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

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Aspects epidemiologiques, cliniques et therapeutiques de la cryptorchidie chez l’enfant: analyse de 123 observations

Buts: Le but de ce travail était de décrire les aspects épidémiologiques, cliniques et thérapeutiques de la cryptorchidie dans le service de Chirurgie Pédiatrique en milieu africain. Patients et méthodes: Il s’agissait d’une étude rétrospective sur 123 cas de cryptorchidie colligés du 1er Mai 2000 au 30 Avril 2008 au service de Chirurgie Pédiatrique du CHU Aristide Le Dantec de Dakar. Les paramètres étudiés étaient la fréquence par rapport aux autres pathologies du canal inguinal, l’âge, les motifs de consultation, l’examen physique, le constat opératoire, la durée d’hospitalisation et les suites opératoires en particulier les résultats cosmétiques et morphologiques. Résultats: La cryptorchidie était la troisième anomalie congénitale du canal inguinal après les hernies (1537 cas) et les hydrocèles (327 cas). L’âge moyen de nos patients était de 5,7 ans. La vacuité scrotal était le principal motif de consultation chez 105 patients (84,5%). La cryptorchidie était unilateral chez 111 patients (90,5%). Dans 34,5% des cas seulement le testicule était palpable. L’exploration chirurgicale avait retrouvé dans 93,43% des cas un testicule en position inguinale et dans 2,5% des cas un testicule en position abdominale. Un sac herniaire a été retrouvé dans 84,7% des cas. La connexion épididymo-testiculaire était mauvaise dans 43,1% des cas. L’abaissement « in dartos » a été realisé dans 97,5% des cas. La durée d’hospitalisation était en moyenne de 14,5 heures. Les suites opératoires étaient simples dans 87,8% des cas. Onze cas de complications ont été notés dont 5 cas de suppuration, 2 cas d’hématome du cordon, 2 cas d’atrophie testiculaire et 2 cas de récidive. Conclusion: La cryptorchidie est vue à un âge tardif dans notre contexte rendant l’intervention immédiate. A cet âge, il existe de possibles lésions dysplasiques justifiant une surveillance prolongée jusqu’à la puberté où un spermogramme sera réalisé

Hernie diaphragmatique droite traumatique chez l’enfant: difficultés diagnostiques

La hernie diaphragmatique droite traumatique est rare chez l’enfant. Elle peut être difficile à mettre en évidence en phase aiguë, car ses signessont peu spécifiques et en particulier dans le cadre d’un polytraumatisme. La nécessité d’un indice élevé de suspicion est soulignée dans lalittérature mais il n’existe pas encore de consensus. Nous rapportons deux cas survenus à la suite d’une contusion thoracoabdominale et exposons les difficultés rencontrées dans notre contexte pour établir un diagnostic précoce. Mots clés : hernie diaphragmatique droite – traumatisme – enfant – diagnostic. Right traumatic diaphragmatic hernia is rare in children. It can be difficult to identify in the acute phase, because its signs are not specific and particularly in the context of a poly trauma. The need for a high index of suspicion is emphasized in the literature but there is no consensusyet. We report two cases occurring after blunt thoracoabdominal trauma and expose the difficulties encountered in our context for early diagnosisKey words : right diaphragmatic hernia -trauma - children - diagnosis

Surveillance of Viral Encephalitis in the Context of COVID-19: A One-Year Observational Study among Hospitalized Patients in Dakar, Senegal

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

Hepatitis B prevention and treatment needs in women in Senegal (ANRS 12356 AmBASS survey)

Abstract Background Although mother-to-child transmission (MTCT) of hepatitis B virus (HBV) is prevalent in West Africa, epidemiological data on HBV infection in women remain scarce. We studied i) hepatitis B surface antigen (HBsAg) prevalence and its correlates, ii) HBV screening history and serological status awareness, iii) MTCT risk and treatment needs in Senegalese women. Methods A cross-sectional population-based serosurvey for HBsAg positivity was conducted in 2018–2019 in the rural area of Niakhar (Fatick region, Senegal). Participants were offered home-based HBV screening and answered face-to-face questionnaires. HBsAg-positive participants underwent clinical and biological assessments. Data were weighted and calibrated to be representative of the area’s population. Logistic regression models helped identify factors associated with HBsAg-positivity in adult women (> 15 years old). Results HBsAg prevalence in adult women was 9.2% [95% confidence interval: 7.0–11.4]. Factors associated with HBsAg-positivity were being 15–49 years old (ref: ≥ 50), living in a household with > 2 other HBsAg-positive members, and knowing someone with liver disease. Only 1.6% of women had already been tested for HBV; no one who tested HBsAg positive was already aware of their serological status. In women 15–49 years old, 5% risked MTCT and none were eligible for long-term antiviral treatment. Conclusions Adult women have a high HBsAg prevalence but a low MTCT risk. Low rates of HBV screening and serological status awareness argue for the adoption of systematic screening during pregnancy using free and rapid diagnostic tests. Additionally, screening household members of HBsAg-positive women may greatly improve the cascade of care in rural Senegal. Trial registration ClinicalTrials.gov identifier (NCT number): NCT03215732

Hepatitis B prevention and treatment needs in women in Senegal (ANRS 12356 AmBASS survey)

International audienceBackground Although mother-to-child transmission (MTCT) of hepatitis B virus (HBV) is prevalent in West Africa, epidemiological data on HBV infection in women remain scarce. We studied i) hepatitis B surface antigen (HBsAg) prevalence and its correlates, ii) HBV screening history and serological status awareness, iii) MTCT risk and treatment needs in Senegalese women. Methods A cross-sectional population-based serosurvey for HBsAg positivity was conducted in 2018–2019 in the rural area of Niakhar (Fatick region, Senegal). Participants were offered home-based HBV screening and answered face-to-face questionnaires. HBsAg-positive participants underwent clinical and biological assessments. Data were weighted and calibrated to be representative of the area’s population. Logistic regression models helped identify factors associated with HBsAg-positivity in adult women (> 15 years old). Results HBsAg prevalence in adult women was 9.2% [95% confidence interval: 7.0–11.4]. Factors associated with HBsAg-positivity were being 15–49 years old (ref: ≥ 50), living in a household with > 2 other HBsAg-positive members, and knowing someone with liver disease. Only 1.6% of women had already been tested for HBV; no one who tested HBsAg positive was already aware of their serological status. In women 15–49 years old, 5% risked MTCT and none were eligible for long-term antiviral treatment. Conclusions Adult women have a high HBsAg prevalence but a low MTCT risk. Low rates of HBV screening and serological status awareness argue for the adoption of systematic screening during pregnancy using free and rapid diagnostic tests. Additionally, screening household members of HBsAg-positive women may greatly improve the cascade of care in rural Senegal. Trial registration ClinicalTrials.gov identifier (NCT number): NCT03215732

Sibling status, home birth, tattoos and stitches are risk factors for chronic hepatitis B virus infection in Senegalese children: A cross‐sectional survey

International audienceSub-Saharan Africa's hepatitis B virus (HBV) burden is primarily due to infection in infancy. However, data on chronic HBV infection prevalence and associated risk factors in children born post-HBV vaccination introduction are scarce. We estimated hepatitis B surface antigen (HBsAg) prevalence and risk factors in Senegalese children born during the HBV vaccination era. In 2018-2019, a community-based cross-sectional survey was conducted in Senegal among children born between 2004 and 2015 (ie after the three-dose HBV vaccine series was introduced (2004) but before the birth dose's introduction (2016)). HBsAg-positive children were identified using dried blood spots. A standardized questionnaire collected socioeconomic information. Data were age-sex weighted and calibrated to be representative of children living in the study area. Risk factors associated with HBsAg positivity were identified using negative binomial regression. Among 1,327 children, 17 were HBsAg-positive (prevalence = 1.23% (95% confidence interval [CI] 0.61-1.85)). Older age (adjusted incidence-rate ratio [aIRR] 1.31 per one-year increase, 95% CI 1.10-1.57), home vs healthcare facility delivery (aIRR 3.55, 95% CI 1.39-9.02), stitches (lifetime) (aIRR 4.79; 95% CI 1.84-12.39), tattoos (aIRR 8.97, 95% CI 1.01-79.11) and having an HBsAg-positive sibling with the same mother (aIRR 3.05, 95% CI 1.09-8.57) were all independently associated with HBsAg positivity. The low HBsAg prevalence highlights the success of the Senegalese HBV vaccination program. To further reduce HBV acquisition in children, high-risk groups, including pregnant women and siblings of HBsAg-positive individuals, must be screened. Vital HBV infection prevention measures include promoting delivery in healthcare facilities, and increasing awareness of prevention and control procedures