Virus World

Coronavirus Disease 2019 (COVID-19) vaccination has resulted in excellent protection against fatal disease, including in older adults. However, risk factors for post-vaccination fatal COVID-19 are largely unknown. We comprehensively studied three large nursing home outbreaks (20–35% fatal cases among residents) by combining severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) aerosol monitoring, whole-genome phylogenetic analysis and immunovirological profiling of nasal mucosa by digital nCounter transcriptomics. Phylogenetic investigations indicated that each outbreak stemmed from a single introduction event, although with different variants (Delta, Gamma and Mu). SARS-CoV-2 was detected in aerosol samples up to 52 d after the initial infection.

Combining demographic, immune and viral parameters, the best predictive models for mortality comprised IFNB1 or age, viral ORF7a and ACE2 receptor transcripts. Comparison with published pre-vaccine fatal COVID-19 transcriptomic and genomic signatures uncovered a unique IRF3 low/IRF7 high immune signature in post-vaccine fatal COVID-19 outbreaks. A multi-layered strategy, including environmental sampling, immunomonitoring and early antiviral therapy, should be considered to prevent post-vaccination COVID-19 mortality in nursing homes. Although vaccination drops COVID-19 mortality in older adults, post-vaccine fatal COVID-19 in nursing home outbreaks was linked to Delta, Gamma and Mu variants, persistently detected in aerosols. Mortality was predicted by IFNB1 or age, ORF7a and ACE2 mRNAs.

Published May 22, 2023: https://doi.org/10.1038/s43587-023-00421-1

New infections of inoculated residents are occurring, signaling the need to maintain safety measures, C.D.C. studies show.  An unvaccinated health care worker set off a Covid-19 outbreak at a nursing home in Kentucky where the vast majority of residents had been vaccinated, leading to dozens of infections, including 22 cases among residents and employees who were already fully vaccinated, a new study reported Wednesday. Most of those who were infected with the coronavirus despite being vaccinated did not develop symptoms or require hospitalization, but one vaccinated individual, who was a resident of the nursing home, died, according to the study released by the Centers for Disease Control and Prevention. Altogether, 26 facility residents were infected, including 18 who had been vaccinated, and 20 health care personnel were infected, including four who had been vaccinated. Two unvaccinated residents also died.  The report underscores the importance of vaccinating both nursing home residents and health care workers who go in and out of the sites, the authors said. While 90 percent of the 83 residents at the Kentucky nursing home had been vaccinated, only half of the 116 employees had been vaccinated when the outbreak was identified in March of this year.

The study, released in tandem with one involving Chicago nursing homes, underscored the importance of maintaining measures like use of protective gear, infection control protocols and routine testing, no matter the level of vaccination rates. The rise of virus variants also has increased concerns. Resistance to vaccines has been steep among nursing home staffs nationwide, and the low acceptance rates of vaccination increase the likelihood of outbreaks in facilities, according to the authors, a team of investigators from the C.D.C. and Kentucky’s public health department. “To protect skilled nursing facility residents, it is imperative that health care providers, as well as skilled nursing facility residents, be vaccinated,” the authors of the Kentucky study wrote. The outbreak involved a variant of the virus that has multiple mutations in the spike protein, of the kind that make the vaccines less effective. Vaccinated residents and health care workers at the Kentucky facility were less likely to be infected than those who had not been vaccinated, and they were far less likely to develop symptoms. The study estimated that the vaccine, identified as Pfizer-BioNTech, showed effectiveness of 66 percent for residents and 75.9 percent for employees, and were 86 percent to 87 percent effective at protecting against symptomatic disease. In the Kentucky outbreak, the virus variant is not on the C.D.C.’s list of those considered variants of concern or interest. But, the study authors note, the variant does have several mutations of importance: D614G, which demonstrates evidence of increased transmissibility; E484K in the receptor-binding domain of the spike protein, which is also seen in B.1.351, the variant first recognized in South Africa, and P.1. of Brazil; and W152L, which might reduce effectiveness of neutralizing antibodies.

In Chicago, meanwhile, routine screening of nursing home residents and staff members identified 627 coronavirus infections in 78 skilled nursing facilities in the city in February, but only 22 were found in individuals who were already fully vaccinated. Two-thirds of the cases in the vaccinated individuals were asymptomatic, the report found, but two residents were hospitalized, and one died. The authors of the Chicago study said their findings demonstrate that nursing homes should continue to follow recommended infection control practices, such as isolation and quarantine, use of personal protective equipment and doing routine testing, regardless of vaccination status. They also emphasized the importance of “maintaining high vaccination coverage among residents and staff members” in order to “reduce opportunities for transmission within facilities and exposure among persons who might not have achieved protective immunity after vaccination.”

23 April — A care-home COVID outbreak shows a vaccine’s powers

In a real-world test, an mRNA-based vaccine protected care-home residents and staff against a new SARS-CoV-2 variant. On 1 March, an unvaccinated health-care worker at a Kentucky care home tested positive for SARS-CoV-2. At that time, 90% of the home’s residents and 53% of its health-care workers had received their second dose of the Pfizer–BioNTech vaccine; the vast majority had received their second shot more than 2 weeks before the worker’s infection was identified. Alyson Cavanaugh at the US Centers for Disease Control and Prevention and her colleagues report that 46 of the 199 people at the care home were infected during the outbreak. (A. M. Cavanaugh et al. Morb. Mortal. Wkly Rep. https://doi.org/f732; 2021). The researchers estimate that the vaccine was 86.5% and 87.1% effective at preventing COVID-19 among residents and staff, respectively, who were more than 2 weeks past their second dose. The shots were even more effective at preventing hospitalization, although one vaccinated resident died. Genome sequencing of samples from 27 individuals identified a variant circulating during the outbreak known as R.1, which contains mutations that have been linked to increased transmissibility and immune evasion.

Findings Published in MMWR (April 21, 2021):

http://dx.doi.org/10.15585/mmwr.mm7017e2

In what is believed to be the first published study of COVID-19 vaccine effectiveness in long-term care facilities such as nursing homes, a research team co-led by the Yale School of Public Health found a widely used vaccine is highly successful in preventing infections. Residents of such facilities, particularly those in skilled nursing facilities (SNFs), have experienced disproportionately high levels of COVID-19–related death and illness since the pandemic first arrived in the United States nearly a year ago.  Despite this, this group was not included in COVID-19 vaccine clinical trials and there is limited post-shot vaccine effectiveness data available for members of this population who are typically older, more frail, and have more underlying medical conditions than the general population. For the study, researchers were able to capitalize on the rapid vaccine rollout in Connecticut's nursing homes facilitated by the state Department of Public Health. Specifically, they examined the "real-world" effectiveness of the Pfizer-BioNTech vaccine among 463 residents in two nursing homes in Connecticut that were experiencing COVID-19 outbreaks. They found that the vaccine had an estimated effectiveness of 63% against SARS-CoV-2 infection among facility residents after the first dose. This is similar to estimated effectiveness for a single dose of COVID-19 vaccine in adults across a range of age groups in non-congregate settings and strongly suggests that a complete two-dose vaccination offers significant protection for medically frail and older adult residents of SNFs.

"This confirms what we had all hoped: This vaccine is highly effective in perhaps the most at-risk group and can potentially save many lives," said Sunil Parikh, an associate professor at the Yale School of Public Health and the study's senior author. "Vaccines work in this highly vulnerable population and their implementation should not be delayed." The findings were published March 15 as an "early release" in the Centers for Disease Control and Prevention's (CDC) Morbidity and Mortality Weekly Report. The study was a joint collaboration with state and federal partners—the Connecticut Department of Public Health and the CDC—and involved two Ph.D. students at YSPH, Jillian Armstrong and Hanna Ehrlich. "This is a great demonstration of the power of collaboration between applied public health at the local and federal levels and academic public health entities," said Parikh. Since the early days of the pandemic, Connecticut has partnered with Parikh and others at the Yale School of Public Health to conduct enhanced surveillance in all Connecticut nursing homes. This surveillance system enabled the rapid detection of outbreaks.

Research published in  MMWR (March 15, 2021):

http://dx.doi.org/10.15585/mmwr.mm7011e2