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

Abstract

The structure and sequence of proteins strongly influence their biological functions. New models and algorithms can help researchers in understanding how the evolution of sequences and structures is related to changes in functions. Recently, studies of SARS-CoV-2 Spike (S) protein structures have been performed to predict binding receptors and infection activity in COVID-19, hence the scientific interest in the effects of virus mutations due to sequence, structure and vaccination arises. However, there is the need for models and tools to study the links between the evolution of S protein sequence, structure and functions, and virus transmissibility and the effects of vaccination. As studies on S protein have been generated a large amount of relevant information, we propose in this work to use Protein Contact Networks (PCNs) to relate protein structures with biological properties by means of network topology properties. Topological properties are used to compare the structural changes with sequence changes. We find that both node centrality and community extraction analysis can be used to relate protein stability and functionality with sequence mutations. Starting from this we compare structural evolution to sequence changes and study mutations from a temporal perspective focusing on virus variants. Finally by applying our model to the Omicron variant we report a timeline correlation between Omicron and the vaccination campaign.

Strategies and Trends in COVID-19 Vaccination Delivery: What We Learn and What We May Use for the Future

“…In response to the insurgence of variants B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta) that have been indicated as variants of concern (VOC), some countries reduced the time interval between vaccine doses. This allowed governments to provide the first dose to a greater number of citizens [ 54 , 55 ]. The planning of an efficient allocation strategy relies on the possibility to simulate the impact of the different choices.…”

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].…”

“…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.…”