ABSTRACT
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
ABSTRACT
Early detection of SARS-CoV-2 infection is crucial to prevent the spread of the virus. In this study, we evaluated the performance of a commercial rapid antigen detection test, BD Veritor, and compared this (and another rapid test, Standard Q) against a gold-standard of nasopharyngeal (NP) swab tested by reverse transcription-polymerase chain reaction (RT-PCR) in prospectively-recruited adults in Dhaka, Bangladesh. We compared the sensitivity and specificity of the two rapid antigen tests against RT-PCR results in 130 symptomatic and 130 asymptomatic adults. In addition, we evaluated the suitability and ease-of-use of the BD Veritor test in a subsample of study participants (n=42) and implementers (n=5). The sensitivity of the BD Veritor rapid antigen test was 70% in symptomatic (95% confidence interval [CI]: 51-85%) and 87% (95% CI: 69-96%) in asymptomatic individuals with positive SARSCoV-2 RT-PCR, for overall sensitivity of 78% (95% CI: 66-88%). The sensitivity of the Standard Q rapid antigen test was 63% (95% CI: 44-80%) in symptomatic and 73% (95% CI: 54-87%) in asymptomatic individuals. One false positive in BD Veritor test (specificity 99.5) and no false positive in Standard Q tests were observed (specificity 100%). The BD Veritor rapid antigen test was 78% sensitive when compared with RT-PCR irrespective of the cycle threshold (Ct) levels in this evaluation in Bangladesh. The implementation evaluation data showed good acceptability in the field settings. This warrants large field evaluation as well as use of the rapid antigen test for quick assessment of SARS-CoV-2 for containment of epidemics in the country.
ABSTRACT
BackgroundThe COVID-19 pandemic has resulted in a need for rapid identification of infectious cases. Testing barriers have prohibited adequate screening for SARS COV2, resulting in significant delays in treatment provision and commencement of outbreak control measures. This study aimed to generate evidence on the performance and implementation characteristics of the BD Veritor rapid antigen test as compared to the gold standard test for diagnosis of SARS COV2 in Kenya. MethodsThis was a field test performance evaluation in symptomatic and asymptomatic adults undergoing testing for SARS COV2. Recruited participants were classified as SARS-CoV2-positive based on the locally implemented gold standard reverse transcription polymerase chain reaction (RT-PCR) test performed on nasopharyngeal swabs. 272 antigen tests were performed with simultaneous gold standard testing, allowing us to estimate sensitivity, specificity, positive and negative predictive values for the BD Veritor rapid antigen test platform. Implementation characteristics were assessed using the Consolidated Framework for Implementation Research for feasibility, acceptability, turn-around time, and ease-of-use metrics. Results and DiscussionWe enrolled 97 PCR negative symptomatic and 128 PCR negative asymptomatic, and 28 PCR positive symptomatic and 19 PCR positive asymptomatic participants. Compared to the gold standard, the sensitivity of the BD Veritor antigen test was 94% (95% confidence interval [CI] 86.6 to 100.0) while the specificity was 98% (95% confidence interval [CI] 96 to 100). The sensitivity of BD Veritor antigen test was higher among symptomatic (100%) compared to asymptomatic (84%) participants, although this difference was not statistically significant. There was also a lack of association between cycle threshold value and sensitivity of BD Veritor test. The BD Veritor test had quick turnaround time and minimal resource requirements, and laboratory personnel conducting testing felt that it was easier to use than the gold standard RT-PCR. ConclusionThe BD Veritor rapid antigen test exhibited excellent sensitivity and specificity when used to detect SARS-CoV-2 infection among both symptomatic and asymptomatic individuals in varied population settings in Kenya. It was feasible to implement and easy to use, with rapid turnaround time.
ABSTRACT
BackgroundEffective vaccine-based containment strategies for SARS-CoV-2 require equitable coverage of communities at greatest risk of infection. We sought to examine the alignment of vaccination and SARS-CoV-2 risk in Massachusetts to inform public health response. MethodsWe aggregated cumulative SARS-CoV-2 testing and vaccination data from the Massachusetts Department of Public Health and the Boston Public Health Commission from January 29, 2020 to April 9, 2021. We used two approaches to assess vaccination equity: vaccination-to-infection risk (VIR) ratio and Lorenz curves. The VIR ratio was calculated for each community as the quotient of the number of fully vaccinated individuals divided by the cumulative number of confirmed SARS-CoV-2 infections. Lorenz curves were used to describe vaccination relative to COVID-19 burden. A multivariable Poisson model was used to assess predictors of VIR ratio. ResultsA total of 607,120 (8.9%) SARS-CoV-2 infections were confirmed in Massachusetts residents and 1,485,266 (21.8%) residents were fully vaccinated. Communities with increased socioeconomic vulnerability had lower VIR ratios indicating less equitable vaccination relative to infection risk. In multivariable analysis, decreased vaccination relative to infection risk was independently associated with increasing socioeconomic vulnerability (aRR 0.82 per quartile increase, 95% CI 0.77 to 0.87) and with greater than 20% of the community identified as Black and/or Latinx (aRR 0.67, 95% CI 0.56 to 0.81). Improved community vaccine delivery was associated with higher community proportion of residents aged 65 or older (aRR 1.23 per 5% increase in proportion, 95% CI 1.15 to 1.31). Lorenz curves indicated considerable inequity (Gini 0.46 between communities). An estimated 330,000 full vaccination courses would need to be diverted to under-vaccinated communities to achieve equity. ConclusionIn conclusion, disparities in vaccine delivery highlight ongoing inequities in our approach to COVID-19 and imperil efforts to control the pandemic.
ABSTRACT
ObjectiveEarly deficiencies in testing capacity contributed to poor control of transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the context of marked improvement in SARS-CoV-2 testing infrastructure, we sought to examine the alignment of testing with epidemic intensity to mitigate subsequent waves of COVID-19 in Massachusetts. MethodsWe compiled publicly available weekly SARS-CoV-2 molecular testing data for period (May 27 to October 14, 2020) following the initial COVID-19 wave. We defined testing intensity as weekly SARS-CoV-2 tests performed per 100,000 population and used weekly test positivity (percent of tests positive) as a measure of epidemic intensity. We considered optimal alignment of testing resources to be matching community ranks of testing and positivity. In communities with a lower rank of testing than positivity in a given week, the testing gap was calculated as the additional tests required to achieve matching ranks. Multivariable Poisson modeling was utilized to assess for trends and association with community characteristics. ResultsDuring the observation period, 4,262,000 tests were reported in Massachusetts and the misalignment of testing with epidemic intensity increased. The weekly testing gap increased 9.0% per week (adjusted rate ratio [aRR]: 1.090, 95% confidence interval [CI]: 1.08-1.10). Increasing levels of community socioeconomic vulnerability (aRR: 1.35 per quartile increase, 95% CI: 1.23-1.50) and the highest quartile of minority and language vulnerability (aRR: 1.46, 95% CI 0.96-1.49) were associated with increased testing gaps, but the latter association was not statistically significant. Presence of large university student population (>10% of population) was associated with a marked decrease in testing gap (aRR 0.21, 95% CI: 0.12-0.38). ConclusionThese analyses indicate that despite objectives to promote equity and enhance epidemic control in vulnerable communities, testing resources across Massachusetts have been disproportionally allocated to more affluent communities. Worsening structural inequities in access to SARS-CoV-2 testing increase the risk for another intense wave of COVID-19 in Massachusetts, particularly among vulnerable communities.
