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

Attitudes of health care providers regarding female genital mutilation and its medicalization in Guinea.

BackgroundGuinea has a high prevalence of female genital mutilation (FGM) (95%) and it is a major concern affecting the health and the welfare of women and girls. Population-based surveys suggest that health care providers are implicated in carrying out the practice (medicalization). To understand the attitudes of health care providers related to FGM and its medicalization as well as the potential role of the health sector in addressing this practice, a study was conducted in Guinea to inform the development of an intervention for the health sector to prevent and respond to this harmful practice.MethodologyFormative research was conducted using a mixed-methods approach, including qualitative in-depth interviews with health care providers and other key informants as well as questionnaires with 150 health care providers. Data collection was carried out in the provinces of Faranah and Labé and in the capital, Conakry.ResultsThe majority of health care providers participating in this study were opposed to FGM and its medicalization. Survey data showed that 94% believed that it was a serious problem; 89% felt that it violated the rights of girls and women and 81% supported criminalization. However, within the health sector, there is no enforcement or accountability to the national law banning the practice. Despite opposition to the practice, many (38%) felt that FGM limited promiscuity and 7% believed that it was a good practice.ConclusionHealth care providers could have an important role in communicating with patients and passing on prevention messages that can contribute to the abandonment of the practice. Understanding their beliefs is a key step in developing these approaches

Impliquer le secteur de la santé dans la prévention et la prise en charge des mutilations génitales féminines: résultats d'une recherche formative en Guinée

Background: Despite efforts to reduce the burden of female genital mutilation (FGM) in Guinea, the practice remains prevalent, and health care providers are increasingly being implicated in its medicalization. This formative study was conducted to understand the factors that facilitate or impede the health sector in providing FGM prevention and care services to inform the development of health sector-based interventions. Methods: Between April and May 2018, a mixed methods formative study was carried out using a rapid assessment methodology in three regions of Guinea—Faranah, Labe and Conakry. A structured questionnaire was completed by one hundred and fifty health care providers of different cadres and 37 semi-structured interviews were conducted with health care providers, women seeking services at public health clinics and key stakeholders, including health systems managers, heads of professional associations and schools of nursing, midwifery, and medicine as well as representatives of the Ministry of Health. Eleven focus group discussions were conducted with female and male community members. Results: This study revealed health systems factors, attitudinal factors held by health care providers, and other factors, that may not only promote FGM medicalization but also impede a comprehensive health sector response. Our findings confirm that there is currently no standardized pre-service training on how to assess, document and manage complications of FGM nor are there interventions to promote the prevention of the practice within the health sector. This research also demonstrates the deeply held beliefs of health care providers and community members that perpetuate this practice, and which need to be addressed as part of a health sector approach to FGM prevention. Conclusion: As integral members of FGM practicing communities, health care providers understand community beliefs and norms, making them potential change agents. The health sector can support them by incorporating FGM content into their clinical training, ensuring accountability to legal and policy standards, and promoting FGM abandonment as part of a multi-sectoral approach. The findings from this formative research have informed the development of a health sector intervention that is being field tested as part of a multi-country implementation research study in Guinea, Kenya, and Somalia.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Women’s report of mistreatment during facility-based childbirth: validity and reliability of community survey measures

Accountability for mistreatment during facility-based childbirth requires valid tools to measure and compare birth experiences. We analyse the WHO 'How women are treated during facility-based childbirth' community survey to test whether items mapping the typology of mistreatment function as scales and to create brief item sets to capture mistreatment by domain. The cross-sectional community survey was conducted at up to 8 weeks post partum among women giving birth at hospitals in Ghana, Guinea, Myanmar and Nigeria. The survey contained items assessing physical abuse, verbal abuse, stigma, failure to meet professional standards, poor rapport with healthcare workers, and health system conditions and constraints. For all domains except stigma, we applied item-response theory to assess item fit and correlation within domain. We tested shortened sets of survey items for sensitivity in detecting mistreatment by domain. Where items show concordance and scale reliability ≥0.60, we assessed convergent validity with dissatisfaction with care and agreement of scale scores between brief and full versions. 2672 women answered over 70 items on mistreatment during childbirth. Reliability exceeded 0.60 in all countries for items on poor rapport with healthcare workers and in three countries for items on failure to meet professional standards; brief scales generally showed high agreement with longer versions and correlation with dissatisfaction. Brief item sets were ≥85% sensitive in detecting mistreatment in each country, over 90% for domains of physical abuse and health system conditions and constraints. Brief scales to measure two domains of mistreatment are largely comparable with longer versions and can be informative for these four distinct settings. Brief item sets efficiently captured prevalence of mistreatment in the five domains analysed; stigma items can be used and adapted in full. Item sets are suitable for confirmation by context and implementation to increase accountability and inform efforts to eliminate mistreatment during childbirth

Highly targeted cholera vaccination campaigns in urban setting are feasible: The experience in Kalemie, Democratic Republic of Congo.

Oral cholera vaccines are primarily recommended by the World Health Organization for cholera control in endemic countries. However, the number of cholera vaccines currently produced is very limited and examples of OCV use in endemic countries, and especially in urban settings, are scarce. A vaccination campaign was organized by Médecins Sans Frontières and the Ministry of Health in a highly endemic area in the Democratic Republic of Congo. This study aims to describe the vaccine coverage achieved with this highly targeted vaccination campaign and the acceptability among the vaccinated communities.We performed a cross-sectional survey using random spatial sampling. The study population included individuals one year old and above, eligible for vaccination, and residing in the areas targeted for vaccination in the city of Kalemie. Data sources were household interviews with verification by vaccination card. In total 2,488 people were included in the survey. Overall, 81.9% (95%CI: 77.9-85.3) of the target population received at least one dose of vaccine. The vaccine coverage with two doses was 67.2% (95%CI: 61.9-72.0) among the target population. The vaccine coverage was higher during the first round (74.0, 95%CI: 69.3-78.3) than during the second round of vaccination (69.1%, 95%CI: 63.9-74.0). Vaccination coverage was lower in male adults. The main reason for non-vaccination was to be absent during the campaign. No severe adverse events were notified during the interviews.Cholera vaccination campaigns using highly targeted strategies are feasible in urban settings. High vaccination coverage can be obtained using door to door vaccination. However, alternative strategies should be considered to reach non-vaccinated populations like male adults and also in order to improve the efficiency of the interventions

Vaccinated and non-vaccinated health areas of the city of Kalemie, Democratic Republic of Congo (base map: Stamen Design).

<p>Vaccinated and non-vaccinated health areas of the city of Kalemie, Democratic Republic of Congo (base map: Stamen Design).</p

Vaccination coverage by age in the areas targeted for vaccination in 2014.

<p>Vaccination coverage by age in the areas targeted for vaccination in 2014.</p

Reasons for non-vaccination in the 2014 campaign (strata 1).

<p>Reasons for non-vaccination in the 2014 campaign (strata 1).</p

Spatial distribution of the vaccination coverage in Kalemie.

<p>Spatial distribution of the vaccination coverage in Kalemie.</p

Correction: Experimental Treatment with Favipiravir for Ebola Virus Disease (the JIKI Trial): A Historically Controlled, Single-Arm Proof-of-Concept Trial in Guinea.

[This corrects the article DOI: 10.1371/journal.pmed.1001967.]