Conserved Pattern and Potential Role of Recurrent Deletions in SARS-CoV-2 Evolution

Abstract

Mutations in SARS-CoV-2 were studied extensively, while only the structure variations on the spike protein were discussed well in previous studies. To study the role of structural variations in virus evolution, we described the distribution of structure variations on the whole genome.

Genetic differentiation and diversity of SARS-CoV-2 Omicron variant in its early outbreak

“…A systemic analysis revealed that deletion in the SARS-CoV-2 had a regional preference. It was also illustrated that the recurrent deletions on the N-terminal Domain of the S protein partially covered the binding domain of some neutralizing antibodies indicating a potential role of the deletions in virus evolution [24] , [25] . Therefore, in preventing and controlling the COVID-19 pandemic, it was necessary to pay more attention to the internal genetic diversity, including nucleotide substitutions and deletions or insertions of the dominant variants.…”

Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021–January 2022

“…Next deletion Y144del is associated with resistance to several S-binding neutralizing antibodies but does not appear to reduce the neutralizing activity of vaccinated persons [ 45 ]. It has been confirmed that Y144del blocks the binding sites of neutralizing antibodies [ 47 ].…”

“…The role of many of these deletions in NSP6 of VOC Alpha/B.1.1.7 lineage is under investigation now, but it is known that deletions of NSP6 in 106–108 showed proliferation advantages for SARS-CoV-2 samples [ 47 ].…”

Research progress of biosensors for detection of SARS-CoV-2 variants based on ACE2

“…Nowadays, many biosensors have been developed to detect SARS-CoV-2 using RNA or proteins as markers for detection [ 34 ]. SARS-CoV-2 has evolved to adapt to human hosts in a variety of ways, including single nucleotide mutations and structural mutations, which have a significant impact on genome structure and protein function [ 35 ]. This may lead to a decrease in the accuracy of detection methods based on genes and marker proteins.…”