Substantial Diversity in Cocirculating Omicron Lineages in Hospital Setting, Porto Alegre, Brazil

Area of Science:

• Virology
• Epidemiology
• Genomic Surveillance

Background:

• The SARS-CoV-2 Omicron variant has rapidly evolved, leading to numerous sublineages with distinct epidemiological characteristics.
• Understanding the genetic diversity and circulation patterns of SARS-CoV-2 variants is crucial for public health interventions.

Purpose of the Study:

• To characterize the genetic diversity of SARS-CoV-2 Omicron lineages circulating in Porto Alegre, Brazil.
• To identify the predominant lineages and their prevalence among healthcare workers and inpatients.

Main Methods:

• Whole-genome sequencing of 272 SARS-CoV-2 positive samples.
• Phylogenetic analysis to identify Omicron lineages.
• Retrospective analysis of samples collected between November 2022 and January 2023.

Main Results:

• A substantial diversity of 23 SARS-CoV-2 Omicron lineages was detected.
• BQ.1 and its related lineages constituted the majority (61.4%) of the sequenced samples.
• BE.9 lineage, first identified in the Amazon region, was also detected (19.1%).

Conclusions:

• The study highlights significant SARS-CoV-2 Omicron variant diversity in Brazil.
• BQ.1 and BE.9 represent important circulating lineages requiring continued surveillance.