Coronavirus outbreak in Kentucky nursing home linked to R.1 variant, prompts concern over vaccine impact

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A so-called R.1 coronavirus lineage variant was detected in an outbreak at a Kentucky nursing facility where nearly all residents were vaccinated, according to one of the latest reports from the Centers for Disease Control and Prevention (CDC). Health departments noted that coronavirus infections cropped up in a quarter of vaccinated residents, raising concerns about vaccine impact.

The unnamed skilled nursing facility offered all residents and staff vaccinations beginning in January, with 90.4% of 83 residents taking up a vaccine and just over half of staffers accepting doses as well.

An investigation by the Kentucky Department of Public Health revealed an unvaccinated, infected staffer initiated the outbreak in early March, ultimately resulting in 46 COVID-19 cases. Of the total, 26 residents were infected, including 18 fully vaccinated individuals, and 20 staffers, including four vaccinated persons.

The report suggested unvaccinated individuals faced a 3 to 4.1 times greater infection risk compared to people who accepted jabs. 

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The recently approved coronavirus vaccines are safe and highly effective, but they are not 100% effective, the CDC notes, and the agency says breakthrough cases, or infections in fully vaccinated persons, is expected. However, the vaccine efficacy proved lower than that seen in real-world vaccine rollout in Israel, though the CDC cautions over comparing results due to small sample size, heightened risk, and testing irrespective to symptoms in the Kentucky nursing facility.

The vaccine was 86.5% protective in tamping down symptomatic illness for residents, and 87.1% protective among staffers, according to the CDC report. The vaccine proved more effective in preventing poor outcomes; the reported vaccine efficacy against hospitalizations was over 94% for residents; no staffers were hospitalized. 

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The R.1 lineage variant is not listed on the CDC’s compiled variants of interest or concern, though it does include several mutations seen in other variants that have previously shown to spread more quickly and resist antibody treatments.

"Although vaccination was associated with decreased likelihood of infection and symptomatic illness, 25.4% of vaccinated residents and 7.1% of vaccinated HCP were infected, supporting concerns about potential reduced protective immunity to R.1," the report reads. "In addition, four possible reinfections were identified, providing some evidence of limited or waning natural immunity to this variant."

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Three residents died, one of whom was vaccinated, and the four possible reinfections were identified among mostly unvaccinated people. All of the possible reinfection cases involved symptomatic illness, and one resident was hospitalized and died.

The CDC urges COVID-19 vaccination uptake among health care providers working in skilled nursing facilities to protect residents and prevent virus transmission. The report had its limitations, like potential discrepancies in health status for staffers who accepted vaccine versus those who did not, which could skew results not controlling for underlying health conditions. It is also possible antigen testing missed some asymptomatic cases, which if true, would affect the vaccine efficacy.