Watch Out for the Case Backfill!

How delays in reporting COVID-19 cases over the winter holidays can skew predictions.

Brendan J. Kelly https://github.com/bjklab
2022-01-03

This week, COVID-19 cases have continued to rise in Philadelphia, Pennsylvania (4119 observed cases on December 28, 2021), despite incidence modelling that predicted a peak closer to 680 cases/day. I wanted to understand how case backfill, the process of updating COVID-19 daily case counts for up to a week after the initial daily case counts are recorded, might impact estimates of the COVID-19 reproductive number (Rt) and predictions of future COVID-19 incidence based on Rt. During the winter holiday season, short staffing may result in data entry and transfer delays that increase the impact of case backfill. To understand the holiday backfill effect, I compared the COVID-19 case data available for Philadelphia, Pennsylvania on 22 December 2021 to the case data available today, 3 January 2022:

In the top panel, the comparison of incidence data demonstrates that case backfill significantly increased cases in the week prior to December 22, 2021. In the bottom panel, the effect of this missing data to skew Rt below 1 can be seen. Rt was estimated using a mean serial interval of 2.2 days (SD 0.8 days), based on the best available data on the Omicron variant, via the EpiEstim R package. The median (line) and 95% confidence interval (shading) for the estimated Rt are shown.

The same model for Rt based on the most recent available data again suggests that Rt is trending down… but this should not be cause for excess optimism in light of the holiday backfill effect seen last week.

Citation

For attribution, please cite this work as

Kelly (2022, Jan. 3). Brendan J. Kelly: Watch Out for the Case Backfill!. Retrieved from https://bjklab.github.io/bjk-distill/index.html/posts/2022-01-03-watch-out-for-the-case-backfill/

BibTeX citation

@misc{kelly2022watch,
  author = {Kelly, Brendan J.},
  title = {Brendan J. Kelly: Watch Out for the Case Backfill!},
  url = {https://bjklab.github.io/bjk-distill/index.html/posts/2022-01-03-watch-out-for-the-case-backfill/},
  year = {2022}
}