Impact of sampling site on diagnostic test accuracy of RT-PCR in diagnosing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection since the emergence of omicron: a systematic review and meta-analysis

Abstract

Nasopharyngeal sampling (NP) is the routine standard for SASR-CoV-2 detection using reverse transcription polymerase chain reaction (RT-PCR). In this systematic review, we assessed diagnostic test accuracy of alternative sampling sites compared to NP for RT-PCR testing of Omicron (sub)-variants.We systematically searched for studies from January 2022 until February 2023 investigating any type of respiratory sample for RT-PCR in people with suspected, known, or known absence of SARS-CoV-2 Omicron infection. Data were pooled for each comparison using the bivariate model, sensitivity and specificity was estimated with 95% confidence intervals (CIs). Risk of bias was assessed with QUADAS-2 tool, certainty of evidence with GRADE.We included three cohort-type cross-sectional studies (1,003 participants). Saliva versus NP sampling in three studies showed a sensitivity of 92% (95% CI 87% to 96%) and a specificity of 94% (95% CI 83% to 98%). AN versus NP sampling in one study showed a sensitivity of 90% (95% CI 82% to 95%) and a specificity of 99% (95% CI 95% to 100%). Certainty of evidence for sensitivity and specificity of both comparisons was low to very low.Based on the current very low- to low-certainty evidence, we are uncertain about accuracy of different sampling sites for RT-PCR.