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1.
Article in English | MEDLINE | ID: mdl-38627964

ABSTRACT

OBJECTIVE: Crimean-Congo haemorrhagic fever (CCHF) is a severe zoonotic arboviral disease that occurs widely in Eastern and Western Europe, Asia and Africa. The disease is becoming of growing public health importance in Senegal. However, analysis of tick infestation, CCHF virus (CCHFV) circulation extent and risk factors during ongoing outbreak are scarce. A thorough outbreak investigation was carried out during a CCHF outbreak in Podor (Northern Senegal) in August 2022. METHODS: Ticks and blood samples were collected from animals (cattle, goats and sheep) randomly selected from confirmed CCHF human cases houses, neighbourhoods and surrounding villages. Blood samples were tested for CCHFV antibodies using a commercial enzyme-linked immunosorbent assay (ELISA) test. Tick samples were screened for CCHFV RNA by RT-PCR. RESULTS: Overall, tick infestation rate (TIR) and CCHFV seroprevalence of livestock were 52.12% (95% confidence interval (CI): 45.54%-58.64%) and 43.28% (95% CI: 36.33%-50.44%), respectively. The TIRs were 87.7% in cattle, 57.6% in sheep and 20.0% in goats. These rates were significantly associated with location, host species and tick control (p < 0.001) but not with animal age and sex (p > 0.7). CCHFV seroprevalence was 80.4% (95% CI: 67.57%-89.77%) in cattle, 35.4% (95% CI: 25.00%-47.01%) in sheep and 21.2% (95% CI: 12.11%-33.02%) in goats. Age, sex, location, animal host and presence of ticks were significantly associated to the presence of antibodies. The 950 ticks collected included among other species, Hyalomma impeltatum (48.84%) and H. rufipes (10.21%). Five pools of Hyalomma ssp. were found CCHFV RT-PCR positive. These infected ticks included 0.86% (4/464) of H. impeltatum collected on cattle and sheep and 1.03% (1/97) of H. rufipes collected on a sheep. CONCLUSIONS: To our knowledge, this is the first report on the extend of tick infestation and CCHFV infection in livestock during an outbreak in Senegal. The results highlight the risk of human infections and the importance of strengthening vector, animal and human surveillance as well as tick control measures in this area to prevent CCHF infections in humans.

2.
Emerg Infect Dis ; 30(4): 770-774, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38526209

ABSTRACT

In 2020, a sylvatic dengue virus serotype 2 infection outbreak resulted in 59 confirmed dengue cases in Kedougou, Senegal, suggesting those strains might not require adaptation to reemerge into urban transmission cycles. Large-scale genomic surveillance and updated molecular diagnostic tools are needed to effectively prevent dengue virus infections in Senegal.


Subject(s)
Dengue Virus , Dengue , Humans , Dengue Virus/genetics , Senegal/epidemiology , Serogroup , Environment , Dengue/epidemiology
3.
Emerg Infect Dis ; 30(4): 805-807, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38526304

ABSTRACT

We report an imported Crimean-Congo hemorrhagic fever case in Senegal. The patient received PCR confirmation of virus infection 10 days after symptom onset. We identified 46 patient contacts in Senegal; 87.7% were healthcare professionals. Strengthening border crossing and community surveillance systems can help reduce the risks of infectious disease transmission.


Subject(s)
Hemorrhagic Fever, Crimean , Humans , Hemorrhagic Fever, Crimean/diagnosis , Hemorrhagic Fever, Crimean/therapy , Case Management , Senegal/epidemiology , Emigration and Immigration , Health Personnel
4.
Trop Med Infect Dis ; 9(2)2024 Jan 27.
Article in English | MEDLINE | ID: mdl-38393121

ABSTRACT

Dengue virus is becoming a major public health threat worldwide, principally in Africa. From 2016 to 2020, 23 outbreaks were reported in Africa, principally in West Africa. In Senegal, dengue outbreaks have been reported yearly since 2017. Data about the circulating serotypes and their spatial and temporal distribution were limited to outbreaks that occurred between 2017 and 2018. Herein, we describe up-to-date molecular surveillance of circulating DENV serotypes in Senegal between 2019 to 2023 and their temporal and spatial distribution around the country. For this purpose, suspected DENV-positive samples were collected and subjected to dengue detection and serotyping using RT-qPCR methods. Positive samples were used for temporal and spatial mapping. A subset of DENV+ samples were then sequenced and subjected to phylogenetic analysis. Results show a co-circulation of three DENV serotypes with an overall predominance of DENV-3. In terms of abundance, DENV-3 is followed by DENV-1, with scarce cases of DENV-2 from February 2019 to February 2022. Interestingly, data show the extinction of both serotype 1 and serotype 2 and the only circulation of DENV-3 from March 2022 to February 2023. At the genotype level, the analysis shows that sequenced strains belong to same genotype as previously described: Senegalese DENV-1 strains belong to genotype V, DENV-2 strains to the cosmopolitan genotype, and DENV-3 strains to Genotype III. Interestingly, newly obtained DENV 1-3 sequences clustered in different clades within genotypes. This co-circulation of strains belonging to different clades could have an effect on virus epidemiology and transmission dynamics. Overall, our results highlight DENV serotype replacement by DENV-3, accompanied by a wider geographic distribution, in Senegal. These results highlight the importance of virus genomic surveillance and call for further viral fitness studies using both in vitro and in vivo models, as well as in-depth phylogeographic studies to uncover the virus dispersal patterns across the country.

5.
Viruses ; 16(2)2024 02 19.
Article in English | MEDLINE | ID: mdl-38400090

ABSTRACT

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.


Subject(s)
Hemorrhagic Fever Virus, Crimean-Congo , Hemorrhagic Fever, Crimean , Ticks , Animals , Humans , Hemorrhagic Fever Virus, Crimean-Congo/genetics , Hemorrhagic Fever, Crimean/epidemiology , Phylogeny , Seroepidemiologic Studies , Senegal/epidemiology , Livestock
6.
Emerg Infect Dis ; 29(9): 1808-1817, 2023 09.
Article in English | MEDLINE | ID: mdl-37610149

ABSTRACT

Historically low levels of seasonal influenza circulation were reported during the first years of the COVID-19 pandemic and were mainly attributed to implementation of nonpharmaceutical interventions. In tropical regions, influenza's seasonality differs largely, and data on this topic are scarce. We analyzed data from Senegal's sentinel syndromic surveillance network before and after the start of the COVID-19 pandemic to assess changes in influenza circulation. We found that influenza shows year-round circulation in Senegal and has 2 distinct epidemic peaks: during January-March and during the rainy season in August-October. During 2021-2022, the expected January-March influenza peak completely disappeared, corresponding to periods of active SARS-CoV-2 circulation. We noted an unexpected influenza epidemic peak during May-July 2022. The observed reciprocal circulation of SARS-CoV-2 and influenza suggests that factors such as viral interference might be at play and should be further investigated in tropical settings.


Subject(s)
COVID-19 , Influenza, Human , Humans , COVID-19/epidemiology , SARS-CoV-2 , Senegal/epidemiology , Influenza, Human/epidemiology , Pandemics
7.
BMJ Glob Health ; 8(6)2023 06.
Article in English | MEDLINE | ID: mdl-37353236

ABSTRACT

The COVID-19 pandemic necessitated the rapid development and implementation of effective surveillance systems to detect and respond to the outbreak in Senegal. In this documentation, we describe the design and implementation of the Community Event-Based Surveillance (CEBS) system in Senegal to strengthen the existing Integrated Disease Surveillance and Response system. The CEBS system used a hotline and toll-free number to collect and triage COVID-19-related calls from the community. Data from the CEBS system were integrated with the national system for further investigation and laboratory testing. From February to September 2020, a total of 10 760 calls were received by the CEBS system, with 10 751 calls related to COVID-19. The majority of calls came from the Dakar region, which was the epicentre of the outbreak in Senegal. Of the COVID-19 calls, 50.2% were validated and referred to health districts for further investigation, and 25% of validated calls were laboratory-confirmed cases of SARS-CoV-2. The implementation of the CEBS system allowed for timely detection and response to potential COVID-19 cases, contributing to the overall surveillance efforts in the country. Lessons learned from this experience include the importance of decentralised CEBS, population sensitisation on hotlines and toll-free usage, and the potential role of Community Health Workers in triaging alerts that needs further analysis. This experience highlights the contribution of a CEBS system in Senegal and provides insights into the design and operation of such a system. The findings can inform other countries in strengthening their surveillance systems and response strategies.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/epidemiology , Senegal/epidemiology , Pandemics , Disease Outbreaks
8.
IJID Reg ; 7: 216-221, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37153883

ABSTRACT

Objectives: Rift Valley Fever and Crimean-Congo Hemorrhagic Fever are two infections classified among the emerging diseases to be monitored with highest priority. Studies undertaken in human and animals have shown endemicity of these two arboviruses in several African countries. However, most of the investigations were carried out on domestic cattle and the studies conducted on human populations are either outdated or limited to a small number of well-known endemic areas. It is then critical to better evaluate the burden of these viruses in Senegal at a national scale. Methods: This work relies on a previous seroprevalence survey undertaken in all regions of Senegal at the end of 2020. The existing biobank was used to determine the immunoglobulin G [IgG] Rift Valley Fever and Crimean-Congo Hemorrhagic Fever seroprevalences by indirect enzyme-linked immunosorbent assay. Results: The crude seroprevalences of Rift Valley Fever and Crimean-Congo Hemorrhagic Fever were 3.94% and 0.7% respectively, with the northern and central part of the countries as the main exposed areas. However, acute infections reported in both high and low exposed regions suggest sporadic introductions. Conclusions: This study gives updated information and could be of interest to support the stakeholders in the management of these zoonoses.

9.
Trop Med Infect Dis ; 8(2)2023 Jan 27.
Article in English | MEDLINE | ID: mdl-36828503

ABSTRACT

The mosquito-borne disease caused by the Rift Valley Fever Virus (RVFV) is a viral hemorrhagic fever that affects humans and animals. In 1987, RVFV emerged in Mauritania, which caused the first RVFV outbreak in West Africa. This outbreak was shortly followed by reported cases in humans and livestock in Senegal. Animal trade practices with neighboring Mauritania suggest northern regions of Senegal are at high risk for RVF. In this study, we aim to conduct a molecular and serological survey of RVFV in humans and livestock in Agnam (northeastern Senegal) by RT-PCR (reverse transcription real-time polymerase chain reaction) and ELISA (Enzyme-Linked Immunosorbent Assay), respectively. Of the two hundred fifty-five human sera, one (0.39%) tested RVFV IgM positive, while fifty-three (20.78%) tested positive for RVFV IgG. For animal monitoring, out of 30 sheep recorded and sampled over the study period, 20 (66.67%) showed seroconversion to RVFV IgG antibodies, notably during the rainy season. The presence of antibodies increased significantly with age in both groups (p < 0.05), as the force of RVF infection (FOI), increased by 16.05% per year for humans and by 80.4% per month for livestock sheep. This study supports the usefulness of setting up a One Health survey for RVF management.

10.
Article in English | MEDLINE | ID: mdl-36554793

ABSTRACT

Dengue virus (DENV) was detected in Senegal in 1979 for the first time. Since 2017, unprecedented frequent outbreaks of DENV were noticed yearly. In this context, epidemiological and molecular evolution data are paramount to decipher the virus diffusion route. In the current study, we focused on a dengue outbreak which occurred in Senegal in 2018 in the context of a large religious gathering with 263 confirmed DENV cases out of 832 collected samples, including 25 life-threatening cases and 2 deaths. It was characterized by a co-circulation of dengue serotypes 1 and 3. Phylogenetic analysis based on the E gene revealed that the main detected serotype in Touba was DENV-3 and belonged to Genotype III. Bayesian phylogeographic analysis was performed and suggested one viral introduction around 2017.07 (95% HPD = 2016.61-2017.57) followed by cryptic circulation before the identification of the first case on 1 October 2018. DENV-3 strains are phylogenetically related, with strong phylogenetic links between strains retrieved from Burkina Faso and other West African countries. These phylogenetic data substantiate epidemiological data of the origin of DENV-3 and its spread between African countries and subsequent diffusion after religious mass events. The study also highlighted the usefulness of a mobile laboratory during the outbreak response, allowing rapid diagnosis and resulting in improved patient management.


Subject(s)
Dengue Virus , Dengue , Humans , Dengue/epidemiology , Dengue Virus/genetics , Serogroup , Phylogeny , Senegal/epidemiology , Bayes Theorem , Disease Outbreaks , Genotype , Burkina Faso
11.
Trop Med Infect Dis ; 7(12)2022 Dec 07.
Article in English | MEDLINE | ID: mdl-36548675

ABSTRACT

Senegal is hyperendemic for dengue. Since 2017, outbreaks have been noticed annually in many regions around the country, marked by the co-circulation of DENV1-3. On 8 October 2021, a Dengue virus outbreak in the Rosso health post (sentinel site of the syndromic surveillance network) located in the north of the country was notified to the WHO Collaborating Center for arboviruses and hemorrhagic fever viruses at Institut Pasteur de Dakar. A multidisciplinary team was then sent for epidemiological and virologic investigations. This study describes the results from investigations during an outbreak in Senegal using a rapid diagnostic test (RDT) for the combined detection of dengue virus non-structural protein 1 (NS1) and IgM/IgG. For confirmation, samples were also tested by real-time RT-PCR and IgM ELISA at the reference lab in Dakar. qRT-PCR positive samples were subjected to whole genome sequencing using nanopore technology. Virologic analysis scored 102 positives cases (RT-PCR, NS1 antigen detection and/or IgM) out of 173 enrolled patients; interestingly, virus serotyping showed that the outbreak was caused by the DENV-1, a serotype different from DENV-2 involved during the outbreak in Rosso three years earlier, indicating a serotype replacement. Nearly all field-tested NS1 positives samples were confirmed by qRT-PCR with a concordance of 92.3%. Whole genome sequencing and phylogenetic analysis of strains suggested a re-introduction in Rosso of a DENV-1 strain different to the one responsible for the outbreak in the Louga area five years before. Findings call for improved dengue virus surveillance in Senegal, with a wide deployment of DENV antigenic tests, which allow easy on-site diagnosis of suspected cases and early detection of outbreaks. This work highlights the need for continuous monitoring of circulating serotypes which is crucial for a better understanding of viral epidemiology around the country.

12.
Emerg Microbes Infect ; 11(1): 2711-2714, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36268900

ABSTRACT

A Crimean-Congo Hemorrhagic Fever Virus (CCHFV) survey in Agnam (North Senegal) permits the detection of three isolates in ticks. These isolates belong genetically to multiple genotypes (I, II, III) and clustered with strains from Uganda, Sudan, Mauritania, and Senegal. The role of ticks in CCHF emergence and widespread is highlighted.


Subject(s)
Hemorrhagic Fever Virus, Crimean-Congo , Hemorrhagic Fever, Crimean , Ticks , Animals , Humans , Hemorrhagic Fever Virus, Crimean-Congo/genetics , Hemorrhagic Fever, Crimean/diagnosis , Senegal/epidemiology , Health Surveys , Genotype
13.
Viruses ; 14(10)2022 10 17.
Article in English | MEDLINE | ID: mdl-36298828

ABSTRACT

We investigated the epidemiology of measles and rubella infections in Senegal based on data from twelve consecutive years of laboratory-based surveillance (2010−2021) and conducted phylogenetic analyses of circulating measles viruses. Sera from measles-suspected cases were collected and tested for measles and rubella-specific IgM antibodies using enzyme-linked immunosorbent assays (ELISA). Throat swabs were collected from patients with clinically diagnosed measles for confirmation by reverse-transcription polymerase chain reaction (RT-PCR) and viral genotyping. Among 8082 laboratory-tested specimens from measles-suspected cases, serological evidence of measles and rubella infection was confirmed in 1303/8082 (16.1%) and 465/6714 (6.9%), respectively. The incidence of rubella is now low­0.8 (95% CI 0.4−1.3) cases per million people in 2021­whereas progress towards measles pre-elimination targets (<1.0 case per million people per year) appears to have stalled; there were 10.8 (95% CI 9.3−12.5) cases per million people in 2021. Phylogenetic analyses revealed that all Senegalese measles strains belonged to genotype B3. The rubella virus sequence obtained in this study was consistent with genotype 1C. Our national surveillance data suggest that despite their low incidence both measles and rubella remain endemic in Senegal with a concerning stagnation in the decline of measles infections that represents a significant challenge to the goal of regional elimination.


Subject(s)
Measles , Rubella , Humans , Molecular Epidemiology , Phylogeny , Incidence , Senegal/epidemiology , Rubella/epidemiology , Measles/epidemiology , Rubella virus/genetics , Measles virus/genetics , Antibodies, Viral , Genotype , Immunoglobulin M
14.
Trop Med Infect Dis ; 7(10)2022 Oct 21.
Article in English | MEDLINE | ID: mdl-36288065

ABSTRACT

Crimean-Congo hemorrhagic fever virus (CCHFV) is widespread in Asia, Europe, and Africa. In Senegal, sporadic cases of CCHFV have been reported since 1960. Bordering Mauritania in northeastern Senegal, Agnam is an arid area in the region of Matam where CCHFV is endemic, which harbors a pastoralist community. Given the drought conditions of Agnam, inhabitants are in constant movement with their animals in search of pasture, which brings them into contact with pathogens such as arboviruses. To identify CCHFV in this area, we established a One Health site in order to analyze animal livestock, ticks and human samples collected over a one-year period by qRT-PCR and ELISA. Our analysis showed one (1/364) patient carried anti-CCHFV IgM and thirty-seven carried anti-CCHFV IgG (37/364). In livestock, anti-CCHFV IgG was detected in 13 (38.24%) of 34 sentinel sheep. The risk of CCHFV infection increased significatively with age in humans (p-value = 0.00117) and sheep (p-value = 1.18 × 10-11). Additional risk factors for CCHFV infection in sheep were dry seasons (p-value = 0.004) and time of exposure (p-value = 0.007). Furthermore, we detected a total of three samples with CCHFV RNA within Rhipicephalus evertsi evertsi and Rhipicephalus guilhoni tick species. Our results highlighted the usefulness of a One Health survey of CCHFV in pastoral communities at risk of arboviruses.

15.
Emerg Infect Dis ; 28(10): 2027-2034, 2022 10.
Article in English | MEDLINE | ID: mdl-36148906

ABSTRACT

Environmental surveillance for poliovirus is increasingly used in poliovirus eradication efforts as a supplement to acute flaccid paralysis (AFP) surveillance. Environmental surveillance was officially established in 2017 in Senegal, where no poliovirus had been detected since 2010. We tested sewage samples from 2 sites in Dakar monthly for polioviruses. We identified a vaccine-derived poliovirus serotype 2 on January 19, 2021, from a sample collected on December 24, 2020; by December 31, 2021, we had detected 70 vaccine-derived poliovirus serotype 2 isolates circulating in 7 of 14 regions in Senegal. Sources included 18 AFP cases, 20 direct contacts, 17 contacts in the community, and 15 sewage samples. Phylogenetic analysis revealed the circulation of 2 clusters and provided evidence on the virus introduction from Guinea. Because novel oral polio vaccine serotype 2 was used for response activities throughout Senegal, we recommend expanding environmental surveillance into other regions.


Subject(s)
Poliomyelitis , Poliovirus , Humans , Environmental Monitoring , Phylogeny , Poliomyelitis/epidemiology , Poliomyelitis/prevention & control , Poliovirus/genetics , Poliovirus Vaccine, Oral/adverse effects , Senegal/epidemiology , Serogroup , Sewage
16.
PLoS One ; 17(9): e0274783, 2022.
Article in English | MEDLINE | ID: mdl-36126041

ABSTRACT

BACKGROUND: The novel coronavirus disease 2019 (COVID-19) pandemic has spread from China to the rest of the world. Africa seems less impacted with lower number of cases and deaths than other continents. Senegal recorded its first case on March 2, 2020. We present here data collected from March 2 to October 31, 2020 in Senegal. METHODS: Socio-demographic, epidemiological, clinical and virological information were collected on suspected cases. To determine factors associated with diagnosed infection, symptomatic disease and death, multivariable binary logistic regression and log binomial models were used. Epidemiological parameters such as the reproduction number and growth rate were estimated. RESULTS: 67,608 suspected cases were tested by the IPD laboratories (13,031 positive and 54,577 negative). All age categories were associated with SARS-CoV-2 infection, but also patients having diabetes or hypertension or other cardiovascular diseases. With diagnosed infection, patients over 65 years and those with hypertension and cardiovascular disease and diabetes were highly associated with death. Patients with co-morbidities were associated with symptomatic disease, but only the under 15 years were not associated with. Among infected, 27.67% were asymptomatic (40.9% when contacts were systematically tested; 12.11% when only symptomatic or high-risk contacts were tested). Less than 15 years-old were mostly asymptomatic (63.2%). Dakar accounted for 81.4% of confirmed cases. The estimated mean serial interval was 5.57 (± 5.14) days. The average reproduction number was estimated at 1.161 (95%CI: 1.159-1.162), the growth rate was 0.031 (95%CI: 0.028-0.034) per day. CONCLUSIONS: Our findings indicated that factors associated with symptomatic COVID-19 and death are advanced age (over 65 years-old) and comorbidities such as diabetes and hypertension and cardiovascular disease.


Subject(s)
COVID-19 , Cardiovascular Diseases , Diabetes Mellitus , Hypertension , Adolescent , Aged , COVID-19/epidemiology , Diabetes Mellitus/epidemiology , Humans , Hypertension/epidemiology , Pandemics , SARS-CoV-2 , Senegal/epidemiology
17.
IJID Reg ; 3: 117-125, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35720135

ABSTRACT

Objectives: A nationwide cross-sectional epidemiological survey was conducted to capture the true extent of coronavirus disease 2019 (COVID-19) exposure in Senegal. Methods: Multi-stage random cluster sampling of households was performed between October and November 2020, at the end of the first wave of COVID-19 transmission. Anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies were screened using three distinct ELISA assays. Adjusted prevalence rates for the survey design were calculated for each test separately, and thereafter combined. Crude and adjusted prevalence rates based on test performance were estimated to assess the seroprevalence. As some samples were collected in high malaria endemic areas, the relationship between SARS-CoV-2 seroreactivity and antimalarial humoral immunity was also investigated. Results: Of the 1463 participants included in this study, 58.8% were female and 41.2% were male; their mean age was 29.2 years (range 0.20-84.8.0 years). The national seroprevalence was estimated at 28.4% (95% confidence interval 26.1-30.8%). There was substantial regional variability. All age groups were impacted, and the prevalence of SARS-CoV-2 was comparable in the symptomatic and asymptomatic groups. An estimated 4 744 392 (95% confidence interval 4 360 164-5 145 327) were potentially infected with SARS-CoV-2 in Senegal, while 16 089 COVID-19 RT-PCR laboratory-confirmed cases were reported by the national surveillance. No correlation was found between SARS-CoV-2 and Plasmodium seroreactivity. Conclusions: These results provide a better estimate of SARS-CoV-2 dissemination in the Senegalese population. Preventive and control measures need to be reinforced in the country and especially in the south border regions.

18.
Open Forum Infect Dis ; 9(3): ofab655, 2022 Mar.
Article in English | MEDLINE | ID: mdl-35198642

ABSTRACT

BACKGROUND: Rift Valley fever virus (RVFV) is an arbovirus that causes epizootics and epidemics among livestock population and humans. Our surveillance system has revealed multiple emergences and re-emergences of RVFV in West Africa over the last decade. METHODS: The Sentinel Syndromic Surveillance Network in Senegal (4S) has been implemented since 2011. Samples from human suspected arbovirus infection in 4S sentinel sites were sent to Institut Pasteur de Dakar (IPD), where arbovirus diagnosis by enzyme-linked immunosorbent assay (ELISA), real-time reverse transcription polymerase chain reaction (RT-PCR), and virus isolation was performed. Overall, IPD has received a total of 1149 samples from arboviral suspected patients through the 4S network from January to December 2020. These samples were screened for 7 arboviruses including RVFV. Whole-genome sequencing of positive RVFV samples by RT-PCR was performed using the Illumina Miseq platform followed by genome assembly. Phylogenetic analyses were performed using MEGA X. RESULTS: Out of the 1149 arbovirus suspected cases, 4 RVFV-positive samples were detected with RT-PCR while 5 RVFV-positive samples were detected by ELISA. Complete genome sequences were obtained for 3 strains among the 4 positive samples by RT-PCR. Phylogenetic analyses indicated an emergence of a virus first described in South Africa during a major outbreak. CONCLUSIONS: This strong surveillance system allowed the detection of an RVFV outbreak in Senegal in 2020. The obtained genomes clustered with strains from South Africa belonging to lineage H. This calls for implementation of a strong surveillance system for wild animals, humans, and livestock simultaneously in all African countries.

19.
Pan Afr Med J ; 43: 204, 2022.
Article in French | MEDLINE | ID: mdl-36942135

ABSTRACT

Introduction: in response to the SARS-CoV-2 pandemic that reached Senegal in March 2020, the country has put in place several strategies to contain its spread. The purpose of this study was to describe the epidemiology and the strategies adopted. Méthods: we conducted a descriptive cross-sectional study of confirmed cases of COVID-19 using RT-PCR test in Senegal from March 2, 2020 to September 30, 2021. Data were collected through a literature review and analyzed with R and QGIS software. Proportions and means with standard deviation were calculated. Results: Senegal has recorded a total of 73,782 confirmed cases and 1,859 deaths from SARS-CoV-2. The temporal evolution was marked by three epidemic waves. The epidemic was concentrated in high-density areas such as Dakar (48,656 cases or 66%), in men (sex-ratio 1:13) and in the age group 25-34 years (16.527 cases or 22.4%). The average age of patients was 43 ± 18 years; the national cumulative incidence was 428 per 100,000 population and the overall case fatality rate was 2.5% (1,859/73,782). Some strategies have been implemented, including staff training, restrictive measures, home-based case management and vaccination. Nine point two percent (840,154/9,128,453) of the target population received 2 doses of vaccine. Conclusion: the epidemic was spread more widely within some population groups. We recommend strengthening preventive measures in high-density cities and mobilizing community networks to encourage immunization.


Subject(s)
COVID-19 , Male , Humans , Adult , Middle Aged , COVID-19/epidemiology , SARS-CoV-2 , Cross-Sectional Studies , Senegal/epidemiology , Pandemics/prevention & control
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