Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

Abstract

In this study, we analyzed the sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which has completely replaced other previously circulating variants in the country due to its transmission advantage. Among all the Delta sublineages that were detected, 81.5 % were classified as AY.20, AY.26, and AY.100. According to publicly available data, these only reached a world prevalence of less than 1%, suggesting a possible Mexican origin. The signature mutations of these sublineages are described herein, and phylogenetic analyses and haplotype networks are used to track their spread across the country. Other frequently detected sublineages include AY.3, AY.62, AY.103, and AY.113. Over time, the main sublineages showed different geographical distributions, with AY.20 predominant in Central Mexico, AY.26 in the North, and AY.100 in the Northwest and South/Southeast. This work describes the circulation, from May to November 2021, of the primary sublineages of the Delta variant associated with the third wave of the COVID-19 pandemic in Mexico and highlights the importance of SARS-CoV-2 genomic surveillance for the timely identification of emerging variants that may impact public health.

Regional epidemic dynamics and Delta variant diversity resulted in varying rates of spread of Omicron-BA.1 in Mexico

“…The spread of BA.1.x sublineages in Mexico did not result in the acquisition of specific new mutations nor the clustering of sequences by sublineage or geographical region, in contrast to previous reports on the spread of Alpha and Delta VOCs, which described the emergence of local specific mutations and sublineages, as well as a solid geographical association with those changes [17,18]. The low diversity of Omicron sublineages was probably associated with its unprecedentedly rapid spread across the country.…”

“…Also, in contrast to the N region, no change was observed between the sublineages circulating previously during the Delta peak and in the inter-wave period [18]. The CN region seems to be a transition zone between the N and the CS and SE regions, as it shares a slower replacement and a higher diversity of Delta with the N region.…”

“…Geographical and prevalence differences in the circulation of distinct lineages in Mexico have been previously reported [16][17][18]. The prevalence of B.1.1.519, which dominated the center and south of the country between February and May 2021, was lower in the north [17].…”

“…This factor, rather than lineage diversity per se, could explain the differences in BA. Notably, in the CS and the SE, the proportion of Delta sublineages that circulated during the fourth wave [18], was practically the same than in the inter-wave (W42-Oct to W50-Dec) period.…”

“…This study examines the entry and spread of Omicron BA.1.x, which caused the fourth wave of the pandemic in Mexico, describing a geographically homogeneous dispersion of BA.1.x lineages in contrast with earlier waves [16][17][18]. In addition, it was found that the rate of spread of the BA.1.x lineages varied by region.…”