Speaker
Description
Vaccine and viral induced immunity place significant multifarious selective pressures on viruses they target. For SARS-CoV-2, the strength of this selection pressure has been in flux over the course of the pandemic as variant specific vaccine efficacy ranged from 30-95%. Monitoring and understanding antigenic evolution of SARS-CoV-2 is therefore crucial for vaccine optimization. Here, antigenic evolution was examined using both intrahost and interhost datasets. Initially, all known samples from the NCBI SRA database with confirmed vaccine status were used to study the influence of vaccines on intrahost evolution. Vaccinated individuals were found to have higher intrahost diversities for most VOCs prior to Omicron emergence. Interestingly, we also found that these differences were dose dependent: those individuals with a single dose showed significantly higher diversities compared to those with two doses. Corroborative selection analyses were performed on all consensus sequences with a confirmed vaccine status from GISAID for each of the variants (Non-VOC =548, Alpha=544, Delta=6,937, and BA.2=2,252). Consistent with intrahost data, in all variants except BA.2, we observed a higher number of sites under positive selection in individuals with a single dose. Furthermore, many sites with a high frequency of intrahost diversification were also found to be under positive selection. These results support evolutionary models in the early stages of the pandemic suggesting that vaccines with high efficacy but insufficient dosing and/or geographic disparities could have led to elevated antigenic selective pressures placed upon the SARS-CoV-2 virus.
