SARS-CoV-2 protein structure and sequence mutations: evolutionary analysis and effects on virus variants

Abstract

Proteins sequence, structure, and function are related, so that any changes in the protein sequence may cause modifications in its structure and function. Thanks to the exponential growth of data availability, many studies have addressed different questions such as: (i) how structure evolves based on the sequence changes, (ii) how structure and function change over time. Computational experiments have contributed to the study of viral protein structures. For instance the Spike (S) protein has been investigated for its role in binding receptors and infection activity in COVID-19, hence the interest of scientific researchers in studying the effects of virus mutations due to sequence, structure and vaccination effects. Protein Contact Networks (PCNs) can be used for investigating protein structures to detect biological properties thorough network topology. We apply topological studies based on graph theory of the PCNs to compare the structural changes with sequence changes, and find that both node centrality and community extraction analysis play a relevant role in changes in protein stability and functionality caused by mutations. We compare the structural evolution to sequence changes and study mutations from a temporal perspective focusing on virus variants. We finally highlight a timeline correlation between Omicron variant identification and the vaccination campaign.

Emergence of SARS-CoV-2 Omicron Variant JN.1 in Tamil Nadu, India - Clinical Characteristics and Novel Mutations

“…The impact of mutations on the protein function is now studied through in silico methods [7,8]. The difference in protein structures induced by mutations resulting in different lineages during the viral evolutionary process [9].…”

Emergence of SARS-CoV-2 Omicron Variant JN.1 in Tamil Nadu, India - Clinical Characteristics and Novel Mutations

“…The impact of mutations on the protein function is now studied through in silico methods 7,8 . The difference in protein structures induced by mutations resulting in different lineages during the viral evolutionary process 9 . Here, we surveyed the population for SARS-CoV-2 Omicron subvariant JN.1 between November and December 2023 as a part of the state's public health genomic surveillance investigation, an ongoing programme of the Directorate of Public Health and Preventive Medicine, Chennai, India since September 2021.…”