3 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
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Validation of two parent-reported autism spectrum disorders screening tools M-CHAT-R and SCQ in Bamako, Mali.
BackgroundEarly screening is crucial for early autism spectrum disorders (ASD) diagnosis and intervention. ASD screening tools have mostly been constructed based on the Western cultural context. We hypothesized that their use in Mali may require a prior validation.ObjectiveTo validate the modified checklist for autism in toddlers-Revised (M-CHAT-R) and the social communication questionnaire (SCQ) in the Malian sociocultural context for ASD screening.Study designWe administered M-CHAT-R and SCQ in 947 toddlers aged 16-30 months old at the district and community health centers in Bamako and 120 patients (60 autistic and 60 age and sex matched controls) aged ≥4 years old at the psychiatry department in Bamako. Toddlers at moderate to high risk of ASD underwent M-CHAT-R/F and clinical evaluation by an ASD multidisciplinary team. M-CHAT-R and SCQ were evaluated for cultural appropriateness by Malian anthropologists. The sensitivity, specificity, PPV, NPV were determined for both M-CHAT-R and SCQ. Health professionals have been trained during ASD seminary on how to use M-CHAT-R and SCQ for ASD screening in Bamako.ResultsWe found for the M-CHAT-R a sensitivity of 50%, a specificity of 100%, a PPV of 100% and a NPV of 87%. The SCQ had a sensitivity of 71%, a specificity of 72%, a PPV of 73% and a NPV of 70%. We have found four out of 20 items on the M-CHAT-R that were culturally inappropriate in the Malian context.DiscussionM-CHAT-R and SCQ can be used for early autism screening in Mali. In the future, we plan to train a descent number of Malian physicians in chief and pediatricians at the district hospitals across the country to integrate the early ASD screening into the national health system.ConclusionM-CHAT-R has a perfect specificity and SCQ a fair diagnostic accuracy for ASD in Mali