Relative prevalence of delH69V70 among SARS-CoV-2 infected individuals during the initial Omicron wave in Ecuador
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Date
2023
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Publisher
PUCE - Quito
Abstract
Background: The SARS-CoV-2 transmission dynamics in Ecuador was profoundly affected by the arrival of the Omicron variant, whose high transmissibility allowed it to overtake the much more virulent Delta variant. The delH69V70 mutation, which is found in the Omicron 21K variant, allows the virus to spread efficiently in the population due to its capability of increase the tolerance of mutations related to the immune escape and improving the infection.
Methods: Between December, 2021, and May 2022, 44,670 samples were analyzed for SARS-CoV-2 infection at the Pontificia Universidad Católica del Ecuador Molecular Diagnostic Laboratory (MLD-PUCE), in Quito, Ecuador. RNA remnants from 1,693 SARS-CoV-2 positive samples were further tested using sets of primers designed to discriminate the presence absence of five specific SARS-CoV-2 mutations (delH69V70, E484K, K417N, L452R and N501Y), which in turn allow for discrimination of six variants (Delta, Mu, Omicron 21K, Omicron 22A/22B, Omicron 21L and Omicron 22C).
Results: Fifty SARS-CoV-2 positive samples did not display any of the mutations detectable with the qPCR testing scheme employed in the study. One-hundred sixty-two samples carried the Delta (L425R) mutation. Five of them carried the MU/GAMMA (N501Y/E484K) mutation pattern. Most of the studied samples (1,375) carried the delH69V70 mutation, suggestive of Omicron 21K. Eighty-five samples carried the N501Y and K417N mutations. Two samples carried delH69V70 and L452R mutations, and 8 of them carried the N501Y, K417N and L452R mutations.
Discussion: Our results indicate that the arrival of the Omicron variant to Ecuador is associated with a sudden increase in cases between December 2021 and March 2022. Our data suggest Omicron replaced Delta as the predominant variant in the country in just 6 days (4 since it was first detected in MDL-PUCE). The prevalence of the Omicron variant among our dataset correlates well with data form the Ecuadorian Ministry of Health indicating a sharp increase of COVID-19 cases in the country. This investigation showcases the impact of Omicron´s transmissibility on the dynamics of COVID-19 in Ecuador.
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Keywords
SARS-CoV-2, COVID-19 (Enfermedad) - Epidemiología, Virus - Variación, Genética viral, Coronavirus - Genética, Reacción en cadena de la polimerasa de transcriptasa inversa, Glicoproteína de la espiga del coronavirus, Transmisión de enfermedad infecciosa - Ecuador