Dataset Information

Clinical Evaluation of Severe Acute Respiratory Syndrome Coronavirus 2 Rapid Antigen Tests During the Omicron Wave in South Africa.

ABSTRACT: We evaluated the performance of nasal and nasopharyngeal Standard Q COVID-19 [coronavirus disease 2019] Ag tests (SD Biosensor) and the Panbio COVID-19 Ag Rapid Test Device (nasal; Abbott) against the Abbott RealTime severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay during the Omicron (clades 21M, 21K, and 21L) wave in South Africa. Overall, all evaluated tests performed well, with high sensitivity (range, 77.78%-81.42%) and excellent specificity values (>99%). The sensitivity of rapid antigen tests increased above 90% in samples with cycle threshold <20, and all 3 tests performed best within the first week after symptom onset.

SUBMITTER: Samsunder N

PROVIDER: S-EPMC9384653 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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Clinical Evaluation of Severe Acute Respiratory Syndrome Coronavirus 2 Rapid Antigen Tests During the Omicron Wave in South Africa.

Samsunder Natasha N de Vos Margaretha M Ngcapu Sinaye S Giandhari Jennifer J Lewis Lara L Kharsany Ayesha B M ABM Cawood Cherie C de Oliveira Tulio T Karim Quarraisha Abdool QA Karim Salim Abdool SA Naidoo Kogieleum K Escadafal Camille C Sivro Aida A

The Journal of infectious diseases 20221001 8

We evaluated the performance of nasal and nasopharyngeal Standard Q COVID-19 [coronavirus disease 2019] Ag tests (SD Biosensor) and the Panbio COVID-19 Ag Rapid Test Device (nasal; Abbott) against the Abbott RealTime severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay during the Omicron (clades 21M, 21K, and 21L) wave in South Africa. Overall, all evaluated tests performed well, with high sensitivity (range, 77.78%-81.42%) and excellent specificity values (>99%). The sensitivity o ...[more]

PMID: 35921539

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Project description:BackgroundThe COVID-19 Omicron BA.2 epidemic wave in Hong Kong peaked in the first quarter of 2022. Following the implementation of stringent public health measures, the daily number of reported cases fell from over 50,000 to below 2000. Although outbreaks steadily receded, the government rolled out a 3-day "voluntary universal rapid testing" campaign to invite all citizens to self-perform a rapid antigen test (RAT) daily to identify undetected prevalent infections.ObjectiveThis study aimed to evaluate the uptake and results of RAT mass screening to estimate the population's residual epidemic burden and assess the risk of further transmission.MethodsA cross-sectional study comprising an open web-based population-based survey was conducted a week after the RAT campaign. Participants were asked to report their COVID-19 vaccination and infection history and the RAT performance and test result during the period. They were also invited to report their coliving individuals' test performance and results. Reasons for nonuptake were enquired. Testing and positive rates were age-adjusted. Determinants of undergoing RAT were identified using univariable and multivariable logistic regression models.ResultsIn total, particulars from 21,769 individuals were reported by 8338 participants. The overall age-adjusted testing rate was 74.94% (95% CI 73.71%-76.18%), with over 80% of participants in the age groups between 45-84 years having self-performed RAT during the campaign period. After age-adjustment, 1.03% (95% CI 0.86%-1.21%) of participants tested positive. The positive rates in the age groups between 20-29 years and >84 years exceeded 2%. Taking into account the positive rate and 5819 reported cases during the period, the cases identified in the campaign might account for 7.65% (95% CI 6.47%-9.14%) of all infections. Testers were more likely to be female, older, not previously diagnosed with COVID-19, and have received COVID-19 vaccination. Adjusting for the number of household members, those living with a child aged <12 years and whose household members were also tested were more likely to have self-performed an RAT. Main reasons for not performing an RAT included the absence of symptoms (598/1108, 53.97%), disbelief of the appropriateness of the campaign as an antiepidemic measure (355/1108, 32.04%), and a recent COVID-19 diagnosis (332/1108, 29.96%).ConclusionsThe residual population burden remained substantial in spite of the clear evidence of a receding epidemic wave. Despite caution in generalization to the Hong Kong population, the high participation rate in mass screening indicated that the voluntary RAT was well accepted, making it a feasible option for implementation as a complementary means of public health surveillance.

Project description:BackgroundRecent studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveal that Omicron variant BA.1 and sub-lineages have revived the concern over resistance to antiviral drugs and vaccine-induced immunity. The present study aims to analyze the clinical profile and genome characterization of the SARS-CoV-2 variant in eastern Uttar Pradesh (UP), North India.MethodsWhole-genome sequencing (WGS) was conducted for 146 SARS-CoV-2 samples obtained from individuals who tested coronavirus disease 2019 (COVID-19) positive between the period of 1 January 2022 and 24 February 2022, from three districts of eastern UP. The details regarding clinical and hospitalized status were captured through telephonic interviews after obtaining verbal informed consent. A maximum-likelihood phylogenetic tree was created for evolutionary analysis using MEGA7.ResultsThe mean age of study participants was 33.9 ± 13.1 years, with 73.5% accounting for male patients. Of the 98 cases contacted by telephone, 30 (30.6%) had a travel history (domestic/international), 16 (16.3%) reported having been infected with COVID-19 in past, 79 (80.6%) had symptoms, and seven had at least one comorbidity. Most of the sequences belonged to the Omicron variant, with BA.1 (6.2%), BA.1.1 (2.7%), BA.1.1.1 (0.7%), BA.1.1.7 (5.5%), BA.1.17.2 (0.7%), BA.1.18 (0.7%), BA.2 (30.8%), BA.2.10 (50.7%), BA.2.12 (0.7%), and B.1.617.2 (1.3%) lineages. BA.1 and BA.1.1 strains possess signature spike mutations S:A67V, S:T95I, S:R346K, S:S371L, S:G446S, S:G496S, S:T547K, S:N856K, and S:L981F, and BA.2 contains S:V213G, S:T376A, and S:D405N. Notably, ins214EPE (S1- N-Terminal domain) mutation was found in a significant number of Omicron BA.1 and sub-lineages. The overall Omicron BA.2 lineage was observed in 79.5% of women and 83.2% of men.ConclusionThe current study showed a predominance of the Omicron BA.2 variant outcompeting the BA.1 over a period in eastern UP. Most of the cases had a breakthrough infection following the recommended two doses of vaccine with four in five cases being symptomatic. There is a need to further explore the immune evasion properties of the Omicron variant.

Dataset Information

Clinical Evaluation of Severe Acute Respiratory Syndrome Coronavirus 2 Rapid Antigen Tests During the Omicron Wave in South Africa.

Publications

Clinical Evaluation of Severe Acute Respiratory Syndrome Coronavirus 2 Rapid Antigen Tests During the Omicron Wave in South Africa.

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