Evidence map›Paper›PMID 36400646›Full record

ArticleIndian journal of medical microbiology

Genome characterization, phylogenomic assessment and spatio-temporal dynamics study of highly mutated BA variants from India.

Poulomi Sarkar, Sarthak Banerjee, Saikat Chakrabarti, Partha Chakrabarti, Arun Bandyopadhyay, Arpita Ghosh Mitra, Soumen Saha, Aviral Roy, Siddik Sarkar

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In one paragraph

Article in Indian journal of medical microbiology. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Poulomi SarkarCSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India.
Sarthak BanerjeeCSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India.
Saikat ChakrabartiCSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India.
Partha ChakrabartiCSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India.
Arun BandyopadhyayCSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India.
Arpita Ghosh MitraMEDICA Super-specialty Hospital, Kolkata, India.
Soumen SahaMEDICA Super-specialty Hospital, Kolkata, India.
Aviral RoyMEDICA Super-specialty Hospital, Kolkata, India.
Siddik SarkarCSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India. Electronic address: siddik.sarkar@iicb.res.in.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

purposeThe emergence of highly mutated and transmissible BA variants has caused an unprecedented surge in COVID-19 infections worldwide. Thorough analysis of its genome structure and phylogenomic evolutionary details will serve as scientific reference for future research.

methodHere, we have analyzed the BA variants from India using whole-genome sequencing, spike protein mutation study, spatio-temporal surveillance, phylogenomic assessment and epitope mapping.

resultsThe predominance of BA.2/BA.2-like was observed in India during COVID-19 third wave. Genome analysis and mutation study highlighted the existence of 2128 amino acid changes within BA as compared to NC_045512.2. Presence of 23 unknown mutation sites (spanning region 61-831) were observed among the Indian BA variants as compared to the global BA strains. Unassigned probable Omicron showed the highest number of mutations (370) followed by BA.1 (104), BA.2.3 (56), and BA.2 (27). Presence of mutations 'Q493R ​+ ​Q498R ​+ ​N501Y', and 'K417 ​N ​+ ​E484A ​+ ​N501Y' remained exclusive to BA.2 as well as unassigned probable Omicron. The time-tree and phylogenomic network assessed the evolutionary relationship of the BA variants. Existence of 424 segregating sites and 113 parsimony informative sites within BA genomes were observed through haplotype network analysis. Epitope mapping depicted the presence of unique antigenic sites within the receptor binding domain of the BA variants that could be exploited for robust vaccine development.

conclusionThese findings provide important scientific insights about the nature, diversity, and evolution of Indian BA variants. The study further divulges in the avenues of therapeutic upgradation for better management and eventual eradication of COVID-19.

Indexed as

COVID-19Amino AcidsHumansIndiaMutationPhylogenyAmino AcidsBA.2/BA.2-likeOmicronPhylogenomic networkSARS-CoV-2Whole genome sequencing (WGS)

Identifiers

PMID36400646
PMCPMC9664238

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