# In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants

## TL;DR

Daily sequencing of a household cohort during the Omicron wave reveals rare but significant selection of spike mutations in SARS-CoV-2 within individual hosts.

## Contribution

Demonstrates that within-host positive selection of SARS-CoV-2 spike variants is rare but detectable during acute infections.

## Key findings

- Individuals showed low viral diversity with genetic drift and purifying selection dominating within-host dynamics.
- Positive selection was rare but concentrated in the spike protein, with 7 of 14 selected loci in spike.
- Detectable immune-mediated selection in acute SARS-CoV-2 infections may be due to a narrow antibody repertoire during the Omicron phase.

## Abstract

SARS-CoV-2 has undergone repeated and rapid evolution to circumvent host immunity. However, outside of prolonged infections in immunocompromised hosts, within-host positive selection has rarely been detected. Here we combine daily longitudinal sampling of individuals with replicate sequencing to increase the accuracy of and lower the threshold for variant calling. We sequenced 577 specimens from 105 individuals in a household cohort during the BA.1/BA.2 variant period. Individuals exhibited extremely low viral diversity, and we estimated a low within-host evolutionary rate. Within-host dynamics were dominated by genetic drift and purifying selection. Positive selection was rare but highly concentrated in spike. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 14 loci with 7 in spike, including S:448 and S:339. This detectable immune-mediated selection is unusual in acute respiratory infections and may be caused by the relatively narrow antibody repertoire in individuals during the early Omicron phase of the SARS-CoV-2 pandemic.

Throughout the SARS-CoV-2 pandemic new variants have continually arisen due to population level immunity from vaccinations and previous infections. A similar process within-hosts may be occurring, where new variants evolve during the course of an infection to escape partial immunity from previous exposures. However, within-host positive selection has rarely been detected in acute SARS-CoV-2 infections. Here we studied individuals from a case-ascertained household cohort during the BA.1/BA.2 wave. Nasal swab specimens were collected daily for 10 days and sequenced in replicate for high accuracy. Individuals exhibited extremely low viral diversity with stochastic processes dominating. Positive selection was rare but highly concentrated in spike. The majority of spike mutations we identified as positively selected have been implicated in immune evasion previously. This infrequent but detectable positive selection may be due to the timing of these infections relative to the emergence of SARS-CoV-2