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

Abstract

A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of concern (VOCs) Alpha, Gamma, Delta, and Omicron. A total of 379 coinfection events were recorded in the dataset (a rate of 1.28 %), resulting in the first such catalogue in Mexico. The most common putative coinfections occurred during the spread of Delta or after the introduction of Omicron BA.2 and its descendants. Coinfections occurred constantly during periods of variant turnover when more than one variant shared the same niche and high infection rate was observed, which was dependent on the local variants and time. Coinfections might occur at a higher frequency than customarily reported, but they are often ignored as only the consensus sequence is reported for lineage identification.

Keywords: Mexico; SARS-CoV-2; coinfections; genomic surveillance; viral quasispecies.

Fig. 1.. Daily average of sequenced genomes produced by CoViGen-Mex and new COVID-19 positive cases in Mexico. The stacked area plots depict the distribution of novel daily genomes sequenced (scale in left y-axis) based on their collection date and coloured by variant group. The dashed line shows the daily positive COVID-19 cases in the official Mexican epidemiological data (scale in the right y-axis). Both sets were reported by collection date and are presented in a sliding 7 day average window with a step of 1 day. Areas are stacked, having no group overlap. Epidemiological waves marked with bars at the bottom are defined as follows: Wave 1 (5 May – 4 October 2020; peak on 18 July 2020 [7 275.29 average daily cases]). Wave 2 (5 October 2020 – 27 April 2021; peak on 10 January 2021 [16 010.00 cases]). Wave 3 (11 June – 4 November 2021; peak on 10 August 2021 [19 305.86 cases]). Wave 4 (23 December 2021 – 22 March 2022; peak on 15 January 2022 [62 134.71 cases]). Wave 5 (15 May 2022 – 6 September 2022; peak on 10 July 2022 [30 824.43 cases]). Wave 6 (22 November 2022 – 27 January 2023; peak on 20 December 2022 [4 850.00 cases]).

Fig. 2.. Genomic distribution of all IPMAVs and major mutations in the CoViGen-Mex set. The height of each line (y-axis) represents the total samples that have a mutation in a specific position in the SARS-CoV-2 genome (x-axis). Major mutations are shown in light colours and IPMAVs are in dark colours. SNPs are shown in shades of blue and continuous lines, deletions in pink/red and dashed lines, and insertions in green on dotted lines. The x-axis shows the genomic map (including genes, UTRs and ORFs).

Fig. 3.. Distributions of total IPMAVs and major mutations per genome. Overlapping histograms show the total genomes (y-axis) having each number of mutations (x-axis). For major mutations, the five most relevant local modes are shown.

Fig. 4.. Description of putative coinfections detected in CoViGen-Mex’s data. All longitudinal data is shown using the same periods (x-axis). (a): The monthly total coinfections (grey transparent bars) are shown over the distribution of samples shown in Fig. 1 (starting on the first of each month and ending on the last day of the month). (b): The black line with circle bullets shows the monthly percentage of detected coinfections out of the total samples available for each month. (c): On top, the collated primary haplotype frequency, by VOCs/VUMs/Recombinant group in all putative coinfections (pie) and their monthly frequency (bars). Similarly, the pie below shows the secondary haplotype collated prevalence, and their monthly frequency (bars). (d): The geographical distribution is shown per state, with the y-axis showing total putative coinfections detected in all sets and coloured by region.