Rapid, early and accurate SARS-CoV-2 detection using RT-qPCR in primary care: a prospective cohort study (REAP-1)

The Diagnostic Performance of Various Clinical Specimens for the Detection of COVID-19: A Meta-Analysis of RT-PCR Studies

BACKGROUND

The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a systematic literature review process.

METHODOLOGY

A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to November 2022. A snowball search on Google, Google Scholar, Research Gate, and MedRxiv, as well as bibliographic research, was performed to identify any other relevant articles. Observational studies that assessed the clinical usefulness of the RT-PCR technique in different human samples for the detection or screening of COVID-19 among patients or patient samples were considered for this review. The primary outcomes considered were sensitivity and specificity, while parameters such as positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient were considered secondary outcomes.

RESULTS

A total of 85 studies out of 10,213 non-duplicate records were included for the systematic review, of which 69 articles were considered for the meta-analysis. The meta-analysis indicated better pooled sensitivity with the nasopharyngeal swab (NPS) than saliva (91.06% vs. 76.70%) and was comparable with the combined NPS/oropharyngeal swab (OPS; 92%). Nevertheless, specificity was observed to be better with saliva (98.27%) than the combined NPS/OPS (98.08%) and NPS (95.57%). The other parameters were comparable among different samples. The respiratory samples and throat samples showed a promising result relative to other specimens. The sensitivity and specificity of samples such as nasopharyngeal swabs, saliva, combined nasopharyngeal/oropharyngeal, respiratory, sputum, broncho aspirate, throat swab, gargle, serum, and the mixed sample were found to be 91.06%, 76.70%, 92.00%, 99.44%, 86%, 96%, 94.4%, 95.3%, 73.63%, and above 98; and 95.57%, 98.27%, 98.08%, 100%, 37%, 100%, 100%, 97.6%, and above 97, respectively.

CONCLUSIONS

NPS was observed to have relatively better sensitivity, but not specificity when compared with other clinical specimens. Head-to-head comparisons between the different samples and the time of sample collection are warranted to strengthen this evidence.

Impact of national-scale targeted point-of-care symptomatic lateral flow testing on trends in COVID-19 infections, hospitalisations and deaths during the second epidemic wave in Austria (REAP3)

BACKGROUND

In October 2020, amidst the second COVID-19 epidemic wave and before the second-national lockdown, Austria introduced a policy of population-wide point-of-care lateral flow antigen testing (POC-LFT). This study explores the impact of this policy by quantifying the association between trends in POC-LFT-activity with trends in PCR-positivity (as a proxy for symptomatic infection), hospitalisations and deaths related to COVID-19 between October 22 and December 06, 2020.

METHODS

We stratified 94 Austrian districts according to POC-LFT-activity (number of POC-LFTs performed per 100,000 inhabitants over the study period), into three population cohorts: (i) high(N = 24), (ii) medium(N = 45) and (iii) low(N = 25). Across the cohorts we a) compared trends in POC-LFT-activity with PCR-positivity, hospital admissions and deaths related to COVD-19; b) compared the epidemic growth rate before and after the epidemic peak; and c) calculated the Pearson correlation coefficients between PCR-positivity with COVID-19 hospitalisations and with COVID -19 related deaths.

RESULTS

The trend in POC-LFT activity was similar to PCR-positivity and hospitalisations trends across high, medium and low POC-LFT activity cohorts, with association with deaths only present in cohorts with high POC-LFT activity. Compared to the low POC-LFT-activity cohort, the high-activity cohort had steeper pre-peak daily increase in PCR-positivity (2.24 more cases per day, per district and per 100,000 inhabitants; 95% CI: 2.0-2.7; p < 0.001) and hospitalisations (0.10; 95% CI: 0.02, 0.18; p = 0.014), and 6 days earlier peak of PCR-positivity. The high-activity cohort also had steeper daily reduction in the post-peak trend in PCR-positivity (-3.6; 95% CI: -4.8, -2.3; p < 0.001) and hospitalisations (-0.2; 95% CI: -0.32, -0.08; p = 0.001). PCR-positivity was positively correlated to both hospitalisations and deaths, but with lags of 6 and 14 days respectively.

CONCLUSIONS

High POC-LFT-use was associated with increased and earlier case finding during the second Austrian COVID-19 epidemic wave, and early and significant reduction in cases and hospitalisations during the second national lockdown. A national policy promoting symptomatic POC-LFT in primary care, can capture trends in PCR-positivity and hospitalisations. Symptomatic POC-LFT delivered at scale and combined with immediate self-quarantining and contact tracing can thus be a proxy for epidemic status, and hence a useful tool that can replace large-scale PCR testing.