2 research outputs found
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
Validity and reliability of a modified short version of a stigma scale for use among Tunisian COVIDâ19 patients after quarantine: A crossâsectional study
Abstract Background and Aim The COVIDâ19 is a stigmatizing infectious disease even after healing. Until now, no COVIDâ19 stigma scale validated in Tunisian Arabic language among the general population is available. Developing such tools is necessary to detect COVIDâ19 stigma and reduce it effectively. Indeed, stigmatization of COVIDâ19 patients could increase the spread of this disease and its related mental health issues. We aimed at testing the validity of a translated and modified version of the 12âitem HIV stigma scale among Tunisian COVIDâ19 patients. Methods A crossâsectional study was conducted between November and December 2020 among a representative sample of COVIDâ19 patients in the governorate of Sousse, Tunisia, after quarantine. The 12âitem HIV stigma scale was translated in Tunisian Arabic and then modified to be adapted to the Tunisian context. The preliminary modified version was administrated to the participants by pretrained medical doctors during phone calls. It consisted on 20 items covering the four stigma dimensions (personalized stigma, disclosure concerns, concerns with public attitudes, and negative selfâimage). The psychometric evaluation of this version included internal consistency as well as principal component analysis (PCA). Results The responses of 346 COVIDâ19 patients were obtained. Their median age was 40âyears (interquartile range: 30â54.5). Females represented 60.4% of them. The PCA resulted in a three factor solution with 14 items. This 14âitem scale demonstrated good internal consistency with a global Cronbach's α of 0.91 and values of 0.94, 0.93, and 0.98 for social stigma, negative selfâimage, and disclosure concerns, respectively. Conclusion This study provides a reliable and valid instrument for stigma measuring among Tunisian COVIDâ19 patients. The use of this scale would contribute in reducing the spread of this new infectious disease and its related mental health issues