Avian Flu Diary: ECDC Influenza Virus Characterisation

Northern Hemisphere Flu As of March 14th, 2021 - Credit WHO

#15,918

As the above chart illustrates, influenza essentially fell off a cliff worldwide when COVID-19 appeared in the spring of 2020, has has been scarcely reported anywhere in world since.

This unprecedented drop in flu activity has been - at least in the short term - a blessing, as it has made diagnosing of COVID much easier, and we've largely avoided the feared complications from co-infection with influenza and COVID.

But its long term impacts are less certain, as community immunity to influenza presumably lessens with each passing month, new flu variants may have a better opportunity to thrive without competition from more established strains, and global flu surveillance has taken a backseat to COVID tracking.

Last February, when flu researchers were tasked with deciding on next fall's Northern Hemisphere flu vaccine components, we discussed the unique challenges during this pandemic (see Recommended composition of influenza virus vaccines for use in the 2021 - 2022 northern hemisphere influenza season).

The ability to watch the trending of different subclades of influenza as they spread around the world is the backbone for predicting which flu strains will likely dominate 6 to 12 months from now, and over the past year almost no data have been available.

The ECDC publishes a monthly (during the northern hemisphere flu season) report on influenza viruses collected from Europe and analyzed by the London WHO Collaborating Centre. Reports during the `off-season' are somewhat less frequent.

While normally we get a highly technical, and detailed, analyses of scores (or even hundreds) of virus samples each month, during the 2020-2021 flu season, only a handful of viruses have been submitted for analysis.

Since week 40/2020, six shipments of specimens (virus isolates and/or clinical specimens) were received at the Crick Worldwide Influenza Centre (WIC), none of which were received in March 2021. The packages contained 20 virus-related samples with collection dates after 31 August 2020 and were made up of nine type A viruses and 11 type B viruses.

The ECDC has published their March 2021 Influenza Characterization report, and as you will see, no new viruses have been analyzed in this latest reporting period. There are concerns raised, however, over new variants of A(H3N2) and B/Victoria-lineage viruses that have emerged outside of the EU region, primarily in Asia and West Africa.

I've reproduced the executive summary below, along with a link to the full (highly technical) report. I'll return with a postscript after the break.

Influenza virus characterisation - Summary Europe, March 2021

Surveillance report
21 Apr 2021

ECDC’s influenza virus characterisation reports are published periodically and give an overview of circulating influenza viruses. They provide details on the current vaccine strains, summarise the development of the viruses since the last report, and closely follow the main developments for the ongoing influenza season. Virus characterisation reports are primarily intended for influenza virologists and epidemiologists.

Executive summary

This is the fifth report for the 2020-2021 influenza season. As of week 12/2021, only 758 influenza detections across the WHO European Region had been reported to The European Surveillance System (TESSy); 50% type A viruses, with A(H3N2) and A(H1N1)pdm09 being equally represented, and 50% type B viruses, with only 12 having been ascribed to a lineage, 10 B/Victoria and two B/Yamagata. This represents a 99.5% drop in detections compared with the same period in 2020, probably due to the COVID-19 pandemic and measures introduced to combat it.

Since the February 2021 characterisation report, no shipments from European Union/European Economic Area (EU/EEA) countries have been received at the London WHO Collaborating Centre, the Francis Crick Worldwide Influenza Centre (WIC): consequently, no new virus characterisation data have been generated. This report therefore focuses on genetic characterisation of the HA genes of seasonal influenza viruses based on sequences deposited and/or released in GISAID during March 2021, compared with the situation reported in the February 2021 characterisation report.

The most recent data continues to show extremely low levels of influenza detections across North America and Europe. Globally, few or no detections of A(H1N1)pdm09 and B/Yamagata-lineage viruses have been reported while new variants of A(H3N2) and B/Victoria-lineage viruses have emerged, with the majority of detections reported by Asian and West African countries with evidence of wider geographic spread.

Influenza virus characterisation - Summary Europe, March 2021 - EN - [PDF-2.19 MB]

The suppression of influenza around the world is likely due to two factors; the first being NPIs (non-pharmaceutical interventions - social distancing, the wearing of face covers, and enhanced hand hygiene, etc.) that have become commonplace during the pandemic.

The second factor is likely `viral interference', a well documented but poorly understood ability of one circulating virus to inhibit or impede the transmission of another (see When Epidemic Viruses Collide).

While reduced surveillance in some parts of the world may be a factor, there are plenty of places actively looking for flu and not finding much.

In 2017's PLoS Comp. Bio.: Spring & Early Summer Most Likely Time For A Pandemic, researchers used `viral interference' and/or the off-season waning of community immunity to explain why historically influenza pandemics almost always emerge in the spring or early summer; after the end of regular flu season.

Whether seasonal influenza returns this fall, or waits until 2022 or beyond, is unknown.

But when flu does return, our collective immune defenses may have waned to a historic low, and if new variants (or worse, subtypes) take center stage, we could find ourselves dealing with yet another public health challenge either following, or along side, COVID-19.