Systematic review with meta-analysis of the accuracy of diagnostic tests for COVID-19

Böger, Beatriz; Fachi, Mariana Millan; Vilhena, Raquel O.; Cobre, Alexandre de Fátima; Tonin, Fernanda S.; Pontarolo, Roberto

doi:10.1016/j.ajic.2020.07.011

Cited by 443 publications

(482 citation statements)

References 36 publications

(99 reference statements)

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“…Furthermore, our rates of growth in prevalence of the virus were similar among symptomatic people and those without symptoms who would be largely ineligible for testing through the routine 'test and trace' programme. An additional limitation is that a nose and throat swab may have limited sensitivity (~70% to 80%) [7] to detect virus, but this should not affect trends in prevalence within or between rounds.…”

Section: Discussionmentioning

confidence: 99%

High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study

Riley

Ainslie

Eales

et al. 2020

Preprint

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Background: REACT-1 is a community survey of PCR confirmed swab-positivity for SARS-CoV-2 among random samples of the population in England. This interim report includes data from the fifth round of data collection currently underway for swabs sampled from the 18th to 26th September 2020. Methods: Repeated cross-sectional surveys of random samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 160,000 people in each round of data collection. Collection of self-administered nose and throat swab for PCR and questionnaire data. Prevalence of swab-positivity by round and by demographic variables including age, sex, region, ethnicity. Estimation of reproduction number (R) between and within rounds, and time trends using exponential growth or decay model. Assessment of geographical clustering based on boundary-free spatial model. Results: Over the 9 days for which data are available, we find 363 positives from 84,610 samples giving a weighted prevalence to date of 0.55% (0.47%, 0.64%) in round 5. This implies that 411,000 (351,000, 478,000) people in England are virus-positive under the assumption that the swab assay is 75% sensitive. Using data from the most recent two rounds, we estimate a doubling time of 10.6 (9.4, 12.0) days covering the period 20th August to 26th September, corresponding to a reproduction number R of 1.47 (1.40, 1.53). Using data only from round 5 we estimate a reproduction number of 1.06 (0.74, 1.46) with probability of 63% that R is greater than 1. Between rounds 4 and 5 there was a marked increase in unweighted prevalence at all ages. In the most recent data, prevalence was highest in the 18 to 24 yrs age group at 0.96% (0.68%, 1.36%). At 65+ yrs prevalence increased ~7-fold between rounds 4 and 5 from 0.04% (0.03%, 0.07%) to 0.29% (0.23%, 0.37%). Prevalence increased in all regions between rounds 4 and 5, giving the highest unweighted prevalence in round 5 in the North West at 0.86% (0.69%, 1.06%). In London, prevalence increased ~5-fold from 0.10% (0.06%, 0.17%) to 0.49% (0.36%, 0.68%). Regional R values ranged from 1.32 (1.16,1.50) in Yorkshire and the Humber to 1.63 (1.42, 1.88) in the East Midlands over the same period. In the most recent data, there was extensive clustering in the North West, Midlands and in and around London with pockets of clustering in other regions including the South West, North East and East of England. Odds of swab-positivity were ~2-fold higher in people of Asian and Black ethnicity compared with white participants. Conclusion: Rapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.

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Section: Discussionmentioning

confidence: 99%

High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study

Riley

Ainslie

Eales

et al. 2020

Preprint

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“…[20] Primary clinical performance data Eight systematic reviews were identified, including one by health technology assessment bodies not listed as a peer-reviewed study, and the primary studies included in the analysis extracted. [6][7][8][9][21][22][23][24] The full list of studies in the FIND and EC databases was retrieved on 22 August 2020. Pubmed was searched on the same date.…”

Section: Resultsmentioning

confidence: 99%

Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020

Walle

Leitmeyer

Broberg

2020

Preprint

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We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width ≤5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity ≤95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Analogously, 9 nucleic acid tests and 25 antibody tests, among which 12 point of care tests, had a clinical specificity of ≤98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid and antigen point of care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width ≤5%, and lower for nucleic acid tests than antibody tests. Manufacturer reported clinical performance was significantly higher than independently assessed in 11/32 (34.4%) and 4/34 (11.8%) cases for sensitivity and specificity respectively, indicating a need for improvement in this area. Continuous monitoring of clinical performance within more clearly defined target populations is needed.

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“…To select the optimal pool size we used the web-based shiny application from Christopher Bilder available at https://www.chrisbilder.com/shiny/ under Hierarchical testing. Assuming a SARS-CoV- 2 prevalence of 4% in our query samples (see later in results section on observed test positivity rate, Figure 1 ), test sensitivity of 90%, test specificity of 98% 18 , adoption of a two stage pooling algorithm ( Figure 2 ) and a pre-specified preferred pool size range of 3-10, the algorithm calculated the optimal testing configuration was a pool size of n=6 followed by individual testing of samples in positive pools.…”

Section: Methodsmentioning

confidence: 99%

Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Agoti¹,

Mutunga²,

Lambisia³

et al. 2020

Wellcome Open Res

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Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.

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Systematic review with meta-analysis of the accuracy of diagnostic tests for COVID-19

Cited by 443 publications

References 36 publications

High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study

High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study

Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020

Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

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