tetano
Editor, Senior Moderator
Pathogens
. 2022 Apr 12;11(4):462.
doi: 10.3390/pathogens11040462.
Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant-Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times
Rok Kogoj[SUP] 1 [/SUP], Misa Korva[SUP] 1 [/SUP], Nataša Knap[SUP] 1 [/SUP], Katarina Resman Rus[SUP] 1 [/SUP], Patricija Pozvek[SUP] 1 [/SUP], Tatjana Avšič-Županc[SUP] 1 [/SUP], Mario Poljak[SUP] 1 [/SUP]
Affiliations
Abstract
Several professional societies advise against using real-time Reverse-Transcription PCR (rtRT-PCR) cycle threshold (Ct) values to guide clinical decisions. We comparatively assessed the variability of Ct values generated by six diagnostic approaches by testing serial dilutions of well-characterized isolates of 10 clinically most relevant SARS-CoV-2 genomic variants: Alpha, Beta, Gamma, Delta, Eta, Iota, Omicron, A.27, B.1.258.17, and B.1 with D614G mutation. Comparison of three fully automated rtRT-PCR analyzers and a reference manual rtRT-PCR assay using RNA isolated with three different nucleic acid isolation instruments showed substantial inter-variant intra-test and intra-variant inter-test variability. Ct value differences were dependent on both the rtRT-PCR platform and SARS-CoV-2 genomic variant. Differences ranging from 2.0 to 8.4 Ct values were observed when testing equal concentrations of different SARS-CoV-2 variants. Results confirm that Ct values are an unreliable surrogate for viral load and should not be used as a proxy of infectivity and transmissibility, especially when different rtRT-PCR assays are used in parallel and multiple SARS-CoV-2 variants are circulating. A detailed turn-around time (TAT) comparative assessment showed substantially different TATs, but parallel use of different diagnostic approaches was beneficial and complementary, allowing release of results for more than 81% of non-priority samples within 8 h after admission.
Keywords: Ct value; coronavirus disease 19 (COVID-19); genomic variant; real-time RT-PCR; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); turn-around time.
. 2022 Apr 12;11(4):462.
doi: 10.3390/pathogens11040462.
Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant-Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times
Rok Kogoj[SUP] 1 [/SUP], Misa Korva[SUP] 1 [/SUP], Nataša Knap[SUP] 1 [/SUP], Katarina Resman Rus[SUP] 1 [/SUP], Patricija Pozvek[SUP] 1 [/SUP], Tatjana Avšič-Županc[SUP] 1 [/SUP], Mario Poljak[SUP] 1 [/SUP]
Affiliations
- PMID: 35456137
- PMCID: PMC9029830
- DOI: 10.3390/pathogens11040462
Abstract
Several professional societies advise against using real-time Reverse-Transcription PCR (rtRT-PCR) cycle threshold (Ct) values to guide clinical decisions. We comparatively assessed the variability of Ct values generated by six diagnostic approaches by testing serial dilutions of well-characterized isolates of 10 clinically most relevant SARS-CoV-2 genomic variants: Alpha, Beta, Gamma, Delta, Eta, Iota, Omicron, A.27, B.1.258.17, and B.1 with D614G mutation. Comparison of three fully automated rtRT-PCR analyzers and a reference manual rtRT-PCR assay using RNA isolated with three different nucleic acid isolation instruments showed substantial inter-variant intra-test and intra-variant inter-test variability. Ct value differences were dependent on both the rtRT-PCR platform and SARS-CoV-2 genomic variant. Differences ranging from 2.0 to 8.4 Ct values were observed when testing equal concentrations of different SARS-CoV-2 variants. Results confirm that Ct values are an unreliable surrogate for viral load and should not be used as a proxy of infectivity and transmissibility, especially when different rtRT-PCR assays are used in parallel and multiple SARS-CoV-2 variants are circulating. A detailed turn-around time (TAT) comparative assessment showed substantially different TATs, but parallel use of different diagnostic approaches was beneficial and complementary, allowing release of results for more than 81% of non-priority samples within 8 h after admission.
Keywords: Ct value; coronavirus disease 19 (COVID-19); genomic variant; real-time RT-PCR; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); turn-around time.