# Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US

## TL;DR

This study examines how new SARS-CoV-2 Omicron variants replaced older ones in Connecticut in 2022, focusing on their ability to spread despite high vaccination and infection rates.

## Contribution

The study integrates genomic and public health data to reveal how Omicron lineages outcompeted others through immune escape or increased shedding.

## Key findings

- New Omicron lineages outcompeted dominant ones through enhanced viral shedding or immune escape.
- Lineage replacement dynamics varied depending on population-level exposure to prior infections and vaccinations.
- The study combined sequencing data with demographic and epidemiological data to provide deeper insights into host-pathogen interactions.

## Abstract

In 2022, consecutive sweeps of highly transmissible SARS-CoV-2 Omicron-derived lineages (B.1.1.529*) maintained viral transmission despite extensive antigen exposure from both vaccinations and infections. To better understand Omicron variant emergence in the context of the dynamic fitness landscape of 2022, we aimed to explore putative drivers behind SARS-CoV-2 lineage replacements. Variant fitness is determined through its ability to either outrun previously dominant lineages or more efficiently circumvent host immune responses to previous infections and vaccinations. By analyzing data collected through our local genomic surveillance program from Connecticut, USA, we compared emerging Omicron lineages’ growth rates, estimated infections, effective reproductive rates, average viral copy numbers, and likelihood for causing infections in recently vaccinated individuals. We find that newly emerging Omicron lineages outcompeted dominant lineages through a combination of enhanced viral shedding or advanced immune escape depending on the population-level exposure state. This analysis integrates individual-level sequencing data with demographic, vaccination, laboratory, and epidemiological data and provides further insights into host–pathogen dynamics beyond public aggregate data.