New COVID variant “Cicada” arrived through SFO airport as Bay Area sees rising infections
A traveler flying from the Netherlands to San Francisco International Airport in June 2025 became the first documented case of COVID variant BA.3.2 in the United States, according to CDC genomic monitoring data. The routine nasal swab revealed a SARS-CoV-2 strain genetically distinct from all variants then circulating in the country.
Ten months later, the variant has spread to 23 countries and at least 25 states, including California. In Germany, Denmark and the Netherlands, BA.3.2 peaked at 30% of all sequenced COVID cases. While its share remains smaller in the US, growth has accelerated rapidly. Stanford’s WastewaterSCAN program shows BA.3.2 comprised 4.1% of samples in February, jumping to 21.2% by late March.
The strain earned the nickname “Cicada” from T. Ryan Gregory, an evolutionary biologist at the University of Guelph in Canada who previously named variants including Cerberus, Kraken and Pirola. The name reflects its unusual origin story: BA.3.2’s ancestor, variant BA.3, emerged with Omicron in late 2021. While four of Omicron’s five branches caused global infection waves, BA.3 disappeared. Scientists believe the virus survived in an immunocompromised person for roughly two years, accumulating mutations before re-emerging — like a cicada living underground before surfacing.
BA.3.2 carries an unprecedented number of mutations. Its spike protein, which the virus uses to enter cells, contains 70-75 substitutions and deletions compared to JN.1 and LP.8.1, the variants used to develop 2025-2026 season vaccines. Previous circulating strains typically had 30-40 such mutations.
These extensive mutations have drawn concern from physicians and virologists. Laboratory studies show antibodies from vaccination neutralize BA.3.2 less effectively than the currently dominant XFG strain.
However, several factors temper these concerns. All available data indicates “Cicada” does not cause more severe illness than other Omicron variants. Symptoms remain consistent: sore throat, cough, fever, body aches and nasal congestion. Distinguishing COVID from flu or RSV without testing remains impossible, confirmed epidemiologist Geeta Sood from Johns Hopkins Bayview Medical Center.
Current vaccines targeting the JN.1 lineage work less effectively against “Cicada” but retain value. T-cell immunity responds to viral components beyond the spike protein that remain unchanged. Vaccination still reduces hospitalization and severe illness risk, according to William Schaffner, an infectious disease specialist at Vanderbilt University Medical Center. “The vaccine’s job is to keep you out of the hospital,” Schaffner said. “It’s less effective at preventing mild illness.”
Antiviral medications continue working against BA.3.2. Paxlovid targets the viral protease Mpro, genetically separate from the spike protein where “Cicada” mutations concentrate. Mount Sinai virologist Adolfo Garcia-Sastre confirmed existing antivirals remain effective.
Early April WastewaterSCAN data for the Bay Area shows SARS-CoV-2 concentrations remain generally low but uneven across the region. San Francisco shows higher levels than other Bay Area counties. The Western region, including California, maintains lower COVID levels compared to the Northeast, where viral concentrations are rising.
BA.3.2 has not achieved dominance. CDC data through late March shows it comprised 7% of national wastewater samples. The dominant strain remains XFG, followed by NB.1.8.1. But “Cicada’s” share grows monthly.
One unusual characteristic: the variant disproportionately affects children. COVID historically impacted older adults more severely, but BA.3.2 shows a different pattern. Scientists do not yet understand why but consider this significant for understanding viral evolution. Children do not experience more severe illness than with other strains.
Germany, where “Cicada” first gained substantial circulation, offers encouraging signals. Icahn School of Medicine virologist Florian Kramer reports BA.3.2 growth in Germany has stalled and appears declining. His team’s research showed vaccine antibodies, while less effective at neutralizing “Cicada,” still combat it sufficiently quickly. The researchers believe this explains why BA.3.2 has not become globally dominant.
University of Missouri molecular microbiology professor Mark Johnson offers a more cautious assessment: “Cicada” could become the dominant strain but will not prove “invasive” like some previous variants.
Practical recommendations for Bay Area residents remain unchanged. Testing remains the only way to distinguish COVID from other respiratory illnesses when symptoms appear. Paxlovid continues working but must begin within 5-7 days of symptom onset. Physicians recommend spring COVID vaccine boosters for people over 65 and those with chronic conditions. The fall 2026 vaccine may include a “Cicada” component, but decisions await data on actual spread patterns, Schaffner said.
COVID levels in the Bay Area remain low. The variant serves as a reminder that the virus continues evolving. A strain considered extinct in 2022 returned three years later with 75 new mutations, finding its first US entry point at SFO.