5 research outputs found
Erratum to: Precision of the Kalon Herpes Simplex Virus Type 2 IgG ELISA: an international inter-laboratory assessment.
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
Precision of the Kalon Herpes Simplex Virus Type 2 IgG ELISA : an international inter-laboratory assessment
CITATION: Patel, Eshan U., et al. 2015. Precision of the Kalon Herpes Simplex Virus Type 2 IgG ELISA : an international inter-laboratory assessment. BMC Infectious Diseases, 15:398, doi:10.1186/s12879-015-1130-6.The original publication is available at http://bmcinfectdis.biomedcentral.comBackground: The commercial Kalon HSV-2 IgG ELISA is currently recommended for research use in sub-Saharan
Africa because of its superior accuracy compared to other serologic assays. However, there are no data on key
precision parameters of Kalon such as inter-operator variation, repeatability, and reproducibility, thus contributing to
a barrier for its acceptance and use in clinical trials in sub-Saharan Africa. We evaluated the analytical and field
precision of the Kalon HSV-2 IgG ELISA.
Methods: A total of 600 HIV-infected and uninfected serum samples from South Africa and Zambia, previously
tested by the gold standard University of Washington HSV western blot (UW-WB), were tested using Kalon by two
technologists in an United States reference laboratory. Aliquots of 183 samples were retested using Kalon by an
on-site technologist in a South African laboratory and a Zambian laboratory.
Results: Intra-assay variation was below 10 %. Intra-assay, intra-laboratory, and inter-laboratory correlation and
agreement were significantly high (p < 0.01). In comparison to the UW-WB, accurate performance of Kalon was
reproducible by each operator and laboratory. Receiver operating characteristic curve analysis indicated high
selectivity of Kalon in the overall study population (area under the curve = 0.95, 95%CI = 0.92–0.97).
Discussion: Kalon is a robust assay with high precision and reproducibility. Accordingly, operator errorlikely does
not contribute to the variability observed in Kalon’s specificity throughout sera from sub-Saharan Africa.
Conclusions: In populations with optimal diagnostic accuracy, Kalon is a reliable stand-alone method for on-site
HSV-2 IgG antibody detection.http://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-015-1130-6Publisher's versio