New variant emerged in Granada outbreak
Hoffman: ‘This is not a variant of concern’
A never-before-seen variant of COVID-19 emerged in Humboldt County during the outbreak at Granada Wellness & Rehabilitation Center in Eureka, but it’s unlikely to be circulating in the community at this time.
“This is not a variant of concern,” Humboldt County Health Officer Dr. Ian Hoffman said in a Thursday media availability video. “It’s different than say the U.K. variant, the South African variant, the Brazilian variants and other variants that we are monitoring. It’s a single mutation and it very much seems to be contained to this one outbreak and did not spread from there.”
Humboldt County Public Health announced last week that 16 samples out of dozens sent to the Chan Zuckerberg Biohub, a nonprofit medical research organization that has been doing genomic surveillance of the novel coronavirus in the state, were determined to have a mutation at the N501Y position of the virus’s spike protein. The mutation allowed the virus to become more highly transmissible.
All 16 samples were from the outbreak at the Granada Rehabilitation & Wellness Center in Eureka. Hoffman said the mutation appeared to have occurred within the facility and was likely responsible for why the virus spread so rapidly through the facility.
“There is no evidence to suggest that this variant was brought in from outside of Granada, and data provided by CZ Biohub indicates that it has not been seen elsewhere in Humboldt County,” Hoffman said in a statement. “The good news is there has been no evidence either through genetic testing or contact investigations to indicate the variant spread into the broader community.”
Another variant that is of concern, L452R, had been detected in Humboldt County first in November and 13 more of those cases were found in the latest round of results returned to the county, Hoffman said in the Thursday media availability video. Researchers are still trying to figure out if the variant is more contagious and resistant to vaccines.
Seeing an increase in the L452R variant in the county isn’t surprising since it’s becoming the dominant strain in the state, accounting for as many as 40% of samples sequenced to date, Hoffman said.
The best way to keep singular mutations from becoming variants of concern is by limiting their spread through safety protocols already being implemented, such as hand-washing, social distancing and masking, as well as containing outbreaks at facilities when they occur as was done at Granada, Hoffman said.
Senior Biosecurity Fellow at CZ Biohub Dr. Patrick Ayscue said in a statement that mutations of viruses are normal and expected during outbreaks, but Public Health’s ability to identify and contain the “potentially dangerous variant” was a credit to the department and its partners.
The Humboldt County Public Health Lab has collaborated with and sent more than 650 samples, approximately 22% of all total cases and 50% of all positive samples, to the CZ Biohub since June 2020 for sequencing.
“After we package and send the samples, our teams work together to analyze the sequencing data and identify any variants of concern,” Public Health’s lab manager Jeremy Corrigan said in a statement. “Sequencing also provides a measure of quality control because we can monitor for mutations that could impact the effectiveness of the (polymerase chain reaction) test we utilize” to detect COVID-19 cases.
Not all samples are able to be sequenced because enough virus has to be present in the sample, which isn’t always the case, Hoffman said. The county currently sends about 100% of samples that are able to be sequenced to CZ Biohub when enough samples are available, he said.
“We really are doing a lot more sequencing than most, both in California and in the country,” Hoffman said. “There is a new national initiative from the Biden administration to increase funding for sequencing, so if there’s a possibility of doing more we’ll certainly look into that. But we’re doing quite a bit already.”