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

Prescription Stimulant Medication Attitudes and Beliefs of Undergraduate Students Involved in Social Sororities

Class of 2016 AbstractObjectives: To first educate undergraduates involved in social sororities about prescription stimulant medications and to evaluate the effectiveness of an educational intervention in influencing the attitudes and beliefs regarding prescription stimulant medication use of undergraduates involved in social sororities. Methods: The intervention, an educational session, was presented to undergraduates involved in social sororities. The questionnaire collected demographic data regarding gender, age, ethnicity, race, undergraduate year, grade point average, type of sorority member, history of an attention-deficit/hyperactivity disorder (ADHD) diagnosis, and previous or current non-medical use of prescription stimulants. The participants’ attitudes and beliefs on nine statements regarding prescription stimulants were queried pre- and post-intervention using a four-point Likert scale ranging from strongly disagree to strongly agree. To analyze changes in attitudes and beliefs, Mann-Whitney test was used. Results: One hundred sixty-three sorority members participated in the study. The average age of participants was 19 years with the majority of respondents identifying as an active sorority member (81%) and in their first year of undergraduate study (69%). There was a statistically significant change in beliefs regarding the safety (p < 0.01) and health risks (p = 0.02) associated with prescription stimulants. There was no significant difference in topics relating to addiction, legal issues of taking someone else’s prescription medications, emotional and academic outcomes from the use of prescription stimulants. Conclusions: The educational program presented by pharmacy students was effective in changing the beliefs and attitudes regarding safety and health risks of prescription stimulants among undergraduate students involved in social sororities.This item is part of the Pharmacy Student Research Projects collection, made available by the College of Pharmacy and the University Libraries at the University of Arizona. For more information about items in this collection, please contact Jennifer Martin, Librarian and Clinical Instructor, Pharmacy Practice and Science, [email protected]

Pathways to work from incapacity benefits A pre-pilot exploration of staff and customer attitudes

Prepared for the Department for Work and PensionsAvailable from British Library Document Supply Centre- DSC:7761. 4795(no 162) / BLDSC - British Library Document Supply CentreSIGLEGBUnited Kingdo

The impact on outcome of the addition of all-trans retinoic acid to intensive chemotherapy in younger patients with nonacute promyelocytic acute myeloid leukemia: overall results and results in genotypic subgroups defined by mutations in NPM1, FLT3, and CEBPA

We investigated the benefit of adding all-trans retinoic acid (ATRA) to chemotherapy for younger patients with nonacute promyelocytic acute myeloid leukemia and high-risk myelodysplastic syndrome, and considered interactions between treatment and molecular markers. Overall, 1075 patients less than 60 years of age were randomized to receive or not receive ATRA in addition to daunorubicin/Ara-C/thioguanine chemotherapy with Ara-C at standard or double standard dose. There were data on FLT3 internal tandem duplications and NPM1 mutations (n = 592), CEBPA mutations (n = 423), and MN1 expression (n = 195). The complete remission rate was 68% with complete remission with incomplete count recovery in an additional 16%; 8-year overall survival was 32%. There was no significant treatment effect for any outcome, with no significant interactions between treatment and demographics, or cytarabine randomization. Importantly, there were no interactions by FLT3/internal tandem duplications, NPM1, or CEBPA mutation. There was a suggestion that ATRA reduced relapse in patients with lower MN1 levels, but no significant effect on overall survival. Results were consistent when restricted to patients with normal karyotype. ATRA has no overall effect on treatment outcomes in this group of patients. The study did not identify any subgroup of patients likely to derive a significant survival benefit from the addition of ATRA to chemotherapy. This study is registered at http://www.controlled-trials.com under ISRCTN17833622

Bone marrow transplantation versus chemotherapy in non-hodgkin's lymphoma

To the Editor: In their study of the efficacy of high-dose chemotherapy and autologous bone marrow transplantation in patients with non-Hodgkin's lymphoma who respond slowly to chemotherapy, Verdonck et al. (April 20 issue) used response criteria that may have influenced the outcome. A variety of criteria have been proposed to assess response in patients with lymphoma, but the most widely accepted are those ratified at the Cotswolds meeting, which define a partial remission as “a decrease by at least 50 percent in the sum of the products of the largest perpendicular diameters of all measurable lesions.” In contrast, Verdonck et