# Within-Host Fitness and Antigenicity Shift Are Key Factors Influencing the Prevalence of Within-Host Variations in the SARS-CoV-2 S Gene

## TL;DR

The study shows that within-host fitness and changes in antigenicity are key factors affecting the prevalence of genetic variations in the SARS-CoV-2 spike gene.

## Contribution

The study identifies within-host fitness and antigenicity shift as key factors influencing the prevalence of SARS-CoV-2 S gene variations.

## Key findings

- Mutational hotspots in the S gene are mainly located in NTD, RBD, TM, and CT domains.
- iSNVs with moderate alternate allele frequencies (0.06–0.12) are more prevalent than those with high frequencies.
- iSNVs that alter antigenicity are more prevalent, highlighting the role of antigenicity shift in variant prevalence.

## Abstract

Within-host evolution plays a critical role in shaping the diversity of SARS-CoV-2. However, understanding the primary factors contributing to the prevalence of intra-host single nucleotide variants (iSNVs) in the viral population remains elusive. Here, we conducted a comprehensive analysis of over 556,000 SARS-CoV-2 sequencing data and prevalence data of different SARS-CoV-2 S protein amino acid mutations to elucidate key factors influencing the prevalence of iSNVs in the SARS-CoV-2 S gene. Within-host diversity analysis revealed the presence of mutational hotspots within the S gene, mainly located in NTD, RBD, TM, and CT domains. Additionally, we generated a single amino acid resolution selection status map of the S protein. We observed a significant variance in within-host fitness among iSNVs in the S protein. The majority of iSNVs exhibited low to no within-host fitness and displayed low alternate allele frequency (AAF), suggesting that they will be eliminated due to the narrow transmission bottleneck of SARS-CoV-2. Notably, iSNVs with moderate AAFs (0.06–0.12) were found to be more prevalent than those with high AAFs. Furthermore, iSNVs with the potential to alter antigenicity were more prevalent. These findings underscore the significance of within-host fitness and antigenicity shift as two key factors influencing the prevalence of iSNVs in the SARS-CoV-2 S gene.