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

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Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.

Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates

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

Availability and Utilization of Digital Health Technology for Improved Patients Care: A Cross-Sectional Study of Nurses’ Perspectives at a State General Hospital in North-Central Nigeria

Digital health technology (DHT), the application and implementation of the digital transformation strategy in the healthcare system, entails incorporating both software and hardware services to facilitate different health needs. In Nigeria's healthcare system, the utilization of digital health technology has not been fully explored resulting in the lagging behind the delivery of healthcare for digitalized, improved patient care, and nursing practice. This research study was designed to assess knowledge, availability and utilization of digital health technology by nurses at a North-Central Hospital, in Kwara state. A descriptive cross-sectional research design was adopted. The researcher used a Self-developed administered questionnaire to elicit responses from a convenient sample of 125 nurses. The data collected were analysed using descriptive and inferential statistics (with a 0.05 level of significance). The study revealed that the majority of the nurses had good knowledge (n= 92; 73.6%) and positive perception (n=90; 72%) about digital health technology with fair adequate utilization (n=74; 59.2%) of the few available digital health technology devices. A significant association was found between the knowledge of nurses about digital health technology and their highest academic qualification with a p-value of 0.022, which is less than a 0.05 level of significance. Also, a significant association was found between the knowledge of nurses and the utilization of digital health technology with a P value of 0.005. In conclusion, digital health technology knowledge among nurses was good and positive respectiviely and the level of utilization of digital health technology was adequate. Therefore, hospital administration and nurses need to advocate for improved provision of adequate digital health technologies for health care and practices especially for nursing care. Hospital administration should continue to improve the knowledge of the health workers and continually enhanced digital health technology utilisation for improved patient care. Résumé: La technologie de la santé numérique (DHT) est l'application et la mise en œuvre de la stratégie de transformation numérique dans le système de santé, qui implique l'incorporation de services logiciels et matériels pour faciliter les différents besoins en matière de santé. Dans le système de santé nigérian, l'utilisation de la technologie de santé numérique n'a pas été pleinement explorée, ce qui entraîne un retard dans la fourniture de soins de santé numérisés, l'amélioration des soins aux patients et la pratique des soins infirmiers. Cette étude a été conçue pour évaluer les connaissances, la disponibilité et l'utilisation des technologies numériques de santé par les infirmières d'un hôpital du centre-nord de l'État de Kwara. Un modèle de recherche transversale descriptive a été adopté. Le chercheur a utilisé un questionnaire auto-élaboré pour obtenir des réponses d'un échantillon de 125 infirmières. Les données recueillies ont été analysées à l'aide de statistiques descriptives et inférentielles (avec un niveau de signification de 0,05). L'étude a révélé que la majorité des infirmières avaient une bonne connaissance (n=92 ; 73,6%) et une perception positive (n=90 ; 72%) de la technologie de santé numérique avec une utilisation adéquate (n=74 ; 59,2%) des quelques dispositifs de technologie de santé numérique disponibles. Une association significative a été trouvée entre les connaissances des infirmières sur les technologies numériques de santé et leur qualification académique la plus élevée avec une valeur p de 0,022, ce qui est inférieur au niveau de signification de 0,05. De même, une association significative a été trouvée entre les connaissances des infirmières et l'utilisation des technologies numériques de santé avec une valeur P de 0,005. En conclusion, les connaissances des infirmières en matière de technologies numériques de santé étaient bonnes et positives respectivement, et le niveau d'utilisation des technologies numériques de santé était adéquat. Par conséquent, l'administration de l'hôpital et les infirmières doivent plaider en faveur d'une meilleure fourniture de technologies numériques de santé adéquates pour les soins de santé et les pratiques, en particulier pour les soins infirmiers. L'administration de l'hôpital devrait continuer à améliorer les connaissances des travailleurs de la santé en améliorant continuellement l'utilisation des technologies numériques de santé pour améliorer les soins aux patients. Mots-clés : Connaissance, disponibilité, DHT, utilisation, soins de santé, amélioration des soins aux patients.

Exploring the Influence of Daily Climate Variables on Malaria Transmission and Abundance of Anopheles arabiensis over Nkomazi Local Municipality, Mpumalanga Province, South Africa

The recent resurgence of malaria incidence across epidemic regions in South Africa has been linked to climatic and environmental factors. An in-depth investigation of the impact of climate variability and mosquito abundance on malaria parasite incidence may therefore offer useful insight towards the control of this life-threatening disease. In this study, we investigate the influence of climatic factors on malaria transmission over Nkomazi Municipality. The variability and interconnectedness between the variables were analyzed using wavelet coherence analysis. Time-series analyses revealed that malaria cases significantly declined after the outbreak in early 2000, but with a slight increase from 2015. Furthermore, the wavelet coherence and time-lagged correlation analyses identified rainfall and abundance of Anopheles arabiensis as the major variables responsible for malaria transmission over the study region. The analysis further highlights a high malaria intensity with the variables from 1998–2002, 2004–2006, and 2010–2013 and a noticeable periodicity value of 256–512 days. Also, malaria transmission shows a time lag between one month and three months with respect to mosquito abundance and the different climatic variables. The findings from this study offer a better understanding of the importance of climatic factors on the transmission of malaria. The study further highlights the significant roles of An. arabiensis on malaria occurrence over Nkomazi. Implementing the mosquito model to predict mosquito abundance could provide more insight into malaria elimination or control in Africa

Exploring the Influence of Daily Climate Variables on Malaria Transmission and Abundance of Anopheles arabiensis over Nkomazi Local Municipality, Mpumalanga Province, South Africa.

The recent resurgence of malaria incidence across epidemic regions in South Africa has been linked to climatic and environmental factors. An in-depth investigation of the impact of climate variability and mosquito abundance on malaria parasite incidence may therefore offer useful insight towards the control of this life-threatening disease. In this study, we investigate the influence of climatic factors on malaria transmission over Nkomazi Municipality. The variability and interconnectedness between the variables were analyzed using wavelet coherence analysis. Time-series analyses revealed that malaria cases significantly declined after the outbreak in early 2000, but with a slight increase from 2015. Furthermore, the wavelet coherence and time-lagged correlation analyses identified rainfall and abundance of Anopheles arabiensis as the major variables responsible for malaria transmission over the study region. The analysis further highlights a high malaria intensity with the variables from 1998-2002, 2004-2006, and 2010-2013 and a noticeable periodicity value of 256-512 days. Also, malaria transmission shows a time lag between one month and three months with respect to mosquito abundance and the different climatic variables. The findings from this study offer a better understanding of the importance of climatic factors on the transmission of malaria. The study further highlights the significant roles of An. arabiensis on malaria occurrence over Nkomazi. Implementing the mosquito model to predict mosquito abundance could provide more insight into malaria elimination or control in Africa

Investigating the resurgence of malaria prevalence in South Africa between 2015 and 2018 : a scoping review

BACKGROUND : Malaria remains a serious concern in most African countries, causing nearly one million deaths globally every year. This review aims to examine the extent and nature of the resurgence of malaria transmission in South Africa. METHODS : Using the Arksey and O'Malley framework, this scoping review includes articles published between the years 2015 and 2018 on the resurgence of malaria occurrence in South Africa. Articles were searched between October 2018 to January 2019 using the following electronic databases: CINAHL, Pubmed, Science Direct and SCOPUS. Grey literature from Google Scholar was also hand searched. Key search terms and subject headings such as climate variables, climate changes, climatic factors, malaria resurgence, malaria reoccurrence and malaria increase over epidemic regions in South Africa were used to identify relevant articles. Three independent reviewers performed the selection and characterization of articles, and the data collected were synthesized qualitatively. RESULTS : A total number of 534 studies were identified. Among these, 24 studies met the inclusion criteria. The results were grouped by factors (four main themes) that influenced the malaria resurgence: Climatic, Epidemiological, Socio-economic, and Environmental factors. Climatic factors were found to be the major factor responsible for the resurgence of malaria, as more than 55% of the selected articles were climate-focused. This was followed by epidemiological, socio-economic and environmental factors, in that order. Grey literature from Google Scholar yielded no results. CONCLUSION : This study shows that malaria transmission in South Africa is more associated with climate. Climate-based malaria models could be used as early warning systems for malaria over the epidemic regions in South Africa. Since epidemiological factors also play significant roles in malaria transmission, regular and unrelaxed use of Indoor Residual Spraying (IRS) should be encouraged in these regions. Individuals should also be educated on the importance and the usefulness of these deliveries. While some studies have indicated that the vectors have developed resistance to insecticides, continuous research on developing new insecticides that could alter the resistance are encouraged. Furthermore, all efforts to eradicate malaria in South Africa must also target malaria-endemic neighbouring countries.The University of Pretoria Institute for Sustainable Malaria Control (UP ISMC) and Malaria Research Control (MRC)https://benthamopen.com/TOPHJ/home/am2021School of Health Systems and Public Health (SHSPH