Omicron-BA.1 Dispersion Rates in Mexico Varied According to the Regional Epidemic Patterns and the Diversity of Local Delta Subvariants

Abstract

Purpose: The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented. Methods: The time to fixation of BA.1, the diversity of Delta sublineages, the population density, and the level of virus circulation during the inter-wave interval were determined to analyze differences in BA.1 spread. Results: BA.1 began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in Mexico. Unlike previous variants, BA.1 did not exhibit a geographically distinct circulation pattern. However, a regional difference in the speed of the replacement of the Delta variant was observed. Conclusions: Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics, in addition to population density. Nonetheless, if there is a significant difference in the fitness of the variants, or if the time allowed for the competition is sufficiently long, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico.

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico

“…The circulation of the SARS-CoV-2 variants in Mexico during the first 2 years of the pandemic has been described previously [25, 39–41]. depicts the relative frequency of subvariants in Mexico between April and August 2022, which includes the last inter-wave period and the fifth wave.…”

“…Genomic surveillance is therefore required to monitor the development and evolution of novel variants, which helps to assess the efficacy of diagnostic methods, the potential of immune escape, and the transmissibility of the virus. As previously described, the BA.1 variant (and its descending subvariants) caused Mexico’s fourth wave of infections [ 25 ]. On the other hand, BA.5 and, to a lesser extent, BA.4 were responsible for the fifth wave.…”

Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover

“…Interestingly, average coinfections dropped during the fourth wave, having the largest record of COVID-19 cases in Mexico so far. This may have been due to the swift turnover event of Omicron’s sweep, which superseded Delta almost entirely in only 2 weeks, leaving no chance for any other variant to compete, as has been suggested previously [ 33 ]. In the period that followed, coinfections mirrored the diversification of the Omicron variants throughout waves five and six, although only the primary variants managed to capture this more accurately.…”

Differences in the Evolution of Clinical, Biochemical, and Hematological Indicators in Hospitalized Patients with COVID-19 According to Their Vaccination Scheme: A Cohort Study in One of the World’s Highest Hospital Mortality Populations

“…During the study period (January 2021 to December 2022), various variants of COVID-19 affected the population of Mexico (research site) [ 24 , 25 , 26 ]. Considering the predominant variants, Figure 2 shows that the severity of the disease did not vary significantly in non-vaccinated patients during different periods ( p = 0.080, ANOVA test).…”

“…In the period when the Delta variant was predominant, vaccinated patients experienced higher severity than the non-vaccinated, exhibiting the opposite trend in other periods. Periods were established based on the predominant variants in the general population of Mexico ([ 24 , 25 , 26 ]; January–July 2021: B.1.1.222; B.1.1.519; and Gamma. August–December 2021: Delta.…”