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

Examining the Development of Latinx Adolescents’ Science Intrinsic and Utility Values: A Family Systems Approach

Due to the importance of motivational beliefs and family support, this dissertation used the situated expectancy-value theory, family systems theory, and the Latino youth development model to focus on motivational and family processes related to science during adolescence among Latinx families. Using the Latinx subsample from a nationally representative dataset, Paper 1 focused on the relations between parent support at 9th grade, adolescents’ 11th grade science intrinsic and utility values, and 11th grade STEM occupational expectations. Moreover, Paper 1 also tested whether these indicators and relations differed by adolescent gender and parent education. Findings indicated that parent science support was related to adolescents’ science utility value and girls’ science intrinsic value, with only adolescents’ science utility value predicting whether they had a STEM occupational expectation. Also, adolescent girls were more likely than boys to have a STEM occupational expectation and adolescents who had parents with a higher education received greater parent support compared to their peers. Expanding upon Paper 1 with a smaller dataset, Paper 2 tested whether parents’ and siblings’ respective familism values and parent education predicted parent and older sibling science support. Also, Paper 2 examined associations between parent and older sibling science support and adolescents’ science intrinsic and utility values. Findings from this study suggested that parents’ and siblings’ familism values were not associated with how much support they gave in science. When compared to each other, parents provided greater support compared to siblings. Lastly, both parent and sibling support predicted adolescents’ science utility value. Finally, using qualitative data that consisted of 14 interviews with Latinas who successfully persisted in science in college, Paper 3 focused on identifying how parents and siblings supported the development of Latina adolescents’ science intrinsic and utility values in high school. The main themes that emerged for both parents and older siblings included conversations, emotional support, and coactivity. Moreover, Latina adolescents with high familism values had greater parent and sibling science support compared to Latina adolescents with low familism values. Also, in families where only older siblings had higher education experience, older siblings gave more support than parents for certain types of support. Findings from these dissertation papers not only unpacked family support by examining the extent to which parents and siblings work together to support adolescents, but it also bridged the gap between literatures on Latinx family support and adolescent science intrinsic and utility values

Developmental Trajectories of Science Identity Beliefs: Within-Group Differences among Black, Latinx, Asian, and White Students.

Though adolescents' science identity beliefs predict positive STEM outcomes, researchers have yet to examine developmental differences within racial/ethnic groups despite theoretical arguments for such studies. The current study examined science identity trajectories for Black (14%), Latinx (22%), Asian (4%), and White (52%) students (N = 21,170; 50% girls) from 9th grade to three years post-high school and the variability within each racial/ethnic group based on gender and college generational status. Contrary to the literature, students' science identities increased over time, and the increases were larger for potential first- versus continuing-generation White students. Potential continuing-generation boys had stronger 9th grade science identities than potential first-generation girls in all groups except Asians. The findings suggest who might benefit from additional supports within each racial/ethnic group

Developmental trajectories of science identity beliefs : Within-group differences among Black, Latinx, Asian, and White Students

Though adolescents’ science identity beliefs predict positive STEM outcomes, researchers have yet to examine developmental differences within racial/ethnic groups despite theoretical arguments for such studies. The current study examined science identity trajectories for Black (14%), Latinx (22%), Asian (4%), and White (52%) students (N = 21,170; 50% girls) from 9th grade to three years post-high school and the variability within each racial/ethnic group based on gender and college generational status. Contrary to the literature, students’ science identities increased over time, and the increases were larger for potential first- versus continuing-generation White students. Potential continuing-generation boys had stronger 9th grade science identities than potential first-generation girls in all groups except Asians. The findings suggest who might benefit from additional supports within each racial/ethnic group

Post-Traumatic Stress Disorder and Blast Exposure in Active-Duty Military Service Members

Objective: Active-duty military personnel in the current wars have experienced unique stressors that deviate from standard PTSD assessment and diagnosis. This situation calls for a refinement of military-related PTSD assessment. To this end, this study assessed the utility of the Trauma Symptom Inventory (TSI) in diagnosing PTSD among active-duty military personnel. The past literature has validated the TSI using populations with a small sample size. Hence, this study aimed to fill the gap by using a large sample size of 670 military members to examine whether the TSI is useful for military populations. Setting: Participants were referred to Carolina Psychological Health Services, in Jacksonville, North Carolina by military neurologists and other qualified medical officers from the Naval Hospital in Camp Lejeune, a military base located in Jacksonville, NC, for neuropsychological evaluation due to reported cognitive deficits related to military deployment (i.e., head injury due to exposure to blast injuries). Participants: Based on clinical diagnosis, comprehensive neuropsychological testing, and self-reported data, personnel were classified into four groups: blast exposure (n = 157), PTSD diagnosis (n = 90), both blast exposure and PTSD (n = 283), and neither blast exposure nor PTSD (n = 140), which helps provide a comprehensive picture of the utility of the TSI. Results: The TSI’s 10 clinical scales could distinguish between all groups. Discriminant function analysis showed that an optimally weighted combination of scales correctly predicted 66.67% of PTSD-positive cases and 35.11% of PTSD-negative cases. Conclusion: These findings provide support for the use of the TSI in the assessment of PTSD in active-duty military personnel. Due to the release of TSI-2, there is a need to replicate this data. However, the validity data has indicated a high concordance between the TSI and TSI-2, bolstering confidence in the current findings of the study