Did Covid-19 Cause Flu Strain to Go Extinct?

SYDNEY – Australian researchers who have spent most of the past two years studying Covid-19 have recently turned their attention to another public health mystery: the possible disappearance of one of the four main strains of influenza that infects humans.

Across the world, labs that use genetic sequencing to identify the strain of influenza that made a patient ill, and upload their results to an international database known as GISAID. Since early last year, none of these labs has confirmed the existence of the Yamagata influenza B strain, the technical name for one of the four strains.

Now, researchers want to know if the Yamagata lineage has become extinct. If it does, it could affect the formulation of annual flu vaccines, which often protect against all four strains. Without Yamagata, vaccine makers could switch back to a three-strain vaccine, or they could try adding protection against another flu variant, which might provide a better defense against one of the remaining strains.

“If he disappears, that’s a big problem,” said Marius Kotsakos, a University of Melbourne research fellow at the Doherty Institute and lead author on a September paper on the possible disappearance of Yamagata. “But the world is a very big place. It could be in a place where we don’t see it.”

Influenza infections have declined globally because lockdowns, social distancing measures and travel restrictions aimed at suppressing Covid-19 have also succeeded in reducing flu transmission. Scientists say this narrowed the genetic diversity of all strains of influenza, not just Yamagata. Doctors are preparing for a worse flu season in the United States this year, with Covid-19 restrictions largely lifted, but predicting the severity of the flu cycle is difficult.

A woman receives a flu shot in Madrid. The extinction of an influenza virus strain is unusual without another strain emerging.


Alberto Ortega / Zuma Press

Several factors could explain Yamagata’s disappearance. The strain more often infects adults than children than the other major strains of influenza B, and many adults work from home and fewer travel abroad. Scientists have determined that Yamagata develops more slowly than the other influenza B strain, making it more susceptible to extermination.

“If there is a positive side to the Covid epidemic, this could be one of them,” said Richard Webby, a virologist at St. Jude Children’s Research Hospital in Memphis, Tennessee.

Influenza B viruses account for about 25% of human influenza infections on average, and another influenza B strain – the Victoria strain – continues to spread. Both breeds were found in the 1980s, and the names refer to the places where they were first identified.

Influenza A viruses, of which there are two main subtypes that circulate in humans – H1N1 and H3N2, named after the main proteins found on the surface of the virus – represent the remaining human influenza cases.

Flu season is approaching and health experts expect it to be worse than last year. Felicia Schwartz of the Wall Street Journal explains why this could be earlier and more severe and what precautions people can take during the Covid-19 pandemic. Photo: Joe Riddell/Getty Images

Scientists believe it will take at least another year to verify whether Yamagata has become extinct. Too much caution about jumping to conclusions, as there is very little flu circulating in the wake of Covid-19 restrictions. They say the strain of influenza that makes up the bulk of cases can vary from year to year.

Meanwhile, some labs that usually test for influenza viruses have focused on Covid-19.

Dr. Koutsakos and colleagues based their research on the GISAID database. Adding to the mystery, another database from the World Health Organization used to track influenza, called FluNet, has recorded 46 cases of Yamagata this year, according to figures from the WHO’s website.

FluNet mostly includes data from laboratories in every country that rely on PCR – a molecular test that detects genetic material using polymerase chain reaction technology. PCR tests are different from sequencing and sometimes produce errors, so FluNet results may be false positives. Scientists now expect to focus more on sequencing influenza B samples to determine which strain is present.

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Influenza infections have declined as Covid-19 lockdowns, social distancing measures and travel restrictions curb flu transmission.


Dinendra Haria / Zuma Press

Ian Barr, deputy director of the WHO Collaborating Center for Reference and Research on Influenza at the Doherty Institute in Melbourne, Australia, said his facility received an unusually low number of influenza samples for genetic sequencing this year. The center obtained about 300 positive influenza samples from countries in the region this year, compared to about 9,300 in 2019, 4,100 in 2018 and 5,900 in 2017, according to the figures it provided.

“Until we can go back to a normal kind of monitoring, I think it’s going to be hard to make sure it’s gone,” he said.

Scientists said the extinction of the influenza virus strain is not unprecedented, but it is unusual for one strain to disappear without another emerging. Influenza A viruses circulate widely in animals, and new copies can spread to humans, causing a pandemic and outstripping existing strains – as happened in 1957, 1968 and 2009. In contrast, influenza B viruses are believed to spread exclusively Almost in humans without an animal host reservoir, the influenza B strain would only be expected to disappear if a more dominant strain evolved naturally in humans.

If the Yamagata goes extinct, scientists will have to work out how that might affect flu vaccines. Twice a year, the WHO panel recommends which of the four major influenza strains should be included in influenza seasons vaccines in the northern and southern hemispheres. The final decision rests with each individual country, but it generally follows the recommendation of the World Health Organization.

The World Health Organization said it does not consider Yamagata to have disappeared as few cases have been reported, albeit without genetic sequencing to confirm. She said there was no discussion about removing Yamagata from the quadruple influenza vaccine at the committee’s most recent meeting in September.

Previously, based on the lack of virus detections, we saw an obvious loss of some data [groups] Only for them to appear again later,” WHO said.

If Yamagata is extinct, some scientists suggest dropping it from the vaccine and including two different types of the H3N2 influenza virus, which in the past were genetically diverse, making choosing the right one difficult.

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If the Yamagata influenza B strain disappears, it could have implications for annual influenza vaccinations.


Inaki Perasalos / Contact Us / Zuma Press

Greg Sylvester, chief medical officer of Seqirus, an Australian-based CSL-owned influenza vaccine manufacturer Ltd.

It is technically feasible to do an injection with three viruses A and B virus, he said.

However, regulators could consider such a formulation to form a new vaccine and require it to go through a lengthy approval process. Some scientists say its efficacy should be shown in clinical trials because it is unclear whether the immune system will focus each H3N2 variant equally and that it may prevail.

Experts are also unsure of the effect of Yamagata’s disappearance on influenza cases in general. Exposure to Yamagata confers some immunity to the Victoria breed. Historically Yamagata was discovered more in temperate regions, so its disappearance could provide more comfort to the people there.

For Dr. Kotsakos, a researcher in Melbourne, there is little to do but wait for the latest genetic sequence.

“Personally, I am frantically updating the database,” he said.

write to Mike Cherney at

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