Measles and Rubella Incidence and Molecular Epidemiology in Senegal: Temporal and Regional Trends during Twelve Years of National Surveillance, 2010-2021.

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 (<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

Rift Valley Fever Outbreak with East-Central African Virus Lineage in Mauritania, 2003

Phylogenetic studies demonstrated that outbreak strains belonged to the East-Central African lineage

Upper respiratory infections in a rural area with reduced malaria transmission in Senegal: a pathogens community study

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

Epidemiology and Molecular Characterization of Human Respiratory Syncytial Virus in Senegal after Four Consecutive Years of Surveillance, 2012-2015.

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

Antibiotic resistance of bacteria responsible of acute respiratory tract infections in children

Background and aims. Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are the most common causative agents of acute respiratory tract infections (RTIs). The objective of this study was to assess their susceptibility to several antibiotics.Materials and methods. A total of 58 strains (16 S. pneumoniae, 19 H. influenzae and 23 M. catarrhalis) were isolated from samples collected in two paediatric centres, and their susceptibility to commonly used antibiotics tested by E-test. Results. Among H. influenzae isolates, 10.5% were resistant to ampicillin (all β-lactamase-positive), and 88.9% were susceptible to cefaclor. High β-lactam resistance rates (penicillin: 31.3% and cephalosporins: 18.7 to 31.3%) had been observed among S. pneumonia strains. Only 50% of isolates were susceptible to azithromycine. 91.3% of M. catarrhalis isolates β-lactamases producers were resistant to ampicillin while susceptible to the most tested antibiotics. Conclusions. Except M. catarrhalis β-lactamases producing strains, frequency of antibiotic resistance was mainly observed among S. pneumoniae, and to a lesser extent among H. influenzae clinical isolates, suggesting the need for continuous surveillance of antimicrobial resistance patterns in the management of RTIs

Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses.

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 <0.05). We noted that HAdV was detected throughout the year at a high level with detection peaks of different amplitudes without any clear seasonality. Phylogenetic analysis revealed species HAdV-C in majority, species HAdV-B and one HAdV- 4 genome type. The 9 HAdV-B species like strains from Senegal grouped with genome types HAdV-7, HAdV-55 and HAdV-11 as shown by a phylogenetic branch with a high bootstrap value of (88%). CONCLUSION:In conclusion, the results of the present study suggest strong year-round HAdV activity in Senegal, especially in children up to 5 years of age. Molecular studies revealed that the dominant species in circulation in patients with ILI appears to be HAdV-C and HAdV-B species. The circulation of though HAdV-7 and HAdV-55 genome types is of note as these serotypes are recognized causes of more severe and even fatal acute respiratory infections

Epidemiology of Non-SARS-CoV2 Human Coronaviruses (HCoVs) in People Presenting with Influenza-like Illness (ILI) or Severe Acute Respiratory Infections (SARI) in Senegal from 2012 to 2020

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

Monthly distribution of RSV A and RSV B infections in patients with ILI in Senegal, over the years of the study (2012–2015).

<p>In green is represented the rainfall during the period of study. Temperatures (mean values of the maxima and the minima ones per month) are also represented.</p