Confirming a COVID-19 Reinfection Using Whole Genome Sequencing


While RT-PCR testing is difficult for confirming a reinfection with the virus, whole genome sequencing may be a more reliable measure.

One of the most important questions that has been asked during the COVID-19 pandemic is that of a possible reinfection with the virus. While there is still not a definitive answer to that question, it seems that most people who had COVID-19 are protected for at least 6 months following their infection.

A study conducted in Denmark showed results in March that suggested those under the age of 65 years old had an 80% chance of protection against being reinfected with COVID-19, while older patients had around 47% protection.

Most COVID-19 cases are detected by real-time reverse-transcription polymerase chain reaction (RT-PCR) tests, which work for several weeks after an infection. However, Discerning persistent RT-PCR positivity versus a COVID-19 reinfection is challenging. Due to this, the frequency of a reinfection is unknown.

Recently a group of investigators set out to determine the frequency of clinically suspected reinfection in our center and confirm reinfection using viral whole genome sequencing (WGS).

The research was presented at The Society for Healthcare Epidemiology of America Conference 2021,

The study included 13,603 patients and took place at the University of Iowa Hospitals and Clinics (UIHC), an 811 bed academic medical center. Patients were identified if they had a previously confirmed case of COVID-19 and sought care for respiratory complaints. Investigators then performed WGS using Oxford Nanopore Technology and protocols from the ARTIC network to confirm the reinfection.

Findings from the study showed that of the patients with a positive RT-PCR test, 296 had a clinical visit for the onset of new symptoms and had a repeat test >45 days from the initial test. Of those, 29 had a positive repeat test and of those, 7 had Ct values < 33, concerning for re-infection.

“In patients with a recent history of COVID-19 infection, repeat testing for respiratory symptoms was infrequent,” the authors wrote. “Some had a positive RT-PCR on repeat testing but only one in four had Ct values suggestive of a reinfection. We confirmed one case of reinfection using WGS.”

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