Nucleic acid amplification tests on respiratory samples for the diagnosis of coronavirus infections: a systematic review and meta-analysis

Hellou, Mona Mustafa; Górska, Anna M.; Mazzaferri, Fulvia; Cremonini, Eleonora; Gentilotti, Elisa; Nardo, Pasquale De; Poran, Itamar; Leeflang, Mariska; Tacconelli, Evelina; Paul, Mical

doi:10.1016/j.cmi.2020.11.002

Cited by 81 publications

(55 citation statements)

References 67 publications

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“…We use the term ‘tentative’ re‐infection because a certain number of these cases might reflect false‐positive results in the testing during the first and/or second wave. This is based on the consideration that the specificity (with 95% confidence region) of PCR tests (nucleic acid amplification tests) for SARS‐CoV‐2 is less than 100%, with 98.1% (95.9 to 99.2%) according to a recent meta‐analysis 16 …”

Section: Methodsmentioning

confidence: 99%

SARS‐CoV‐2 re‐infection risk in Austria

Pilz

Chakeri

Ioannidis

et al. 2021

Eur J Clin Investigation

142

179

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Background A key question concerning coronavirus disease 2019 (COVID‐19) is how effective and long lasting immunity against this disease is in individuals who were previously infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). We aimed to evaluate the risk of SARS‐CoV‐2 re‐infections in the general population in Austria. Methods This is a retrospective observational study using national SARS‐CoV‐2 infection data from the Austrian epidemiological reporting system. As the primary outcome, we aim to compare the odds of SARS‐CoV‐2 re‐infections of COVID‐19 survivors of the first wave (February to April 30, 2020) versus the odds of first infections in the remainder general population by tracking polymerase chain reaction (PCR)‐confirmed infections of both groups during the second wave from September 1 to November 30, 2020. Re‐infection counts are tentative, since it cannot be excluded that the positive PCR in the first and/or second wave might have been a false positive. Results We recorded 40 tentative re‐infections in 14 840 COVID‐19 survivors of the first wave (0.27%) and 253 581 infections in 8 885 640 individuals of the remaining general population (2.85%) translating into an odds ratio (95% confidence interval) of 0.09 (0.07 to 0.13). Conclusions We observed a relatively low re‐infection rate of SARS‐CoV‐2 in Austria. Protection against SARS‐CoV‐2 after natural infection is comparable with the highest available estimates on vaccine efficacies. Further well‐designed research on this issue is urgently needed for improving evidence‐based decisions on public health measures and vaccination strategies.

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Section: Methodsmentioning

confidence: 99%

SARS‐CoV‐2 re‐infection risk in Austria

Pilz

Chakeri

Ioannidis

et al. 2021

Eur J Clin Investigation

142

179

View full text Add to dashboard Cite

show abstract

“…This is based on the consideration that the specificity (with 95% confidence region) of PCR tests (nucleic acid amplification tests) for SARS-CoV-2 is less than 100%, with 98.1% (95.9 to 99.2%) according to a recent meta-analysis. 16 The group size of "COVID-19 survivors" was calculated as all individuals who had a positive PCR test result for SARS-CoV-2 minus all reported COVID-19 deaths All rights reserved. No reuse allowed without permission.…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 re-infection risk in Austria

Pilz

Chakeri

Ioannidis

et al. 2021

Preprint

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Background: A key question concerning coronavirus disease 2019 (COVID-19) is how effective and long lasting immunity against this disease is in individuals who were previously infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to evaluate the risk of SARS-CoV-2 re-infections in the general population in Austria. Methods: This is a retrospective observational study using national SARS-CoV-2 infection data from the Austrian epidemiological reporting system. As the primary outcome, we aim to compare the odds of SARS-CoV-2 re-infections of COVID-19 survivors of the first wave (February to April 30, 2020) versus the odds of first infections in the remainder general population by tracking polymerase chain reaction (PCR)-confirmed infections of both groups during the second wave from September 1 to November 30, 2020. Re-infection counts are tentative, since it cannot be excluded that the positive PCR in the first and/or second wave might have been a false positive. Results: We recorded 40 tentative re-infections in 14,840 COVID-19 survivors of the first wave (0.27%) and 253,581 infections in 8,885,640 individuals of the remaining general population (2.85%) translating into an odds ratio (95% confidence interval) of 0.09 (0.07 to 0.13). Conclusions: We observed a relatively low re-infection rate of SARS-CoV-2 in Austria. Protection against SARS-CoV-2 after natural infection is comparable to the highest available estimates on vaccine efficacies. Further well-designed research on this issue is urgently needed for improving evidence-based decisions on public health measures and vaccination strategies.

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“…Reverse-transcriptase PCR (RT-PCR) tests, which identify viral RNA, are the current gold standard for diagnosis of SARS-CoV-2 infection but pose different challenges including test speed and the requirement of a skilled laboratory operator (7) . LAMP (loop-mediated isothermal amplification) assays improve on RT-PCR timings but with an associated reduction in sensitivity (8) . All current viral detection tests rely on swabbing of nasopharyngeal and/or oropharyngeal mucosa, the effectiveness of which is operator-dependent and prone to sampling variability.…”

Section: Introductionmentioning

confidence: 99%

Blood transcriptional biomarkers of acute viral infection for detection of pre-symptomatic SARS-CoV-2 infection

Rosenheim

Bell

et al. 2021

Preprint

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We hypothesised that host-response biomarkers of viral infections may contribute to early identification of SARS-CoV-2 infected individuals, critical to breaking chains of transmission. We identified 20 candidate blood transcriptomic signatures of viral infection by systematic review and evaluated their ability to detect SARS-CoV-2 infection, compared to the gold-standard of virus PCR tests, among a prospective cohort of 400 hospital staff subjected to weekly testing when fit to attend work. The transcriptional signatures had limited overlap, but were mostly co-correlated as components of type 1 interferon responses. We reconstructed each signature score in blood RNA sequencing data from 41 individuals over sequential weeks spanning a first positive SARS-CoV-2 PCR, and after 6-month convalescence. A single blood transcript for IFI27 provided the highest accuracy for discriminating individuals at the time of their first positive viral PCR result from uninfected controls, with area under the receiver operating characteristic curve (AUROC) of 0.95 (95% confidence interval 0.91–0.99), sensitivity 0.84 (0.7–0.93) and specificity 0.95 (0.85–0.98) at a predefined test threshold. The test performed equally well in individuals with and without symptoms, correlated with viral load, and identified incident infections one week before the first positive viral PCR with sensitivity 0.4 (0.17–0.69) and specificity 0.95 (0.85–0.98). Our findings strongly support further urgent evaluation and development of blood IFI27 transcripts as a biomarker for early phase SARS-CoV-2 infection, for screening individuals such as contacts of index cases, in order to facilitate early case isolation and early antiviral treatments as they emerge.

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Nucleic acid amplification tests on respiratory samples for the diagnosis of coronavirus infections: a systematic review and meta-analysis

Cited by 81 publications

References 67 publications

SARS‐CoV‐2 re‐infection risk in Austria

SARS‐CoV‐2 re‐infection risk in Austria

SARS-CoV-2 re-infection risk in Austria

Blood transcriptional biomarkers of acute viral infection for detection of pre-symptomatic SARS-CoV-2 infection

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