Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice.

TitleEvaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice.
Publication TypeJournal Article
Year of Publication2023
AuthorsChaves-Blanco, L, de Salazar, A, Fuentes, A, Viñuela, L, Perez-Florido, J, Dopazo, J, García, F
JournalEpidemiol Infect
Volume151
Paginatione201
Date Published2023 Nov 24
ISSN1469-4409
KeywordsAlleles; COVID-19; COVID-19 Testing; Humans; Real-Time Polymerase Chain Reaction; SARS-CoV-2; Sensitivity and Specificity
Abstract

This study aimed to assess the ability of a real-time reverse transcription polymerase chain reaction (RT-PCR) with multiple targets to detect SARS-CoV-2 and its variants in a single test. Nasopharyngeal specimens were collected from patients in Granada, Spain, between January 2021 and December 2022. Five allele-specific RT-PCR kits were used sequentially, with each kit designed to detect a predominant variant at the time. When the Alpha variant was dominant, the kit included the HV69/70 deletion, E and N genes. When Delta replaced Alpha, the kit incorporated the L452R mutation in addition to E and N genes. When Omicron became dominant, L452R was replaced with the N679K mutation. Before incorporating each variant kit, a comparative analysis was carried out with SARS-CoV-2 whole genome sequencing (WGS). The results demonstrated that RT-PCR with multiple targets can provide rapid and effective detection of SARS-CoV-2 and its variants in a single test. A very high degree of agreement (96.2%) was obtained between the comparison of RT-PCR and WGS. Allele-specific RT-PCR assays make it easier to implement epidemiological surveillance systems for effective public health decision making.

DOI10.1017/S095026882300184X
Alternate JournalEpidemiol Infect
PubMed ID37997654
PubMed Central IDPMC10753446