Severe Acute Respiratory Syndrome Coronavirus-2 genome sequence variations relate to morbidity and mortality in Coronavirus Disease-19
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Abstract
Outcome of infection with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) may depend on the host, virus or the host-virus interaction-related factors. Complete SARS-CoV-2 genome was sequenced using Illumina and Nanopore platforms from naso-/oro-pharyngeal ribonucleic acid (RNA) specimens from COVID-19 patients of varying severity and outcomes, including patients with mild upper respiratory symptoms (n=35), severe disease ad-mitted to intensive care with respiratory and gastrointestinal symptoms (n=21), fatal COVID-19 outcome (n=17) and asymptomatic (n=42). Of a number of genome variants observed, p.16L>L (Nsp1), p.39C>C (Nsp3), p.57Q>H (ORF3a), p.71Y>Y (Membrane glycoprotein), p.194S>L (Nucleocapsid protein) were observed in similar frequencies in different patient subgroups. However, seventeen other variants were observed only in symptomatic patients with severe and fatal COVID-19. Out of the latter, one was in the 5’UTR (g.241C>T), eight were synonymous (p.14V>V and p.92L>L in Nsp1 protein, p.226D>D, p.253V>V, and p.305N>N in Nsp3, p.34G>G and p.79C>C in Nsp10 protein, p.789Y>Y in Spike protein), and eight were non-synonymous (p.106P>S, p.157V>F and p.159A>V in Nsp2, p.1197S>R and p.1198T>K in Nsp3, p.97A>V in RdRp, p.614D>G in Spike protein, p.13P>L in nucleocapsid). These were completely absent in the asymptomatic group. SARS-CoV-2 genome variations have a significant impact on COVID-19 presentation, severity and outcome.
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SciScore for 10.1101/2021.05.24.445374: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Patients: The experimental protocols were approved by the Institutional Ethics Committee of Sanjay Gandhi Postgraduate Institute of Medical Sciences.
Field Sample Permit: All methods were carried out in accordance with relevant guidelines and regulations.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Illumina’s MiSeq platform was used for sequencing. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Miseq data analysis: The raw reads generated on MiSeq were checked for quality using FASTQC (version 0.11.8, Babraham Institute, Cambridge, UK). FASTQCsuggested: (FastQC, …SciScore for 10.1101/2021.05.24.445374: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Patients: The experimental protocols were approved by the Institutional Ethics Committee of Sanjay Gandhi Postgraduate Institute of Medical Sciences.
Field Sample Permit: All methods were carried out in accordance with relevant guidelines and regulations.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Illumina’s MiSeq platform was used for sequencing. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Miseq data analysis: The raw reads generated on MiSeq were checked for quality using FASTQC (version 0.11.8, Babraham Institute, Cambridge, UK). FASTQCsuggested: (FastQC, RRID:SCR_014583)HISAT2 was used to map the reads to the viral genome. HISAT2suggested: (HISAT2, RRID:SCR_015530)Consensus fasta sequence was generated using samtools (version 1.9) and BCFtools on SARS-CoV-2 aligned files. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)The variants in the samples were called using BCFtools and VarScan. VarScansuggested: (VARSCAN, RRID:SCR_006849)Sequencing flow cell was primed using flow cell priming kit (EXP-FLP002), and sequencing was performed on MinION Mk1B platform (Oxford Nanopore Technologies, Oxford, UK) MinIONsuggested: (MinION, RRID:SCR_017985)All the genome sequences (3181) were subsequently aligned in MAFFT (https://mafft.cbrc.jp/alignment/server/). MAFFTsuggested: (MAFFT, RRID:SCR_011811)For the alignment containing 3020 full length genome sequences, nucleotide composition, codon usage, single-tons and CpG were calculated in MEGA v7.0. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)Protein based annotation: Specific amino acid changes as a result of a mutation were annotated using SnpEff (version 4.5) 13. SnpEffsuggested: (SnpEff, RRID:SCR_005191)The analysis to figure out the conservation of these amino acids, multiple sequence alignment of the full-length sequences of six other coronaviruses was undertaken using Clustal Omega 14. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:We did not find a significant difference in the age of symptomatic patients from asymptomatic; nevertheless, the lack of adjustment of data for patient age, host genetic factors, microbiome and comorbidities is a limitation of our study. In conclusion, the comparison of virus genotype across symptomatic and asymptomatic COVID-19 patients identified a clustering of unique viral genome variants in the symptomatic classes, which were completely absent in the asymptomatic class. However, these variants did not differ in frequency across the symptomatic classes showing no correlation with the degree of morbidity within the symptomatic class. Out of these variants, we would like to emphasize on the potential importance of the mutations observed in all three categories of the symptomatic patients. Among these g.241 C>T mutation in the 5’UTR, p.1197 S>R and p.1198 T>K in the Nsp3 protein, p.97 A>V in RdRp, p.614 D>G and p.789 Y>Y in the spike protein could be potentially important for disease severity. 5’UTR mutation g.241 C>T could affect the stability of the transcript, and the synonymous mutation (p.789 Y>Y) could affect translation by differences in codon usage preference in humans. Among other mutations, p.1197 S>R and p.1198 T>K in the Nsp3 protein, p.97 A>V in RdRp and p.614 D>G in the spike protein lie in crucial domains of the polymerase of the spike protein. D614G has already been reported to affect viral infectivity, and perhaps affects virulence as well. With available da...
Results from TrialIdentifier: No clinical trial numbers were referenced.
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Results from scite Reference Check: We found no unreliable references.
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