Covid Update: Variant Varieties

Hospitalizations due to COVID-19 infections have had two peaks this year, one in January and a second in August. Rates in California were higher than the national average, but they have begun to decline as of the beginning of September. New COVID virus variants (nicknamed FLiRT for the changes in the virus spike protein) were responsible for the summer surge in infections. The new COVID vaccines available since late August should help protect against the FLiRT and closely related variants, so it is important to get a booster shot if you haven’t already done so.

A recent publication in Nature Communications (PubMedID 39174553) provided new insight into the generation of sequence variants during COVID infection. It has long been suspected that variants arise during chronic infection of individuals with poor immune responses, and this publication provides the data to support this concept. Variants occur in the spike protein of the virus that mediates entry into human cells. When the genes for the spike protein were sequenced from COVID infections of persons without HIV or with HIV but preserved immunity, each individual had a single spike gene sequence. In marked contrast to this finding, HIV-infected individuals with more advanced disease and lower immunity had a median of 46 spike mutations per person! This virus genetic diversity was detected as soon as COVID-19 symptoms appeared, and it was associated with prolonged release of COVID virus. Importantly, the virus variation continued during infection with appearance of key changes in functionally important parts of the spike protein.

Because COVID infection is so prevalent and immune suppression due to HIV infection, old age, cancer therapy, or autoimmune disease is not uncommon, emergence of new COVID virus variants is certain to occur. The latest variant, XEC, has just arrived in the US, and it may fuel a surge in infections later this fall. It is not too different from the FLiRT variants, so the current vaccine may provide some protection, but it is time for vulnerable individuals to consider masking and avoiding crowds to lessen the risk of infection.