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

Research PaperReliability of self report questionnaires for epidemiological investigations of adolescent mental health in Cape Town, South Africa

Objective: This study aimed to assess the reliability of a number of self report questionnaires for epidemiological investigations of adolescents’ mental health in Cape Town, South Africa. The scales used were: the Short Mood and Feelings Questionnaire (SMFQ), Zung Self-rating Anxiety Scale (SAS), Self-esteem Questionnaire (SEQ), Harvard Trauma Questionnaire (HTQ) and Multi-Dimensional Scale of Perceived Social Support (MSPSS).Method: The self-report questionnaire (available in Afrikaans, English and isiXhosa) was administered to 237 grade 8 students (14–15 years) on 2 occasions in metropolitan Cape Town high schools. The mean interval between first and second administration of the questionnaire was 8.3 days. Test-retest reliability was assessed using Cohen’s kappa and observed agreement. Pearson’s correlation coefficients were used to assess consistency across total scores between occasion 1 and occasion 2. Cronbach’s alpha was used to assess the internal consistency of each scale. Results: All items had at least fair test-retest reliability (kappa > 0.20) apart from two items on the Self-rating Anxiety Scale and one item on the Harvard Trauma questionnaire. Test-retest reliability was strong for the HTQ (Pearson’s correlation coefficient >0.75), moderate for the SAS, SEQ and MSPSS (0.50–0.74) and weak for the SMFQ (0.25–0.49). Cronbach’s alpha for all scales was acceptable (>0.60). Analysis by the different language versions (Afrikaans/English and isi-Xhosa/English) of the questionnaire indicated good internal consistency for most measures for all three languages.Conclusions: The results indicate that many of these instruments may be used reliably in South Africa to assess adolescent mental health and that the different language versions of the instruments used in the questionnaire are generally reliable for use in South African schools. However, some caution is required with the use of the SAS and SEQ in different language groups.Journal of Child and Adolescent Mental Health 2011, 23(2): 119–12