Seroepidemiological and genomic investigation of COVID-19 spread in North East region of India

  1. Romi Wahengbam
  2. Pankaj Bharali
  3. Prasenjit Manna
  4. Tridip Phukan
  5. Moirangthem Goutam Singh
  6. Gayatri Gogoi
  7. Yasmin Begam Tapadar
  8. Anil Kumar Singh
  9. Rituraj Konwar
  10. Channakeshavaiah Chikkaputtaiah
  11. Natarajan Velmurugan
  12. Selvaraman Nagamani
  13. Hridoy Jyoti Mahanta
  14. Himakshi Sarma
  15. Ravi Kumar Sahu
  16. Prachurjya Dutta
  17. Sawlang Borsingh Wann
  18. Jatin Kalita
  19. G Narahari Sastry

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Abstract

Seroepidemiology and genomics are valuable tools to investigate the transmission of COVID-19. We utilized qRT-PCR, serum antibody immunoassays, and whole genome sequencing to examine the spread of SARS-CoV-2 infections in North East (NE) region of India during the first and second pandemic waves (June 2020 to September 2021). qRT-PCR analysis was performed on a selected population from NE India during June 2020 to July 2021, and metadata were collected for the region. Seroprevalence and neutralizing antibody immunoassay were studied on selected individuals (n=2026) at three time points (August 2020, February 2021 and June 2021), as well as in a cohort (n=35) for a year (August 2020 to August 2021). SARS-CoV-2 genomes of 914 qRT-PCR positive samples (June 2020 to September 2021) were sequenced and assembled, and those obtained from the sequence databases were analyzed. Test positivity rates in first and second waves were 6.34% and 6.64% in the state of Assam, respectively, and a similar pattern was observed in other NE states. Seropositivity in August 2020, February 2021, and June 2021 were 10.63%, 40.3% and 46.33% respectively, and neutralizing antibody prevalence were 90.91%, 52.14%, and 69.30% respectively. The cohort group showed the presence of stable neutralizing antibody throughout the year. Normal variants dominated the first wave, while the variant of concerns (VOCs) B.1.617.2 and AY-sublineages dominated the second wave, and identified mostly among vaccinated individuals. All eight states of NE India reported numerous incidences of SARS-CoV-2 VOCs, especially B.1.617.2 and AY sublineages, and their prevalence co-related well with high TPR and seropositivity rate in the region. High infection and seroprevalence of COVID-19 in NE India during the second wave was associated with the emergence of VOCs. Natural infection prior to vaccination provided higher neutralizing activity than vaccination alone.

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  1. ScreenIT

    SciScore for 10.1101/2022.01.25.22269702: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Ethical statement: All subjects participated on a voluntarily basis and written informed consent was obtained from each participants.
    IRB: The study was approved by the Institutional Human Ethics Committee of CSIR-NEIST (IHEC/NEIST20-21/201).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    IgG-N antibodies were measured using Elecsys Anti-SARS-CoV-2 kit (Roche Diagnostics, Germany) as per manufacturer’s protocol.
    Anti-SARS-CoV-2
    suggested: None
    IgG-S and IgM-S antibodies were detected using VoxPress New Corona Virus (COVID-19) IgG / IgM Rapid Test kit (
    IgG-S
    suggested: (Icosagen AS Cat# A1-900-100, RRID:AB_11135309)
    IgM-S
    suggested: None
    COVID-19 ) IgG
    suggested: None
    Samples that were seropositive for IgG-N, IgG-S and/or IgM-S were further tested for neutralizing antibody response against spike protein using GENScriptcPass SARS-CoV-2 Neutralization Antibody Detection Kit (GenScript, USA), according to the manufacturer’s protocol.
    IgG-N , IgG-S
    suggested: None
    Software and Algorithms
    SentencesResources
    Nine hundred and fourteen qRT-PCR positive samples from first wave (July-August 2020) and second wave (May-September 2021) were sequenced on a MinION Mk1c sequencer (Oxford Nanopore Technologies) using NEB Next ARTIC SARS-CoV-2
    MinION
    suggested: (MinION, RRID:SCR_017985)
    The sequence alignment files of the genomes were used to construct maximum-likelihood phylogenetic tree using IQ-TREE server (version 1.6.12) and visualized in Fig Tree version 1.4.4.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)

    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.

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  2. Version published to 10.1101/2022.01.25.22269702v1 on medRxiv