Differences in human immunodeficiency virus-1C viral load and drug resistance mutation between plasma and cerebrospinal fluid in patients with human immunodeficiency virus-associated cryptococcal meningitis in Botswana.

To determine effects of cryptococcal meningitis (CM) on human immunodeficiency virus (HIV)-1C cerebrospinal fluid (CSF) viral escape, CSF/plasma viral discordance, and drug resistance mutation (DRM) discordance between CSF and plasma compartments, we compared CSF and plasma viral load (VL) and DRMs in individuals with HIV-associated CM in Botswana.This cross-sectional study utilized 45 paired CSF/plasma samples from participants in a CM treatment trial (2014-2016). HIV-1 VL was determined and HIV-1 protease and reverse transcriptase genotyping performed. DRMs were determined using the Stanford HIV database. CSF viral escape was defined as HIV-1 ribonucleic acid ≥0.5 log10 higher in CSF than plasma and VL discordance as CSF VL > plasma VL.HIV-1 VL was successfully measured in 39/45 pairs, with insufficient sample volume in 6; 34/39 (87.2%) participants had detectable HIV-1 in plasma and CSF, median 5.1 (interquartile range: 4.7-5.7) and 4.6 (interquartile range:3.7-4.9) log10 copies/mL, respectively (P≤.001). CSF viral escape was present in 1/34 (2.9%) and VL discordance in 6/34 (17.6%). Discordance was not associated with CD4 count, antiretroviral status, fungal burden, CSF lymphocyte percentage nor mental status. Twenty-six of 45 (57.8%) CSF/plasma pairs were successfully sequenced. HIV-1 DRM discordance was found in 3/26 (11.5%); 1 had I84IT and another had M46MI in CSF only. The third had K101E in plasma and V106 M in CSF.Our findings suggest that HIV-1 escape and DRM discordance may occur at lower rates in participants with advanced HIV-disease and CM compared to those with HIV associated neurocognitive impairment

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

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The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time 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 shed light on 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 re-emerging 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

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

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

Body Image Dissatisfaction Is Increased in Male andOverweight/Obese Adolescents in Botswana

Introduction:The purpose of this study was to examine linkages between obesity, physical activity, and body image dissatisfaction,with consideration of socioeconomic status (SES) and urbanization in adolescents in Botswana. Materials and Methods.A nationally representative, cross-sectional survey in 707 secondary school students included measured height and weight to determine overweight (OW) or obesity (OB) using World Health Organization standards; physical activity (PA) using the International Physical Activity Questionnaire; and body image satisfaction using the Body Ideals Questionnaire. SES was described by private school versus public school attendance. Results and Discussion. OW/OB students felt farther from ideal and greater dissatisfaction with their weight and body proportions than optimal weight students. Boys felt greater difference from ideal and more dissatisfaction with muscle tone, chest size, and strength than girls. Lower SES students and those from rural villages had more minutes of PA than higher SES or urban students. In this rapidly developing African country, these trends reflect the nutrition transition and offer opportunity to motivate OW/OB students and boys for PA as a health promotion obesity prevention behavior. Conclusions. As urbanization and improved SES are desirable and likely to continue, the public health system will be challenged to prevent obesity while preserving a healthy body image

Association between socioeconomic status indicators and obesity in adolescent students in B otswana, an A frican country in rapid nutrition transition

Objective: The purpose of this study was to examine two separate socioeconomic status (SES) indicators of obesity in Botswana, an African country that has experienced rapid economic development and where the prevalence of human immunodeficiency virus/acquired immune deficiency syndrome is high. Methods: We conducted a nationally representative, cross-sectional study of 707 adolescent secondary school students in Botswana. Measured height and weight were used to compute World Health Organization age- and sex-specific body mass index z-scores. SES was described by private vs. public school attendance and a survey of assets/facilities within the home. Results: Overall, private school students and those with more assets had a higher prevalence of overweight and obesity than public school students (private: 27.1%, 95% confidence interval [CI]: 20.4-34.5; public: 13.1%, 95% CI: 9.8-16.8) and those with fewer assets (more assets: 20.0%, 95% CI: 16.0-24.4; fewer assets: 11.2%, 95% CI: 6.6-16.9). Conclusions: Public health interventions in developing countries may need to be targeted differently to low or high SES individuals in order to treat already high obesity rates in higher SES groups and to prevent the development of obesity in lower SES communities undergoing economic transition

Adolescent Obesity Prevention in Botswana: Beliefs and Recommendations of School Personnel

The study’s objectives were to gain school personnel’s (1) perceptions on diet, physical activity, body size, and obesity, (2) description of school food and physical activity practices, and (3) recommendations for programs to prevent adolescent obesity. The study took place in six junior secondary schools of varying socioeconomic status in Gaborone, Botswana. Using a qualitative descriptive design, semistructured interviews were conducted with key school personnel. Directed content analysis was used to summarize the findings. School personnel believed that obesity was an important problem. They felt that school food was unhealthy and that physical activity was provided insufficiently. Participants shared enthusiasm for a school-based health-promoting intervention that must be fun and include active engagement and education on healthy lifestyles for all students. Participants supported on-site food shop inventory changes and physical activity programs. Potential barriers listed were schools’ financial resources, interest of students, and time limitations of all involved