Vectors. 2023;16:133.\u003c/li\u003e\n\u003cli\u003eTsetsarkin KA, Chen R, Weaver SC. Interspecies transmission and chikungunya virus emergence. Curr Opin Virol. 2016;16:143\u0026ndash;50.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-infectious-diseases","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"infd","sideBox":"Learn more about [BMC Infectious Diseases](http://bmcinfectdis.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/infd","title":"BMC Infectious Diseases","twitterHandle":"#bmcinfectdis","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Chikungunya outbreak, epidemic chikungunya vector, wild Aedes vectors, chikungunya amplification, Aedes furcifer","lastPublishedDoi":"10.21203/rs.3.rs-6865029/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6865029/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eChikungunya fever (CHIK) caused by the mosquito-borne chikungunya virus (CHIKV) and transmitted by \u003cem\u003eAedes\u003c/em\u003e mosquitoes, remains a public health burden throughout the tropics. During the CHIK outbreak in the southeastern Senegal in August 2023, an entomologic investigation was conducted to identify the vector(s) and characterize the virus strains.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e \u003cp\u003eAdult mosquitoes were collected indoors and outdoors from houses of confirmed CHIK cases and their immediate neighborhoods using Prokopack aspirators and double-net traps and all water containers were inspected for aquatic stages. Mosquito pools were tested for CHIKV by RT-qPCR and positive samples were subjected to whole genome sequencing using Illumina iSeq system.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eAnimal watering points; bricks and tree holes were the most common sites for \u003cem\u003eAedes aegypti\u003c/em\u003e larvae and pupae. While immature \u003cem\u003eAe. aegypti\u003c/em\u003e were found in all affected villages, with Breteau and Container indices exceeded the WHO epidemic thresholds, \u003cem\u003eAe. furcifer\u003c/em\u003e emerged as the most abundant host-seeking species in domestic areas. CHIKV was detected in 31 mosquito pools, primarily in \u003cem\u003eAe. furcifer\u003c/em\u003e (22 pools) and only one pool of \u003cem\u003eAe. aegypti\u003c/em\u003e. Other \u003cem\u003eAedes\u003c/em\u003e species accounted for 8 positive pools and \u003cem\u003eAnopheles gambiae\u003c/em\u003e, the primary malaria vector, one pool. Phylogenetic analysis confirmed the close relationship between 2023 CHIKV strains circulating in humans and mosquitoes, and those responsible for the 2015 outbreak.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e \u003cp\u003eOur study highlights the urgent need to include sylvatic mosquitoes in surveillance and control programs that until now have mainly focused on \u003cem\u003eAe. aegypti\u003c/em\u003e. Moreover, the potential role of \u003cem\u003eAnopheles gambiae\u003c/em\u003e in the CHIKV transmission in Senegal warrants further investigation.\u003c/p\u003e","manuscriptTitle":"Challenging the notion of Aedes aegypti as the primary chikungunya virus vector: insights from Kédougou, Southeastern Senegal","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-07-01 10:43:15","doi":"10.21203/rs.3.rs-6865029/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-07-07T04:34:26+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-07-06T19:53:25+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-07-04T19:45:43+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-07-03T16:13:33+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"13352087672697827456491482771258901","date":"2025-06-26T17:05:43+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"289486141410581842387753027478214187300","date":"2025-06-25T14:17:22+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"127961869060965333324887235284746826184","date":"2025-06-25T13:33:34+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-06-25T13:30:38+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-06-24T10:57:20+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-06-24T02:39:49+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-06-24T02:39:03+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Infectious Diseases","date":"2025-06-10T16:14:48+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-infectious-diseases","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"infd","sideBox":"Learn more about [BMC Infectious Diseases](http://bmcinfectdis.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/infd","title":"BMC Infectious Diseases","twitterHandle":"#bmcinfectdis","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"1fa302d3-d013-4350-904e-15c26c8e788a","owner":[],"postedDate":"July 1st, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-09-08T16:05:57+00:00","versionOfRecord":{"articleIdentity":"rs-6865029","link":"https://doi.org/10.1186/s12879-025-11402-7","journal":{"identity":"bmc-infectious-diseases","isVorOnly":false,"title":"BMC Infectious Diseases"},"publishedOn":"2025-09-03 15:57:36","publishedOnDateReadable":"September 3rd, 2025"},"versionCreatedAt":"2025-07-01 10:43:15","video":"","vorDoi":"10.1186/s12879-025-11402-7","vorDoiUrl":"https://doi.org/10.1186/s12879-025-11402-7","workflowStages":[]},"version":"v1","identity":"rs-6865029","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6865029","identity":"rs-6865029","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}