First Case of Community Acquired Omicron Variant in San Diego

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Officials at the San Diego County Health and Human Services Agency, working in collaboration with scientists at University of California San Diego and Scripps Research, have announced the second confirmed case — and first locally acquired infection — of the Omicron variant of SARS-CoV-2, the virus that causes COVID-19.

The San Diego County man, in his 30s, does not have a travel history or known exposure. He had mild symptoms at testing, which have resolved, but he remains at home in isolation. He did not require hospitalization. He was fully vaccinated and had received his booster shot two weeks before the infection was diagnosed.

Molecular representations of the Delta and Omicron SARS-CoV-2 spike proteins from top down (upper row) and membrane view. The spike protein is shown in transparent white ribbons, with single point mutations depicted as blue surfaces, amino acid deletions as red surfaces and amino acid insertions in white surfaces. Photo credit: Mia Rosenfeld, Fiona Kearns, Lorenzo Casalino, Rommie Amaro/UC San Diego

“With our first known case of community acquired Omicron, it’s clear that the variant is here and it will be spreading,” said Christopher Longhurst, MD, chief medical officer, UC San Diego Health. “That means the usual precautions, measures and common sense still apply, maybe even more so.” 

The announcement comes roughly 24 hours after confirmation of the first Omicron case, a San Diego County resident who tested positive on December 8, 2021 and who had recently traveled abroad. Health officials said the traveler had been vaccinated and had received a booster, was not hospitalized and was currently was in isolation. 

Tracing efforts have begun to identify others who may have been in close contact with either infected person.  

At last count, 22 states had reported Omicron cases. The Omicron variant has already been detected in at least 57 countries, according to the World Health Organization (WHO), since first being identified in South Africa in late-November. 

The second case was first detected through the Expedited Covid Identification Environment (EXCITE) lab at UC San Diego, which runs thousands of diagnostic tests daily on human and environmental samples taken at UC San Diego, local schools and communities. It was sequenced and confirmed by investigators at Scripps Research, partners in the San Diego Epidemiology and Research for COVID Health (SEARCH) Alliance.  

Few places in the country and world are better equipped to detect new viral variants than San Diego, where researchers at UC San Diego School of Medicine and Scripps Research, working with county public health officials, health systems and others, collaborate to create a viral variant surveillance system.  

“It’s not random chance that the SEARCH Alliance was the first to detect Omicron in San Diego. We have been monitoring individual COVID-19 testing results and the wastewater for it very closely since the new variant was first announced,” said Rob Knight, PhD, professor and director of the Center for Microbiome Innovation at UC San Diego. 

“And because we already had highly trained testing staff monitoring test results for the tell-tale ‘S-drop,’ an efficient viral sequencing process built into our workflow, as well as the required regulatory approvals in place to allow for sharing of patient samples and data among multiple organizations, we were able to identify and confirm this case extremely quickly.”

Knight co-leads the SEARCH alliance with Louise Laurent, MD, PhD, professor of obstetrics, gynecology and reproductive sciences, vice chair for translational research and co-director of the Center for Perinatal Discovery at UC San Diego School of Medicine; Gene Yeo, PhD, professor of cellular and molecular medicine at UC San Diego School of Medicine; and Kristian Andersen, PhD, professor at Scripps Research. 

"Everyone has been working around the clock to monitor for the variant," said Mark Zeller, PhD, a staff scientist in the Andersen lab who leads the sequencing efforts for the SEARCH Alliance at Scripps Research. "We have in place the technology and effective processes that enabled us to detect the first confirmed case of Omicron, even while its prevalence is still thought to be currently low."

Additional key partners in the viral sequencing process are the UC San Diego Institute for Genomic Medicine Genomics Center, led by Kristen Jepsen, PhD, and the UC San Diego Center for Computational Biology and Bioinformatics, led by Kathleen Fisch, PhD.

At UC San Diego, teams run thousands of COVID-19 PCR tests daily on samples collected from campus faculty, staff and students; local K-12 school staff and students; and even the wastewater flushed from campus and school buildings. The qPCR test they use is different than those used in many labs: It can detect a specific pattern that might indicate a variant, such as Omicron. 

After testing, the team sequences the viral genome of all positive samples to track variants. Positive samples with qPCR results consistent with variants of concern are transferred for rapid sequencing first at Scripps Research, and also sequenced again for confirmation back at UC San Diego School of Medicine. 

In January, this research partnership announced the first evidence that the B.1.1.7 or Alpha variant was present in California. It was initially detected by personnel at the EXCITE COVID-19 clinical testing lab at UC San Diego as part of its Return to Learn program, then immediately sequenced by Scripps Research scientists. The sample came from a local man in his 30s who had not recently traveled, indicating that the variant was already present in the community. 

Background and Looking Ahead

The Omicron variant was first identified in Botswana and South Africa, and prompted immediate concern among researchers and public health authorities because an unusually high number of spike protein mutations (30) make the strain potentially more transmissible and less susceptible to current vaccines. 

Officially, the variant is called B.1.1.529, but is also known as Omicron after the 15th letter in the Greek alphabet. 

The WHO has dubbed Omicron a “variant of concern” and warned of heightened global risk. Cases have been identified in at least 57 countries so far, including parts of Europe. 

This rapid spread and the multiple mutations present in its genome have led to concerns that the transmission or virulence of the Omicron variant may be different compared to prior variants. Indeed, emerging evidence suggests greater transmissibility and infectiousness, but a milder disease outcome. 

At this point, health experts caution that much remains to be learned about Omicron, including its degree of transmissibility, its capacity to cause serious illness and whether it can infect vaccinated or previously infected persons more readily than other variants. 

“Since we are seeing a lot of Omicron infection in vaccinated, and even recently boosted, individuals, we need to take a multi-pronged approach,” said Laurent. “This includes not only vaccination and boosting, but also masking and social distancing, serial testing in high-risk situations (like group homes, dorms, and schools), prompt isolation and testing for anyone who has symptoms, even minor ones like headaches or low-grade fevers.”  

“If a person has mild symptoms and tests negative, and then their symptoms continue or get worse, they should retest.”

Davey Smith, MD, a translational research virologist and head of Infectious Diseases and Global Public Health at UC San Diego School of Medicine, said that despite numerous pressing questions, the overall situation with the Omicron variant is better than in the past with other emerging variants. 

“We are in much better shape than last year at this time, but how much better is still unclear.” 

Protections

Health authorities continue to emphasize that current mitigation efforts remain effective against virus infection, including:

• Getting a booster shot. The Centers for Disease Control now recommends everyone 18 years and older receive a booster at least six months after completing the primary COVID-19 vaccination series (Pfizer or Moderna) or at least two months after the single-dose Johnson & Johnson vaccine. Persons can receive any vaccine as booster, regardless of original vaccine used. 
• Continued masking in poorly ventilated indoors areas or in crowds. “It is critical that we convey the importance of wearing well-fitted KN95 masks to prevent transmission, even for folks who have received boosters,” said Amaro.
• Social distancing.
• Registration in CA Notify, a free service that informs users if they have been exposed to COVID-19.