H3N2 flu variant spreads across Brazil with reduced vaccine protection

Rio de Janeiro's grip tightened in December as a strain of influenza called H3N2—specifically what researchers call the Darwin variant—began spreading beyond the state's borders into São Paulo, Salvador, and across Brazil. The timing could not have been worse. Brazilians were preparing to travel, to gather with family, to move through airports and buses and homes. Health authorities watched with visible concern, knowing that this virus was moving through a population already exhausted by COVID-19, and that the vaccines most people had received offered only partial defense against what was coming.

The numbers told the story plainly. In São Paulo's first two weeks of December, the municipal health department counted 82 percent of the entire month of November's flu cases—roughly half of those also carried COVID-19. Salvador had already confirmed an outbreak. The Fundação Oswaldo Cruz, Brazil's premier research institution, issued a warning on December 9th: the influenza virus and the coronavirus were now circulating together, and the country was not prepared.

H3N2 is one of several subtypes of influenza A, distinguished from its cousin H1N1 by differences in the proteins that coat its surface. The virus itself was not new. Scientists had first isolated this particular strain in Australia in 1999. But beginning in recent months, it had circulated with new intensity across the Northern Hemisphere, prompting the World Health Organization in September to recommend that Southern Hemisphere countries update their flu vaccines for 2022 to include protection against it. Brazil had not done so in time.

Alexandre Naime Barbosa, an infectious disease specialist and department head at São Paulo State University, explained the problem with clinical precision. The Darwin variant now spreading through Brazil was not the same H3N2 included in the current flu vaccine. The vaccine might offer low to moderate cross-immunity—protection that was better than nothing but far from complete. This explained why vaccinated people could still contract the flu. But the unvaccinated remained far more vulnerable to severe illness. And vaccination rates had been dismal. Only 42 percent of the target population nationally had received the flu shot by July, when the Health Ministry expanded eligibility to the general public. São Paulo had managed just 40 percent coverage by June.

Part of the problem was bureaucratic. Until late September, the Health Ministry had required a two-week interval between COVID-19 and flu vaccines, pushing people to choose one over the other. Most chose COVID protection. When the ministry finally allowed simultaneous vaccination at month's end, uptake did not increase. By mid-December, reporters calling health clinics in São Paulo found no flu vaccines available in the public system, though private pharmacies still had stock.

People who contracted the virus reported symptoms of striking intensity. High fever, profound weakness, a sense of malaise so complete that patients described feeling as though they might die. Barbosa distinguished this from COVID-19, which typically developed more gradually. Influenza struck suddenly and violently—the fever higher, the muscular weakness more pronounced, the prostration more complete. The patient could not leave bed. The difference was not subtle.

Yet vaccination remained worthwhile, Barbosa insisted. Even imperfect protection was protection. The alternative was to wait and hope, and hope was not a strategy during a dual outbreak. For those who did fall ill, treatment existed. Oseltamivir, an antiviral drug, could reduce both the duration and severity of symptoms if administered within 72 hours of symptom onset. It was particularly important for the elderly, for pregnant women, for anyone with underlying illness. But first, a person had to recognize they were sick and seek care—and they had to know the difference between flu and COVID, which required testing. The public system had rapid tests but could not distinguish between flu types. The private system could.

Prevention remained the simplest tool: physical distance, masks, hand hygiene—the same measures that had defined two years of pandemic life. But those measures had been loosening for two months, researchers noted. The relaxation of restrictions, combined with holiday travel and family gatherings, had created conditions for the virus to move freely. What happened next would depend on how many people chose vaccination, how quickly they sought care, and whether the country's health system could absorb another surge.