Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover.
Microb Genom
; 10(3)2024 Mar.
Article
in En
| MEDLINE
| ID: mdl-38512312
ABSTRACT
A total of 14â973 alleles in 29â661 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 1.28â%), 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.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Coinfection
/
COVID-19
Limits:
Humans
Country/Region as subject:
Mexico
Language:
En
Journal:
Microb Genom
/
Microb. genom
/
Microbial genomics
Year:
2024
Document type:
Article
Affiliation country:
Country of publication: