Connecticut Patient Had COVID for 471 Days, Evolved 3 New Lineages: Study

A Connecticut cancer patient was chronically infected with COVID-19 for at least 471 straight days, and during that time evolved at least three distinct lineages of the virus in their bloodstream, according to a new study from researchers at Yale.

The report highlights the potential for immunocompromised people to serve as hosts for COVID's evolution, much as South African scientists speculated last year that the omicron variant may have come from one chronically ill person.

The pre-print study, which has not been peer-reviewed, was led by Yale scientists in conjunction with teams in Australia and North Carolina. It was published online Saturday.

According to the authors, their regular surveillance of COVID variants detected a lineage known as B.1.517 in Connecticut well after it largely stopped being seen around the world. Subsequent tracing led back to a person in their 60s with lymphoma.

The patient first tested positive for COVID in Nov. 2020, and continued to be positive for the virus through at least March of this year.

"The patient continues to test positive for SARS-CoV-2 471 days and counting after the initial diagnosis," the authors wrote, adding that the person was infectious and had high viral loads essentially throughout the period. (They also noted that the patient had a few days of mild symptoms when first diagnosed, and has otherwise been fine since.)

But it was not just the persistent infection that caught their attention, it was the fact that the virus was quickly evolving inside the patient as time passed, with three distinct, new lineages emerging.

Using sophisticated data analysis of the patient's tests and global databases, the authors concluded that the virus might be evolving twice as fast inside the patient as it did in the general population.

"These findings show that this chronic infection resulted in accelerated SARS-CoV-2
evolution and divergence, a mechanism potentially contributing to the emergence of genetically diverse SARS-CoV-2 variants, including Omicron, Delta, and Alpha," they wrote.

Of the variants that evolved in the patient, the authors added "(these) distinct genotypes appeared to emerge as early as within the first three months of the infection, although new genotypes were detected after nearly ten months, suggesting multiple novel variants may simultaneously emerge and potentially spread from the same immunocompromised individual over a longer sampling period."