Crimean–Congo hemorrhagic fever (CCHF), the most widespread tick-borne viral human infection, poses a threat to global health. In this study, clinical samples collected through national surveillance systems were screened for acute CCHF virus (CCHFV) infection using RT-PCR and for exposure using ELISA. For any CCHF-positive sample, livestock and tick samples were also collected in the neighborhood of the confirmed case and tested using ELISA and RT-PCR, respectively. Genome sequencing and phylogenetic analyses were also performed on samples with positive RT-PCR results. In Eastern Senegal, two human cases and one Hyalomma tick positive for CCHF were identified and a seroprevalence in livestock ranging from 9.33% to 45.26% was detected. Phylogenetic analyses revealed that the human strain belonged to genotype I based on the available L segment. However, the tick strain showed a reassortant profile, with the L and M segments belonging to genotype I and the S segment belonging to genotype III. Our data also showed that our strains clustered with strains isolated in different countries, including Mauritania. Therefore, our findings confirmed the high genetic variability inside the CCHF genotypes and their introduction to Senegal from other countries. They also indicate an increasing CCHF threat in Senegal and emphasize the need to reinforce surveillance using a one-health approach.

Rift Valley fever (RVF) is a re-emerging vector-borne zoonosis with a high public health and veterinary impact. In West Africa, many lineages were previously detected, but since 2020, lineage H from South Africa has been the main cause of the outbreaks. In this study, clinical samples collected through national surveillance were screened for RVF virus (RVFV) acute infection by RT-PCR and IgM ELISA tests. Sequencing, genome mapping and in vitro phenotypic characterization in mammal cells were performed on RT-PCR positive samples in comparison with other epidemic lineages (G and C). Four RVFV human cases were detected in Senegal and the sequence analyses revealed that the strains belonged to lineage H. The in vitro kinetics and genome mapping showed different replication efficiency profiles for the tested RVFV lineages and non-conservative mutations, which were more common to lineage G or specific to lineage H. Our findings showed the re-emergence of lineage H in Senegal in 2022, its high viral replication efficiency in vitro and support the findings that genetic diversity affects viral replication. This study gives new insights into the biological properties of lineage H and calls for deeper studies to better assess its potential to cause a future threat in Senegal.

: Crimean–Congo hemorrhagic fever (CCHF) is a lethal zoonotic disease transmitted through tick bites and contact with infected animals or humans. As CCHF continues to expand worldwide, we report on the first severe outbreak in Senegal (Podor, Saint-Louis region) in 2022. We conducted a comprehensive outbreak investigation after a confirmed CCHF human case in Podor. This included sample collections from humans, animals, and ticks from the household and surrounding area. Human and animal samples were tested by ELISA for antibodies to CCHF virus and by reverse transcription polymerase chain reaction (RT-PCR) for CCHF virus RNA, whereas tick samples underwent CCHF RT-PCR only. Positive RT-PCR samples underwent viral genome sequencing for genetic characterization. We determined three CCHF human cases, with two deaths, as well as virus circulation in 11 ticks and in livestock, with an overall seroprevalence of 42.5%. CCHF IgG antibodies were detected in human contact cases, showing its prior prevalence in the area. Phylogenetic analyses revealed high genetic diversity within CCHF genotypes, with existence of reassortants and cocirculation of two different isolates from various origins in Mboyo and Nenette villages, where human cases were detected. The data showed a correlation between the strains identified in humans and ticks in each village, showing two independent emergences in Podor. The outbreak in Podor was probably because of the high abundance of animal hosts in this sylvopastoral area, the diversity of tick populations with the presence of the main CCHF vectors, and the increasing prevalence of CCHF virus. The surveillance in this area needs to be strengthened.

: Hepatitis E, caused by hepatitis E virus (HEV), is a highly endemic disease with a major public health impact. In Senegal, the first HEV outbreak was identified in 2014 in Kedougou, and a recent study focusing on pregnant women showed a seroprevalence of 7.8%. Apart from these data, very little is known about its burden in Senegal, and there is no specific surveillance program. We describe HEV prevalence among acute febrile jaundice patients in Senegal. A retrospective analysis using jaundice samples (2008–2020) collected through the national yellow fever surveillance program were tested for HEV by IgM/IgG ELISA and reverse transcription polymerase chain reaction (RT-PCR). Sequencing and phylogenetic analyses were performed on RT-PCR-positive samples. Statistical tools were used to analyze the HEV prevalence. In total, 2,387 samples were tested, and 174 IgG, 135 IgM/IgG, and 29 IgM positive samples were detected. Among the IgM-positive samples, 74 were positive by RT-PCR. The results showed an overall HEV prevalence of 14% in febrile jaundice patients in Senegal. Phylogenetic analyses showed the circulation of genotype 2b. Our data confirmed the HEV outbreak in Kedougou in 2014 and showed the detection of acute cases in other regions. We also detected in these regions genotype 2b, which is usually associated with large outbreaks in many African countries, suggesting a high risk of HEV outbreak occurrence in Senegal. Finally, our data showed that the yellow fever surveillance program, which is based on jaundice and already exists in many countries, could be a valuable tool for HEV surveillance.

Ticks are major vectors of numerous pathogens affecting both livestock and humans. In Senegal, data on the diversity of tick‐borne pathogens (TBPs) in ruminant‐associated ticks remain limited. In total, 1703 ticks were collected from goats, sheep, and cattle across three ecological zones of Senegal (Sudanian, Sahelian, and Sudano‐Sahelian). Tick species were identified morphologically, and 300 individuals were screened for 36 microorganisms using a high‐throughput microfluidic real‐time PCR system. DNA was successfully extracted and amplified from 289 ticks. The most abundant species were Rhipicephalus evertsi evertsi (32.3%), Hyalomma truncatum (19.6%), R. guilhoni (15.6%), H. rufipes (11.6%), and Amblyomma variegatum (11.0%). Among the screened ticks, 226 (78.9%) were positive for at least one microorganism. True pathogens of veterinary and/or zoonotic importance included Anaplasma ovis (30.8%), Coxiella spp. (23.9%), Rickettsia aeschlimannii (13.1%), Theileria spp. (11.1%), and Ehrlichia canis (4.8%), with sporadic detections of Anaplasma marginale , A. bovis , and Babesia spp. (0.3% each). In addition, non‐pathogenic Francisella ‐like endosymbionts (FLEs) were detected at high prevalence (37.4%) across all ecological zones. The presence of TBPs and/or endosymbionts was significantly associated only with the tick’s host in the multivariable logistic regression model. Ticks collected from goats (OR = 7.82; p = 0.024) and sheep (OR = 7.70; p = 0.015) were significantly more likely to be infected than those collected from cattle (reference group). A total of 96 cases of microorganism co‐occurrence were recorded across different tick species. Co‐infections were more frequent in ticks collected from the Sudano‐Sahelian zone (48.2%) and in those from sheep (32.0%). None of the detected microorganism species showed a significant associated with tick sex. This study represents the first large‐scale molecular survey of TBPs in ruminant‐associated ticks in Senegal, revealing both a high diversity of pathogens and a widespread presence of tick endosymbionts. While endosymbionts, such as FLEs, are not known to be pathogenic, their abundance may influence tick physiology and vector competence. The detection of zoonotic pathogens, such as E. canis and R. aeschlimannii , underscores the need to strengthen tick surveillance and investigate their potential public health implications.