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In December 2023, we observed through hospital-based surveillance a severe outbreak of enterovirus D68 infection in pediatric inpatients in Dakar, Senegal. Molecular characterization revealed that subclade B3, the dominant lineage in outbreaks worldwide, was responsible for the outbreak. Enhanced surveillance in inpatient settings, including among patients with neurologic illnesses, is needed.

Objectives: Several factors can cause acute flaccid paralysis cases including non-polio enteroviruses. In Senegal, few studies on non-polio enteroviruses (NPEV) have been performed. Methods: Our study assess the molecular epidemiology of non-polio enteroviruses in Senegal from 2013 to 2021 through the previously existing programs for surveillance of polioviruses. Results: A total of 3815 stool samples and 281 sewage samples were collected. After virus isolation by cell culture, non-polio enteroviruses-positive isolates were confirmed by reverse transcriptase-quantitative polymerase chain reaction. Following this detection, the positive samples were subjected to molecular characterization. Our data showed that 15.22% and 52.66% were positive in cell culture for non-polio enteroviruses in acute flaccid paralysis surveillance and environmental surveillance, respectively. These non-polio enteroviruses-positive isolates were detected all year round but tend to unequal peaks of circulation, and the age group 0-5 years was more vulnerable to infection (84.4%). Genetic characterization revealed the circulation of enteroviruses species infecting humans (Enterovirus A – Enterovirus D): Enterovirus A (29.2%) and Enterovirus B (63.1%) isolates from both the acute flaccid paralysis surveillance and environmental surveillance while Enterovirus C (5.3%) and Enterovirus D (2.4%) were only isolated from the acute flaccid paralysis surveillance. However, the highly prevalent Enterovirus B species from the acute flaccid paralysis surveillance included echovirus 7 and echovirus 13, whereas coxsackievirus A6 was the predominant species from the environmental surveillance. Conclusion: This first 8-year period study of NPEV in Senegal showed that NPEV represent important viral etiologies associated with acute flaccid paralysis cases and circulating in environmental surveillance in Senegal and highlighted the need to promote effective long-term strategies for monitoring of non-polio enteroviruses infections.

Chikungunya virus has caused millions of cases worldwide over the past 20 years, with recent outbreaks in Kedougou region in the southeastern Senegal, West Africa. Genomic characterization highlights that an ongoing epidemic in Kedougou in 2023 is not due to an introduction event but caused by the re-emergence of an endemic strain evolving linearly in a sylvatic context.

Abstract In 2022, many regions around the world experienced a severe respiratory syncytial virus (RSV) epidemic with an earlier-than-usual start and increased numbers of paediatric patients in emergency departments. Here we carried out this study to describe the epidemiology and genetic characteristics of RSV infection in patients hospitalized with severe acute respiratory infections in 2022. Samples were tested for RSV by multiplex real time reverse transcription polymerase chain reaction. Subsequently, a subset of RSV positive samples was selected for NGS sequencing. RSV was detected in 16.04%, among which RSV-A was confirmed in 7.5% and RSV-B in 76.7%. RSV infection were more identified in infants aged ≤ 11 months (83.3%) and a shift in the circulation pattern was observed, with highest incidences between September–November. Phylogenetic analyses revealed that all RSV-A strains belonged to GA2.3.5 genotype and all RSV-B strains to GB5.0.5a genotype. Three putative N-glycosylation sites at amino acid positions 103, 135, 237 were predicted among RSV-A strains, while four N-linked glycosylation sites at positions 81, 86, 231 and 294 were identified in RSV-B strains. Globally, our findings reveal an exclusive co-circulation of two genetic lineages of RSV within the pediatric population in Senegal, especially in infants aged ≤ 11 months.

BackgroundWith growing use of parasitological tests to detect malaria and decreasing incidence of the disease in Africa; it becomes necessary to increase the understanding of causes of non-malaria acute febrile illness (NMAFI) towards providing appropriate case management. This research investigates causes of NMAFI in pediatric out-patients in rural Guinea-Bissau.MethodsChildren 0–5 years presenting acute fever (≥38°) or history of fever, negative malaria rapid diagnostic test (mRDT) and no signs of specific disease were recruited at the out-patient clinic of 3 health facilities in Bafatá province during 54 consecutive weeks (dry and rainy season). Medical history was recorded and blood, nasopharyngeal, stool and urine samples were collected and tested for the presence of 38 different potential aetiological causes of fever.ResultsSamples from 741 children were analysed, the protocol was successful in determining a probable aetiological cause of acute fever in 544 (73.61%) cases. Respiratory viruses were the most frequently identified pathogens, present in the nasopharynx samples of 435 (58.86%) cases, followed by bacteria detected in 167 (22.60%) samples. Despite presenting negative mRDTs, P. falciparum was identified in samples of 24 (3.25%) patients.ConclusionsThis research provides a description of the aetiological causes of NMAFI in West African context. Evidence of viral infections were more commonly found than bacteria or parasites.

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.

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.

Abstract During the COVID-19 pandemic in Senegal, contact tracing was done to identify transmission clusters, their analysis allowed to understand their dynamics and evolution. In this study, we used information from the surveillance data and phone interviews to construct, represent and analyze COVID-19 transmission clusters from March 2, 2020, to May 31, 2021. In total, 114,040 samples were tested and 2153 transmission clusters identified. A maximum of 7 generations of secondary infections were noted. Clusters had an average of 29.58 members and 7.63 infected among them; their average duration was 27.95 days. Most of the clusters (77.3%) are concentrated in Dakar, capital city of Senegal. The 29 cases identified as super-spreaders, i.e., the indexes that had the most positive contacts, showed few symptoms or were asymptomatic. Deepest transmission clusters are those with the highest percentage of asymptomatic members. The correlation between proportion of asymptomatic and degree of transmission clusters showed that asymptomatic strongly contributed to the continuity of transmission within clusters. During this pandemic, all the efforts towards epidemiological investigations, active case-contact detection, allowed to identify in a short delay growing clusters and help response teams to mitigate the spread of the disease.

Abstract Profiling of the antibody responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) proteins in African populations is scarce. Here, we performed a detailed IgM and IgG epitope mapping study against 487 peptides covering SARS-CoV-2 wild-type structural proteins. A panel of 41 pre-pandemic and 82 COVID-19 RT-PCR confirmed sera from Madagascar and Senegal were used. We found that the main 36 immunodominant linear epitopes identified were (i) similar in both countries, (ii) distributed mainly in the Spike and the Nucleocapsid proteins, (iii) located outside the RBD and NTD regions where most of the reported SARS-CoV-2 variant mutations occur, and (iv) identical to those reported in European, North American, and Asian studies. Within the severe group, antibody levels were inversely correlated with the viral load. This first antibody epitope mapping study performed in patients from two African countries may be helpful to guide rational peptide-based diagnostic assays or vaccine development.

Acute respiratory viruses (ARVs) are the leading cause of diseases in humans worldwide. High-risk individuals, including children and the elderly, could potentially develop severe illnesses that could result in hospitalization or death in the worst case. The most common ARVs are the Human respiratory syncytial virus, Human Metapneumovirus, Human Parainfluenza Virus, rhinovirus, coronaviruses (including SARS and MERS CoV), adenoviruses, Human Bocavirus, enterovirus (-D68 and 71), and influenza viruses. The olfactory deficits due to ARV infection are a common symptom among patients. This review provides an overview of the role of SARS-CoV-2 and other common ARVs in the development of human olfactory pathophysiology. We highlight the critical need to understand the signaling underlying the olfactory dysfunction and the development of therapeutics for this wide-ranging category of AVRs to restore the altered or loss of smell in affected patients.

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.

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.

Abstract Early predictions forecasted large numbers of severe acute respiratory syndrome coronavirus (SARS-CoV-2) cases and associated deaths in Africa. To date, Africa has been relatively spared. Various hypotheses were postulated to explain the lower than anticipated impact on public health in Africa. However, the contribution of pre-existing immunity is yet to be investigated. In this study, the presence of antibodies against SARS-CoV-2 spike (S) and nucleocapsid (N) proteins in pre-pandemic samples from Africa, Europe, South and North America was examined by ELISA. The protective efficacy of N specific antibodies isolated from Central African donors was tested by in vitro neutralization and in a mouse model of SARS-CoV-2 infection. Antibodies against SARS-CoV-2 S and N proteins were rare in all populations except in Gabon and Senegal where N specific antibodies were prevalent. However, these antibodies failed to neutralize the virus either in vitro or in vivo. Overall, this study indicates that cross-reactive immunity against SARS-CoV-2 N protein was present in Africa prior to the pandemic. However, this pre-existing humoral immunity does not impact viral fitness in rodents suggesting that other human immune defense mechanisms could be involved. In Africa, seroprevalence studies using the N protein are over-estimating SARS-CoV-2 circulation.

This overview of severe acute respiratory syndrome coronavirus 2 circulation over 1.5 years in Guinea demonstrates that virus clades and variants of interest and concern were progressively introduced, mostly by travellers through Conakry, before spreading through the country. Sequencing is key to following virus evolution and establishing efficient control strategies.

We conducted an active influenza surveillance in the single pig slaughterhouse in Dakar to investigate the epidemiology and genetic characteristics of influenza A viruses (IAVs) and to provide serologic evidence of avian influenza virus (AIV) infection in pigs at interfaces with human populations in Senegal. Nasal swab and blood samples were collected on a weekly basis from the same animal immediately after slaughter. Influenza A viruses were diagnosed using RT-qPCR and a subset of positive samples for H3 and H1 subtypes were selected for full genome amplification and NGS sequencing. Serum samples were tested by HI assay for the detection of antibodies recognizing four AIVs, including H9N2, H5N1, H7N7 and H5N2. Between September 2018 and December 2019, 1691 swine nasal swabs were collected and tested. Influenza A virus was detected in 30.7% (520/1691), and A/H1N1pdm09 virus was the most commonly identified subtype with 38.07% (198/520), followed by A/H1N2 (16.3%) and A/H3N2 (5.2%). Year-round influenza activity was noted in pigs, with the highest incidence between June and September. Phylogenetic analyses revealed that the IAVs were closely related to human IAV strains belonging to A/H1N1pdm09 and seasonal H3N2 lineages. Genetic analysis revealed that Senegalese strains possessed several key amino acid changes, including D204 and N241D in the receptor binding site, S31N in the M2 gene and P560S in the PA protein. Serological analyses revealed that 83.5% (95%CI = 81.6–85.3) of the 1636 sera tested were positive for the presence of antibodies against either H9N2, H5N1, H7N7 or H5N2. Influenza H7N7 (54.3%) and H9N2 (53.6%) were the dominant avian subtypes detected in Senegalese pigs. Given the co-circulation of multiple subtypes of influenza viruses among Senegalese pigs, the potential exists for the emergence of new hybrid viruses of unpredictable zoonotic and pandemic potential in the future.

Abstract Background Influenza is a major cause of morbidity and mortality in Africa. However, a lack of epidemiological data remains for this pathology, and the performances of the influenza-like illness (ILI) case definitions used for sentinel surveillance have never been evaluated in Senegal. This study aimed to i) assess the performance of three different ILI case definitions, adopted by the WHO, USA-CDC (CDC) and European-CDC (ECDC) and ii) identify clinical factors associated with a positive diagnosis for Influenza in order to develop an algorithm fitted for the Senegalese context. Methods All 657 patients with a febrile pathological episode (FPE) between January 2013 and December 2016 were followed in a cohort study in two rural villages in Senegal, accounting for 1653 FPE observations with nasopharyngeal sampling and influenza virus screening by rRT-PCR. For each FPE, general characteristics and clinical signs presented by patients were collected. Sensitivity, Specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV) for the three ILI case definitions were assessed using PCR result as the reference test. Associations between clinical signs and influenza infection were analyzed using logistic regression with generalized estimating equations. Sore throat, arthralgia or myalgia were missing for children under 5 years. Results WHO, CDC and ECDC case definitions had similar sensitivity (81.0%; 95%CI: 77.0–85.0) and NPV (91.0%; 95%CI: 89.0–93.1) while the WHO and CDC ILI case definitions had the highest specificity (52.0%; 95%CI: 49.1–54.5) and PPV (32.0%; 95%CI: 30.0–35.0). These performances varied by age groups. In children

A substantial amount of epidemiological data has been reported on Enterovirus D68 (EV-D68) infections after the 2014 outbreak. Our goal was to map the case fatality rate (CFR) and prevalence of current and past EV-D68 infections. We conducted a systematic review (PROSPERO, CRD42021229255) with published articles on EV-68 infections in PubMed, Embase, Web of Science and Global Index Medicus up to January 2021. We determined prevalences using a model random effect. Of the 4,329 articles retrieved from the databases, 89 studies that met the inclusion criteria were from 39 different countries with apparently healthy individuals and patients with acute respiratory infections, acute flaccid myelitis and asthma-related diseases. The CFR estimate revealed occasional deaths (7/1353) related to EV-D68 infections in patients with severe acute respiratory infections. Analyses showed that the combined prevalence of current and past EV-D68 infections was 4% (95% CI = 3.1–5.0) and 66.3% (95% CI = 40.0–88.2), respectively. The highest prevalences were in hospital outbreaks, developed countries, children under 5, after 2014, and in patients with acute flaccid myelitis and asthma-related diseases. The present study shows sporadic deaths linked to severe respiratory EV-D68 infections. The study also highlights a low prevalence of current EV-D68 infections as opposed to the existence of EV-D68 antibodies in almost all participants of the included studies. These findings therefore highlight the need to implement and/or strengthen continuous surveillance of EV-D68 infections in hospitals and in the community for the anticipation of the response to future epidemics. Author summary Enterovirus D68 (EV-D68) infections represent a global public health concern. EV-D68 are detected in apparently healthy subjects and patients with acute respiratory illnesses, acute flaccid myelitis, and asthma-related illnesses. Enterovirus D68 was first described in 1962 and exhibited sporadic circulation until August 2014 when outbreaks of EV-D68 infections were reported in the USA and Canada mainly in children with acute flaccid myelitis and severe acute respiratory disease. We systematically reviewed the literature on EV-D68 infections globally in the present study to determine the case fatality rate and prevalence of current and past infections. Our results show sporadic deaths in patients with severe acute respiratory EV-D68 infections. Our data also show a low prevalence of EV-D68 in current infections unlike the presence of EV-D68 antibodies (past infections) in almost all individuals of all ages. EV-D68 infections were more prevalent in hospital outbreaks, industrialized countries, children < 5 years, and patients with acute flaccid myelitis and asthma-related diseases. These data highlight the need to strengthen the surveillance of EV-D68 infections.

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.

We tested for enterovirus D68 in fecal samples collected during June–September 2016 from 567 patients with acute flaccid paralysis in 7 West Africa nations. Children

ABSTRACTThe H9N2 influenza virus has become one of the dominant subtypes of influenza virus circulating in poultry, wild birds, and can occasionally cross the mammalian species barrier. Here, we report the first human A/H9N2 in Sub-Saharan Africa. The patient was a child of 16 months' old living in the South-West of Senegal. He had no influenza vaccination history and no other disease history. He had symptoms of fever with an auxiliary temperature of 39.1°C. Respiratory symptoms were an intense cough, runny nose and pulmonary crackles. All eight genome segments belonged to the A/H9N2 AIV subtype and the strain characyerized as of low pathogenicity with a RSSR/GLF amino acids mo­tif. Phylogenetic analysis of both complete HA and NA gene segments showed that the A/H9N2 subtype virus from Senegal belonged to the G1 lineage. This human case highlights the weakness of influenza surveillance in animals and the need for enhanced surveillance using a one-health approach.

In addition to emerging coronaviruses (SARS-CoV, MERS, SARS-CoV-2), there are seasonal human coronaviruses (HCoVs): HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1. With a wide distribution around the world, HCoVs are usually associated with mild respiratory disease. In the elderly, young children and immunocompromised patients, more severe or even fatal respiratory infections may be observed. In Africa, data on seasonal HCoV are scarce. This retrospective study investigated the epidemiology and genetic diversity of seasonal HCoVs during nine consecutive years of influenza-like illness surveillance in Senegal. Nasopharyngeal swabs were collected from ILI outpatients or from SARI hospitalized patients. HCoVs were diagnosed by qRT-PCR and the positive samples were selected for molecular characterization. Among 9337 samples tested for HCoV, 406 (4.3%) were positive: 235 (57.9%) OC43, 102 (25.1%) NL63, 58 (14.3%) 229E and 17 (4.2%) HKU1. The four types circulated during the study period and a peak was noted between November and January. Children under five were the most affected. Co-infections were observed between HCoV types (1.2%) or with other viruses (76.1%). Genetically, HCoVs types showed diversity. The results highlighted that the impact of HCoVs must be taken into account in public health; monitoring them is therefore particularly necessary both in the most sensitive populations and in animals.

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 low—0.8 (95% CI 0.4–1.3) cases per million people in 2021—whereas progress towards measles pre-elimination targets (

The spread of severe acute respiratory syndrome coronavirus 2 began later in Africa than in Asia and Europe. Senegal confirmed its first case of coronavirus disease on March 2, 2020. By March 4, a total of 4 cases had been confirmed, all in patients who traveled from Europe.

Objective: There is extensive evidence that SARS-CoV-2 replicates in the gastrointestinal tract. However, the infectivity of virions in feces is poorly documented. Although the primary mode of transmission is airborne, the risk of transmission from contaminated feces remains to be assessed. Design: The persistence of SARS-CoV-2 (infectivity and RNA) in human and animal feces was evaluated by virus isolation on cell culture and RT-qPCR, respectively. The exposure of golden Syrian hamsters to experimentally contaminated feces through intranasal inoculation has also been tested to assess the fecal-oral transmission route. Results: For periods that are compatible with average intestinal transit, the SARS-CoV-2 genome was noticeably stable in human and animal feces, contrary to the virus infectivity that was reduced in a time- and temperature-dependent manner. In human stools, this reduction was variable depending on the donors. Viral RNA was excreted in the feces of infected hamsters, but exposure of naïve hamsters to feces of infected animals did not lead to any productive infection. Conversely, hamsters could be experimentally infected following exposure to spiked fresh feces. Conclusion: Infection following exposure to naturally contaminated feces has been suspected but has not been established so far. The present work demonstrates that SARS-CoV-2 rapidly lost infectivity in spiked or naturally infected feces. Although the possibility of persistent viral particles in human or animal feces cannot be fully ruled out, SARS-CoV-2 transmission after exposure to contaminated feces is unlikely.

To retrospectively investigate enterovirus D68 circulation in Senegal during the 2014 US outbreak, we retrieved specimens from 708 persons, mostly children, who had acute respiratory symptoms during September–December 2014. Enterovirus D68 was detected in 14 children (2.1%); most cases occurred in October. Phylogenetic analysis revealed that all strains clustered within subclade A1.

Abstract Background Human metapneumovirus (HMPV) is a causal agent of acute respiratory infection, especially in primarily children. At the clinical level, HMPV is associated to several diseases including bronchitis, croup, pneumonia, bronchiolitis, reactive airway disease, chronic obstructive pulmonary disease and asthma exacerbations, specifically in children less than 5 years. Here, we carried out a retrospective pilot study, based on the processing of nasopharyngeal swabs, with a focus on the epidemiology and molecular characteristics of HMPV in Senegal. Methods This retrospective study was conducted from January 2012 to December 2016. Briefly, all outpatients presenting to healthcare sentinel sites were screened for surveillance enrollment and included if they met criteria for ILI. Naso-oropharyngeal swabs were collected from eligible participants. For viral respiratory pathogens detection, including HMPV, the Anyplex™ II RV16 Detection kit was used. A fragment of the hMPV F gene was targeted for sequencing. Results In total, 8209 patients with ILI were enrolled. Half of them (49.7%) were children under 5 years. Fever was the most common symptom followed by cough, and rhinitis. Three hundred eight patients were positive for HMPV (3.75%). 89 (28.9%) were detected as single infection. In co-infection cases, the most common co-infecting viruses were influenza, adenovirus and rhinovirus. HMPV detection rates in the different age groups varied significantly with the children under 5 years group accounting for 71.7% of positive patients. The temporal distribution pattern for HMPV infection showed a clear seasonal pattern with a higher activity during the rainy period (July–September). Phylogenetic analyses revealed that HMPV specimens circulating in Senegal were distributed into the two main genetic lineages, A and B. We also noted a co-circulation of both genetic lineages during the whole study period except in 2014. Conclusion In summary, the present study characterized the recent prevalence, seasonality and genetic diversity of HMPV in a large outpatient population presented with ILI in Senegal between 2012 and 2016. Globally our results show a clear seasonal circulation pattern of HMPV in Senegal. Our findings identified children less than 5 years as more susceptible group to HMPV infection. Molecular studies identified A2, B1 and B2 as the major genotypes circulating.

Polioviruses have been eliminated in many countries; however, the number of acute flaccid paralysis cases has not decreased. Non-polio enteroviruses are passively monitored as part of the polio surveillance program. Previous studies have shown that some enteroviruses do not grow in conventional cell lines used for the isolation of poliovirus according to the WHO guidelines. In order to evaluate the presence of enteroviruses, real-time RT-PCR was performed on Human Rhabdomyosarcoma (RD)-positive and RD-negative stool samples. A total of 310 stool samples, collected from children under the age of 15 years with acute flaccid paralysis in Senegal in 2017, were screened using cell culture and real-time RT-PCR methods. The selected isolates were further characterized using Sanger sequencing and a phylogenetic tree was inferred based on VP1 sequences. Out of the 310 stool samples tested, 89 were positive in real-time RT-PCR. A total of 40 partial VP1 sequences were obtained and the classification analysis showed that 3 (13%), 19 (82.6%), and 1 (4.4%) sequences from 23 RD-positive non-polio enterovirus isolates and 3 (17.6%), 7 (41.1%), and 7 (41.1%) sequences from 17 RD-negative stool samples belonged to the species EV-A, B, and C, respectively. Interestingly, the EV-B sequences from RD-negative stool samples were grouped into three separate phylogenetic clusters. Our data exhibited also a high prevalence of the EV-C species in RD-negative stool samples. An active country-wide surveillance program of non-polio enteroviruses based on direct RT-PCR coupled with sequencing could be important not only for the rapid identification of the involved emergence or re-emergence enteroviruses, but also for the assessment of AFP’s severity associated with non-polio enteroviruses detected in Senegal.

Influenza virus types A and B are responsible for acute viral infections that affect annually 1 billion people, with 290,000 to 650,000 deaths worldwide. In this study, we investigated the circulation of influenza B viruses over a 10-year period (2010–2019). Specimens from patients suspected of influenza infection were collected. Influenza detection was performed following RNA extraction and real-time RT-PCR. Genes coding for hemagglutinin (HA) and neuraminidase (NA) of influenza B viruses were partially sequenced, and phylogenetic analyses were carried out subsequently. During the study period, we received and tested a total of 15,156 specimens. Influenza B virus was detected in 1322 (8.7%) specimens. The mean age of influenza B positive patients was 10.9 years. When compared to reference viruses, HA genes from Senegalese circulating viruses showed deletions in the HA1 region. Phylogenetic analysis highlighted the co-circulation of B/Victoria and B/Yamagata lineage viruses with reassortant viruses. We also noted a clear seasonal pattern of circulation of influenza B viruses in Senegal.

Enterovirus A71 (EV-A71) is a non-polio enterovirus that currently represents a major public health concern worldwide. In Africa, only sporadic cases have been reported. Acute flaccid paralysis and environmental surveillance programs have been widely used as strategies for documenting the circulation of polio and non-polio enteroviruses. To date, little is known about the molecular epidemiology of enterovirus A71 in Africa where resources and diagnostic capacities are limited. To fill this gap in Senegal, a total of 521 non-polio enterovirus isolates collected from both acute flaccid paralysis (AFP) and environmental surveillance (ES) programs between 2013 and 2020 were screened for enterovirus A71 using real-time RT-PCR. Positive isolates were sequenced, and genomic data were analyzed using phylogeny. An overall rate of 1.72% (9/521) of the analyzed isolates tested positive for enterovirus A71. All positive isolates originated from the acute flaccid paralysis cases, and 44.4% (4/9) of them were isolated in 2016. The nine newly characterized sequences obtained in our study included eight complete polyprotein sequences and one partial sequence of the VP1 gene, all belonging to the C genogroup. Seven out of the eight complete polyprotein sequences belonged to the C2 subgenotype, while one of them grouped with previous sequences from the C1 subgenotype. The partial VP1 sequence belonged to the C1 subgenotype. Our data provide not only new insights into the recent molecular epidemiology of enterovirus A71 in Senegal but also point to the crucial need to set up specific surveillance programs targeting non-polio enteroviruses at country or regional levels in Africa for rapid identification emerging or re-emerging enteroviruses and better characterization of public health concerns causing acute flaccid paralysis in children such as enterovirus A71. To estimate the real distribution of EV-A71 in Africa, more sero-epidemiological studies should be promoted, particularly in countries where the virus has already been reported.

The burden of encephalitis and its associated viral etiology is poorly described in Africa. Moreover, neurological manifestations of COVID-19 are increasingly reported in many countries, but less so in Africa. Our prospective study aimed to characterize the main viral etiologies of patients hospitalized for encephalitis in two hospitals in Dakar. From January to December 2021, all adult patients that met the inclusion criteria for clinical infectious encephalitis were enrolled. Cerebrospinal fluids, blood, and nasopharyngeal swabs were taken and tested for 27 viruses. During the study period, 122 patients were enrolled. Viral etiology was confirmed or probable in 27 patients (22.1%), with SARS-CoV-2 (n = 8), HSV-1 (n = 7), HHV-7 (n = 5), and EBV (n = 4) being the most detected viruses. Age groups 40–49 was more likely to be positive for at least one virus with an odds ratio of 7.7. The mortality was high among infected patients, with 11 (41%) deaths notified during hospitalization. Interestingly, SARS-CoV-2 was the most prevalent virus in hospitalized patients presenting with encephalitis. Our results reveal the crucial need to establish a country-wide surveillance of encephalitis in Senegal to estimate the burden of this disease in our population and implement strategies to improve care and reduce mortality.

Dengue virus (DENV) is the most prevalent arboviral threat worldwide. This virus belonging to genus Flavivirus, Flaviviridae family, is responsible for a wide spectrum of clinical manifestations, ranging from asymptomatic or mild febrile illness (dengue fever) to life-threatening infections (severe dengue). Many sporadic cases and outbreaks have occurred in Senegal since 1970. Nevertheless, this article describes a field investigation of suspected dengue cases, between 05 September 2017 and 17 December 2017 made possible by the deployment of a Mobile Biosafety Laboratory (MBS-Lab). Overall, 960 human sera were collected and tested in the field for the presence of viral RNA by real-time RT-PCR. Serotyping, sequencing of complete E gene, and phylogenetic analysis were also performed. Out of 960 suspected cases, 131 were confirmed dengue cases. The majority of confirmed cases were from Louga community. Serotyping revealed two serotypes, Dengue 1 (100/104; 96, 15%) and Dengue 2 (04/104; 3, 84%). Phylogenetic analysis of the sequences obtained indicated that the Dengue 1 strain was closely related to strains isolated, respectively, in Singapore (Asia) in 2013 (KX380803.1) outbreak and it cocirculated with a Dengue 2 strain closely related to strains from a Burkina Faso dengue outbreak in 2016 (KY62776.1). Our results showed the co-circulation of two dengue virus serotypes during a single outbreak in a short time period. This co-circulation highlighted the need to improve surveillance in order to prevent future potential severe dengue cases through antibody-dependent enhancement (ADE). Interestingly, it also proved the reliability and usefulness of the MBS-Lab for expedient outbreak response at the point of need, which allows early cases management.

Background: Past and recent outbreaks have highlighted the vulnerability of humans to infectious diseases, which represent serious economic and health security threats. A paradigm shift in the management of sanitary crises is urgently needed. Based on lessons from the 2014 Ebola outbreak, the Praesens Foundation has developed an all-terrain mobile biosafety laboratory (MBS-Lab) for effective field diagnostics capabilities. Objective: The aim of the study was to train African teams and run a field evaluation of the MBS-Lab, including robustness, technical and operational sustainability, biosafety, connectivity, turn-around times for testing and result delivery. Methods: The MBS-Lab was deployed in Senegal in October 2017 for a six-month field assessment under various ecological conditions and was mobilised during the dengue outbreaks in 2017 and 2018. Results: The MBS-Lab can be considered an off-grid solution that addresses field challenges with regard to working conditions, mobility, deployment, environment and personnel safety. Blood (n = 398) and nasal swab (n = 113) samples were collected from 460 study participants for molecular screening for acute febrile illnesses and respiratory infections. The results showed that malaria (particularly in Kédougou) and upper respiratory tract infections remain problematic. Suspected dengue samples were tested on board during the dengue outbreaks in 2017 (882 tests; 128 confirmed cases) and 2018 (1736 tests; 202 confirmed cases). Conclusion: The MBS-Lab is an innovative solution for outbreak response, even in remote areas. The study demonstrated successful local ownership and community engagement. The MBS-Lab can also be considered an open mobile healthcare platform that offers various opportunities for field-deployable, point-of-care technologies for surveillance programmes.

Abstract Background Acute Respiratory Infections (ARI) are common causes of febrile illnesses in many settings in Senegal. These infections are usually managed presumptively due to lack of appropriate diagnostic tools. This situation, can lead to poor management of febrile illness or antibiotic misuse. In addition, there are limited data on the spectrum of pathogens commonly responsible for these ARI. This study was conducted to explore the pathogens community among patients with acute respiratory infection in a rural area in Senegal. Methods A cross sectional study was conducted from August to December 2015. Children and adult patients attending Keur Socé health post for signs suggestive of acute respiratory infection were enrolled after providing inform consent. Eligible participants were recruited using a consecutive sampling method. Paired nose and throat swabs were collected for pathogen detection. Samples were processed using a multiplex PCR designed to identify 21 pathogens including both virus and bacteria. Results Two hundred and fifty patients participated in the study. Samples positivity rate was evaluated at 95.2% (238/250). Streptococcus pneumoniae was the predominant pathogen (74%) and was present in all months and all age-groups, followed by Staphylococcus aureus (28,8%) and rhinovirus (28,4%). Respiratory syncytial virus (RSV) was detected only among children under 5 years old in August and September while coronavirus was present in all age groups, during the months of October and December. Conclusion This pilot study revealed a diversity of pathogens over the time and across all age groups, highlighting the need for further exploration. A pathogen community approach including both virus and bacteria at a larger scale becomes crucial for a better understanding of transmission dynamics at population level in order to help shape ARI control strategies.

As of today, little data is available on COVID-19 in African countries, where the case management relied mainly on a treatment by association between hydroxychloroquine (HCQ) and azithromycin (AZM). This study aimed to understand the main clinical outcomes of COVID-19 hospitalized patients in Senegal from March to October 20202. We described the clinical characteristics of patients and analysed clinical status (alive and discharged versus hospitalized or died) at 15 days after Isolation and Treatment Centres (ITC) admission among adult patients who received HCQ plus AZM and those who did not receive this combination. A total of 926 patients were included in this analysis. Six hundred seventy-four (674) (72.8%) patients received a combination of HCQ and AZM. Results showed that the proportion of patient discharge at D15 was significantly higher for patients receiving HCQ plus AZM (OR: 1.63, IC 95% (1.09–2.43)). Factors associated with a lower proportion of patients discharged alive were: age ≥ 60 years (OR: 0.55, IC 95% (0.36–0.83)), having of at least one pre-existing disorder (OR: 0.61, IC 95% (0.42–0.90)), and a high clinical risk at admission following NEWS score (OR: 0.49, IC 95% (0.28–0.83)). Few side effects were reported including 2 cases of cardiac rhythmic disorders in the HCQ and AZM group versus 13 in without HCQ + AZM. An improvement of clinical status at 15 days was found for patients exposed to HCQ plus AZM combination.

BACKGROUND:Human adenoviruses (HAdVs) are highly contagious pathogens that are associated with a wide spectrum of human illnesses involving the respiratory tract. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases. METHODOLOGY AND RESULTS:From January 2012 to December 2015 swabs were collected from consenting ILI outpatients. Adenoviral detection is performed by rRT-PCR with the Anyplex™ II RV16 Detection kit (Seegene) and molecular characterization was performed using a partial hexon gene sequence. 6381 samples were collected. More than half of patients (51.7%; 3297/6381) were children of ≤ 5 years. 1967 (30.8%) were positive for HAdV with 1561 (79.4%) found in co-infection with at least one another respiratory virus. The most common co-detections were with influenza viruses (53.1%; 1045/1967), rhinoviruses (30%; 591/1967), enteroviruses (18.5%; 364/1967) and RSV (13.5%; 266/1967). Children under 5 were the most infected group (62.2%; 1224/1967; p

The burden of respiratory syncytial virus (RSV) infection remains poorly defined in Africa. To address this, we carried out a descriptive and retrospective pilot study, with a focus on the epidemiology of RSV in Senegal after 4 years of surveillance.From January 2012 to October 2015 swabs were collected from consenting ILI outpatients. Viral detection was performed using RV16 kit enabling direct subtyping of RSV-A and B. For the molecular characterization of HRSV, the second hypervariable region of the Glycoprotein (G) gene was targeted for sequencing. We enrolled 5338 patients with 2803 children younger than five years of age (52.5%). 610 (11.4%) were positive for RSV infection: 276 (45.2%) were group A infections, 334 (54.8%) were group B infections and 21 (3.4%) were A/B co-infections. RSV detection rate is significantly higher (P < 0.0001) in children below 5 years. We noted that the annual distribution of RSV varied substantially by season and for the predominant subtype. Globally, results show a clear circulation pattern in the second half of each year; between June and September and possibly extended into November. The majority of RSV-A strains from Senegal clustered with strains that were previously assigned NA1 and novel ON1 genotype sequences. RSV-B sequences from Senegal clustered with the BA9 genotype. At the amino acid level, RSV-A strains from Senegal show proximity with the genotype ON1 characterized by a 72 nt insertion in G, resulting in 24 extra amino acids of which 23 are duplications of aa 261-283.Globally our results show a clear circulation pattern of RSV in the second half of each year, between June and September and possibly extending into November, with children under 5 being more susceptible. Molecular studies identified the novel strains ON1 and BA9 as the major genotypes circulating in Senegal between 2012 and 2015.

BackgroundIn Senegal, with the variable routine vaccination coverage, the risk for illness and death from measles still exists as evidenced by the measles epidemic episode in 2009. Since 2002 a laboratory-based surveillance system of measles was established by the Ministry of Health and the Institut Pasteur de Dakar. The present study analysed the data collected over the 10 years inclusive between 2004-2013 in order to define a measles epidemiological profile in Senegal, and we carried out a phylogenetic analysis of measles virus circulating in Senegal over the period 2009-2012.Methodology and resultsA total number of 4580 samples were collected from suspected cases, with the most cases between 2008 and 2010 (2219/4580; 48.4%). The majority of suspected cases are found in children from 4-6 years old (29%). 981 (21.4%) were measles laboratory-confirmed by IgM ELISA. The measles confirmation rate per year is very high during 2009-2010 periods (48.5% for each year). Regarding age groups, the highest measles IgM-positivity rate occurred among persons aged over 15 years with 39.4% (115/292) followed by 2-3 years old age group with 30.4% (323/1062) and 30% (148/494) in children under one year old group. The majority of suspected cases were collected between February and June and paradoxically confirmed cases rates increased from July (77/270; 28.6%) and reached a peak in November with 60% (93/155). Phylogenetic analysis showed that all the 29 sequences from strains that circulated in Senegal between 2009 and 2012 belong to the B3 genotype and they are clustered in B3.1 (2011-2012) and B3.3 (2009-2011) sub-genotypes according to a temporal parameter.ConclusionImprovements in the measles surveillance in Senegal are required and the introduction of oral fluid and FTA cards as an alternative to transportation of sera should be investigated to improve surveillance. The introduction of a national vaccine database including number of doses of measles-containing vaccine will greatly improve efforts to interrupt and ultimately eliminate measles virus transmission in Senegal.

African populations are considered to be particularly vulnerable to fever illnesses, including malaria, and acute respiratory disease, owing to limited resources and overcrowding. However, the overall burden of influenza in this context is poorly defined and incidence data for African countries are scarce. We therefore studied the fever syndrome incidence and more specifically influenza incidence in a cohort of inhabitants of Dielmo and Ndiop in Sokone district, Senegal.Daily febrile-illness data were prospectively obtained from January 2012 to December 2013 from the cohort of the villages of Dielmo and Ndiop, initially dedicated to the study of malaria. Nasopharyngeal swabs were collected from, and malaria diagnosis tests (thick blood smears) carried out on, every febrile individual during clinical visits; reverse transcriptase-polymerase chain reaction was used to identify influenza viruses in the samples. Binomial negative regression analysis was used to study the relationship between the monthly incidence rate and various covariates.In Dielmo and Ndiop, the incidence of malaria has decreased, but fever syndromes remain frequent. Among the 1036 inhabitants included in the cohort, a total of 1,129 episodes of fever were reported. Influenza was present all year round with peaks in October-December 2012 and August 2013. The fever, ILI and influenza incidence density rates differed significantly between age groups. At both sites, the adjusted incidence relative risks for fever syndromes and ILI were significantly higher in the [6-24 months) than other age groups: 7.3 (95%CI: [5.7-9.3]) and 16.1 (95%CI: [11.1-23.3]) respectively. The adjusted incidence relative risk for influenza was significantly higher for the [0-6 months) than other age groups: 9.9 (95%CI: [2.9-33.6]). At both sites, incidence density rates were lowest among adults > = 50 years.In this rural setting in Senegal, influenza was most frequent among the youngest children. Preventive strategies targeting this population should be implemented.

Influenza surveillance in African countries was initially restricted to the identification of circulating strains. In Senegal, the network has recently been enhanced (i) to include epidemiological data from Dakar and other regions and (ii) to extend virological surveillance to other respiratory viruses. Epidemiological data from the sentinel sites is transmitted daily by mobile phone. The data include those for other febrile syndromes similar to influenza-like illnesses (ILI), corresponding to integrated approach. Also, clinical samples are randomly selected and analyzed for influenza and other respiratory viruses. There were 101,640 declared visits to the 11 sentinel sites between week 11-2012 and week 35-2013; 22% of the visits were for fever syndromes and 23% of the cases of fever syndrome were ILI. Influenza viruses were the second most frequent cause of ILI (20%), after adenoviruses (21%) and before rhinoviruses (18%) and enteroviruses (15%). Co-circulation and co-infection were frequent and were responsible for ILI peaks. The first months of implementation of the enhanced surveillance system confirmed that viruses other the influenza make large contributions to influenza-like illnesses. It is therefore important to consider these etiologies in the development of strategies to reduce respiratory infections. More informative tools and research studies are required to assess the burden of respiratory infections in developing countries.