One of the Most Common Seasonal Flu Strains May Have Become Extinct Due to Covid

The appearance of the pandemic coronavirus struck widespread damage; not even seasonal flu viruses were immune. The 2020-2021 flu season was all but canceled due to travel restrictions, quarantines, closures, physical separation, masks, enhanced hand washing, and disinfection.

This resulted in not only an unparalleled global drop in the number of flu patients but also a substantial decline in the genetic variety of circulating flu strains. Many viral subtypes have all but vanished. But, perhaps most notably, one entire lineage — one of only four flu families targeted by seasonal flu vaccines — went completely dark, appearing to be extinct.

Researchers noticed the absence last year when the flu was still struggling to recover from the pandemic. However, the flu has returned, threatening to kick off an especially bad season in the Northern Hemisphere.

According to a study published this week in the journal Eurosurveillance, the B/Yamagata lineage is still lacking. Since April 2020, it has not been definitively detected. And the question of whether it truly went extinct remains unanswered.

What the absence of B/Yamagata means for future flu seasons and flu vaccinations is still unknown. In recent years, four major kinds of seasonal flu have been circulating among individuals globally. Two types of influenza A viruses exist in subtypes of H1N1 and H3N2 viruses.

The other two viruses are influenza type B strains from the Victoria and Yamagata lineages. (For a more extensive description of flu, see our page here.) Current quadrivalent vaccinations target seasonal variants of each of these four flu viruses.

With fewer flu viruses around, future vaccines may be easier to match to circulating viruses, making seasonal shots more effective. A surprise re-emergence of B/Yamagata, on the other hand, could become more harmful as people lose their immunity. But before health officials can plan for future flu seasons, they need to know if B/Yamagata is truly gone.

disappeared virus

Researchers in the Netherlands searched the most recent worldwide flu surveillance data until August 31, 2022, in a report published this week in the journal Eurosurveillance. They point out that GISAID, a global database of influenza virus genetic sequences that gets millions of flu sequences each year, has not received any B/Yamagata sequences with sample collection data beyond March 2020.

There were 43 reports of the missing lineage in 2021, largely from China, and eight sporadic cases from four countries in 2022, according to the World Health Organization’s FluNet surveillance data. In comparison, there were more than 51,000 B/Yamagata detections in 2018.

The scientists speculate that the modest number of instances reported in the last two years may have been false alarms. Rather than releasing viruses into the wild, they can simply identify B/Yamagata signatures in vaccinations containing live attenuated influenza viruses.

They could also be the result of genetic contamination from inactivated viral vaccinations. This is not a hypothetical situation. The authors point out that several B/Yamagata detections in the United States and Scotland were caused by live attenuated flu vaccinations rather than true cases of circulating virus.

The researchers are urging flu surveillance labs to increase their efforts to discover Yamagata cases in order to determine whether the virus is truly gone or simply low.

“From a laboratory standpoint,” they conclude, “we believe it would be prudent to increase the ability and capacity to determine the lineage of all influenza B viruses detected around the world, as this is crucial to detecting the lack of B/Yamagata lineage viruses.”

They also propose that the World Health Organization develop standards for determining when a lineage can be proclaimed “extinct” and the implications of such a pronouncement.

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