Effi cacy of a Russian-backbone live attenuated infl uenza vaccine among children in Senegal: a randomised, double-blind, placebo-controlled trial

Background Live attenuated infl uenza vaccines have been shown to signifi cantly reduce infl uenza in diverse populations of children, but no effi cacy studies have been done in resource-poor tropical settings. In Senegal, we assessed the effi cacy and safety of a live attenuated infl uenza vaccine based on Russian-derived master donor viruses and licensed as a single dose. Methods In this double-blind, placebo-controlled, parallel group, single-centre trial done near Niakhar, Senegal, generally healthy children aged 2–5 years were randomly allocated (2:1) to receive a single intranasal dose of masked trivalent live attenuated infl uenza vaccine or placebo. The allocation sequence was computer-generated by PATH with block sizes of three. The manufacturer provided vaccine and placebo in coded vials to preserve blinding. Participants were monitored through the predictable infl uenza season in Senegal for adverse events and signs and symptoms of infl uenza using weekly home visits and surveillance in clinics. The primary outcome was symptomatic laboratoryconfi rmed infl uenza caused by any strain and occurring from 15 days post-vaccination to the end of the study. The primary analysis was per protocol. This study is registered with ClinicalTrials.gov, number NCT01854632. Findings Between May 23, and July 1, 2013, 1761 children were randomly assigned, 1174 to receive live attenuated infl uenza vaccine and 587 to receive placebo. The per-protocol set included 1173 vaccinees and 584 placebo recipients followed up to Dec 20, 2013. Symptomatic infl uenza was laboratory-confi rmed in 210 (18%) of 1173 recipients of live attenuated infl uenza vaccine and 105 (18%) of placebo recipients, giving a vaccine effi cacy of 0·0% (95% CI –26·4 to 20·9). Adverse events were balanced between the study groups. Two girls who had received live attenuated infl uenza vaccine died, one due to anasarca 12 days postvaccination and one due to malnutrition 70 days postvaccination. Interpretation Live attenuated infl uenza vaccine was well tolerated in young children in Senegal, but did not provide protection against infl uenza. Further study in such populations, which might experience extended periods of infl uenza circulation, is warranted

Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures

International audienceThe microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the genome identified only 3 of the 22 expected rDNA units. While chromosome end assembly remains a difficult process in most eukaryotic genomes, it is of significant importance for pathogens because these regions encode factors important for virulence and host evasion

Antibiotic susceptibility profile of Streptococcus pneumoniae isolated from acute respiratory infection in Dakar: a cross sectional study

Streptococcus pneumoniae is a pathogen causing pneumonia, meningitis, otitis and bacteraemia. Nowadays, S. pneumoniae is developing antibacterial resistance, particularly for those with reduced susceptibility to penicillin. The objective of this study was to assess the susceptibility profile of S. pneumoniae strains isolated from acute respiratory infections (ARIs) in children younger than 5 years of age in Dakar, Senegal. S. pneumoniae strains were isolated from broncho-alveolar lavages (BALs), nasopharyngeal swabs, and middle ear secretion from children in the Paediatric Department of Abass Ndao University Teaching Hospital and Paediatric Department of Roi Baudouin Hospital in Dakar, Senegal. The strains were cultivated on Columbia agar supplemented with 5% of horse blood and gentamicin (6 mg/L). Antibiotic susceptibility testing was performed using E-test method. A total of 34 strains of S. pneumoniae were isolated and identified in this study, among them 7 strains (20.58%) showed penicillin-resistance. Antibiotics such as amoxicillin/clavulanic acid (MIC90=0.036 μg/mL), cefuroxim (MIC90=0.38 μg/mL), cefixim (MIC90=1.5 μg/mL), as well as macrolides (azithromycin MIC90=1.5 μg/mL, clarithromycin MIC90=0.125 μg/mL) and fluoroquinolone (levofloxacin MIC90=1 μg/mL, ofloxacin MIC90=2 μg/mL) were mostly active. However, all S. pneumoniae strains were resistant to sulfamethoxazole/trimethoprim (MIC90: 32 μg/mL). Except of S. pneumoniae strains penicillin-resistance or reduced susceptibility, most strains were susceptible to β-lactams antibiotics commonly used in ARI treatment. Continuous surveillance of antimicrobial resistance patterns of pneumococcus strains is still crucial for effective control of ARIs in children

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

Crimean-Congo Hemorrhagic Fever, Mauritania

A hospital outbreak of CCHF in Mauritania alerted authorities to sporadic cases occurring in the community; in all, 38 persons were infected

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

Results from the second WHO external quality assessment for the molecular detection of respiratory syncytial virus, 2019-2020

BACKGROUND: External quality assessments (EQAs) for the molecular detection of human respiratory syncytial virus (RSV) are necessary to ensure the standardisation of reliable results. The Phase II, 2019-2020 World Health Organization (WHO) RSV EQA included 28 laboratories in 26 countries. The EQA panel evaluated performance in the molecular detection and subtyping of RSV-A and RSV-B. This manuscript describes the preparation, distribution, and analysis of the 2019-2020 WHO RSV EQA. METHODS: Panel isolates underwent whole genome sequencing and in silico primer matching. The final panel included nine contemporary, one historical virus and two negative controls. The EQA panel was manufactured and distributed by the UK National External Quality Assessment Service (UK NEQAS). National laboratories used WHO reference assays developed by the United States Centers for Disease Control and Prevention, an RSV subtyping assay developed by the Victorian Infectious Diseases Reference Laboratory (Australia), or other in-house or commercial assays already in use at their laboratories. RESULTS: An in silico analysis of isolates showed a good match to assay primer/probes. The panel was distributed to 28 laboratories. Isolates were correctly identified in 98% of samples for detection and 99.6% for subtyping. CONCLUSIONS: The WHO RSV EQA 2019-2020 showed that laboratories performed at high standards. Updating the composition of RSV molecular EQAs with contemporary strains to ensure representation of circulating strains, and ensuring primer matching with EQA panel viruses, is advantageous in assessing diagnostic competencies of laboratories. Ongoing EQAs are recommended because of continued evolution of mismatches between current circulating strains and existing primer sets

Data Influenza Burden

Complete data used for the articl

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