tetano
Editor, Senior Moderator
PLoS One
. 2024 Jan 12;19(1):e0294271.
doi: 10.1371/journal.pone.0294271. eCollection 2024. Monitoring SARS-CoV-2 genetic variability: A post-market surveillance workflow for combined bioinformatic and laboratory evaluation of commercial RT-PCR assay performance
Barbara Kosińska-Selbi[SUP] 1 [/SUP], Justyna Kowalczyk[SUP] 1 [/SUP], Jagoda Pierscińska[SUP] 1 [/SUP], Jarosław Wełeszczuk[SUP] 1 [/SUP], Luis Peñarrubia[SUP] 2 [/SUP], Benjamin Turner[SUP] 3 [/SUP], Josep Pareja[SUP] 2 [/SUP], Roberto Porco[SUP] 2 [/SUP], Rubi Diaz-Hernandez[SUP] 2 [/SUP], Martí Juanola-Falgarona[SUP] 2 [/SUP], Melisa Rey[SUP] 2 [/SUP], Davide Manissero[SUP] 4 [/SUP], Anna Blacha[SUP] 4 [/SUP]
Affiliations
Objective: The speed at which Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is mutating has made it necessary to frequently assess how these genomic changes impact the performance of diagnostic real-time polymerase chain reaction (RT-PCR) assays. Herein, we describe a generic three-step workflow to assess the effect of genomic mutations on inclusivity and sensitivity of RT-PCR assays.
Methods: Sequences collected from the Global Initiative on Sharing All Influenza Data (GISAID) were mapped to a SARS-CoV-2 reference genome to evaluate the position and prevalence of mismatches in the oligonucleotide-binding sites of the QIAstat-Dx, an RT-PCR panel designed to detect SARS-CoV-2. The frequency of mutations and their impact on melting temperature were assessed, and sequences flagged by risk-based criteria were examined in vitro.
Results: Out of 8,900,393 SARS-CoV-2 genome sequences analyzed, only 173 (0.0019%) genomes contained potentially critical mutations for the QIAstat-Dx; follow-up in-vitro testing confirmed no impact on the assays' performance.
Conclusions: The current study demonstrates that SARS-CoV-2 genetic variants do not affect the performance of the QIAstat-Dx device. It is recommended that manufacturers incorporate this workflow into obligatory post-marketing surveillance activities, as this approach could potentially enhance genetic monitoring of their product.
. 2024 Jan 12;19(1):e0294271.
doi: 10.1371/journal.pone.0294271. eCollection 2024. Monitoring SARS-CoV-2 genetic variability: A post-market surveillance workflow for combined bioinformatic and laboratory evaluation of commercial RT-PCR assay performance
Barbara Kosińska-Selbi[SUP] 1 [/SUP], Justyna Kowalczyk[SUP] 1 [/SUP], Jagoda Pierscińska[SUP] 1 [/SUP], Jarosław Wełeszczuk[SUP] 1 [/SUP], Luis Peñarrubia[SUP] 2 [/SUP], Benjamin Turner[SUP] 3 [/SUP], Josep Pareja[SUP] 2 [/SUP], Roberto Porco[SUP] 2 [/SUP], Rubi Diaz-Hernandez[SUP] 2 [/SUP], Martí Juanola-Falgarona[SUP] 2 [/SUP], Melisa Rey[SUP] 2 [/SUP], Davide Manissero[SUP] 4 [/SUP], Anna Blacha[SUP] 4 [/SUP]
Affiliations
- PMID: 38215170
- PMCID: PMC10786374
- DOI: 10.1371/journal.pone.0294271
Objective: The speed at which Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is mutating has made it necessary to frequently assess how these genomic changes impact the performance of diagnostic real-time polymerase chain reaction (RT-PCR) assays. Herein, we describe a generic three-step workflow to assess the effect of genomic mutations on inclusivity and sensitivity of RT-PCR assays.
Methods: Sequences collected from the Global Initiative on Sharing All Influenza Data (GISAID) were mapped to a SARS-CoV-2 reference genome to evaluate the position and prevalence of mismatches in the oligonucleotide-binding sites of the QIAstat-Dx, an RT-PCR panel designed to detect SARS-CoV-2. The frequency of mutations and their impact on melting temperature were assessed, and sequences flagged by risk-based criteria were examined in vitro.
Results: Out of 8,900,393 SARS-CoV-2 genome sequences analyzed, only 173 (0.0019%) genomes contained potentially critical mutations for the QIAstat-Dx; follow-up in-vitro testing confirmed no impact on the assays' performance.
Conclusions: The current study demonstrates that SARS-CoV-2 genetic variants do not affect the performance of the QIAstat-Dx device. It is recommended that manufacturers incorporate this workflow into obligatory post-marketing surveillance activities, as this approach could potentially enhance genetic monitoring of their product.