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

Failing the rights: sexual vulnerability, access to services and barriers to contraceptives among adolescents in Narok County, Kenya

Purpose: Around one in five girls in Kenya, aged 15 to 19 years old are either pregnant or have given birth. Of 47 counties, adolescent pregnancy is highest in Narok, where about 40% of girls aged 15 to 19 years old have begun childbearing. This study aims to explore drivers to sexual activity, access to sexual and reproductive health (SRH) services and barriers to contraceptive use among adolescents in Narok County, Kenya to inform the design of SRH interventions and safeguard young people’s rights to sexual health. Design/methodology/approach: A cross-sectional mixed methods study was conducted in December 2019. Quantitative data were collected through structured questionnaires among girls aged 15 to 19 years old who were either pregnant or had given birth and those who had not and boys aged 15 to 19 years old. Qualitative data were collected through focus group discussions with adolescent girls and boys and through structured key informant interviews with parents, community leaders and health workers. Findings: The mean age at first sexual intercourse for both genders was 15 years. While the majority of girls and boys knew where to access SRH services, few used contraception during their last sexual activity. There was no significant difference in the condom or other contraceptive methods use between girls who had begun child bearing and those who had not (p = 0.549 and p = 0.563, respectively). Key drivers for sexual activity among young people were poverty and peer pressure. Cultural practices such as female genital mutilation and early marriage contributed to early sex. Community attitudes toward contraception discouraged young people from taking up contraceptives. Originality/value: This mixed methods study explores the drivers of adolescent pregnancy in Narok, Kenya, the county with the highest rates of adolescent pregnancy; twice the national pregnancy rates. Understanding the drivers of pregnancy and the underlying human rights violations will help policymakers and health leaders to design interventions which will improve outcomes

Prevalence and correlates of depressive disorders in commercially sexual exploited children: A cross-sectional study in Mombasa, Kenya

Background: Commercial sexual exploitation of children (CSEC) is a global concern and is among the common forms of sexual violence against children. In Kenya, about 32 % of girls and 16 % of boys experience sexual violence before the age of 18 years. While much has been written about the impact of child sexual exploitation, there’s little on the prevalence of depressive disorders among CSE children. Objectives: This study was conducted to assess the prevalence and correlates of depressive disorders among CSE children in Mombasa, Kenya. Participants and setting: The study was conducted among CSE children (10–17 years) in Mombasa County. Methods: A cross-sectional study conducted between May 2021 and June 2022. A total of 409 CSE children were enrolled, using a case management approach. Data was collected using the child identification tool and the Patient Health Questionnaire (PHQ-9), at the first counselling session to determine the prevalence of depression levels. Results: Of the 409 children, 367 (90 %) were girls while 42 (10 %) were boys. The mean age was 15 years (10–17) (SD = 1.4, t = 0.765). In 286 (70 %) ‘Depression unlikely’ was recorded, while 123 (30 %) ‘Depression likelihood.’ Prevalence of mild to severe depression was significantly higher in girls than boys (p = 0.002). Other determinants of depression were having a primary level of education (p = 0.03) and being an orphan. (p = 0.03). Conclusion: It is important to prioritize mental health interventions such as screening and early diagnosis of mental health among CSE children in order to prevent and manage both short and long term effects