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

Significance of hematologic abnormalities in COVID-19 severity among infected patients in Lagos, Nigeria

Abstract Background There have been suggestions that hematologic abnormalities in COVID-19 are linked with the progression and severity of diseases and mortality. Lymphopenia, sepsis, and thrombocytopenia were highly reported in patients with COVID-19. This study investigated the significance of hematologic abnormalities in patients with COVID-19 in Lagos, Nigeria, and its potential as a diagnostic tool for COVID-19 severity. Results This was a retrospective observational study with a total of 340 patients with COVID-19 (236 patients included in the analysis). These patients were categorized into two groups, comprising 71 patients with severe COVID-19 (SCP) and 165 patients with non-severe COVID-19 (NSCP). The majority were males in both categories (SCP 74.6% and NSCP 63.6%). The mean ± SD ages for SCP and NSCP were 52.28 ± 16.87 and 42.44 ± 17.18 years, respectively. The SCP (52.1%) and NSCP (20.0%) had underlying health conditions. The SCP exhibited significantly higher neutrophil counts (P < 0.05) and significantly lower mean hemoglobin, red blood cell (RBC), packed cell volume (PCV), and lymphocyte values (P < 0.05). Anemia and lymphocytopenia were more prominent in the SCP group than in the NSCP group (P < 0.05). Hemoglobin, RBC, PCV, and lymphocytes were inversely correlated with age-group in the SCP, while only lymphocytes and platelets were inversely correlated with age-group in the NSCP. The highest area under the ROC curve (AUC) for neutrophils was 0.739 with a sensitivity of 62.0% and specificity of 80.0%, while white blood cells had an AUC of 0.722 with a sensitivity of 73.2% and specificity of 61.2%. The AUC for neutrophil–lymphocyte ratio (NLR) was 0.766 with a sensitivity of 63.3% and specificity of 83.5%, while that for the platelet–lymphocyte ratio (PLR) was 0.695 with a sensitivity and specificity of 61.7% and 77.8%. Conclusions COVID-19 affected the levels of hemoglobin, RBC, PCV, and lymphocytes in the blood, and the differences were significant between the SCP and NSCP. The significant changes in neutrophil and lymphocyte counts may be useful in the prognosis and management of COVID-19 severity in hospital settings. Furthermore, NLR and PLR may be used in the prognosis and management of severe COVID-19 infection, as well as provide an objective basis for early identification and management in low-resource settings

Experience of quality management system in a clinical laboratory in Nigeria

Issues: Quality-management systems (QMS) are uncommon in clinical laboratories in Nigeria, and until recently, none of the nation’s 5 349 clinical laboratories have been able to attain the certifications necessary to begin the process of attaining international accreditation. Nigeria’s Human Virology Laboratory (HVL), however, began implementation of a QMS in 2006, and in 2008 it was determined that the laboratory conformed to the requirements of ISO 9001:2000 (now 2008), making it the first diagnostic laboratory to be certified in Nigeria. The HVL has now applied for the World Health Organization (WHO) accreditation preparedness scheme. The experience of the QMS implementation process and the lessons learned therein are shared here. Description: In 2005, two personnel from the HVL spent time studying quality systems in a certified clinical laboratory in Dakar, Senegal. Following this peer-to-peer technical assistance, several training sessions were undertaken by HVL staff, a baseline assessment was conducted, and processes were established. The HVL has monitored its quality indicators and conducted internal and external audits; these analyses (from 2007 to 2009) are presented herein. Lessons learned: Although there was improvement in the pre-analytical and analytical indicators analysed and although data-entry errors decreased in the post-analytical process, the delay in returning laboratory test results increased significantly. There were several factors identified as causes for this delay and all of these have now been addressed except for an identified need for automation of some high-volume assays (currently being negotiated). Internal and external audits showed a trend of increasing non-conformities which could be the result of personnel simply becoming lax over time. Application for laboratory accreditation, however, could provide the renewed vigour needed to correct these non-conformities. Recommendation: This experience shows that sustainability of the QMS at present is a cause for concern. However, the tiered system of accreditation being developed by WHO–Afro may act as a driving force to preserve the spirit of continual improvement