Study finds minimal impact of SARS-CoV-2 genome variability on current diagnostic molecular systems ResearchSquare ELTE_UNI embl emblebi
By Neha MathurMar 29 2023Reviewed by Lily Ramsey, LLM *Important notice: Research Square publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.
As different variants emerge with multiple genetic mutations, it might reduce the effectiveness of a specific RT-PCR primer set targeted to detect them in the SARS-CoV-2 viral populations spread across different geographical regions furthermore. Also, it might result in false-negative results during RT-PCR detection. Thus, it is crucial to continuously monitor the genetic variations in RT-PCR primer/probe regions using genomic sequences from SARS-CoV-2 isolates collected worldwide.
They retrieved 987,138 samples from the CoVEO database collected between 1 January and 31 December 2021. This database compiles data of good-quality genomic samples of highly-reliable variants, which helped the researchers distinguish between harmless/neutral and possibly damaging mutations. In addition, the CoVEO database provided a fast and direct mutation retrieval compared to databases containing only the consensus sequences of the samples.
To monitor whether samples with high-risk mutations in the TRs of the different primer sets were becoming more frequent, they plotted the proportion of samples having a slight chance of misclassification and being susceptible to misclassification. In addition, examining the type and location of the detected variants in the TRs of different primer systems helped the researchers categorize them as high or moderate-risk mutations.
Strikingly, the frequency of samples prone to misclassification changed during the study period with the advent of SARS-CoV-2 VoCs with highly diverse mutational profiles. Thus, there is a need for continuously reevaluating RT-PCR efficacy and updating the primer sets used in clinical and commercial settings, as required.
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