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

Training Mode’s Influence on the Relationships between Training-Load Models During Basketball Conditioning

Purpose: To compare perceptual and physiological training load responses during various basketball training modes. Methods: Eight semi-professional male basketball players (age: 26.3 ± 6.7 years; height: 188.1 ± 6.2 cm; body mass: 92.0 ± 13.8 kg) were monitored across a 10-week period in the preparatory phase of the training plan. Player session ratings of perceived exertion (sRPE) and heart rate (HR) responses were gathered across base, specific, and tactical/game-play training modes. Pearson correlations were used to determine the relationships between the sRPE model and two HR-based models, the training impulse (TRIMP) and summated-heart-rate-zones (SHRZ). One-way ANOVAs were used to compare training loads between training modes for each model. Results: Stronger relationships between perceptual and physiological models were evident during base (sRPE-TRIMP: r = 0.53, P < 0.05; sRPE-SHRZ: r = 0.75, P < 0.05) and tactical/game-play conditioning (sRPE-TRIMP: r = 0.60, P < 0.05; sRPE-SHRZ: r = 0.63; P < 0.05) than during specific conditioning (sRPE-TRIMP: r = 0.38, P < 0.05; sRPE-SHRZ: r = 0.52; P < 0.05). Further, the sRPE model detected greater increases (126-429 AU) in training load than the TRIMP (15-65 AU) and SHRZ models (27-170 AU) transitioning between training modes. Conclusions: While the training load models were significantly correlated during each training mode, weaker relationships were observed during specific conditioning. Comparisons suggest the HR-based models were less effective in detecting periodized increases in training load, particularly during court-based, intermittent, multidirectional drills. The practical benefits and sensitivity of the sRPE model support its use across different basketball training modes

Receptor-defined subtypes of breast cancer in indigenous populations in Africa: a systematic review and meta-analysis.

BACKGROUND: Breast cancer is the most common female cancer in Africa. Receptor-defined subtypes are a major determinant of treatment options and disease outcomes but there is considerable uncertainty regarding the frequency of poor prognosis estrogen receptor (ER) negative subtypes in Africa. We systematically reviewed publications reporting on the frequency of breast cancer receptor-defined subtypes in indigenous populations in Africa. METHODS AND FINDINGS: Medline, Embase, and Global Health were searched for studies published between 1st January 1980 and 15th April 2014. Reported proportions of ER positive (ER+), progesterone receptor positive (PR+), and human epidermal growth factor receptor-2 positive (HER2+) disease were extracted and 95% CI calculated. Random effects meta-analyses were used to pool estimates. Fifty-four studies from North Africa (n=12,284 women with breast cancer) and 26 from sub-Saharan Africa (n=4,737) were eligible. There was marked between-study heterogeneity in the ER+ estimates in both regions (I2>90%), with the majority reporting proportions between 0.40 and 0.80 in North Africa and between 0.20 and 0.70 in sub-Saharan Africa. Similarly, large between-study heterogeneity was observed for PR+ and HER2+ estimates (I2>80%, in all instances). Meta-regression analyses showed that the proportion of ER+ disease was 10% (4%-17%) lower for studies based on archived tumor blocks rather than prospectively collected specimens, and 9% (2%-17%) lower for those with ≥ 40% versus those with <40% grade 3 tumors. For prospectively collected samples, the pooled proportions for ER+ and triple negative tumors were 0.59 (0.56-0.62) and 0.21 (0.17-0.25), respectively, regardless of region. Limitations of the study include the lack of standardized procedures across the various studies; the low methodological quality of many studies in terms of the representativeness of their case series and the quality of the procedures for collection, fixation, and receptor testing; and the possibility that women with breast cancer may have contributed to more than one study. CONCLUSIONS: The published data from the more appropriate prospectively measured specimens are consistent with the majority of breast cancers in Africa being ER+. As no single subtype dominates in the continent availability of receptor testing should be a priority, especially for young women with early stage disease where appropriate receptor-specific treatment modalities offer the greatest potential for reducing years of life lost. Please see later in the article for the Editors' Summary

The relationship between physical fitness and shooting accuracy of professional basketball players

The aim of this study was to examine the relationships among physical fitness of professional Bosnianbasketball players (n = 38) and shooting accuracy during one basketball season. A related, secondary aim was toexamine relationships between basketball shooting assessments and competitive shooting accuracy during game play.Physical fitness components included: muscular endurance and aerobic endurance, lower and upper-body power,speed, agility, anaerobic capacity and anaerobic power. The specific basketball shooting accuracy was assessed bystationary and dynamic shooting assessments. Competitive shooting accuracy was represented by data collected duringone basketball season for each player (free throw, field goal, and three-point %). Results of the regression analysesshowed that there were significant positive relationships among shooting assessments and competitive shooting accuracyduring game play. The relationship was stronger when the dynamic shooting tests were applied compared tothe stationary tests. However, few or weak relationships existed among physical fitness components and competitiveshooting accuracy. Only the power tests showed to be good predictors for shooting over longer distances. The findingssupport the inclusion of the dynamic basketball shooting accuracy tests in regular basketball assessment proceduresas a valuable testing instrument.A relação entre aptidão física e precisão de arremesso dos jogadores profissionais de basquetebol.“ Oobjetivo do presente estudo foi identificar a relação entre a condição física de basquetebolistas profissionais bósnios(n=38) na precisão de arremesso no decorrer de uma temporada competitiva. Adicionalmente, pretendeu-se verificara relação entre a avaliação específica e a precisão de arremessos durante os jogos. As variáveis de condição físicaforam as seguintes: resistência de força, resistência aeróbia, potência dos membros inferiores e superiores, velocidade,agilidade, capacidade e potência anaeróbia. A avaliação específica do arremesso foi testada através da utilização dearremessos estáticos e dinâmicos. A precisão dos arremessos durante os jogos foi realizada no decorrer da temporadacompetitiva mediante análise das seguintes variáveis: lance-livre, arremessos de quadra, e percentagem de arremessosde três pontos. As análises de regressão indicaram a existência de uma relação positiva entre as avaliações específicasdos arremessos e a precisão durante os jogos, a qual foi mais forte nas situações de arremessos dinâmicos comparadosaos estáticos. Contudo, as relações existentes entre as variáveis de condição física e a precisão de arremesso duranteos jogos foram menores e pouco significativas. Apenas os testes de potência mostraram ser bons preditores para osarremessos efetuados a longas distâncias. Os resultados obtidos apoiam a inclusão de testes de avaliação da precisãode arremessosrealizados de forma dinâmica em procedimentos regulares de avaliação no basquetebol, constituindo-secomo instrumentos valiosos para ocontrole do rendimento.La relación entre la aptitud física y precisión de tiro de los jugadores profesionales de baloncesto.” El objetivo de este estudio fue examinar la relación entre la condición física de los jugadores profesionales de baloncesto de Bosnia (n=38) y la precisión de tiro durante una temporada de baloncesto. Paralelamente, el objetivo secundario fue examinar las relaciones entre las evaluaciones de lanzamiento de baloncesto y la precisión de tiro durante el partido. Los componentes de la aptitud física incluían: la resistencia muscular y la resistencia aeróbica, la potencia de los miembros inferiores y superiores del cuerpo, la velocidad, la agilidad, la capacidad anaeróbica y la potencia anaeróbica. La pre­cisión específica de tiro de baloncesto se evaluó mediante lanzamiento estático y evaluaciones de tiro en movimiento. La precisión de tiro en competición estuvo representada por los datos recogidos durante una temporada de baloncesto para cada jugador (tiro libre, tiro de campo y triple %). Posteriores análisis de los resultados mostraron que había una significativa relación positiva entre las evaluaciones de tiro y la precisión de tiro durante el partido. La relación era más fuerte cuando las pruebas de tiro en movimiento se compararon con las pruebas de tiro estático. Sin embargo, existían pocas o débiles relaciones entre los componentes de la aptitud física y la precisión de tiro en competición. Sólo las pruebas de potencia mostraron ser buenas predictoras para lanzamientos de mayor distancia. Los resultados apoyan la inclusión de los entrenamientos de precisión de tiro en movimiento en los procedimientos habituales de evaluación de baloncesto, como un valioso instrumento de prueba