SARS-CoV-2 Omicron Variant Wave in India: Advent, Phylogeny and Evolution
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Abstract
SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was responsible for disease in patients without comorbidity(97%), while Omicron BA.2 caused disease primarily in those with comorbidity(77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could possibly be due to evolutionary trade-off and explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2.
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SciScore for 10.1101/2022.05.14.491911: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. 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 The fragment sizes of the pooled libraries were assessed with DNA HS Kit (Agilent Technologies, Santa Clara, USA) on Agilent Bioanalyser. Agilent Bioanalysersuggested: NoneThe pooled library was further normalized to 4nM concentration, denatured and loaded onto a Miseq V3 Flow Cell (150 cycles) to carry out paired end sequencing with a read length of 2×75 on MiSeq platform. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)The whole-genome sequences were aligned using were aligned using MAFFT v7.475 12, the aligned … SciScore for 10.1101/2022.05.14.491911: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. 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 The fragment sizes of the pooled libraries were assessed with DNA HS Kit (Agilent Technologies, Santa Clara, USA) on Agilent Bioanalyser. Agilent Bioanalysersuggested: NoneThe pooled library was further normalized to 4nM concentration, denatured and loaded onto a Miseq V3 Flow Cell (150 cycles) to carry out paired end sequencing with a read length of 2×75 on MiSeq platform. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)The whole-genome sequences were aligned using were aligned using MAFFT v7.475 12, the aligned sequences were further used as input for IQ-TREE program build in nextstrain pipeline and downstream analysis steps were followed to generate the phylogenetic tree. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Generated tree file were visualized using the FigTree program v1.4.4 (available at: http://tree.bio.ed.ac.uk/software/figtree/). FigTreesuggested: (FigTree, RRID:SCR_008515)To determine the phylogenetic clade, isolated SARS-CoV-2 genomes were compared against the global Nextstrain database (https://nextstrain.org/ncov/global) using the combined package of Augur, the MAFFT and the IQ-tree software embedded in Nextstrain pipeline. IQ-treesuggested: (IQ-TREE, RRID:SCR_017254)Results from OddPub: Thank you for sharing your data.
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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