Computer program to analyze prevalence of SARS-CoV-2 Spike mutations at sites of N-linked glycosylation

Abstract: Functional and epidemiological data suggest that N-linked glycans on the SARS-CoV-2 Spike protein may contribute to viral infectivity. To analyze this, we downloaded SARS-CoV-2 Spike protein sequences from GISAID (all available data up to 06/28/2022; EPI_SET_220803fo). The number of mutations in this protein at sites of N-linked glycosylation were enumerated using a program scripted using MATLAB. The program is provided as part of this repository. Data analyzed are available from GISAID.org.

Methods: Data were collected by independent laboratories and other GISAID contributors. These were available from GISAID.org. A script was written to process these data in order to quantify mutation rates on Spike glycoprotein, with focus on mutations that occur at sites of N-liked glycosylation.

Usage Notes: Data files are in .txt/.fasta format and can be opened using any plain text-reading software. The script is written using MATLAB, a common program commonly available in research universities.