Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

Barrett, Chelsea T.; Neal, Hadley E.; Edmonds, Kearstin; Moncman, Carole L.; Thompson, Rachel; Branttie, Jean Mawuena; Boggs, Kerri Beth; Wu, Cheng-Yu; Leung, Daisy W.; Dutch, Rebecca Ellis

doi:10.1101/2021.01.24.428007

Cited by 6 publications

(4 citation statements)

References 108 publications

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“…The S2 is markedly conserved among CoVs, and have a low mutation rate indicating that most mutations are likely to impact viral entry. Moreover, it is less antigenic, probably due to the extensive N-linked glycosylation, therefore not under much selective pressure compared to S1 ( 9 , 27 ). However, studies show the HR2 region can elicit an antibody response that is cross-reactive with other CoVs ( 28 ).…”

Section: Variations In Sars-cov-2 Genome and Proteomementioning

confidence: 99%

SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines

Thakur¹,

Sasi²,

et al. 2022

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With the high rate of COVID-19 infections worldwide, the emergence of SARS-CoV-2 variants was inevitable. Several mutations have been identified in the SARS-CoV-2 genome, with the spike protein as one of the mutational hot spots. Specific amino acid substitutions such as D614G and N501Y were found to alter the transmissibility and virulence of the virus. The WHO has classified the variants identified with fitness-enhancing mutations as variants of concern (VOC), variants of interest (VOI) or variants under monitoring (VUM). The VOCs pose an imminent threat as they exhibit higher transmissibility, disease severity and ability to evade vaccine-induced and natural immunity. Here we review the mutational landscape on the SARS-CoV-2 structural and non-structural proteins and their impact on diagnostics, therapeutics and vaccines. We also look at the effectiveness of approved vaccines, antibody therapy and convalescent plasma on the currently prevalent VOCs, which are B.1.17, B.1.351, P.1, B.1.617.2 and B.1.1.529. We further discuss the possible factors influencing mutation rates and future directions.

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Section: Variations In Sars-cov-2 Genome and Proteomementioning

confidence: 99%

SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines

Thakur¹,

Sasi²,

et al. 2022

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“…Notably, during the evolution of SARS-CoV-2, the S1-NTD in the present study additionally organized many mutations, including deletions idel69/70 and del 142/144. Similarly, frequently deleted regions in the NTD were those positioned at 69-70, 141-144, 146, 210, and 243-244; reported in the previous study most NTD mutations were found to change antigenicity or eliminate epitopes, enabling immune escape (52).…”

Section: Resultsmentioning

confidence: 54%

Phylogenetic, Sequencing, and Mutations Analysis of the SARS-CoV-2 Omicron (BA.1) and Sub-variants (BA.1.1, BA.2) during the Fifth Wave of the Pandemic in the Iraqi Kurdistan Region

Taher,

Abdo,

Merza

2023

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in humans in Wuhan City at the end of December 2019. Since then, it has spread to all the countries. Therefore, global interest has been focused on discovering treatments and developing successful vaccines. This study sequenced the complete genome of the SARS-COV-2 Omicron Omicron (BA.1) and sub-variants (BA.1.1, BA.2), which were isolated from 40 individuals in Duhok, Iraq. Ninety-five different mutations were identified when the complete genome of the SARS-COV-2 virus discovered in Wuhan, China (accession number: NC 045512.2) was matched to the virus sequence using sequencing technology (Illumina, USA). Sequence analysis revealed 38 mutations in spike glycoprotein (S), 30 of which were found in ORF1a. Additionally, 11 mutations were found in ORF1b, and 7,3,2,1 mutations were found in Nucleocapsid (N), membrane protein (M), Open Reading Frames 6 (ORF6), Open Reading Frames 9 (ORF9), and Envelope (E) genes, respectively. Phylogenetic analysis and transmission further confirmed that the isolates found in Iraq had distinct infection origins and were closely related to those from other countries and states. According to the findings of this study, a new vaccine can be developed based on identifying new Omicron variant mutations and sub-variants such as BA.2, which were identified for the first time in Iraq.

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“…reported in the previous study, most NTD mutations were found to change antigenicity or eliminate epitopes, enabling immune escape. (32).…”

Section: Resultsmentioning

confidence: 99%

Whole Genome Sequence Analysis of SARS-COV-2 Isolated from COVID-19 Patients in Duhok Province, Iraq

Taher¹,

Abdo²,

Merza³

2023

Preprint

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Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in people in the city of Wuhan at the end of December 2019, and it has since spread to all continents. Global interest has been focused on discovering a treatment and developing a successful coronavirus vaccine as a result of the emergence of this new coronavirus. In this research, we sequenced the whole genome of the SARS-COV-2 virus that were isolated from 40 patients in Duhok, Iraq. 95 different mutations were identified in our isolation when such the whole genome sequence of the SARS-COV-2 isolated from the city of Wuhan, China (Accession number: NC 045512.2) was matched to the virus's sequence using Sequencing technology (Illumina , USA ) and Assembly method (iVar 1.3.1). Sequence analysis revealed that 38 mutations were found at spike glycoprotein (S), 30 of which were found in the ORF1b , 11 mutations were found in ORF1b ,7,3,2,1 mutations were found in ( N,M,ORF6 ,ORF9 /E ) genes which had been linked to structural changes at various places. The conclusion that the cases in Iraq were of different origins of infections and had a close relationship with the isolates from different country and state were further confirmed by phylogenetic analysis and transmission. The whole genome sequence of the SARS-CoV-2 , which were identified from the Iraqi Kurdistan region, and reported as a first study in Kurdistan region.

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Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

Cited by 6 publications

References 108 publications

SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines

SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines

Phylogenetic, Sequencing, and Mutations Analysis of the SARS-CoV-2 Omicron (BA.1) and Sub-variants (BA.1.1, BA.2) during the Fifth Wave of the Pandemic in the Iraqi Kurdistan Region

Whole Genome Sequence Analysis of SARS-COV-2 Isolated from COVID-19 Patients in Duhok Province, Iraq

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