Predicting virologically confirmed influenza using school absences in PA

Methods The Allegheny County Department of Health provided virologically confirmed influenza data collected from all emergency departments and outpatient providers in the county for 2007 and 2011-2016. All-cause school absence rates were collected from nine school districts within Allegheny County for 2010-2015. For a subset of these schools, in addition to all-cause absences, influenza-like illness (ILI)-specific absences were collected using a standard protocol: 10 K-5 schools in one school district (2007-2008), nine K-12 schools in two school districts (2012-2013), and nine K-12 schools from three school districts (2015-2016). We used negative binomial regression to predict weekly county-level influenza cases in Allegheny County, Pennsylvania, during the 2010-2015 influenza seasons. We included the following covariates in candidate models: all-cause school absence rates with different lags (weekly, 1-3 week lags, assessed in separate models using all other covariates) and administrative levels (county, school type, and grade), week and month of the year (assessed in separate models), average weekly temperature, and average weekly relative humidity. Separately, for the three districts for which ILI-specific and all-cause absences were available, we predicted weekly county-level influenza cases using all-cause and ILI-specific absences with all previously stated covariates. We used several crossvalidation approaches to assess models, including leave 20% of weeks out, leave 20% of schools out, and leave 52-weeks out.