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

Mass measles vaccination in urban Burkina Faso, 1998

OBJECTIVE: To assess the impact of the National Immunization Days (NIDs) on measles vaccine coverage in Burkina Faso in 1998. METHODS: During the week after the campaign, in which measles vaccine was offered to children aged 9-59 months in six cities regardless of vaccination history, a cluster survey was conducted in Ouagadougou and Bobo Dioulasso, the country?s two largest cities. Interviewers visited the parents of 1267 children aged up to 59 months and examined vaccination cards. We analysed the data using cluster sample methodology for the 1041 children who were aged 9-59 months. FINDINGS: A total of 604 (57%) children had received routine measles vaccination prior to the campaign, and 823 (79%) were vaccinated during the NIDs. Among those who had previously had a routine vaccination, 484 (81%) were revaccinated during the NIDs. Among those not previously vaccinated, 339 (78%) received one dose during the NIDs. After the campaign, 943 (91%) children had received at least one dose of measles vaccine. Better socioeconomic status was associated with a higher chance of having been vaccinated routinely, but it was not associated with NID coverage. CONCLUSION: The mass campaign enabled a substantial increase in measles vaccine coverage to be made because it reached a high proportion of children who were difficult to reach through routine methods

Incidence et risque résiduel de transmission des virus de l’hépatite B et C par transfusion sanguine à Bobo-Dioulasso (Burkina Faso) : Étude de cohorte

l’objectif de notre étude était d’évaluer l’incidence et le risque de  transmission des virus des hépatites B et C par transfusion. nous avons conduit une étude de cohorte rétrospective de janvier 2009 à décembre 2014 portant sur les dons de 12 969 donneurs bénévoles et réguliers de sang au Centre Régional de Transfusion Sanguine de Bobo-dioulasso. le diagnostic de l’infection par le VhC ou le VhB était obtenu par technique eliSa devant la présence dans le sérum des anticorps anti-VhC pour le VhC ou de l’antigène hBs pour ce qui est du VhB. le taux d’incidence du VhB était de 2,16 pour 100 donneurs-années et celui du VhC était de 2,59 pour 100 donneurs-années. le risque de transmission du VhB était estimé à 1 pour 302 dons et celui du VhC à 1 pour 213 dons. un renforcement de la sélection des donneurs de sang s’avère indispensable devant un risque élevé de transmission des virus de l’hépatite B et/ou C par don de sang provenant des donneurs bénévoles réguliers.Mots-clés : incidence, Risque résiduel, hépatite B/C, don de sang,  Bobo-dioulasso.The objective of our study was to assess the incidence and risk of   transmission of hepatitis B and C viruses by transfusion. we conducted a retrospective cohort study from January 2009 to december 2014 on the donations of 12,969 volunteer and regular blood donors to the  Bobo-dioulasso Regional Blood Transfusion Center. The diagnosis of infection with hCV or hBV was obtained by eliSa in the presence of serum hCV antibodies for hCV or hBs antigen for hBV. The incidence rate of hBV was 2.16 per 100 years and hCV was 2.59 per 100 years. The risk of transmission of hBV was estimated at 1 for 302 donations and for hCV at 1 for 213 donations. Strengthening the selection of blood donors is essential in view of the high risk of transmission of hepatitis B and / or C viruses through the donation of blood from regular voluntary donors.Keywords: incidence, Residual risk, hepatitis B / C, Blood donation,  Bobo-dioulasso

Global Retinoblastoma Presentation and Analysis by National Income Level

This cross-sectional analysis reports the retinoblastoma stage at diagnosis across the world during a single year, investigates associations between clinical variables and national income level, and investigates risk factors for advanced disease at diagnosis. Key PointsQuestionIs the income level of a country of residence associated with the clinical stage of presentation of patients with retinoblastoma? FindingsIn this cross-sectional analysis that included 4351 patients with newly diagnosed retinoblastoma, approximately half of all new retinoblastoma cases worldwide in 2017, 49.1\% of patients from low-income countries had extraocular tumor at time of diagnosis compared with 1.5\% of patients from high-income countries. MeaningThe clinical stage of presentation of retinoblastoma, which has a major influence on survival, significantly differs among patients from low-income and high-income countries, which may warrant intervention on national and international levels. ImportanceEarly diagnosis of retinoblastoma, the most common intraocular cancer, can save both a child's life and vision. However, anecdotal evidence suggests that many children across the world are diagnosed late. To our knowledge, the clinical presentation of retinoblastoma has never been assessed on a global scale. ObjectivesTo report the retinoblastoma stage at diagnosis in patients across the world during a single year, to investigate associations between clinical variables and national income level, and to investigate risk factors for advanced disease at diagnosis. Design, Setting, and ParticipantsA total of 278 retinoblastoma treatment centers were recruited from June 2017 through December 2018 to participate in a cross-sectional analysis of treatment-naive patients with retinoblastoma who were diagnosed in 2017. Main Outcomes and MeasuresAge at presentation, proportion of familial history of retinoblastoma, and tumor stage and metastasis. ResultsThe cohort included 4351 new patients from 153 countries; the median age at diagnosis was 30.5 (interquartile range, 18.3-45.9) months, and 1976 patients (45.4\%) were female. Most patients (n=3685 {[}84.7\%]) were from low- and middle-income countries (LMICs). Globally, the most common indication for referral was leukocoria (n=2638 {[}62.8\%]), followed by strabismus (n=429 {[}10.2\%]) and proptosis (n=309 {[}7.4\%]). Patients from high-income countries (HICs) were diagnosed at a median age of 14.1 months, with 656 of 666 (98.5\%) patients having intraocular retinoblastoma and 2 (0.3\%) having metastasis. Patients from low-income countries were diagnosed at a median age of 30.5 months, with 256 of 521 (49.1\%) having extraocular retinoblastoma and 94 of 498 (18.9\%) having metastasis. Lower national income level was associated with older presentation age, higher proportion of locally advanced disease and distant metastasis, and smaller proportion of familial history of retinoblastoma. Advanced disease at diagnosis was more common in LMICs even after adjusting for age (odds ratio for low-income countries vs upper-middle-income countries and HICs, 17.92 {[}95\% CI, 12.94-24.80], and for lower-middle-income countries vs upper-middle-income countries and HICs, 5.74 {[}95\% CI, 4.30-7.68]). Conclusions and RelevanceThis study is estimated to have included more than half of all new retinoblastoma cases worldwide in 2017. Children from LMICs, where the main global retinoblastoma burden lies, presented at an older age with more advanced disease and demonstrated a smaller proportion of familial history of retinoblastoma, likely because many do not reach a childbearing age. Given that retinoblastoma is curable, these data are concerning and mandate intervention at national and international levels. Further studies are needed to investigate factors, other than age at presentation, that may be associated with advanced disease in LMICs