Genomic analysis of SARS-CoV-2 breakthrough infections from Varanasi, India

  1. Lamuk Zaveri
  2. Royana Singh
  3. Priyoneel Basu
  4. Sofia Banu
  5. Payel Mukherjee
  6. Shani Vishwakarma
  7. Chetan Sahni
  8. Manpreet Kaur
  9. Nitish Kumar Singh
  10. Abhay Kumar Yadav
  11. Ajay Kumar Yadav
  12. Ashish
  13. Shivani Mishra
  14. Shivam Tiwari
  15. Surendra Pratap Mishra
  16. Amareshwar Vodapalli
  17. Himasri Bollu
  18. Debashruti Das
  19. Prajjval Pratap Singh
  20. Gyaneshwer Chaubey
  21. Divya Tej Sowpati
  22. Karthik Bharadwaj Tallapaka

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Abstract

Studies worldwide have shown that the available vaccines are highly effective against SARS-CoV-2. However, there are growing laboratory reports that the newer variants of concerns (VOCs e.g. Alpha, Beta, Delta etc) may evade vaccine induced defense. In addition to that, there are few ground reports on health workers having breakthrough infections. In order to understand VOC driven breakthrough infection we investigated 14 individuals who tested positive for SARS-CoV-2 after being administered a single or double dose of Covishield (ChAdOx1, Serum Institute of India) from the city of Varanasi, which is located in the Indian state of Uttar Pradesh. Genomic analysis revealed that 78.6% (11/14) of the patients were infected with the B.1.617.2 (Delta) variant. Notably, the frequency (37%) of this variant in the region was significantly lower (p<0.01), suggesting that the vaccinated people were asymmetrically infected with the Delta variant. Most of the patients tested displayed mild symptoms, indicating that even a single dose of the vaccine can help in reducing the severity of the disease. However, more comprehensive epidemiological studies are required to understand the effectiveness of vaccines against the newer VOCs.

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  1. ScreenIT

    SciScore for 10.1101/2021.09.19.21262487: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: Ethical approval: This study was approved by the local institutional ethical committee.
    Consent: Written consent was taken from patients wherever applicable.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Data processing: Basecalling was performed on raw image data using bcl2fastq v2.20.0.422 (Illumina).
    bcl2fastq
    suggested: (bcl2fastq , RRID:SCR_015058)
    Quality control of FASTQ files was performed using FASTQC v0.11.9 [8].
    FASTQC
    suggested: (FastQC, RRID:SCR_014583)
    Poor quality bases and adapters were trimmed using Trimmomatic [9].
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Alignment of reads to the indexed reference genome NC_045512.2 was done using HISAT2 v2.1.0 [10].
    HISAT2
    suggested: (HISAT2, RRID:SCR_015530)
    Coverage across the genome was calculated using samtools depth.
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    PANGO v3.0.5 was used to assign lineages to the consensus sequences [11].
    PANGO
    suggested: None
    The sequences were aligned against the WH1 reference genome using MAFFT and IQTREE was used to construct a phylogenetic time tree using the sequence collection date [13,14].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    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.
    • 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.

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

    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 10.1101/2021.09.19.21262487v1 on medRxiv