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ObjectivesTo assess the real-world diagnostic performance of nasal and nasopharyngeal swabs for SD Biosensor STANDARD Q COVID-19 Antigen Rapid Diagnostic Test (Ag-RDT). MethodsIndividuals [≥]5 years with COVID-19 compatible symptoms or history of exposure to SARS-CoV-2 presenting at hospitals in Lesotho received two nasopharyngeal and one nasal swab. Ag-RDT from nasal and nasopharyngeal swabs were performed as point-of-care on site, the second nasopharyngeal swab used for polymerase chain reaction (PCR) as the reference standard. ResultsOut of 2198 participants enrolled, 2131 had a valid PCR result (61% female, median age 41 years, 8% children), 84.5% were symptomatic. Overall PCR positivity rate was 5.8%. The sensitivity for nasopharyngeal, nasal, and combined nasal and nasopharyngeal Ag-RDT result was 70.2% (95%CI: 61.3-78.0), 67.3% (57.3-76.3) and 74.4% (65.5-82.0), respectively. The respective specificity was 97.9% (97.1-98.4), 97.9% (97.2-98.5) and 97.5% (96.7-98.2). For both sampling modalities, sensitivity was higher in participants with symptom duration [≤] 3days versus [≤] 7days. Agreement between nasal and nasopharyngeal Ag-RDT was 99.4%. ConclusionsThe STANDARD Q Ag-RDT showed high specificity. Sensitivity was, however, below the WHO recommended minimum requirement of [≥] 80%. The high agreement between nasal and nasopharyngeal sampling suggests that for Ag-RDT nasal sampling is a good alternative to nasopharyngeal sampling. Highlights- Prospective study on real-world diagnostic performance of nasal and nasopharyngeal SD Biosensor STANDARD Q COVID-19 Ag Test in 2131 participants in a rural African setting - The sensitivity of the STANDARD Q COVID-19 Ag Test was below the World Health Organization requirement of [≥] 80% but met the specificity requirement of [≥]97%. - Sensitivity was higher in the following subpopulations: persons with symptoms [≤]3 days, and Ct value < 25. - In head-to-head comparison nasal and nasopharyngeal sampling had comparable sensitivity and specificity and an overall test agreement of 99.4%, indicating that the more convenient nasal sampling could be used for SARS-CoV-2 rapid antigen tests. - 24 of the 2131 participants with COVID-19 symptoms had pulmonary tuberculosis with a positive Xpert Ultra test on sputum.
RESUMO
Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks. One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.