Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh

  1. Pallavali Roja Rani
  2. Mohamed Imran
  3. J. Vijaya Lakshmi
  4. Bani Jolly
  5. S. Afsar
  6. Abhinav Jain
  7. Mohit Kumar Divakar
  8. Panyam Suresh
  9. Disha Sharma
  10. Nambi Rajesh
  11. Rahul C. Bhoyar
  12. Dasari Ankaiah
  13. Sanaga Shanthi Kumari
  14. Gyan Ranjan
  15. Valluri Anitha Lavanya
  16. Mercy Rophina
  17. S. Umadevi
  18. Paras Sehgal
  19. Avula Renuka Devi
  20. A. Surekha
  21. Pulala Chandra Sekhar
  22. Rajamadugu Hymavathy
  23. P.R. Vanaja
  24. Vinod Scaria
  25. Sridhar Sivasubbu

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Abstract

Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13,324X. We identified 564 high-quality SARS-CoV-2 variants, out of which 15 are novel. A total of 18 variants mapped to RT-PCR primer/probe sites, and 4 variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (94%), while 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.

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  1. ScreenIT

    SciScore for 10.1101/2021.01.22.427775: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study is in compliance with relevant laws and institutional guidelines and in accordance with the ethical standards of the Declaration of Helsinki and approved by Institutional Human Ethics Committee (RC.No.03/IHC/kmcknl/2020, dated 03/08/2020).
    Consent: The patient consent has been waived by the ethics committee.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Briefly, raw FASTQ files underwent quality control with average Phred score quality of Q30 and read length of 30 bps with adapter trimming using Trimmomatic (version 0.39)6.
    Phred
    suggested: (Phred, RRID:SCR_001017)
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    The primer and probe sequences were mapped to the Wuhan-Hu-1 reference genome using BLAST to get their genomic loci.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)

    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: 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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.01.22.427775v1 on bioRxiv
  3. Version published to 10.1017/s0950268821001424