Immunoinformatic analysis of structural and epitope variations in the spike and Orf8 proteins of SARS‐CoV‐2/B.1.1.7

Hussain, Mushtaq; Shabbir, Sanya; Amanullah, Anusha; Raza, Fozia; Imdad, Muhammad J.; Zahid, Sahar

doi:10.1002/jmv.26931

Cited by 12 publications

(10 citation statements)

References 29 publications

(83 reference statements)

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“…The ORF8 gene encodes a rapidly evolving protein of SARS-CoV-2, and many variants of this protein have been reported ( Alkhansa et al, 2021 ; Fahmi et al, 2021 ; Hussain et al, 2021 ; Pereira, 2021 ; Zinzula, 2021 ). A recent X-ray crystallography study of ORF8 reported found that SARS-COV-2 ORF8 can form dimers or unique large-scale assemblies through Cys20 and 73YIDI76 motifs ( Flower et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

The ORF8 Protein of SARS-CoV-2 Modulates the Spike Protein and Its Implications in Viral Transmission

et al. 2022

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COVID-19 is currently global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Accompanying the rapid spread of the error-prone RNA-based genome, several dominant SARS-CoV-2 variants have been genetically identified. The mutations in the spike protein, which are essential for receptor binding and fusion, have been intensively investigated for their contributions to viral transmission. Nevertheless, the importance of other viral proteins and their mutations in SARS-CoV-2 lifecycle and transmission remains fairly understood. Here, we report the strong potency of an accessory protein ORF8 in modulating the level and processing of the spike protein. The expression of ORF8 protein does not affect propagation but expression of spike protein, which may lead to pseudovirions with less spike protein on the surface, therefore less infection potential. At the protein level, ORF8 expression led to downregulation and insufficient S1/S2 cleavage of the spike protein in a dose-dependent manner. ORF8 exhibits a strong interaction with the spike protein mainly at S1 domains and mediates its degradation through multiple pathways. The dominant clinical isolated ORF8 variants with the reduced protein stability exhibited the increased capacity of viral transmission without compromising their inhibitory effects on HLA-A2. Although the increase in spike protein level and Spike pseudovirus production observed by using highly transmissible clinical spike variants, there was no significant compromise in ORF8-mediated downregulation. Because ORF8 is important for immune surveillance and might be required for viral fitness in vivo, the alteration of the spike protein might be an optional strategy used by SARS-CoV-2 to promote viral transmission by escaping the inhibitory effects of ORF8. Therefore, our report emphasized the importance of ORF8 in SARS-CoV-2 spike protein production, maturation, and possible evolution.

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Section: Resultsmentioning

confidence: 99%

The ORF8 Protein of SARS-CoV-2 Modulates the Spike Protein and Its Implications in Viral Transmission

et al. 2022

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“…SC-2 variant B.1.1.7 contains numerous synonymous and nonsynonymous mutations, of which the spike gene mutations 69-70del, N501Y, and P681H received most attention due to their potential effect on virus infectivity ( 12 , 13 ). For diagnostic purposes, however, the N501Y mutation is not variant-specific, as it was identified in several variants other than variant B.1.1.7, such as B.1.351 and the P.1 variant ( 14 ).…”

Section: Discussionmentioning

confidence: 99%

Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351

et al. 2021

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“…However, the capacity to distinguish between different lineages in a time scale of hours is currently possible only using qPCR. SC-2 variant B.1.1.7 contains numerous synonymous and non-synonymous mutations, of which the Spike gene mutations 69-70del, N501Y, and P681H received most attention due to their potential effect on virus infectivity (14)(15). For diagnostic purposes, however, the N501Y mutation is not variant-specific, as it was identified in several variants other than variant B.1.1.7, such as B.1.351 and the P.1 variant first discovered in Brazil (16).…”

Section: Discussionmentioning

confidence: 99%

Rapid And high throughput RT-qPCR assay for identification and differentiation between SARS-CoV-2 variants B.1.1.7 and B.1.351

Erster

Mendelson

Levy

et al. 2021

Preprint

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Emerging SARS-CoV-2 (SC-2) variants with increased infectivity and vaccine resistance are of major concern. Rapid identification of such variants is important for the public health activities and provide valuable data for epidemiological and policy decision making. We developed a multiplex quantitative RT-qPCR (qPCR) assay that can specifically identify and differentiate between the emerging B.1.1.7 and B.1.351 SC-2 variants. In a single assay, we combined four reactions: one that detects SC-2 RNA independently of the strain, one that detects the D3L mutation, which is specific to variant B.1.1.7, and one that detects the 242-244 deletion, which is specific to variant B.1.351. The fourth reaction identifies human RNAseP gene, serving as an endogenous control for RNA extraction integrity. We show that the strain-specific reactions target mutations that are strongly associated with the target variants, and not with other major known variants. The assay specificity was tested against a panel of respiratory pathogens (n=16), showing high specificity towards SC-2 RNA. The assay sensitivity was assessed using both In-vitro transcribed RNA and clinical samples, and was determined to be between 20 and 40 viral RNA copies per reaction. The assay performance was corroborated with Sanger and whole genome sequencing, showing complete agreement with the sequencing results. The new assay is currently implemented in the routine diagnostic work at the Central Virology Laboratory, and may be used in other laboratories to facilitate the diagnosis of these major worldwide circulating SC-2 variants.

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Immunoinformatic analysis of structural and epitope variations in the spike and Orf8 proteins of SARS‐CoV‐2/B.1.1.7

Cited by 12 publications

References 29 publications

The ORF8 Protein of SARS-CoV-2 Modulates the Spike Protein and Its Implications in Viral Transmission

The ORF8 Protein of SARS-CoV-2 Modulates the Spike Protein and Its Implications in Viral Transmission

Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351

Rapid And high throughput RT-qPCR assay for identification and differentiation between SARS-CoV-2 variants B.1.1.7 and B.1.351

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