Outbreak or pseudo-outbreak? Integrating SARS-CoV-2 sequencing to validate infection control practices in a dialysis facility

Abstract

Background: The COVID-19 pandemic poses a particularly high risk for End Stage Renal Disease (ESRD) patients so rapid identification of case clusters in ESRD facilities is essential. Nevertheless, with high community prevalence, a series of ESRD patients may test positive contemporaneously for reasons unrelated to their shared ESRD facility. Here we describe a series of 5 cases detected within 11 days 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 to evaluate links between cases.

Methods: Four patient cases and one staff case were identified in symptomatic individuals by RT-PCR. Facility-wide screening was conducted using rapid SARS-CoV-2 antigen tests. SARS-CoV-2 genome sequences were obtained from residual diagnostic specimens.

Results: Facility-wide screening of 47 staff and 107 patients identified no additional cases. Residual specimens from 4 of 5 cases were available for genetic sequencing. Clear genetic differences proved that these contemporaneous cases were not linked.

Conclusions: With high community prevalence, epidemiological data alone is insufficient to deem a case cluster an outbreak. Cluster evaluation with genomic data, when available with a short turn-around time, can play an important role in infection prevention and control response programs.

Keywords: COVID-19; End stage renal disease; Epidemiology; Genome sequencing; Infection prevention.

Fig 1

Schematic representation of the ESRD facility showing the location of treatment stations used by COVID-19-positive individuals. Cases are identified by an ID (P = Patient, S = Staff), which of 2 non-overlapping dialysis schedules was utilized (A or B) and the date of diagnosis relative to the diagnosis date of the initial patient of this cluster investigation. The 5 cases comprising the current cluster investigation are highlighted in yellow. Two cases that were detected subsequent to the current investigation are shown in gray.

Fig 2

Four genetically distinct viral genomes sequenced from patient and staff in this ESRD cluster investigation. (A) Comparison of each of the 4 genomes to the original Wuhan SARS-CoV-2 reference genome with bases not matching this reference genome highlighted in color. This clearly indicates the genetic differences between the 4 sequenced strains in this cluster investigation. Specimens are identified using the code described in Figure 1. (B) Radial phylogenetic tree representing 1,120 SARS-CoV-2 genomes sequenced at our institution between March and November 2020, with cases relevant to this cluster investigation highlighted. The tip of each branch represents a case and more genetically similar genomes cluster together.