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

Gombak and its patients: provision of healthcare to the Orang Asli (indigenous minority) of Peninsular Malaysia

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Local barriers and solutions to improve care-seeking for childhood pneumonia, diarrhoea and malaria in Kenya, Nigeria and Niger: a qualitative study.

We present qualitative research findings on care-seeking and treatment uptake for pneumonia, diarrhoea and malaria among children under 5 in Kenya, Nigeria and Niger. The study aimed to determine the barriers caregivers face in accessing treatment for these conditions; to identify local solutions that facilitate more timely access to treatment; and to present these findings as a platform from which to develop context-specific strategies to improve care-seeking for childhood illness. Kenya, Nigeria and Niger are three high burden countries with low rates of related treatment coverage, particularly in underserved areas. Data were collected in Homa Bay County in Nyanza Province, Kenya; in Kebbi and Cross River States, Nigeria; and in the Maradi and Tillabéri regions of Niger. Primary caregivers of children under 5 who did not regularly engage with health services or present their child at a health facility during illness episodes were purposively selected for interview. Data underwent rigorous thematic analysis. We organise the identified barriers and related solutions by theme: financial barriers; distance/location of health facilities; socio-cultural barriers and gender dynamics; knowledge and information barriers; and health facility deterrents. The relative importance of each differed by locality. Participant suggested solutions ranged from community-level actions to facility-level and more policy-oriented actions, plus actions to change underlying problems such as social perceptions and practices and gender dynamics. We discuss the feasibility and implications of these suggested solutions. Given the high burden of childhood morbidity and mortality due to pneumonia, diarrhoea and malaria in Kenya, Nigeria and Niger, this study provides important insights relating to demand-side barriers and locally proposed solutions. Significant advancements are possible when communities participate in both problem identification and resolution, and are engaged as important partners in improving child health and survival

The burden of diarrhoea, pneumonia and malaria and related indicators, Kenya, Niger and Nigeria (various years).

<p><b>Footnote for </b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100038#pone-0100038-t001" target="_blank"><b>table 1</b><b>:</b></a></p>a<p>) UN Inter-agency Group for Child Mortality Estimation (2013) Levels & trends in child mortality.</p><p>Report 2013. New York, UNICEF. 30 p.</p>b<p>) Child Health Epidemiology Reference Group.</p><p>Child causes of death annual estimates by country, 2000–2010. Unpublished estimates available at <a href="http://cherg.org/datasets.html" target="_blank">http://cherg.org/datasets.html</a>. Accessed 31 May 2013.</p>c<p>) UNICEF (2012) Pneumonia and diarrhoea: tackling the deadliest diseases for the world's poorest children.</p><p>UNICEF: New York. 77 p.</p>d<p>) UNICEF (2013) State of the world's children 2013.</p><p>Children with disabilities. UNICEF: New York. 164 p.</p

Demand-side barriers identified by participants in all three settings.

<p>Demand-side barriers identified by participants in all three settings.</p

Barriers and related solutions identified by caregivers in Nigeria.

<p>Barriers and related solutions identified by caregivers in Nigeria.</p

Overview of participants per data collection method in each study site.

<p>Overview of participants per data collection method in each study site.</p

Barriers and related solutions identified by caregivers in Kenya.

<p>Barriers and related solutions identified by caregivers in Kenya.</p

Map of Nigeria fieldsites.

<p>Map of Nigeria fieldsites.</p