Impact of the COVID-19 nonpharmaceutical interventions on influenza and other respiratory viral infections in New Zealand

  1. Q. Sue Huang
  2. Tim Wood
  3. Lauren Jelley
  4. Tineke Jennings
  5. Sarah Jefferies
  6. Karen Daniells
  7. Annette Nesdale
  8. Tony Dowell
  9. Nikki Turner
  10. Priscilla Campbell-Stokes
  11. Michelle Balm
  12. Hazel C. Dobinson
  13. Cameron C. Grant
  14. Shelley James
  15. Nayyereh Aminisani
  16. Jacqui Ralston
  17. Wendy Gunn
  18. Judy Bocacao
  19. Jessica Danielewicz
  20. Tessa Moncrieff
  21. Andrea McNeill
  22. Liza Lopez
  23. Ben Waite
  24. Tomasz Kiedrzynski
  25. Hannah Schrader
  26. Rebekah Gray
  27. Kayla Cook
  28. Danielle Currin
  29. Chaune Engelbrecht
  30. Whitney Tapurau
  31. Leigh Emmerton
  32. Maxine Martin
  33. Michael G. Baker
  34. Susan Taylor
  35. Adrian Trenholme
  36. Conroy Wong
  37. Shirley Lawrence
  38. Colin McArthur
  39. Alicia Stanley
  40. Sally Roberts
  41. Fahimeh Rahnama
  42. Jenny Bennett
  43. Chris Mansell
  44. Meik Dilcher
  45. Anja Werno
  46. Jennifer Grant
  47. Antje van der Linden
  48. Ben Youngblood
  49. Paul G. Thomas
  50. NPIsImpactOnFlu Consortium
  51. Richard J. Webby

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Abstract

Stringent nonpharmaceutical interventions (NPIs) such as lockdowns and border closures are not currently recommended for pandemic influenza control. New Zealand used these NPIs to eliminate coronavirus disease 2019 during its first wave. Using multiple surveillance systems, we observed a parallel and unprecedented reduction of influenza and other respiratory viral infections in 2020. This finding supports the use of these NPIs for controlling pandemic influenza and other severe respiratory viral threats.

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  1. ScreenIT

    SciScore for 10.1101/2020.11.11.20228692: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Data analyses: Study data were captured using REDCap electronic data capture tools.
    REDCap
    suggested: (REDCap, RRID:SCR_003445)
    24 Analyses were performed in Stata 16.1 (StataCorp LLC).
    StataCorp
    suggested: (Stata, RRID:SCR_012763)

    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: We detected the following sentences addressing limitations in the study:
    Our study has several limitations. Firstly, this is an observational study. Multiple simultaneous measures were applied depending on alert levels, making it difficult to understand the relative contribution of each of these measures. Secondly, during the COVID-19 laboratory response, some laboratories prioritised testing for COVID-19 and reduced testing for influenza and other respiratory viruses. Additionally, those samples ordered by clinicians for hospital inpatients and outpatients during normal clinical practices were based on clinician’s judgement, rather than a systematic sampling approach. This may result in selection bias. Thirdly, the government set up a number of community-based testing centres around the country to provide access to safe and free sampling for COVID-19. The usual flow and processes established for sentinel general practice based influenza-like illness surveillance may have been interrupted as many ILI patients would visit these centres instead of sentinel GP clinics. Additionally, national sentinel GP-based ILI surveillance requires swabbing from an ILI patient. This may contribute to the lower GP participation for this surveillance during the COVID-19 pandemic. These factors probably resulted in lower consultation and reporting and sample collection for sentinel ILI surveillance in 2020. However, the SARI surveillance system and SHIVERS-II&III cohorts operated as usual and showed the same apparent elimination of influenza virus circulation. In con...

    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.

    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 10.1038/s41467-021-21157-9
  3. ScreenIT

    SciScore for 10.1101/2020.11.11.20228692: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    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: We detected the following sentences addressing limitations in the study:

    Our study has several limitations. Firstly, this is an observational study. Multiple simultaneous measures were applied depending on alert levels, making it difficult to understand the relative contribution of each of these measures. Secondly, during the COVID-19 laboratory response, some laboratories prioritised testing for COVID-19 and reduced testing for influenza and other respiratory viruses. Additionally, those samples ordered by clinicians for hospital inpatients and outpatients during normal clinical practices were based on clinician’s judgement, rather than a systematic sampling approach. This may result in selection bias. Thirdly, the government set up a number of community-based testing centres around the country to provide access to safe and free sampling for COVID-19. The usual flow and processes established for sentinel general practice based influenza-like illness surveillance may have been interrupted as many ILI patients would visit these centres instead of sentinel GP clinics. Additionally, national sentinel GP-based ILI surveillance requires swabbing from an ILI patient. This may contribute to the lower GP participation for this surveillance during the COVID-19 pandemic. These factors probably resulted in lower consultation and reporting and sample collection for sentinel ILI surveillance in 2020. However, the SARI surveillance system and SHIVERS-II&III cohorts operated as usual and showed the same apparent elimination of influenza virus circulation. In con...

    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.

    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.

  4. Version published to 10.1101/2020.11.11.20228692v1 on medRxiv