#15,859
Two weeks ago flu experts from around the world were called upon to make their recommendations for the vaccine viruses to be contained in next fall's northern hemisphere flu shot (see Recommended composition of influenza virus vaccines for use in the 2021 - 2022 northern hemisphere influenza season).
This normally difficult task was made even more daunting by the unprecedented lack of flu activity around the world for the past 12 months (see WHO epi chart above), supplanted largely by COVID-19.
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 WHO addresses these shortcoming in their Vaccine Q&A document.
18. How has the COVID-19 pandemic impacted the 2021-2022 northern hemisphere influenza vaccine recommendation?The volume of data available from recently circulating influenza viruses and the geographic representation have been significantly lower for this northern hemisphere vaccine recommendation meeting than is typical. The reduced number of viruses available for characterization raises uncertainties regarding the full extent of the genetic and antigenic diversity of circulating influenza viruses and those likely to pose a threat in forthcoming seasons. Nevertheless, new groups of A(H3N2) viruses were identified, some of which had spread internationally. Consequently, the A(H3N2) component recommendation has been updated.
Even during years with the best of surveillance, we've been blindsided by a rapidly evolving seasonal flu strain (see 2014's CDC HAN Advisory On `Drifted’ H3N2 Seasonal Flu Virus). Whether flu returns as normal later this year, or is delayed even longer by COVID, is unknowable, but there is little reason to believe this respite will last for very long.
All of which brings us to the 4th, and most recent, update from the ECDC on seasonal influenza surveillance in the 2020-2021 season. So far, they report a 99.5% drop in detections compared to the same period in 2020, which means there is a dearth of data available.
Influenza virus characterisation - Summary Europe, February 2021
Surveillance report
11 Mar 2021
Publication series: Influenza Virus Characterisation
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 fourth report for the 2020-2021 influenza season. As of week 8/2021, only 712 influenza detections across the WHO European Region had been reported to TESSy; 51% type A viruses, with A(H3N2) and A(H1N1)pdm09 being equally represented, and 49% type B viruses, with only 10 having been ascribed to a lineage, eight B/Victoria and two B/Yamagata. This represents a 99.5% drop in detections compared to the same period in 2020, probably due to the COVID-19 pandemic and measures introduced to combat it.
Since the December 2020 characterisation report1, six shipments from European Union/European Economic Area (EU/EEA) countries, containing a total of 20 influenza-positive specimens, have been received at the London WHO Collaborating Centre, the Francis Crick Worldwide Influenza Centre (WIC). This report therefore focuses mainly on genetic characterisation of the HA genes of influenza viruses with the most recent collection dates (after 31 August 2020) based on sequences deposited in GISAID up to 28 February 2021.
Of the 27 A(H1N1)pdm09 HA sequences in GISAID for viruses collected after 31 August 2020, two from the United States of America (US) fell in the 6B.1A5B group; one from Ghana fell in the basal 6B.1A5A group; two, one each from China and Ghana, fell in the 6B.1A5A+156K subgroup represented by A/Victoria/2570/2019, the vaccine virus for the southern hemisphere 2021 and northern hemisphere 2021-2022 seasons; and 22, two from Japan, three from Ghana and 17 from Togo, fell in the 6B.1A5A+187V/A subgroup represented by A/Guangdong-Maonan/SWL1536/2019, the vaccine virus for the northern hemisphere 2021-2022 season. The 20 viruses from West Africa in the 6B.1A5A+187V/A subgroup all contained additional HA1 amino acid substitutions of I166T and A186T.
Of the 162 A(H3N2) HA sequences in GISAID for viruses collected after 31 August 2020, one fell in the 3C.2a1b+T135K-B subgroup represented by A/Hong Kong/2671/2019, the vaccine virus for the northern hemisphere 2021-2022 and southern hemisphere 2021 seasons; 24, one from France and 23 from West Africa fell in the 3C.2a1b+T135K-a subgroup represented by the reference virus A/Denmark/3264/2019; and 137 fell in the 3C.2a1b+T131K-A subgroup.
The viruses in the 3C.2a1b+T135K-A subgroup formed two clusters: the first contained 96 viruses, 84 being from Bangladesh, with HA1 amino acid substitutions of Y159N, T160I (loss of a glycosylation site), L164Q, G186D, D190N, F193S and Y195F; and the second contained 40 viruses, 22 being from Cambodia, with HA1 amino acid substitutions of G186S, F193S, Y195F and S198P, with 39 HAs also having K171N. Viruses in these two clusters were antigenically distinct from one another, and from those in other A(H3N2) genetic groups, and A/Cambodia/e0826360/2020 was recommended as the vaccine virus for the northern hemisphere 2021-2022 influenza season.
Although the highly detailed and technical monthly report is of most interest to epidemiologists and influenza virologists, you can download it in its entirety at the link below. I'll have a brief postscript when you return.
Influenza virus characterisation Summary Europe, February 2021 - EN - [PDF-9 MB]
Our recent lack of seasonal flu activity is arguably a good thing - as it makes things far less complicated during the COVID-19 pandemic and flu is a killer in its own right - but there is a potential downside.
One that is mostly theoretical right now, but is at least plausible.
The longer we go without seasonal influenza, the lower community immunity to seasonal H1N1 and H3N2 drops. As long as there is very little flu circulating, that isn't a problem, but presumably influenza will eventually return in the months or years ahead.
And that could mean that the next real flu season we see could be unusually severe, or could be dominated by a virus not well covered by the current vaccine.
There are studies that suggest that novel flu viruses may have a better chance of emerging when seasonal influenza activity is low, and community immunity to influenza is reduced (see PLoS Comp. Bio.: Spring & Early Summer Most Likely Time For A Pandemic,).
Admittedly, its mostly theoretical.
But this COVID pandemic has changed the viral status quo of our world in ways we are just beginning to fathom, and we should be prepared for surprises going forward.
