Frequency of SARS-CoV-2 variants identified by real-time PCR in the AUNA healthcare network, Peru

Abstract

IntroductionIn Peru, on 11 February 2023, the Ministry of Health registered 4 million patients infected with COVID-19 and around 219,260 deaths. In 2020, the SARS-CoV-2 virus was acquiring mutations that impacted the properties of transmissibility, infectivity, and immune evasion, leading to new lineages. In the present study, the frequency of COVID-19 variants was determined during 2021 and 2022 in patients treated in the AUNA healthcare network.MethodsThe methodology used to detect mutations and identify variants was the Allplex™ SARS-CoV-2 Variants Assay I, II, and VII kit RT-PCR. The frequency of variants was presented by epidemiological weeks.ResultsIn total, 544 positive samples were evaluated, where the Delta, Omicron, and Gamma variants were identified. The Delta variant was found in 242 (44.5%) patients between epidemiological weeks 39 and 52 in 2021. In the case of Gamma, it was observed in 8 (1.5%) patients at weeks 39, 41, 43, 45, and 46 of 2021. The Omicron variant was the most frequent with 289 (53.1%) patients during weeks 49 to 52 of 2021 and 1 to 22 of 2022. During weeks 1 through 22 of 2022, it was possible to discriminate between BA. 1 (n = 32) and BA.2 (n = 82).ConclusionThe rapid identification of COVID-19 variants through the RT-PCR methodology contributes to timely epidemiological surveillance, as well as appropriate patient management.