Dispersion of SARS-CoV-2 lineage BA.5.1.25 and its descendants in Peru during two COVID-19 waves in 2022

Area of Science:

• Virology
• Genomic Epidemiology
• Public Health Surveillance

Background:

• Persistent SARS-CoV-2 transmission during the third pandemic year in Peru led to the emergence of immune-evasive Omicron sublineages.
• The BA.5.1.25 Omicron sublineage, later designated DJ.1, showed increased prevalence during the fourth COVID-19 wave.

Purpose of the Study:

• To investigate the introduction, emergence, and time to the most recent common ancestor (tMRCA) of SARS-CoV-2 Omicron sublineages BA.5.1.25 and its descendants (DJ.1, DJ.1.1, DJ.1.2, DJ.1.3).
• To analyze the time lags between the emergence and identification of these sublineages by the Peruvian National Institute of Health.

Main Methods:

• Genomic surveillance of SARS-CoV-2 by the Peruvian National Institute of Health.
• Phylogenetic analysis to determine the introduction, emergence, and tMRCA of identified Omicron sublineages.
• Analysis of time lags between sublineage emergence and official identification.

Main Results:

• Detection of spike mutations in the circulating Omicron BA.5.1.25 sublineage, leading to its designation as DJ.1.
• Observed increase in DJ.1 prevalence during the fourth COVID-19 wave, with subsequent branching into new sublineages (DJ.1.1, DJ.1.2, DJ.1.3).
• Characterization of the introduction, emergence timing, and identification time lags for these evolving sublineages.

Conclusions:

• Ongoing genomic surveillance of SARS-CoV-2 is crucial for understanding viral phylogenetic evolution.
• Continuous monitoring facilitates the timely detection and characterization of emerging SARS-CoV-2 variants and sublineages.