Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development

Abstract

The rapid spread of the COVID-19 demands immediate response from the scientific communities. Appropriate countermeasures mean thoughtful and educated choice of viral targets (epitopes). There are several articles that discuss such choices in the SARS-CoV-2 proteome, other focus on phylogenetic traits and history of the Coronaviridae genome/proteome. However none consider viral protein low complexity regions (LCRs). Recently we created the first methods that are able to compare such fragments. We show that five low complexity regions (LCRs) in three proteins (nsp3, S and N) encoded by the SARS-CoV-2 genome are highly similar to regions from human proteome. As many as 21 predicted T-cell epitopes and 27 predicted B-cell epitopes overlap with the five SARS-CoV-2 LCRs similar to human proteins. Interestingly, replication proteins encoded in the central part of viral RNA are devoid of LCRs. Similarity of SARS-CoV-2 LCRs to human proteins may have implications on the ability of the virus to counteract immune defenses. The vaccine targeted LCRs may potentially be ineffective or alternatively lead to autoimmune diseases development. These findings are crucial to the process of selection of new epitopes for drugs or vaccines which should omit such regions. Author summaryThe outbreak of the COVID-19 disease affects humans all over the globe. More and more people get sick and many die because of the deadly SARS-CoV-2 virus. The whole machinery of this pathogen is enclosed in a short sequence of nucleotides, building blocks for both RNA and DNA strands. This RNA virus encodes less than 30 protein sequences that change the fate of our societies. Its proteins are composed of 20 amino acids (building bricks) that are usually used quite freely by proteins. However, there are fragments where only one or a few amino acids are used. We name those low complexity regions (LCRs). We invented the first programmes able to compare such LCRs. Using this new methodology we were able to show similarity of some viral proteins to human ones. This discovery has a serious implication when designing vaccines or drugs. It means that companies should not use these very LCRs as targets because it may trigger an autoimmune disease. On the other hand this specific similarity may suggest some kind of disguise of viral proteins into the machinery of human cells.