Severe Acute Respiratory Syndrome Coronavirus-2 genome sequence variations relate to morbidity and mortality in Coronavirus Disease-19

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   ScreenIT

   May 26, 2021

   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.	MiSeq suggested: (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).	FASTQC suggested: (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.	MiSeq suggested: (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).	FASTQC suggested: (FastQC, RRID:SCR_014583)
   HISAT2 was used to map the reads to the viral genome.	HISAT2 suggested: (HISAT2, RRID:SCR_015530)
   Consensus fasta sequence was generated using samtools (version 1.9) and BCFtools on SARS-CoV-2 aligned files.	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   The variants in the samples were called using BCFtools and VarScan.	VarScan suggested: (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)	MinION suggested: (MinION, RRID:SCR_017985)
   All the genome sequences (3181) were subsequently aligned in MAFFT (https://mafft.cbrc.jp/alignment/server/).	MAFFT suggested: (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.	MEGA suggested: (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.	SnpEff suggested: (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 Omega suggested: (Clustal Omega, RRID:SCR_001591)

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   Results from OddPub: Thank you for sharing your data.

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   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...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
   • No protocol registration statement was detected.

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   Results from scite Reference Check: We found no unreliable references.

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   Version published to 10.1101/2021.05.24.445374v1 on bioRxiv

   May 24, 2021