A never-before-seen COVID-19 variant has been identified in Humboldt County, but Public Health officials say current evidence suggests it was contained to a single outbreak and there is no indication it has spread to the broader community.
In late January, Humboldt County Public Health submitted dozens of samples from individuals who tested positive for COVID-19 at the Granada Rehabilitation and Wellness Facility, along with dozens of random samples from the Humboldt County Public Health Lab (PHL), for routine genomic surveillance. Genomic sequencing of the samples was conducted by Chan Zuckerberg Biohub (CZ Biohub), a nonprofit medical research organization that has been responsible for about 45% of the genomic surveillance in California.
CZ Biohub determined that 16 of those samples had the same mutation of the virus’s spike protein at the N501Y position, which is common among other COVID-19 variants, and Public Health linked all 16 back to the Granada facility. Lab studies suggest that this mutation makes the virus “sticky” or easier for the virus to attach to a cell’s receptors, which could result in a higher rate of transmission.
Humboldt County Health Officer Dr. Ian Hoffman said that it appears the mutation occurred within the Granada facility as the virus spread among staff and residents. “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,” he said. “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.”
Senior Biosecurity Fellow at CZ Biohub Dr. Patrick Ayscue said, “Mutation is a natural feature of viruses, so it is not unexpected that we will see variants occasionally arise in outbreaks.” Dr. Ayscue went on to say, “What is pretty remarkable here is Humboldt County Public Health was in a position to identify a new and potentially dangerous variant, contain it and successfully stop it before it had the opportunity to spread more broadly. It’s really a credit to the hard work of local public health and their partners."
The Humboldt County PHL has been collaborating with CZ Biohub since June 2020, and the nonprofit has sequenced more than 650 samples from Humboldt County, accounting for approximately 22% of total cases. PHL Laboratory Manager Dr. Jeremy Corrigan said, “After we package and send the samples, our teams work together to analyze the sequencing data and identify any variants of concern. Sequencing also provides a measure of quality control because we can monitor for mutations that could impact the effectiveness of the PCR test we utilize,” referring to the polymerase chain reaction test used by the PHL. Dr. Corrigan noted that these kinds of partnerships are a great opportunity to leverage expertise and resources to better understand local COVID-19 conditions.
Dr. Hoffman described the outbreak at Granada as heartbreaking for residents, their families and caregivers as well as the community at large. Identifying this variant, he said, offers a better understanding of why the virus was able to spread through the facility so quickly. “Genomic sequencing is a tool we’ll continue to use to help us monitor for and contain variants before they become a problem,” he said.
With variants of concern on the rise around the world and here in California, Dr. Hoffman said, prevention measures are vital to keeping the spread of COVID-19 in check. “Please continue to wear a mask when in public, maintain physical distance and wash your hands regularly.”
Read more about CZ Biohub’s genomic sequencing at czbiohub.org.
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