SARS‐CoV‐2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents

Ghaleh, Samira Salami; Rahimian, Karim; Mahmanzar, Mohammadamin; Mahdavi, Bahar; Tokhanbigli, Samaneh; Sisakht, Mahsa Mollapour; Farhadi, Amin; Bakhtiari, Mahsa Mousakhan; Kuehu, Donna Lee; Deng, Youping

doi:10.1016/j.virusres.2022.199016

Cited by 12 publications

(5 citation statements)

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“…Thus, E87 seems to be involved in a crucial relay of interactions from N to the C-terminal ends of NSP1. Our results are corroborated by earlier studies, which indicate the unequivocal role of E87D in structural stability [45,50]. The H45Y mutation was discovered to be the most stabilizing mutation, possibly as a result of a favorable ring-stacking interaction with the adjacent F31 and the subsequent stabilization of the α1 helix (Figure 2).…”

Section: Mutational Analysis Of Nsp1supporting

confidence: 91%

“…It was discovered that, of all viral proteins, NSP1 had the greatest impact on host viability in human lung cells. It targets the 40S ribosomal subunit to stall translation during initiation and is involved in the cleavage of host RNA to accelerate degradation [45]. In our study, a total of 3161 mutations were observed in NSP1 (PDB: 7K3N, [46]), out of which 17 were filtered as having significant occurrence.…”

Section: Mutational Analysis Of Nsp1mentioning

confidence: 92%

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SARS-COV-2: Analysis of mutational impacts on non-structural proteins

Senthilazhagan

Sakthimani

Kallanja

et al. 2023

Preprint

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The global pandemic that peaked in 2019 was caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus), which had China as its whenua. The whys and wherefores of this outbreak are attributed to the structural competency of the single-stranded RNA virus that continues to evolve posing major health concerns. SARS-CoV-2 with an increased level of genetic mutations alters the characteristics of the virus, such as transmissibility, and antigenicity alongside the development of drug and vaccine resistance. The deeper examination of prominent mutating sites and structures of the virus can give insights into the development of better and more efficient vaccine candidates. This research is steered to delve into the viral dynamics using full genome sequences and decode the genesis behind the structural and functional variances. The genomic data of SARS-CoV-2 variants were obtained from the Global Initiative on Sharing Avian Influenza Data (GISAID), and a set of significant mutations in each of the non-structural proteins (NSPs) 1 through 16 and structural proteins, including envelope, nucleocapsid, membrane, and spike, were identified. The mutations were characterized as stabilizing or destabilizing and their significance was analyzed with respect to self and in the context of interacting partners. Among all the proteins, NSP6 stands out as a dark horse with extremely high mutability. The results augment our understanding of how mutational events influence virus pathogenicity and evolution.

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Section: Mutational Analysis Of Nsp1supporting

confidence: 91%

Section: Mutational Analysis Of Nsp1mentioning

confidence: 92%

SARS-COV-2: Analysis of mutational impacts on non-structural proteins

Senthilazhagan

Sakthimani

Kallanja

et al. 2023

Preprint

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“…The N protein mutations, including P13L, R203K and G204R/K, may assist with increasing the transmission of the SARS-CoV-2 but also be associated with reduced severity of disease and, therefore, lower mortality rates when compared to individuals with the wild-type N protein [ 40 , 41 , 42 ]. In the nsp1 protein, the E102K mutation encourages attachment to viral RNA, increasing replication and thereby increasing infectivity [ 43 ]. While del141-143 in nsp1, also reported in Omicron BA.4 lineages during the fifth wave in SA and described in Delta AY.63 in Norway, extends the duration of infection [ 5 , 44 ].…”

Section: Discussionmentioning

confidence: 99%

Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages

Subramoney

Mtileni

Giandhari

et al. 2023

Viruses

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SARS-CoV-2 lineages and variants of concern (VOC) have gained more efficient transmission and immune evasion properties with time. We describe the circulation of VOCs in South Africa and the potential role of low-frequency lineages on the emergence of future lineages. Whole genome sequencing was performed on SARS-CoV-2 samples from South Africa. Sequences were analysed with Nextstrain pangolin tools and Stanford University Coronavirus Antiviral & Resistance Database. In 2020, 24 lineages were detected, with B.1 (3%; 8/278), B.1.1 (16%; 45/278), B.1.1.348 (3%; 8/278), B.1.1.52 (5%; 13/278), C.1 (13%; 37/278) and C.2 (2%; 6/278) circulating during the first wave. Beta emerged late in 2020, dominating the second wave of infection. B.1 and B.1.1 continued to circulate at low frequencies in 2021 and B.1.1 re-emerged in 2022. Beta was outcompeted by Delta in 2021, which was thereafter outcompeted by Omicron sub-lineages during the 4th and 5th waves in 2022. Several significant mutations identified in VOCs were also detected in low-frequency lineages, including S68F (E protein); I82T (M protein); P13L, R203K and G204R/K (N protein); R126S (ORF3a); P323L (RdRp); and N501Y, E484K, D614G, H655Y and N679K (S protein). Low-frequency variants, together with VOCs circulating, may lead to convergence and the emergence of future lineages that may increase transmissibility, infectivity and escape vaccine-induced or natural host immunity.

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“…A table within the ‘Worldwide Mutation Distribution’ tab shows the counts of SAVs in each country/area. A case study was conducted on NSP1 mutation virulence and natural selection including evolutionary trends from six continents ( 21 ). This publication represents an examination of the potential applications of available data within the present database and expands researchers understanding of the tracking of mutations across different geographical regions.…”

Section: Resultsmentioning

confidence: 99%

SARS2Mutant: SARS-CoV-2 amino-acid mutation atlas database

Rahimian

Arefian

Mahdavi

et al. 2023

NAR Genomics and Bioinformatics

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The coronavirus disease 19 (COVID-19) is a highly pathogenic viral infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in the global pandemic of 2020. A lack of therapeutic and preventive strategies has quickly posed significant threats to world health. A comprehensive understanding of SARS-CoV-2 evolution and natural selection, how it impacts host interaction, and phenotype symptoms is vital to develop effective strategies against the virus. The SARS2Mutant database (http://sars2mutant.com/) was developed to provide valuable insights based on millions of high-quality, high-coverage SARS-CoV-2 complete protein sequences. Users of this database have the ability to search for information on three amino acid substitution mutation strategies based on gene name, geographical zone, or comparative analysis. Each strategy is presented in five distinct formats which includes: (i) mutated sample frequencies, (ii) heat maps of mutated amino acid positions, (iii) mutation survivals, (iv) natural selections and (v) details of substituted amino acids, including their names, positions, and frequencies. GISAID is a primary database of genomics sequencies of influenza viruses updated daily. SARS2Mutant is a secondary database developed to discover mutation and conserved regions from the primary data to assist with design for targeted vaccine, primer, and drug discoveries.

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SARS‐CoV‐2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents

Cited by 12 publications

References 50 publications

SARS-COV-2: Analysis of mutational impacts on non-structural proteins

SARS-COV-2: Analysis of mutational impacts on non-structural proteins

Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages

SARS2Mutant: SARS-CoV-2 amino-acid mutation atlas database

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