Nipah Virus Outbreak in Kerala State, India Amidst of COVID-19 Pandemic

  1. Pragya D. Yadav
  2. Rima R. Sahay
  3. Anukumar Balakrishnan
  4. Sreelekshmy Mohandas
  5. Chandni Radhakrishnan
  6. Mangesh D. Gokhale
  7. R. Balasubramanian
  8. Priya Abraham
  9. Nivedita Gupta
  10. A. P. Sugunan
  11. Rajan Khobragade
  12. Kalpana George
  13. Anita Shete
  14. Savita Patil
  15. Ullas Padinjaremattathil Thankappan
  16. Hitesh Dighe
  17. Jijo Koshy
  18. Vivek Vijay
  19. R. Gayathri
  20. P. Jayesh Kumar
  21. Asma Rahim
  22. A. Naveen
  23. Sarala Nair
  24. V. R. Rajendran
  25. V. Jayasree
  26. Triparna Majumdar
  27. Rajlaxmi Jain
  28. Prasanth Viswanathan
  29. Deepak Y. Patil
  30. Abhinendra Kumar
  31. Dimpal A. Nyayanit
  32. Prasad Sarkale
  33. Ashwini Waghmare
  34. Shrikant Baradkar
  35. Pranita Gawande
  36. Poonam Bodke
  37. Kaumudi Kalele
  38. Jyoti Yemul
  39. Sachin Dhaigude
  40. Manjunath Holepannawar
  41. Sanjay Gopale
  42. Ganesh Chopade
  43. Shilpa Ray
  44. Priyanka Waghmare
  45. Jitendra Narayan
  46. Basavaraj Mathapati
  47. Manoj Kadam
  48. Abhimanyu Kumar
  49. Annasaheb Suryawanshi
  50. Beena Philomina Jose
  51. Saritha Sivadas
  52. N. P. Akash
  53. T. V. Vimisha
  54. K. V. Keerthi

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Abstract

We report here a Nipah virus (NiV) outbreak in Kozhikode district of Kerala state, India, which had caused fatal encephalitis in a 12-year-old boy and the outbreak response, which led to the successful containment of the disease and the related investigations. Quantitative real-time reverse transcription (RT)-PCR, ELISA-based antibody detection, and whole genome sequencing (WGS) were performed to confirm the NiV infection. Contacts of the index case were traced and isolated based on risk categorization. Bats from the areas near the epicenter of the outbreak were sampled for throat swabs, rectal swabs, and blood samples for NiV screening by real-time RT-PCR and anti-NiV bat immunoglobulin G (IgG) ELISA. A plaque reduction neutralization test was performed for the detection of neutralizing antibodies. Nipah viral RNA could be detected from blood, bronchial wash, endotracheal (ET) secretion, and cerebrospinal fluid (CSF) and anti-NiV immunoglobulin M (IgM) antibodies from the serum sample of the index case. Rapid establishment of an onsite NiV diagnostic facility and contact tracing helped in quick containment of the outbreak. NiV sequences retrieved from the clinical specimen of the index case formed a sub-cluster with the earlier reported Nipah I genotype sequences from India with more than 95% similarity. Anti-NiV IgG positivity could be detected in 21% of Pteropus medius ( P. medius ) and 37.73% of Rousettus leschenaultia ( R. leschenaultia ). Neutralizing antibodies against NiV could be detected in P. medius . Stringent surveillance and awareness campaigns need to be implemented in the area to reduce human-bat interactions and minimize spillover events, which can lead to sporadic outbreaks of NiV.

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  1. Version published to 10.3389/fpubh.2022.818545
  2. ScreenIT

    SciScore for 10.1101/2021.12.09.21267278: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: The sampling was performed with the prior approval from the Institutional Animal Ethics Committee, Institutional Biosafety Committee of ICMR-NIV, Pune and the Principal Chief Conservator of Forests, Government of Kerala.
    Sex as a biological variableCase history: In August 2021, an adolescent male (index case) resident of Kozhikode district, Kerala state, India developed low grade fever (Supplementary Figure.1).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Briefly, the microtiter plates were coated with 1: 100 diluted anti-human IgM antibodies (Sigma, USA) overnight at 40C.
    anti-human IgM
    suggested: None
    The plates were washed and anti-NiV biotinylated antibodies were added and incubated for one hour.
    anti-NiV
    suggested: None
    After washing, 100 micro litre of 1:15000 dilution of anti-human IgG HRP antibodies were added and incubated for one hr at 37°C.
    anti-human IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    After washing with wash buffer for four times, inactivated NiV antigen (positive antigen) and Vero-CCL81 cell lysate (negative antigen) were added and incubated for one hr at 37°C.
    Vero-CCL81
    suggested: None
    Anti-Nipah human IgG ELISA: Briefly, microtiter plates were coated with 0.1 ml of inactivated NiV antigen and normal Vero CCL81 cell lysate as negative antigen in carbonate buffer (pH 9.2, 0.025 M) overnight at 4°C.
    Vero CCL81
    suggested: None
    The mixture was incubated for 1 hour and was added to 24-well tissue culture plate containing a confluent monolayer of Vero CCL-81 cells.
    Vero CCL-81
    suggested: None
    Software and Algorithms
    SentencesResources
    Whole Genome Sequencing (WGS): To identify the NiV genotype, WGS was carried out on different clinical samples obtained from the patient.
    WGS
    suggested: None

    Results from OddPub: Thank you for sharing your data.

    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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  3. Version published to 10.1101/2021.12.09.21267278v1 on medRxiv