A new coronavirus strain is making headlines this week after being linked to an outbreak at a Kentucky nursing home, where the variant, known as R.1, infected both vaccinated and unvaccinated people.
The variant is still not widespread. Just over 2,000 R.1 cases have been detected across 47 states in the U.S. — including a few in California — since March 2020, representing less than 0.05% of cases nationwide. Its presence has tapered off since August of this year, data shows.
But the variant — which was first detected in Japan — had not been found in Kentucky before the outbreak in March affecting 46 people according to the U.S. Centers for Disease Control and Prevention. Here’s what we know so far.
Why is R.1 concerning?
The R.1 variant has characteristics that could make it more transmissible and better at evading antibodies, but evidence so far shows that coronavirus vaccines are still effective against it.
A CDC report showed that the R.1 variant was linked to an outbreak in March 2021 at a skilled nursing facility in Kentucky, where it infected both vaccinated and unvaccinated residents and health care personnel. At the facility, 90% of residents were vaccinated at the time of the outbreak, and around 50% of employees were.
The R.1 variant has what the CDC calls “multiple spike protein mutations,” which means that it might be able to evade antibodies produced either naturally or by the vaccine more easily. In other words, a vaccinated person could be more likely to get infected with R.1 than with other variants. It also showed evidence of increased transmissibility.
Still, in the case of the Kentucky outbreak, vaccinated people were less likely to get the virus than the unvaccinated, even with the R.1 strain. The vaccine was also found to prevent symptomatic cases, severe illness and death.
Is R.1 in California? The Bay Area?
Because the R.1 variant is not yet listed as a variant of interest or of concern, it is not yet listed on California’s variant tracker.
As of Thursday, a total of 53 cases with the R.1 variant sequence had been found in California — and 51 of those were reported before May 2021, the California Department of Public Health noted in an email.
Bay Area health departments that track variants — Marin, Santa Clara and Sonoma counties — also do not have the variant on their trackers yet.
“We have not detected the R.1 variant in Sonoma County, although we continue to do genotyping and monitor for all variants,” a spokesperson for the Sonoma County health department said. “Right now, our highest concern remains the delta variant, which is responsible for the majority of our current cases.”
Marin County has also not had any cases of the R.1 variant, public information officer Laine Hendricks said, adding that for the past five weeks, all of the sequenced samples in the county have been the delta variant.
What is a variant of interest, and why isn’t R.1 one?
The World Health Organization and the CDC use two main distinctions for COVID-19 variants: variants of interest and variants of concern.
A variant of interest has genetic changes that are likely to affect virus characteristics such as transmissibility, immune system evasion or disease severity. The variant may also be considered “an emerging risk to global public health” if it caused significant community transmission or multiple clusters in multiple countries, according to WHO.
A strain becomes a variant of concern when there’s scientific evidence showing that a strain may be associated with higher transmissibility or disease severity, or may reduce the effectiveness of treatments, testing or vaccines “at a degree of global public health significance.”
WHO designates variants with a Greek letter when they fall into either of these two categories, which is why R.1 — not yet on these lists — is not named yet. Scientists say that R.1 should be studied further to determine whether it should become a variant of interest.
A subset of the U.S. Department of Health and Human Services meets regularly to evaluate variants and decide how to classify them, according to the CDC.
Danielle Echeverria is a San Francisco Chronicle staff writer. Email: danielle.echeverria@sfchronicle.com Twitter: @DanielleEchev