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

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

Immunological and hematological reference intervals among HIV-seronegative pregnant women in northwest Ethiopia

Meaza Genetu,1 Debasu Damtie,1 Meseret Workineh,1 Biniam Mathewos Tebeje,1,2 Bamlaku Enawgaw,3 Tekalign Deressa1 1Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia; 2Molecular Parasitology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia; 3Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia Background: Pregnancy is a state characterized by profound physiological hematological changes. However, hematological reference intervals being used in clinical practice in Ethiopia are derived from nonlocal general populations, despite the significant variations reported previously. The aim of this study was to determine the immunological and hematological reference intervals in healthy pregnancy among HIV-seronegative pregnant women in northwest Ethiopia.Materials and methods: A total of 200 healthy, HIV-seronegative pregnant women were enrolled from February 2015 to June 2015 in a cross-sectional study setting at Gondar University Hospital. Sociodemographic and obstetric data were collected using a structured questionnaire. Blood samples collected from each participant were used to define the immunological and hematological parameters. The mean, median, and 95% interval values were calculated for the immunological and hematological parameters. P-value <0.05 was considered statistically significant for all variables.Results: This study found that there were changes in CD4+ T-cell count, platelet count, and hematocrit (HCT) values as pregnancy advances. The calculated combined reference intervals for the absolute CD4+ T-cell count and platelet count were 712.47–760.67 and 221.25–240.14, respectively. A progressive decline in the platelet count was observed as pregnancy advanced, with 95% intervals of 224.53–253.21, 209.50–237.38, and 213.70–247.86 in the first, second, and third trimesters, respectively (P=0.27). There was a statistically significant increase in mean (±standard deviation [SD]) HCT with gestational age, being 39.18±6.70, 41.96±3.70, and 40.53±3.77 in the first, second, and third trimesters, respectively (P=0.03). The overall 95% interval for hemoglobin (HB) concentration was 12.99–13.36 g/dL, HCT 40.19%–41.49%, mean corpuscular volume (MCV) 93.33–94.63 fL, and mean corpuscular hemoglobin (MCH) 28.88–34.81 pg. Compared with the reference ranges derived from other studies, we found considerable variations in CD4+ T-cell count, HB, HCT, and MCV values.Conclusion: The findings of this study highlight the differences in immunohematological profile among pregnant women and nonpregnant women from Ethiopia and other countries, in addition to suggesting the need for such establishment of local reference values for different populations. Keywords: immunological parameter, hematological parameter, pregnant women, reference range, immunohematological reference intervals&nbsp

Analysis of Immune Responses against a Wide Range of Mycobacterium tuberculosis Antigens in Patients with Active Pulmonary Tuberculosis

Immunogenetics and cellular immunology of bacterial infectious disease