Retrospective screening for SARS‐CoV‐2 among influenza‐like illness hospitalizations: 2018–2019 and 2019–2020 seasons, Valencia region, Spain

  1. Ainara Mira‐Iglesias
  2. Beatriz Mengual‐Chuliá
  3. Laura Cano
  4. Javier García‐Rubio
  5. Miguel Tortajada‐Girbés
  6. Mario Carballido‐Fernández
  7. Juan Mollar‐Maseres
  8. Germán Schwarz‐Chavarri
  9. Sandra García‐Esteban
  10. Joan Puig‐Barberà
  11. Javier Díez‐Domingo
  12. F. Xavier López‐Labrador

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Abstract

On 9 March 2020, the World Health Organization (WHO) Global Influenza Programme (GIP) asked participant sites on the Global Influenza Hospital Surveillance Network (GIHSN) to contribute to data collection concerning severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). We re‐analysed 5833 viral RNA archived samples collected prospectively from hospital admissions for influenza‐like illness (ILI) in the Valencia Region of Spain by the Valencia Hospital Surveillance Network for the Study of Influenza and Other Respiratory Viruses (VAHNSI) network (four hospitals, catchment area population 1 118 732) during the pre‐pandemic 2018/2019 ( n  = 4010) and pandemic 2019/2020 ( n  = 1823) influenza seasons for the presence of SARS‐CoV‐2. We did not find evidence for community‐acquired SARS‐CoV‐2 infection in hospital admissions for ILI in our region before early March 2020.

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  1. Version published to 10.1111/irv.12899
  2. ScreenIT

    SciScore for 10.1101/2021.05.24.21257402: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Finally, patients need to be in hospital between 8 and 48 hours to be enrolled and swabbed (combined nasopharyngeal and oropharyngeal in universal transport medium), after written informed consent.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Recombinant DNA
    SentencesResources
    The limit of detection of the assay was established to 35 copies using the SARS-CoV-2 E-gene as reference material either as an insert in a pCDNA plasmid (a gift from Luis Enjuanes, Coronavirus laboratory, CNB-CSIC, Madrid, Spain) or as encapsulated RNA (a gift from Charité Medical Center, Berlin, though the European Virus Archive program).
    pCDNA
    suggested: RRID:Addgene_105932)

    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. First, the VAHNSI network was designed for detecting influenza cases, therefore COVID19 cases presenting a symptomatology different from influenza were not detected. Second, the pandemic disruption situation forced the interruption of hospital surveillance activities in mid-March, just after the declaration of the state of alarm by the Spanish Government. More cases of SARS-CoV-2 would have been detected should the study had not been stopped. Finally, it is possible that pooled testing for 2018-19 samples led to lower RT-PCR sensitivity. However, pool sizes of up to 10 samples have been proven to maintain high performance when compared with individual sample testing (23, 32). Despite these limitations, here we show how influenza surveillance networks are a powerful resource to analyse the presence of the new respiratory viruses sharing the ILI / SARI symptomatology, because routine collection and storage of samples months (and eventually years) before the occurrence of a new virus introduction. Using these networks will allow us to expand surveillance of SARS-CoV-2, to detect unexpected pathogens in the future, and to elaborate a better map and seasonality for SARS-CoV-2 circulation during the next influenza season. The transition of influenza surveillance networks to other respiratory viruses is thus warranted.

    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.

  3. Version published to 10.1101/2021.05.24.21257402v2 on medRxiv
  4. Version published to 10.1101/2021.05.24.21257402v1 on medRxiv