Proteomic analysis of SARS-CoV-2 responsible for COVID-19 in Algeria (in silico study)

The high variability of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) genome presents a challenge to scientists on molecular diagnosis, treatment and vaccination. 

In this work, we have characterized the proteomic mutations of SARS-CoV-2 responsible for COVID-19 in Algeria present during the period March 2020 to July 2021.

We extracted 44 sequences from the GISAID platform's database (Global Initiative on Sharing Avian Influenza Data). The search for virus variants was performed on the GISAID and PANGO platforms (Global Outbreak: cov-lineages.org/). 

The proteins with the most mutations were Spike, N (Nucleoprotein), NSP3 (Non-Structural Protein 3) and NSP12 (Non-Structural Protein 12). The most frequent mutations were D614G and P323L, found in the Spike and NSP12 proteins, respectively. However, positions S-614 and NSP12-323 were less mutable than those of the accessory NS7a/b proteins, which are involved, in the immune escape. Among the mutations found in the Spike, five were associated with the VOCs "Variants Of Concern" and four with the VOIs "Variants Of Interest".

The study of the GISAID clades revealed that the G, GH and GR clades were present at the start of the pandemic and replaced by the GK corresponding to the Delta variant, which is currently predominant in Algeria.