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

The Effect of Omega-3 Docosahexaenoic Acid Supplementation on Gestational Length: Randomized Trial of Supplementation Compared to Nutrition Education for Increasing n-3 Intake from Foods

Objective. DHA supplementation was compared to nutrition education to increase DHA consumption from fish and DHA fortified foods. Design. This two-part intervention included a randomized double-blind placebo controlled DHA supplementation arm and a nutrition education arm designed to increase intake of DHA from dietary sources by 300 mg per day. Setting. Denver Health Hospitals and Clinics, Denver, Colorado, USA. Population. 871 pregnant women aged 18–40 were recruited between16 and 20 weeks of gestation of whom 564 completed the study and complete delivery data was available in 505 women and infants. Methods. Subjects received either 300 or 600 mg DHA or olive oil placebo or nutrition education. Main Outcome Variable. Gestational length. Results. Gestational length was significantly increased by 4.0–4.5 days in women supplemented with 600 mg DHA per day or provided with nutrition education. Each 1% increase in RBC DHA at delivery was associated with a 1.6-day increase in gestational length. No significant effects on birth weight, birth length, or head circumference were demonstrated. The rate of early preterm birth (1.7%) in those supplemented with DHA (combined 300 and 600 mg/day) was significantly lower than in controls. Conclusion. Nutrition education or supplementation with DHA can be effective in increasing gestational length

Adapting and Implementing a Long-Term Nutrition and Physical Activity Curriculum to a Rural, Low-Income, Biethnic Community

This study adapted an urban-based school nutrition program for delivery in a rural community. Specific aims were to adapt the curriculum; expand it to include physical activity; determine effectiveness on students’ attitudes, knowledge, and self-efficacy; and assess teachers’ impressions. Three cohorts were established: 173 students taught by a resource teacher, 170 students taught by classroom teachers, and 187 students who did not receive the curriculum. Pre- and posttest surveys measured outcomes, and classroom teachers were observed and interviewed. The curriculum was shown to be effective in enhancing student outcomes for both the resource teacher and classroom teacher cohorts. Teachers reported that lessons needed to be simplified and that children enjoyed them. Findings support the transferability of an urban-based nutrition curriculum to a rural community and the need for students to receive health education annually

Field testing a questionnaire assessing parental psychosocial factors related to consumption of calcium-rich foods by Hispanic, Asian, and Non-Hispanic white young adolescent children

Intervention strategies to increase calcium intake of parents and young adolescent children could be improved by identifying psychosocial factors influencing intake. The objective was to develop a tool to assess factors related to calcium intake among parents and Hispanic, Asian, and non-Hispanic white young adolescent children (10–13 years) meeting acceptable standards for psychometric properties. A parent questionnaire was constructed from interviews conducted to identify factors. Parents (n = 166) in the United States completed the questionnaire, with seventy-one completing it twice. Two constructs (Attitudes/Preferences and Social/Environmental) were identified and described by eighteen subscales with Cronbach’s alpha levels from.50 to.79. Test-retest coefficients ranged from.68 to.85 (p < .001). Several subscales were statistically significantly associated with parent characteristics consistent with theory and published literature. This tool shows promise as a valid and reliable measure of factors associated with calcium-rich food intake among parents and young adolescent children