Genomic surveillance of SARS-CoV-2 in Mexico pre-vaccination

Context

In the early stages of the COVID-19 pandemic, understanding the genetic evolution of SARS-CoV-2 was crucial for public health responses. This study focused on the phylogenomic and population genomic analysis of SARS-CoV-2 in Mexico during the pre-vaccination period.

Collaborators

A multidisciplinary team from various Mexican research institutions, including Cinvestav-IPN.

Challenge

Limited genomic data on SARS-CoV-2 variants circulating in Mexico hindered the ability to track the virus's evolution and inform public health strategies.

Approach:

• Collected and sequenced SARS-CoV-2 samples from symptomatic and asymptomatic individuals across Mexico.

• Performed phylogenomic analyses to identify circulating variants and mutations.

• Conducted population genomic studies to assess the distribution and frequency of specific mutations.

  
  

Key Findings

• Identified variants of interest, including B.1.1.28.4 and B.1.1.222/B.1.1.519, circulating in Mexico.

• Detected the nucleocapsid mutation S194L, which was associated with symptomatic cases.

• Observed mutations in the spike protein, such as E484K, T478K, and P681R/H, which have implications for transmissibility and immune escape.

  
  

Impact

This study provided critical insights into the genetic diversity of SARS-CoV-2 in Mexico, highlighting the importance of genomic surveillance in tracking virus evolution and informing public health interventions.

Publication

Barona-Gómez, F., Delaye, L., Díaz-Valenzuela, E., et al. (2021). Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Microbial Genomics, 7(11). https://doi.org/10.1099/mgen.0.000684