Methods

Search strategy and selection criteria

This systematic review was reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline (Text S1) and Synthesis without meta-analysis in systematic reviews (SWiM) reporting guideline (Text S2). The protocol of this review was registered in International Prospective Register of Systematic Review (PROSEPRO) with registration number CRD42021283045. We searched the following electronic databases: MEDLINE, EMBASE, Web of Science, the WHO COVID-19 Global literature on coronavirus disease database, China National Knowledge Infrastructure (CNKI), WanFang, CqVip, and Sinomond for relevant publications from January 1, 2020 to December 31, 2021 using a tailored search strategy (Text S3). No restrictions on language were applied. The reference lists of eligible studies were also examined for eligibility. The following selection criteria were applied.

Inclusion criteria

Population-based studies reporting any laboratory-confirmed co-infections with influenza or RSV in COVID-19 patients; AND
At least one of the following outcomes should be reported separately in co-infection group (i.e., SARS-CoV-2 and influenza / RSV) and mono-infection group (i.e., SARS-CoV-2): need or use of supplemental oxygen, ICU admission, mechanical ventilation (including invasive and non-invasive ventilation) and deaths.

Exclusion criteria

Systematic literature review

Two reviewers (BC and SD) independently screened titles, abstracts and full-texts of the retrieved records from the literature search, and extracted data using tailored data extraction template. The data extraction template consisted of two parts: the first part collected study-level characteristics such as the study location, period, number of subjects, age of subjects, statistical method, disease severity outcomes reported, clinical specimens, viral diagnostic techniques and so on; the second part collected data on the clinical outcomes by mono- infection group and co-infection group. Any discrepancies during data screening and extraction were resolved among YL, BC and SD.

Quality assessment

Quality assessment was conducted for all included studies independently by two reviewers (BC and SD). The questionnaire used for the quality assessment was modified based on the Critical Appraisal Skills Programme (CASP) checklist for cohort studies12. The modified questionnaire contained the following seven questions: 1. Did the study address a clearly focused issue?, 2. Were the subjects recruited in an acceptable way?, 3. Was the exposure accurately measured to minimize bias?, 4. Was the outcome accurately measured to minimize bias?, 5. Have the authors used multivariable analysis method to adjust for confounders?, 6. Can the results be applied to the local population?, 7. Do the results of this study fit with other available evidence? The questionnaire contained seven questions and answer to each of the questions could be “Yes”, “No”, or “Can’t tell”, corresponding to 1, 0 and 0 points, respectively. We calculated the overall score for each study after assessing each criterion as listed above. Studies with 7, 5-6 and ≤4 points were defined as “high quality”, “moderate quality” and “low quality”, respectively. Any discrepancies during quality assessment were resolved among YL, BC and SD.

Data analysis

A narrative synthesis was conducted for all outcomes of interest. The outcomes were compared between the mono-infection group and the co-infection group. A random-effect meta-analysis of the corresponding odds ratios was conducted if three or more studies were available per comparison (i.e., influenza and SARS-CoV-2 co-infection vs SARS-CoV-2 mono-infection, and RSV and SARS-CoV-2 co-infection vs SARS-CoV-2 mono-infection). The choice of conducting a random-effect meta-analysis (rather than fixed-effect meta-analysis) was based on the anticipation that populations included in the studies differed by region, age, study period (in relation to the COVID-19 pandemic), clinical specimens and diagnostic methods. We applied a continuity correction of 0.5 if no one had severity outcomes in any group 13. This allowed calculation of an OR for these instances, and enabled inclusion within subsequent meta–analyses. When odds ratios could be obtained both from univariate analysis and multivariate analysis in a report, the one from the multivariate analysis was included in the meta-analysis. For influenza and SARS-CoV-2 co-infection, the subgroup analysis was conducted by influenza type (i.e., influenza A and influenza B) if data allowed. Sensitivity analyses excluding studies with small sample sizes (defined as ≤ 5 subjects in any of the mono-infection and co-infection groups) and excluding those low-quality studies were performed. Symmetry of funnel plot and Egger’s regression method were used to evaluate the presence of small study effects 14. Heterogeneity was evaluated by I2 values; I2 value of >50% and >75% suggested moderate and high heterogeneity, respectively 15. All statistical analyses and data visualizations were performed with R version 4.1.0.