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.

Keywords: SARS-CoV-2; delta variant; genomic surveillance; variants of concern.

Figure 1

SARS-CoV-2 cases and diversity of Delta variant viruses in Mexico. (A) Confirmed cases, deaths, and total genomes sequenced between 1 March 2020, and 30 November 2021 in the country. (B) Stacked area plot showing the lineage diversity from April to November 2021. Vertically, lineages are stacked on top of one another. The black line corresponds to the total Delta genomes reported and the dashed red line to the number of confirmed cases for context.

Figure 2

Density plots of relative lineage distribution by geographical region, considering sequences from January to November 2021. (A) Northwest, (B) Northeast, (C) Central North, (D) Central South, (E) West, (F) South, and (G) Southeast.

Figure 3

Frequency of aa changes in SARS-CoV-2 genome sequences of Mexico compared with the Wuhan reference genome (NC_045512). Only changes above 5% prevalence in at least one of the sublineages are shown. * Denotes an stop codon. The Delta-defining substitutions are marked with #.

Figure 4

Haplotype network using mutations from AY.20, AY.26, and AY.100 sublineages in Mexico and worldwide. Colors indicate the Mexican regions sequences were isolated, with yellow and gray circles representing the USA and the rest of the world, respectively. The size of the circles indicates the number of samples within the same haplotype (scale is provided). Main subclusters within each lineage are marked with black discontinuous circles, and their specific mutations are indicated in blue.

Figure 5

Map series showing the spatiotemporal distribution of the most prevalent Delta sublineages in Mexico. (A) Sublineage AY.20, (B) sublineage AY.26, (C) sublineage AY.100. The prevalence was calculated for each state over time.