Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks

These authors contributed equally: Alpha K. Keita, Fara R. Koundouno, Martin Faye, Ariane Düx, Julia Hinzmann.International audienc

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

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

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

Squamous Cell Carcinoma in African Children with Xeroderma Pigmentosum: Three Case Reports

Introduction: Xeroderma pigmentosum is a rare autosomal recessive genetic disease. This disease predisposes patients to early-onset skin cancers, particularly squamous cell carcinoma. Here, we report 3 pediatric cases, including 2 deaths. Observation: The subjects included 2 boys and 1 girl with skin type VI. All subjects were from consanguineous marriages, and the average age was 7.6 years. The patients all had ulcerative budding tumor lesions in the cephalic region, and the mean disease duration was 18 months. In all 3 cases, the diagnosis of xeroderma pigmentosum was made before the poikilodermal appearance of sun-exposed areas and photophobia. Neurological-type mental retardation was noted in 1 case. Histology confirmed squamous cell carcinoma in all 3 cases. The evolutions were marked by the death of 2 children (cases 1 and 3). In one case, the outcome was favorable following cancer excision and subsequent chemotherapy with adjuvant radiotherapy. Conclusion: Squamous cell carcinoma is a serious complication related to xeroderma pigmentosum in Sub-Saharan Africa. Prevention is based on the early diagnosis of xeroderma pigmentosum, black skin photoprotection, screening and early treatment of lesions, and genetic counseling

High and Rapid Increase in Seroprevalence for SARS-CoV-2 in Conakry, Guinea: Results From 3 Successive Cross-Sectional Surveys (ANRS COV16-ARIACOV)

Abstract We conducted 3 successive seroprevalence surveys, 3 months apart, using multistage cluster sampling to measure the extent and dynamics of the severe acute respiratory syndrome coronavirus 2 epidemic in Conakry, the capital city of Guinea. Seroprevalence increased from 17.3% (95% CI, 12.4%–23.8%) in December 2020 during the first survey (S1) to 28.9% (95% CI, 25.6%–32.4%) in March/April 2021 (S2), then to 42.4% (95% CI, 39.5%–45.3%) in June 2021 (S3). This significant overall trend of increasing seroprevalence (P &amp;lt; .0001) was also significant in every age class, illustrating a sustained transmission within the whole community. These data may contribute to defining cost-effective response strategies.</jats:p

Low prevalence of lipodystrophy in HIV-infected Senegalese children on long-term antiretroviral treatment: the ANRS 12279 MAGGSEN Pediatric Cohort Study

Abstract Background The long-term benefits of antiretroviral treatment (ART) are associated with metabolic complications, especially lipodystrophy, which has been well described among HIV-infected adults and children on ART in developed settings. Specifically, stavudine, and to a lesser extent zidovudine and protease inhibitors (PI), have been consistently implicated in the development of lipodystrophy. In 2006, following advice from the WHO, Senegal began phasing out stavudine from first-line ART. The objectives of this cross-sectional analysis are to assess and identify risk factors affecting the prevalence of lipodystrophy in Senegalese children and adolescents on long-term ART participating in a cohort study. Methods Lipodystrophy was clinically assessed in two- to 18-year-old children on ART for at least six months and with no concurrent severe acute malnutrition. Risk factors for lipodystrophy were identified using stepwise multivariable logistic regression. Explanatory variables included clinical and personal data, immunovirologic status, and therapeutic history. Results Overall, 254 children were assessed for lipodystrophy. The median age was 10.9 years (IQR: 8.1–14.2) and the median duration on ART was 54 months (32–84). Only 18% had been previously treated with stavudine, with a median treatment duration of 8 months (5–25). Ongoing treatment included 76% of children receiving zidovudine (median duration of 48 months (26–74)) and 27% receiving PI (lopinavir/ritonavir; median duration of 49 months (23–59)). Mild signs of lipodystrophy were observed in 33 children (13%): 28 with lipoatrophy, 4 with lipohypertrophy and one with combined type. Boys were more likely to present with lipoatrophy than girls (aOR: 4.3, 95% CI: 1.6–11.7). Children previously treated with stavudine for ≥1 year had a greater risk for lipoatrophy than those never exposed (3.8, 1.0–14.0), although the association was weak. There was no association between lipodystrophy and age or current or cumulative treatment with lopinavir/ritonavir or zidovudine. Conclusions We report low prevalence of mild lipodystrophy in children and adolescents on long-term ART receiving a stavudine-sparing regimen. These findings are reassuring for clinicians in low-income settings where zidovudine is massively prescribed and lopinavir/ritonavir is the only widely available PI. Trial registration ClinicalTrials.gov identifier: NCT01771562 (registration date: 01/18/2013)

Ebola virus circulation in a non-epidemic Guinean rural area: a mixed-method approach to assessing endemicity

International audienceObjectivesThis study aimed to investigate the prevalence of orthoebolavirus antibodies in Madina Oula, a non-epidemic rural area in Guinea, in 2022.(...)ConclusionSerological data in a region unaffected by recent Ebola outbreaks indicate possible orthoebolavirus endemicity, emphasizing the need for preparedness against known or novel orthoebolaviruses with potential cross-reactivity