The Spatiotemporal Distribution and Molecular Characterization of Circulating Dengue Virus Serotypes/Genotypes in Senegal from 2019 to 2023.

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.

First hepatitis E outbreak in Southeastern Senegal.

The Rapid proliferation of traditional gold mining sites in the Kedougou region has led to massive migration of people from neighbouring West African countries and the establishment of several small villages where poor hygiene and sanitation conditions exist. In this context, a Hepatitis E virus outbreak was reported in Kedougou in 2014 with several cases among the traditional mining workers. Herein, we described epidemiological and laboratory data collected during the outbreak's investigation from February 2012 to November 2014. Any suspected, contact or probable case was investigated, clinical and epidemiological data were collected. In our study, sera were collected and tested for viral RNA and anti-Hepatitis E virus (HEV) IgM. Archived serum samples from Kedougou were retrospectively screened by real-time polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). A total of 65 water samples collected from ponds and wells surrounding gold panners' sites and habitats and 75 tissues samples from rats captured in the environment of traditional gold mining sites were also tested. A total of 1617 sera were collected from 698 suspected cases, 862 contacts and 57 persons with missing information. The median age was 20 (1-88 years-old) and the sex ratio was 1.72. An overall rate of 64.62% (1045/1617) of these patients tested positive for HEV with a high case fatality rate in pregnant women. All water samples and animal tissues tested negative for HEV. Our data help not only determining of the beginning of the HEV outbreak to March 2012, but also identifying risk factors associated to its emergence. However, there is a need to implement routine diagnosis, surveillance and training of health personnel in order to reduce mortality especially among pregnant women. In addition, further studies are needed to identify the virus reservoir and environmental risk factors for HEV in the Kedougou region.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Individual and healthcare supply-related HIV transmission factors in HIV-positive patients enrolled in the antiretroviral treatment access program in the Centre and Littoral regions in Cameroon (ANRS-12288 EVOLCam survey).

BACKGROUND: Despite great progress in antiretroviral treatment (ART) access in recent decades, HIV incidence remains high in sub-Saharan Africa. We investigated the role of individual and healthcare supply-related factors in HIV transmission risk in HIV-positive adults enrolled in 19 HIV services in the Centre and Littoral regions of Cameroon. METHODS: Factors associated with HIV transmission risk (defined as both unstable aviremia and inconsistent condom use with HIV-negative or unknown status partners) were identified using a multi-level logistic regression model. Besides socio-demographic and behavioral individual variables, the following four HIV-service profiles, identified using cluster analysis, were used in regression analyses as healthcare supply-related variables: 1) district services with large numbers of patients, almost all practicing task-shifting and not experiencing antiretroviral drugs (ARV) stock-outs (n = 4); 2) experienced and well-equipped national reference services, most practicing task-shifting and not experiencing ARV stock-outs (n = 5); 3) small district services with limited resources and activities, almost all experiencing ARV stock-outs (n = 6); 4) small district services with a wide range of activities and half not experiencing ARV stock-outs (n = 4). RESULTS: Of the 1372 patients (women 67%, median age [Interquartile]: 39 [33-44] years) reporting sexual activity in the previous 12 months, 39% [min-max across HIV services: 25%-63%] were at risk of transmitting HIV. The final model showed that being a woman (adjusted Odd Ratio [95% Confidence Interval], p-value: 2.13 [1.60-2.82], p<0.001), not having an economic activity (1.34 [1.05-1.72], p = 0.019), having at least two sexual partners (2.45 [1.83-3.29], p<0.001), reporting disease symptoms at HIV diagnosis (1.38 [1.08-1.75], p = 0.011), delayed ART initiation (1.32 [1.02-1.71], p = 0.034) and not being ART treated (2.28 [1.48-3.49], p<0.001) were all associated with HIV transmission risk. Conversely, longer time since HIV diagnosis was associated with a lower risk of transmitting HIV (0.96 [0.92-0.99] per one-year increase, p = 0.024). Patients followed in the third profile had a higher risk of transmitting HIV (1.71 [1.05-2.79], p = 0.031) than those in the first profile. CONCLUSIONS: Healthcare supply constraints, including limited resources and ARV supply chain deficiency may impact HIV transmission risk. To reduce HIV incidence, HIV services need adequate resources to relieve healthcare supply-related barriers and provide suitable support activities throughout the continuum of care.

The first year of the COVID-19 pandemic in the ECOWAS region.

Objective: to analyse the pandemic after one year in terms of the evolution of morbidity and mortality and factors that may contribute to this evolution. Design: This is a secondary analysis of data gathered to respond to the COVID-19 pandemic. The number of cases, incidence rate, cumulative incidence rate, number of deaths, case fatality rate and their trends were analysed during the first year of the pandemic. Testing and other public health measures were also described according to the information available. Settings: The 15 States members of the Economic Community of West African States (ECOWAS) were considered. Results: As of 31st March 2021, the ECOWAS region reported 429,760 COVID-19 cases and 5,620 deaths. In the first year, 1,110.75 persons were infected per million, while 1.31% of the confirmed patients died. The ECOWAS region represents 30% of the African population. One year after the start of COVID-19 in ECOWAS, this region reported 10% of the cases and 10% of the deaths in the continent. Cumulatively, the region has had two major epidemic waves; however, countries show different patterns. The case fatality rate presented a fast growth in the first months and then decreased to a plateau. Conclusion: We learn that the context of COVID-19 is specific to each country. This analysis shows the importance of better understanding each country's response. During this first year of the pandemic, the problem of variants of concern and the vaccination were not posed. Funding: The study was funded by the International Development Research Centre (IDRC) under CATALYSE project.

The first year of the COVID-19 pandemic in the ECOWAS region

Objective: to analyse the pandemic after one year in terms of the evolution of morbidity and mortality and factors that may contribute to this evolution Design: This is a secondary analysis of data gathered to respond to the COVID-19 pandemic. The number of cases, incidence rate, cumulative incidence rate, number of deaths, case fatality rate and their trends were analysed during the first year of the pandemic. Testing and other public health measures were also described according to the information available. Settings: The 15 States members of the Economic Community of West African States (ECOWAS) were considered. Results: As of 31st March 2021, the ECOWAS region reported 429,760 COVID-19 cases and 5,620 deaths. In the first year, 1,110.75 persons were infected per million, while 1.31% of the confirmed patients died. The ECOWAS region represents 30% of the African population. One year after the start of COVID-19 in ECOWAS, this region reported 10% of the cases and 10% of the deaths in the continent. Cumulatively, the region has had two major epidemic waves; however, countries show different patterns. The case fatality rate presented a fast growth in the first months and then decreased to a plateau. Conclusion: We learn that the context of COVID-19 is specific to each country. This analysis shows the importance of better understanding each country's response. During this first year of the pandemic, the problem of variants of concern and the vaccination were not posed.

Risk of Fecal Incontinence Following Receptive Anal Intercourse: Survey of 21,762 Men Who Have Sex With Men.

BACKGROUND: The prevalence of receptive anal intercourse (RAI) is increasing. A few studies, with heterogeneous designs, have investigated the associated risk of fecal incontinence (FI). AIM: The primary objective of this study was to determine FI prevalence in a population of men who have sex with men (MSM) engaging in RAI. The secondary objective was to identify risk factors for severe FI. METHODS OUTCOMES: An online survey of 24,308 MSM was performed in 2019. Demographic and socioeconomic data were collected, together with information about RAI sexual practices, and FI defined by: "During the last month, have you experienced any involuntary leakage of stools?" RESULTS CLINICAL IMPLICATIONS: In total, 1,734 (8%) of the 21,762 participants reported FI. Mean age was 35.3 years. The prevalence of FI was correlated with RAI frequency: 12.7% (if RAI ≥ 1 /wk) versus 5.7% (if no RAI). In multivariate analysis, the factors associated with FI were age (OR: 1.01), low socioeconomic status (OR 1.32 to 1.40), HIV-seropositivity (OR: 1.78), high RAI frequency (OR: 1.64), chemsex (OR: 1.67) and fist-fucking (OR: 1.61). STRENGTHS AND LIMITATIONS: Main strengths of our study are population size and assessment of detailed modalities of sexual practices. Main limitations are the use of a convenience non-random sample and the assessment of FI only during the past month. CONCLUSION: This study of a large MSM population, highlights risk factors for FI among RAI practices: RAI ≥ 1 /wk, chemsex, fist-fucking, low socioeconomic status. Garros A, Bourrely M, Sagaon-Teyssier L, et al. Risk of Fecal Incontinence Following Receptive Anal Intercourse: Survey of 21,762 Men Who Have Sex With Men. J Sex Med 2021;18:1880-1890.

Intimate partner violence by men living with HIV in Cameroon: Prevalence, associated factors and implications for HIV transmission risk (ANRS-12288 EVOLCAM).

OBJECTIVES: Intimate partner violence (IPV) against women is frequent in Central Africa and may be a HIV infection risk factor. More data on HIV-positive men (MLHIV) committing IPV are needed to develop perpetrator-focused IPV and HIV prevention interventions. We investigated the relationship between IPV and HIV transmission risk and IPV-associated factors. METHODS: We used data from the cross-sectional survey EVOLCam which was conducted in Cameroonian outpatient HIV structures in 2014. The study population comprised MLHIV declaring at least one sexual partner in the previous year. Using principal component analysis, we built three variables measuring, respectively, self-reported MLHIV-perpetrated psychological and physical IPV (PPV), severe physical IPV (SPV), and sexual IPV (SV). Ordinal logistic regressions helped investigate: i) the relationship between HIV transmission risk (defined as unstable aviremia and inconsistent condom use) and IPV variables, ii) factors associated with each IPV variable. RESULTS: PPV, SPV and SV were self-reported by 28, 15 and 11% of the 406 study participants, respectively. IPV perpetrators had a significantly higher risk of transmitting HIV than non-IPV perpetrators. Factors independently associated with IPV variables were: i) socio-demographic, economic and dyadic factors, including younger age (PPV and SPV), lower income (PPV), not being the household head (SPV and SV), living with a main partner (SPV), and having a younger main partner (SPV); ii) sexual behaviors, including ≥2 partners in the previous year (PPV and SPV), lifetime sex with another man (SPV), inconsistent condom use (SV), and >20 partners during lifetime (SV); iii) HIV-related stigma (PPV and SV). CONCLUSION: IPV perpetrators had a higher risk of transmitting HIV and having lifetime and recent risky sexual behaviors. Perpetrating IPV was more frequent in those with socioeconomic vulnerability and self-perceived HIV-related stigma. These findings highlight the need for interventions to prevent IPV by MLHIV and related HIV transmission to their(s) partner(s).

How does the West African Health Organisation (WAHO) contribute to the evidence based decision-making and practice during COVID-19 pandemic in ECOWAS region?

The COVID-19 pandemic required policy makers to make urgent decisions to limit the spread of the disease. International and regional health bodies and research institutions have a role in supporting decision makers and health actors in providing accurate and timely research evidence and guidance in decision making and practice. In ECOWAS region, the West African Health Organisation (WAHO) has experience in promoting evidence use decision making and practice as part of its role as Health Policy and Research Organisation. Promoting the use of evidence to influence policy and practice is possible through various approaches including training, the development of guides and policy briefs, the synthesis and sharing of evidence, and the organisation of meetings to share experiences. In the context of the COVID-19 pandemic, WAHO has deployed several approaches to bring the use of evidence to decision-makers and stakeholders to influence policy and practice. To improve practices, WAHO has organized regional training workshops on laboratory diagnostic, surveillance and simulation exercises of outbreak response for key actors, as well as webinars on different aspects of COVID-19 pandemic surveillance, coordination and management. In addition, a synthesis of the most recent evidence and epidemiologic models were developed to enlighten decision makers in selecting and implementation response interventions.

Seoul Orthohantavirus in Wild Black Rats, Senegal, 2012-2013.

Hantaviruses cause hemorrhagic fever in humans worldwide. However, few hantavirus surveillance campaigns occur in Africa. We detected Seoul orthohantavirus in black rats in Senegal, although we did not find serologic evidence of this disease in humans. These findings highlight the need for increased surveillance of hantaviruses in this region.

Who are the persons living with HIV who might refuse to participate in HIV cure-related clinical trials with treatment interruption?

: Achieving a HIV cure has become a research priority. As any improvement of knowledge, which could help scientists design new HIV cure-related clinical trials (HCRCT) depends on the risks potential participants are willing to accept, it is important to understand who will agree or refuse to participate and in which proportions. By providing insights into factors associated with reluctance toward HCRCT participation, our results may help clinicians in patient recruitment.

Changes in the Transmission Dynamic of Chikungunya Virus in Southeastern Senegal.

In Senegal, chikungunya virus (CHIKV) is maintained in a sylvatic cycle and causes sporadic cases or small outbreaks in rural areas. However, little is known about the influence of the environment on its transmission. To address the question, 120 villages were randomly selected in the Kedougou region of southeastern Senegal. In each selected village, 10 persons by randomly selected household were sampled and tested for specific anti-CHIKV IgG antibodies by ELISA. We investigated the association of CHIKV seroprevalence with environmental variables using logistic regression analysis and the spatial correlation of village seroprevalence based on semivariogram analysis. Fifty-four percent (51%-57%) of individuals sampled during the survey tested positive for CHIKV-specific IgG. CHIKV seroprevalence was significantly higher in populations living close to forested areas (Normalized Difference Vegetation Index (NDVI), Odds Ratio (OR) = 1.90 (1.42-2.57)), and was negatively associated with population density (OR = 0.76 (0.69-0.84)). In contrast, in gold mining sites where population density was >400 people per km2, seroprevalence peaked significantly among adults (46% (27%-67%)) compared to all other individuals (20% (12%-31%)). However, traditional gold mining activities significantly modify the transmission dynamic of CHIKV, leading to a potential increase of the risk of human exposition in the region.

Multinomial Logistic Model for Coinfection Diagnosis Between Arbovirus and Malaria in Kedougou.

In tropical regions, populations continue to suffer morbidity and mortality from malaria and arboviral diseases. In Kedougou (Senegal), these illnesses are all endemic due to the climate and its geographical position. The co-circulation of malaria parasites and arboviruses can explain the observation of coinfected cases. Indeed there is strong resemblance in symptoms between these diseases making problematic targeted medical care of coinfected cases. This is due to the fact that the origin of illness is not obviously known. Some cases could be immunized against one or the other of the pathogens, immunity typically acquired with factors like age and exposure as usual for endemic area. Thus, coinfection needs to be better diagnosed. Using data collected from patients in Kedougou region, from 2009 to 2013, we adjusted a multinomial logistic model and selected relevant variables in explaining coinfection status. We observed specific sets of variables explaining each of the diseases exclusively and the coinfection. We tested the independence between arboviral and malaria infections and derived coinfection probabilities from the model fitting. In case of a coinfection probability greater than a threshold value to be calibrated on the data, long duration of illness and age are mostly indicative of arboviral disease while high body temperature and presence of nausea or vomiting symptoms during the rainy season are mostly indicative of malaria disease.

Role of monkeys in the sylvatic cycle of chikungunya virus in Senegal.

Arboviruses spillover into humans either as a one-step jump from a reservoir host species into humans or as a two-step jump from the reservoir to an amplification host species and thence to humans. Little is known about arbovirus transmission dynamics in reservoir and amplification hosts. Here we elucidate the role of monkeys in the sylvatic, enzootic cycle of chikungunya virus (CHIKV) in the region around Kédougou, Senegal. Over 3 years, 737 monkeys were captured, aged using anthropometry and dentition, and tested for exposure to CHIKV by detection of neutralizing antibodies. Infant monkeys were positive for CHIKV even when the virus was not detected in a concurrent survey of mosquitoes and when population immunity was too high for monkeys alone to support continuous transmission. We conclude that monkeys in this region serve as amplification hosts of CHIKV. Additional efforts are needed to identify other hosts capable of supporting continuous circulation.

Chikungunya Outbreak in Kedougou, Southeastern Senegal in 2009-2010.

BACKGROUND: In Senegal, Chikungunya virus (CHIKV), which is an emerging mosquito-borne alphavirus, circulates in a sylvatic and urban/domestic cycle and has caused sporadic human cases and epidemics since 1960s. However, the real impact of the CHIKV sylvatic cycle in humans and mechanisms underlying its emergence still remains unknown. METHODOLOGY: One thousand four hundred nine suspect cases of CHIKV infection, recruited from 5 health facilities located in Kedougou region, south-eastern Senegal, between May 2009 to March 2010, together with 866 serum samples collected from schoolchildren from 4 elementary schools in May and November 2009 from Kedougou were screened for anti-CHIKV immunoglobulin (Ig)M antibodies and, when appropriate, for viral nucleic acid by real-time polymerase chain reaction (rPCR) and virus isolation. In addition, mosquitoes collected in the same area from May 2009 to January 2010 were tested for CHIKV by rPCR and by virus isolation, and 116 monkeys sera collected from March 2010 to May 2010 were tested for anti-CHIKV IgM and neutralizing antibodies. RESULTS: The main clinical manifestations of the CHIKV suspect cases were headache, myalgia, and arthralgia. Evidence for CHIKV infection was observed in 1.4% (20 of 1409) of patients among suspect cases. No significant difference was observed among age or sex groups. In addition, 25 (2.9%) students had evidence of CHIKV infection in November 2009. Chikungunya virus was detected in 42 pools of mosquitoes, mainly from Aedes furcifer, and 83% of monkeys sampled were seropositive. CONCLUSIONS: Our findings further documented that CHIKV is maintained in a sylvatic transmission cycle among monkeys and Aedes mosquitoes in Kedougou, and humans become infected by exposure to the virus in the forest.

Asymptomatic Plasmodium vivax infections among Duffy-negative population in Kedougou, Senegal.

BACKGROUND: In the southeastern Senegal, the report of Plasmodium vivax infections among febrile patients in Kedougou constitutes a new emerging health problem. METHODS: Samples from 48 asymptomatic schoolchildren sampled twice a year over 2 years were used to explore the reservoir of P. vivax parasite infections in this region. Both Duffy genotyping and Plasmodium species diagnostic assays were performed. RESULTS: PCR assays detected Plasmodium genomic DNA in 38.5% (74/192) of samples. Pure P. falciparum and P. vivax infections were identified in 79.7% (59/74) and 20.3% (15/74) of samples, respectively. All schoolchildren were classified as Duffy-negative by genotyping. P. vivax infections were detected in five children: in two children during both years, in one child in 2010 and on May 2011, and only in 2010 for the remaining two children. CONCLUSIONS: This unexpectedly high proportion of P. vivax infections in asymptomatic Duffy-negative children highlights to consider vivax malaria as an emerging problem in Senegal.

Unexpected high circulation of Plasmodium vivax in asymptomatic children from Kédougou, southeastern Senegal.

BACKGROUND: Malaria in Senegal is due essentially to infections by Plasmodium falciparum and, to a lesser extent to Plasmodium malariae and Plasmodium ovale. By the use of molecular methods, detection of Plasmodium vivax has been recently reported in the region of Kedougou, raising the question of appraisal of its potential prevalence in this setting. METHODS: A retrospective serological study was carried out using 188 samples taken from 2010 to 2011 in a longitudinal school survey during which 48 asymptomatic children (9-11 years) were recruited. Four collections of samples collected during two successive dry and rainy seasons were analysed for antibody responses to P. vivax and P. falciparum. Recombinant P. falciparum and P. vivax MSP1 antigens and total P. falciparum schizont lysate from African 07/03 strain (adapted to culture) were used for ELISA. Nested PCR amplification was used for molecular detection of P. vivax. RESULTS: A surprising high prevalence of IgG responses against P. vivax MSP1 was evidenced with 53% of positive samples and 58% of the individuals that were found positive to this antigen. There was 77% of responders to P. falciparum outlined by 63% of positive samples. Prevalence of responders did not differ as function of seasons. Levels of antibodies to P. falciparum fluctuated with significant increasing between dry and rainy season (P < 0.05), contrary to responses to P. vivax. There was a significant reciprocal relationship (P < 10-3) between antibody responses to the different antigens, but with weak coefficient of correlation (Rho around 0.3) underlining a variable profile at the individual level. Clear molecular signature was found in positive IgG to P. vivax msp1 samples by PCR. CONCLUSION: This cross-sectional longitudinal study highlights the unexpected high circulation of P. vivax in this endemic area. Sero-immunology and molecular methods are powerful additive tools to identify endemic sites where relevant control measures have to be settled and monitored.