Outbreak or pseudo-outbreak? Integrating SARS-CoV-2 sequencing to validate infection control practices in an end stage renal disease facility

Pfaff, B. L.; Richmond, C. S.; Sabin, A. P.; Athas, D. M.; Adams, J. C.; Meller, M. E.; Usha, K.; Schmitz, S. A.; Simmons, B. J.; Borgert, A. J.; Kenny, P. A.

Background: The COVID-19 pandemic of 2020 poses a particularly high risk for End Stage Renal Disease (ESRD) patients and led to a need for facility-wide control plans to prevent introduction and spread of infection within ESRD facilities. Rapid identification of clusters of contemporaneous cases is essential, as these may be indicative of within-facility spread. Nevertheless, in a setting of high community COVID-19 prevalence, a series of ESRD patients may test positive at around the same time without their shared ESRD facility being the nexus for disease spread. Here we describe a series of five cases occurring within an eleven-day period in November 2020 in a hospital-based 32-station ESRD facility in southwest Wisconsin, the subsequent facility-wide testing, and the use of genetic sequence analysis of positive specimens to evaluate whether these cases were linked. Methods: Four patient cases and one staff case were identified in symptomatic individuals by RT-PCR. Facility-wide screening was initiated at the request of local public health and conducted using Abbot BinaxNOW antigen tests. SARS-CoV-2 genome sequences were obtained from residual diagnostic test specimens using an amplicon-based approach on an Ion Torrent S5 sequencer. Results: Residual specimens from 4 of 5 cases were available for sequence analysis. Each sequence was very clearly genetically distinct from the others, indicating that these contemporaneous cases were not linked. Facility-wide screening of 47 staff and 107 patients did not identify any additional cases. Conclusions: These data indicate that despite the outward appearance of a case cluster, the facility did not experience within-facility spread nor serve as the epicenter of a new outbreak, suggesting that the enacted rigorous infection control procedures (screening, masking, distancing) practiced stringently by patients and staff were sufficient to permit dialysis to proceed safely in a very high-risk population under pressure from increasing community spread. These data also demonstrate the utility of rapid turnaround SARS-CoV-2 sequencing in outbreak investigations in settings like ESRD facilities.