An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2
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Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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SciScore for 10.1101/2021.05.25.445557: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Truncated ORF8 protein (T-ORF8) sequences (complete) from five continents (Asia, Africa, Europe, South America, and North America) were downloaded in Fasta format (as of May 18, 2021) from the National Center for Biotechnology Information (NCBI) database (http://www.ncbi.nlm.nih.gov/). http://www.ncbi.nlm.nih.gov/suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)Then sequence homology of these sequences was derived using the Clustal Omega web-suite and then associated with nearest neighborhood phylogenetic relationship among the unique T-ORF8 variants. Clusta…SciScore for 10.1101/2021.05.25.445557: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Truncated ORF8 protein (T-ORF8) sequences (complete) from five continents (Asia, Africa, Europe, South America, and North America) were downloaded in Fasta format (as of May 18, 2021) from the National Center for Biotechnology Information (NCBI) database (http://www.ncbi.nlm.nih.gov/). http://www.ncbi.nlm.nih.gov/suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)Then sequence homology of these sequences was derived using the Clustal Omega web-suite and then associated with nearest neighborhood phylogenetic relationship among the unique T-ORF8 variants. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Prediction of molecular and physicochemical properties: Theoretical pI (PI), extinction coefficient (EC), instability index (II), aliphatic index (AI), protein solubility (PS), grand average of hydropathicity (GRAVY), and the number of tiny, small, aliphatic, aromatic, non-polar, polar, charged, basic and acidic residues of all unique T-ORF8 proteins were calculated using the web-servers ‘ProtParam’, ‘Protein-sol’ and EMBOSS Pepstats [43, 44, 45]. 2.5. EMBOSSsuggested: (EMBOSS, RRID:SCR_008493)Finding functional motifs: The Eukaryotic Linear Motif (ELM) resource (http://elm.eu.org/) was used for finding functional sites in proteins [48]. http://elm.eu.org/suggested: (Eukaryotic Linear Motif, RRID:SCR_003085)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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