New COVID Variant With Unique Mutations Detected in Kentucky Nursing Home

Experts have shed new light on a variant of COVID-19 discovered in a nursing home in Kentucky, which has infected at least 45 residents and health care staff. The strain has five mutations seen in other variants, plus many unique ones.

Many residents of the Kentucky nursing home were fully vaccinated, but the evolved virus was able to circumvent their anti-body protection.

An investigation by the Kentucky Department of Public Health revealed an unvaccinated, infected staff member initiated the outbreak in early March, resulting in the wave of infections.

An article published on Forbes written by William A. Haseltine, a former Harvard Medical School professor, reported that the new variant—named R.1—was first found in Japan. It has infected more than 10,000 people globally, according to GISAID SARS-CoV-2 database.

Haseltine warned that the new variant has additional mutations that could give it an advantage in transmission, replication and immune suppression.

WHO and the Centers for Disease Control and Prevention (CDC) have three categories of COVID variants that make up their watch lists: variants of interest, variants of concern—which include alpha, beta, delta and gamma—and variants of high consequence.

The R.1 variant has a mutation that can lead to "increased resistance to antibodies," according to Forbes, which could make it better able to evade anti-bodies generated by the vaccine and those who have been infected by the virus already.

This mutation in the spike protein, called E484K, is present in the Beta, Gamma, Eta, Iota and Mu variants of COVID-19, the article said.

R.1 contains the W152L mutation in the N-terminal domain, a region of the spike protein that is the target of neutralizing antibodies in convalescent sera and is the target of several neutralizing monoclonal antibodies. The W152L mutation is present in one of the minor variants of the Delta strain found in India. The same amino acid is also mutant in several variants first detected in California, B.1427/429.

R.1 shared a common origin with all variants of interest or concern— in that they are all marked with three mutations: one the 5' untranslated region: C241U, a second in the viral polymerase NSP12: P323L, and the third D614G in the exterior S1 domain of the spike protein. The D614G mutation increases infectiousness, while it is not known what the other two mutations mean. Coronaviruses with these three mutations quickly superseded the original Wuhan strain.

The COVID-19 pandemic has infected more than 229 million people and killed more than 4.55 million as of Tuesday, according to data from Johns Hopkins University.

TEM image from America's first COVID-19 case.
File photo: A transmission electron microscopic (TEM) image of an isolate from the first US case of COVID-19 in March, 2020. The spherical viral particles, colorized blue, contain cross-sections through the viral genome, seen as black dots. CDC/Smith Collection/Gado/Getty Images