Virus World

The Omicron SARS-CoV-2 has three distinct sublineages, among which sublineage BA.1 is responsible for the initial Omicron surge and is now being replaced by BA.2 worldwide, whereas BA.3 is currently at a low frequency. The ongoing BA.1-to-BA.2 replacement underscores the importance to understand the cross-neutralization among the three Omicron sublineages. Here we tested the neutralization of BA.1-infected human sera against BA.2, BA.3, and USA/WA1-2020 (a strain isolated in late January 2020). The BA.1-infected sera neutralized BA.1, BA.2, BA.3, and USA/WA1-2020 SARS-CoV-2s with geometric mean titers (GMTs) of 445, 107, 102, and 16, respectively. Thus, the neutralizing GMTs against heterologous BA.2, BA.3, and USA/WA1-2020 were 4.2-, 4.4-, and 28.4-fold lower than the GMT against homologous BA.1, respectively. These findings have implications for vaccine strategy.

Preprint available in bioRxiv (March 31, 2022):

https://doi.org/10.1101/2022.03.30.486409 

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.”

Half of the elementary school students in an unvaccinated teacher’s classroom developed COVID-19 after the teacher — infected and symptomatic — worked for 2 days and read to the students while not wearing a mask, according to researchers. The exposures led to a larger outbreak at the California school in May that was associated with the delta variant, with many cases occurring among children not eligible for vaccination, illustrating a continued need for nonpharmaceutical prevention strategies during the pandemic, the researchers wrote in MMWR.  The outbreak location was an elementary school in Marin County, California, which serves 205 students in prekindergarten through eighth grade, with most students unable to receive the vaccine to due age limits. The school was also reported as having 24 staff members, with all but two of the teachers being vaccinated. One of the two unvaccinated teachers, whom the study identifies as the index patient, reported becoming symptomatic on May 19, having attended social events the previous few days without any known COVID-19 exposures. “The teacher continued working during May 17-21, subsequently experiencing cough, subjective fever, and headache,” the researchers wrote. “The school required teachers and students to mask while indoors; interviews with parents of infected students suggested that students’ adherence to masking and distancing guidelines in line with CDC recommendations was high in class. However, the teacher was reportedly unmasked on occasions when reading aloud in class.”

On May 23, the teacher notified the school that they had tested positive for COVID-19 on May 21 and self-isolated until May 30. The study said the teacher did not receive a second COVID-19 test but reported fully recovering during isolation. “The index patient’s students began experiencing symptoms on May 22,” the study said, and 22 of the teacher’s 24 students were tested for COVID-19, with 12 testing positive, including eight who began having symptoms between May 22 and 26. According to the researchers, desks in the classroom were separated by 6 feet and arranged in five rows. The attack rate was higher the closer students sat to the teacher’s desk — eight out of 10 students sitting in the first two rows tested positive vs. three of 14 in the back three rows. On May 26 and June 2, the Marin County Department of Public Health held testing events at the school as part of outbreak control. During these 2 days, 231 people were tested, including 194 of the 205 students, 21 of 24 staff members and teachers, and 16 parents and siblings of students. A total of 18 people tested positive for the delta variant at the time, and five more tested positive later on. The study’s authors said further transmission might have been prevented by high levels of community vaccination — at the time of this outbreak, approximately 72% of eligible individuals in the city where the school is located were fully vaccinated.

“In addition to vaccination of eligible persons, implementation of and strict adherence to multipronged nonpharmaceutical prevention strategies including proper masking, routine testing, ventilation, and staying home while symptomatic are important to ensure safe school instruction,” the study said. With school set to return in the coming weeks in many areas of the country, the CDC is encouraging districts to follow guidelines to decrease transmission.  In a briefing Friday, CDC Director Rochelle Walensky, MD, MPH cited a second MMWR study that demonstrated that schools in Los Angeles County with safety measures in place during the winter peak of the pandemic experienced rates of COVID-19 that were around 3.5 times lower than the rates in the surrounding community. “While symptoms and severe case in children remain less common than in other age groups, we have seen increases in pediatric cases and hospitalizations over the last few weeks, which is likely the result of overall increases in community transmission generally and more specifically the delta variant’s increased transmissibility,” Walensky said. Walensky said schools should implement as many prevention measures as possible simultaneously, such as ensuring that eligible children and adults are vaccinated, that everyone is wearing a mask, and that appropriate ventilation, distancing, cohorting, screening and testing measures are followed.

“This serves to protect our children even if there are inevitable breaches in any single protection layer,” Walensky said.

Study Cited Published in MMWR (August 27, 2021):

http://dx.doi.org/10.15585/mmwr.mm7035e2