Integrated genomic view of SARS-CoV-2 in India
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Abstract
Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India.
Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred.
Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster.
Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.
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SciScore for 10.1101/2020.06.04.128751: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Samples from each group were selected and further processed for WGS of the SARS-CoV-2. WGSsuggested: NoneIllumina’s MiSeq platform was used for sequencing. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Phylogeny and network analysis: The fasta sequences were aligned using MAFFT considering the MN90894.3 version as the reference sequence. MAFFTsuggested: (MAFFT, RRID:SCR_011811)FIGTREE was used for the graphical visualisation of Phylogenetic analysis … SciScore for 10.1101/2020.06.04.128751: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Samples from each group were selected and further processed for WGS of the SARS-CoV-2. WGSsuggested: NoneIllumina’s MiSeq platform was used for sequencing. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Phylogeny and network analysis: The fasta sequences were aligned using MAFFT considering the MN90894.3 version as the reference sequence. MAFFTsuggested: (MAFFT, RRID:SCR_011811)FIGTREE was used for the graphical visualisation of Phylogenetic analysis (http://tree.bio.ed.ac.uk/software/figtree). FIGTREEsuggested: (FigTree, RRID:SCR_008515)Pheatmap and complex heatmap packages from R were used to plot the heatmaps. Pheatmapsuggested: (pheatmap, RRID:SCR_016418)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: Please consider improving the rainbow (“jet”) colormap(s) used on page 23. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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