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

Insetos-pragas, produtos e métodos de controle utilizados na cultura de mandioca em Ivinhema, Mato Grosso do Sul

The objective of this research was to determine which are the insect pests, products and methods of control used in the cultivation of cassava in Ivinhema, State of Mato Grosso do Sul were interviewed 30 farmers in the Municipality during April and May 2011. Data were obtained with the aid of a script and the questions asked directly and individually with each producer. In the present study can be seen that the insect pests most common occurrence in cassava are leaf cutter ants (Atta spp.) Mandarova (Erinnyis spp.), the whitefly (Bemisia spp.), and the bug (Vatiga spp.). Based on data obtained 97% producers perform some kind of control in the cassava agroecosystem, which may be chemical or biological control. It is worth noting that the lack of chemical and biological control of insects is one of the problems faced by farmers. The pest control is performed without any technical assistance and most of the time with products for veterinary use which impairs the efficiency of the method and reduces the yield.O objetivo da pesquisa foi verificar quais são os insetos-praga, produtos e métodos de controle utilizados na cultura de mandioca em Ivinhema, Estado de Mato Grosso do Sul. Foram entrevistados 30 agricultores do município no período de Abril e Maio de 2011. As informações foram obtidas com auxilio de um roteiro e as perguntas efetuadas de forma direta e individualmente com cada produtor. No presente estudo pode-se constatar que os insetos-praga de maior ocorrência na cultura de mandioca são as formigas cortadeiras (Atta spp.), mandarová (Erinnyis spp.), a mosca- branca (Bemisia spp.), e o percevejo-de- renda (Vatiga spp.). Com base nos dados obtidos 97% produtores realizam algum tipo de controle no agroecossistema mandioqueiro, podendo ser o controle químico ou biológico. Ressalta-se ainda que a escassez de produtos químicos e biológicos para o controle desses insetos é um dos problemas enfrentados pelos agricultores. O controle das pragas é efetuado sem nenhuma assistência técnica e na maioria das vezes com produtos de uso veterinário o que prejudica a eficiência do método e diminui a produtividade da cultura

Sequential sampling of Bemisia tuberculata (Bondar, 1923) (Hemiptera: Aleyrodidae) on cassava crop

Estimate efficiently of the whitefly population (Bemisia tuberculata Bondar) in cassava, to assist in decision making of pest control is one of the advantages of sequential sampling plans. Therefore, the objective of this study was to determine a sequential sampling plan according to two methods of pest management, using biological and/or chemical control. Samples were obtained in a commercial field of 2.500,00 m2, divided into 100 plots. The visualization method was used for sampling of the upper leaves by counting the number of adults. In total 15 samples were taken weekly from January to April 2012. The spatial distribution model which best fit to the behavior of B. tuberculata adults was the negative binomial distribution. Levels adapted for biological and chemical control were five and twenty adults per plant, respectively. Sampling plans resulted in two decisions for each proposed method. Thus, for population control the upper limit was defined as S1 = 4.2056 + 2.1540n (biological) and S1 = 20.219 + 10.4306n (chemical); and the lower limit where the pest control is not recommended was defined by S0 = -4.2056 + 2.1540n (biological) and S0 = -20.219 + 10.4306n (chemical). Sequential sampling estimated the maximum number of sample units necessary for decision-making of three samples with 1.34 adults for biological control and 3.85 sample units with 7.39 adult pests for chemical control

Occurrence of lace bug Vatiga illudens and Vatiga manihotae (Hemiptera: Tingidae) in Mato Grosso do Sul, midwestern Brazil

Nymphs and adults of the lace bug (Hemiptera: Tingidae) have been found in cassava crops (Manihot esculenta) in Mato Grosso do Sul State, Brazil. The insects were collected in the field and taken to the laboratory where they were identified based on some morphological traits of the species Vatiga manihotae (Drake) and V. illudens (Drake), which are first reported in the aforementioned state

Physicians' guideline adherence is associated with long-term heart failure mortality in outpatients with heart failure with reduced ejection fraction: the QUALIFY international registry

Background: Physicians' adherence to guideline-recommended therapy is associated with short-term clinical outcomes in heart failure (HF) with reduced ejection fraction (HFrEF). However, its impact on longer-term outcomes is poorly documented. Here, we present results from the 18-month follow-up of the QUALIFY registry. Methods and results: Data at 18 months were available for 6118 ambulatory HFrEF patients from this international prospective observational survey. Adherence was measured as a continuous variable, ranging from 0 to 1, and was assessed for five classes of recommended HF medications and dosages. Most deaths were cardiovascular (CV) (228/394) and HF-related (191/394) and the same was true for unplanned hospitalizations (1175 CV and 861 HF-related hospitalizations, out of a total of 1541). According to univariable analysis, CV and HF deaths were significantly associated with physician adherence to guidelines. In multivariable analysis, HF death was associated with adherence level [subdistribution hazard ratio (SHR) 0.93, 95% confidence interval (CI) 0.87–0.99 per 0.1 unit adherence level increase; P = 0.034] as was composite of HF hospitalization or CV death (SHR 0.97, 95% CI 0.94–0.99 per 0.1 unit adherence level increase; P = 0.043), whereas unplanned all-cause, CV or HF hospitalizations were not (all-cause: SHR 0.99, 95% CI 0.9–1.02; CV: SHR 0.98, 95% CI 0.96–1.01; and HF: SHR 0.99, 95% CI 0.96–1.02 per 0.1 unit change in adherence score; P = 0.52, P = 0.2, and P = 0.4, respectively). Conclusion: These results suggest that physicians' adherence to guideline-recommended HF therapies is associated with improved outcomes in HFrEF. Practical strategies should be established to improve physicians' adherence to guidelines. © 2019 The Authors. European Journal of Heart Failure © 2019 European Society of Cardiolog