# VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19

## TL;DR

This paper introduces a new software tool called VOE to identify variants in SARS-CoV-2 epitopes, which helps improve the accuracy of diagnostic tests and vaccines for COVID-19.

## Contribution

The novel contribution is the development of the VOE software for automated variant epitope analysis in SARS-CoV-2.

## Key findings

- Variants with high or moderate impact were found on most epitopes except KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK.
- Epitopes APGQTGK and DSKVGGNYN showed significantly lower sensitivity in variant detection.
- The epitope GGDGKMKD on the N gene is suggested for use in serodiagnostic tests.

## Abstract

The development of serodiagnostic tests and vaccines for COVID-19 depends on the identification of epitopes from the SARS-CoV-2 genome. An epitope is the specific part of an antigen that is recognized by the immune system and can elicit an immune response. However, when the genetic variants contained in epitopes are used to develop rapid antigen tests (Ag-RDTs) and DNA or RNA vaccines, test sensitivity and vaccine efficacy can be low.

Here, we developed a “variant on epitope (VOE)” software, a new Python script for identifying variants located on an epitope. Variant analysis and sensitivity calculation for seven recommended epitopes were processed by VOE. Variants in 1,011 Omicron SRA reads from two variant databases (BCFtools and SARS-CoV-2-Freebayes) were processed by VOE.

A variant with HIGH or MODERATE impact was found on all epitopes from both variant databases except the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK on the S gene and ORF7a gene. All epitope variants from the BCFtools and SARS-CoV-2 Freebayes variant databases showed about 100% sensitivity except epitopes APGQTGK and DSKVGGNYN on the S gene, which showed respective sensitivities of 28.4866% and 6.8249%, and 87.7349% and 71.1177%.

Therefore, the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK may be useful for the development of an epitope-based peptide vaccine and GGDGKMKD on the N gene may be useful for the development of serodiagnostic tests. Moreover, VOE can also be used to analyze other epitopes, and a new variant database for VOE may be further established when a new variant of SARS-CoV-2 emerges.