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Winning Solution: Dialysis Facility Safety Validation with Rapid COVID-19 Sequencing

Genetic sequencing of COVID-19 cases to determine patterns of spread and inform infection control practices

Paraic Kenny, PhD; Gundersen Medical Foundation

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KidneyX Competition:

COVID-19 Kidney Care Challenge

About the Solution

Routine clinical COVID-19 testing simply yields positive or negative results. Accordingly, determining patterns of spread or risk factors leading to failure to prevent spread requires considerable effort via contact tracing and other assessments which, inevitably, lead to suboptimal judgements based on incomplete data.

In contrast, genetic sequencing can illuminate very precisely the links, if any, between sets of cases. We have recently demonstrated the utility of this approach in an investigation of a potential COVID-19 outbreak in an ESRD facility. Our ability to rapidly sequence cases demonstrated that, in this particular instance, the apparent cluster merely consisted of a collection of unlinked cases acquired by the patients in the community and that no spread had occurred within the ESRD facility. This affirmed for staff and patients that this ESRD facility was a safe place in which to work and receive care. In contrast, if the data had shown that some or all cases were linked, the enhanced detail provided by the sequencing information would have provided a much more robust framework within which to address potential infection control failures, thereby increasing the probability that effort would be focused on remediating the most likely risks rather than more evenly distributed among several competing possibilities.

If widely deployed, this approach would bring infection control in dialysis facilities into a rigorous new era. By helping to identify actual failure points, it would ultimately increase patient safety. By affirming the infection control interventions that are working well, it will reward staff with the knowledge that the burdensome measures they are taking are worthwhile, thereby further reinforcing good practices. In our recent investigation, rapid provision of sequence data prevented at least one additional round of facility-wide screening, preserving both effort and expense for higher-value interventions and preventing unnecessary, invasive testing of patients.
COVID-19 sequencing is relatively straightforward to implement in any clinical or public health laboratory that is already performing next-generation sequencing for other purposes (e.g., germline diagnostics, cancer testing). Many state public health laboratories have developed this capability and the Centers for Disease Control and Prevention (CDC) is providing support to expand this. Accordingly, depending on location, many ESRD facilities should currently be able to reach out to a regional partner, most likely a public health laboratory, to perform testing. State public health laboratories have a strong mandate to prevent disease spread and are likely to be willing to incorporate ESRD specimens into their workflows, as they do with other outbreak investigations. Large commercial laboratories (e.g., Quest) are also performing COVID-19 sequencing so it will likely also be available soon as a fee-for-service test.

A key challenge will be obtaining the diagnostic specimen from the cases so that it can be sent for sequencing. In our integrated healthcare system with centralized testing, this was straightforward. It may be more difficult in a community where individuals are likely to be tested at multiple sites. The facility should be prepared to resample some patients if the original specimen cannot be secured in a timely fashion. We have found that anterior nares specimens are generally quite sufficient for sequencing, so the more invasive nasopharyngeal swabs are not required. While our analysis benefited somewhat from a background set of more than 1,100 cases from our region, the conclusion that cases are either linked or unlinked can generally be made with high confidence from an analysis restricted to just the set of cases under investigation.

At the ESRD facility management level, no particular expertise in the interpretation of genetic data would be required, as results provided by the testing lab can simply indicate which cases, if any, are genetically identical. We note that this pathogen sequencing technology has found widespread uptake in the tracking of organisms causing food-borne illness through food supply chains that spread across the nation. If it can be used successfully in that very challenging setting, we have every confidence that it can be efficiently deployed and used in the more contained environment of local healthcare settings. Our per genome sequencing cost (including labor) is $165 per case, so cost should not be a barrier to more widespread implementation of this technology.

About the Winner

Paraic Kenny is the Director of the Kabara Cancer Research Institute of the Gundersen Medical Foundation and is a Clinical Adjunct Associate Professor of Medicine at the University of Wisconsin School of Medicine and Public Health in Madison and an Adjunct Associate Professor of Biology at the University of Wisconsin – La Crosse. The KCRI also houses the CAP-accredited Gundersen Cancer Biobank with more than 15,000 solid tumor specimens.