Monday, August 24, 2020

ECDC: Influenza Virus Characterisation - Summary Europe, July 2020



As we head into our first full flu season under the shadow of COVID-19 there are a lot of open questions over how this winter's twin  epidemics will interact. While there remain genuine concerns over seeing a  `twindemic' - one that could overburden our already stretched medical system - globally, influenza reporting has been greatly subdued since the arrival of our novel coronavirus. 

The most recent WHO Influenza update (below) shows - for the first time I've ever seen - a blank flu map, and indicates only 40 positive flu samples were received by their laboratories over the month of July (a 90-fold decrease over July 2019). 

Influenza update - 374
17 August 2020 - Update number 374, based on data up to 02 August 2020

Information in this report is categorized by influenza transmission zones, which are geographical groups of countries, areas or territories with similar influenza transmission patterns. For more information on influenza transmission zones, see the link below:

  • The current influenza surveillance data should be interpreted with caution as the ongoing COVID-19 pandemic might have influenced to varying extents health seeking behaviours, staffing/routines in sentinel sites, as well as testing priorities and capacities in Member States. The various hygiene and physical distancing measures implemented by Member States to reduce SARS-CoV-2 virus transmission might also have played a role in mitigating influenza virus transmission.
  • Globally, influenza activity was reported at lower levels than expected for this time of the year. In the temperate zones of the southern hemisphere, the influenza season has not commenced. Despite continued or even increased testing for influenza in some countries in the southern hemisphere, very few influenza detections were reported.
  • In the temperate zone of the northern hemisphere, influenza activity remained below inter-seasonal levels.
  • In the Caribbean and Central American countries, sporadic influenza detections were reported. Severe acute respiratory infection (SARI) activity remained elevated in some reporting countries.
  • In tropical South America and tropical Africa, there were sporadic influenza virus or no detections across reporting countries.
  • In Southern Asia and South East Asia, no influenza detections were reported.
  • Worldwide, of the very low numbers of detections reported, seasonal influenza A viruses accounted for the majority of detections.
National Influenza Centres (NICs) and other national influenza laboratories from 65 countries, areas or territories reported data to FluNet for the time period from 20 July 2020 to 02 August 2020 (data as of 2020-08-19 09:14:02 UTC). The WHO GISRS laboratories tested more than 2050491 specimens during that time period.
A total of 40 specimens were positive for influenza viruses, of which 20 (50%) were typed as influenza A and 20 (50%) as influenza B. Of the sub-typed influenza A viruses, 3 (25%) were influenza A(H1N1)pdm09 and 9 (75%) were influenza A(H3N2). Of the characterized B viruses, 0 (0%) belonged to the B-Yamagata lineage and 8 (100%) to the B-Victoria lineage.


Admittedly, not a lot of information to go on.  And it isn't entirely clear whether all of this massive decline in reported global  flu activity reflects reality, or is the result of public health resources being diverted to the COVID-19 pandemic. 

That said, social distancing, hand hygiene, and face covers used against COVID-19 covers undoubtedly suppress flu transmission as well.  At this point, no one really knows what to expect this fall and winter. 

One source of additional information we do have comes from the ECDC's Monthly Influenza Virus Characterisation Report, which provides us with some of the most detailed analysis of influenza virus samples submitted by EU countries.  

But this year, the ECDC report has analysed fewer virus samples than usual.

All of this is important, not only to give us an idea of what to expect this fall and winter in the Northern Hemisphere, but also to guide flu experts in selecting the vaccine components in September for next year's Southern Hemisphere flu vaccine. 

While the number of virus samples tested remains small, and are submitted from a limited geographic region, three trends have appeared over the past few ECDC reports.

  • We are seeing more diversity among H1N1 viruses sampled, with only 73% (down from 91% last March) well recognized by antisera from the 2019-2020 flu vaccine (A/Brisbane/02/2018).
  • Only 57% of H3N2 viruses sampled in this report (down from 76% last month) were well recognized by antisera from the 2019-2020 flu vaccine (egg propagated A/Kansas/14/2017).
  • Nearly all influenza B viruses detected were B/Victoria. Of 32 tested - 4 showed poor reactivity to the 2019-2020 vaccine virus. 
Since all three (H1N1, H3N2, B/Victoria) vaccine virus components have been updated for the 2020-2021 Northern Hemisphere's flu shot, we won't know until January or February of next year how effective they are going to be in preventing infection.  

The full 29-page PDF report will be tough sledding for non-experts, so I've only posted the executive summary below.  I'll have a brief postscript when you return.

Influenza virus characterisation - Summary Europe, July 2020

Surveillance report
24 Aug 2020
Time period covered: Week 40/2019 - week 30/2020 

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 ninth report for the 2019 20 influenza season. As of week 30 / 164887 influenza detections had been reported across the WHO European Region ; 73% type A viruses, with A(H1N1)pdm09 prevailing over A(H3N2), and 27% type B viruses, with 4479 (98%) of 4 5 68 ascribed to a B/Victoria lineage.

Since the June 2020 characterisation report report1, three shipments of influenza positive specimens from EU/EEA countries have been received at the London WHO collaborating Centre , the Francis Crick Worldwide Influenza Centre (WIC). In total (since week 40/2019) 2019), 1661 virus specimens have been received , with collection dates after 31 August 2019.

Of the 49 A(H1N1)pdm09 viruses from EU/EEA countries characterised antigenically since the June report, 36 were well recognised by antisera raised against the 2019 20 vaccine virus, A/Brisbane/02/2018. The 13 viruses showing poor reactivity generally carried amino acid substitutions (notably N156K) in the HA1 150 loop region. The 468 EU/EEA test viruses with collection dates from week 40/2019 genetically characterised at the WIC have fallen within subclades of clade 6B.1A: 425 6B.1A5A, 30 6B.1A5B, 1 6B.1A6 and 12 6B.1A7.

The majority ( 39 ) of the 68 A(H3N2) viruses from EU/EEA countries characterised antigenically i n July were clade 3C.3a and were well recognised by antiserum raised against egg propagated A/Kansas/14/2017, the current vaccine virus. Globally approximately equal proportions of clade 3C.3a and subgroups 3C.2a1b+T131K and 3C.2a1b+T135K viruses have bee n detected, but for viruses detected since 1 February 2020, subgroups 3c.2a1b+T135KA/B have prevailed in the USA while those of clade 3C.3a and subgroup 3C.2a1b+T131K have dominated in Europe. In total, 500 viruses from EU/EEA countries have been characterised genetically at the WIC: 2 82 were clade 3C.3a, 1 37 were 3C.2a1b+T131K, 61 were 3C.2a1b+T135K A and 20 were 3C.2a1b+T135K B.

Thirty two B/Victoria lineage viruses from EU/EEA countries were antigenically characterised in July , all were subclade 1A(Δ3)B. Four viruses were not recognised well by antiserum raised against B/Washington/02/2019, the vaccine virus for the 2020 2021 northern hemisphere influenza season. Poor recognition was associated with HA1 a mino acid substitutions of either N126K or T155A . 

In total, 306 EU/EEA viruses have been characterised genetically at the WIC: 290 were sub clade 1A(Δ3)B and 16 were subclade 1A(Δ2). A single B/Yamagata lineage virus from France , with a collection date in February 2020 , was antigenically characterised in July. As for all recently circulating B/Yamagata lineage viruses a ll eight EU/EEA viruses characterised genetically at the WIC since week 40/2019 belong to genetic clade 3 and contain at least two HA amino acid substitutions (HA1 L172Q and M251V) compared to B/Phuket/3073/2013, the antigenic effects of which have been minimal as assessed in earlier reports.

PDF File

Influenza virus characterisation - Summary Europe, July 2020 - EN - [PDF-3.08 MB]

A bad flu season, combined with COVID-19, could easily overwhelm our medical system, and so a great deal of emphasis is being placed on this year's flu vaccination campaign, with the CDC reporting a record 194 million to 198 million doses of influenza vaccine  on order this year.

This fall's vaccination campaign also will serve as a dress rehearsal for next year's anticipated COVID-19 vaccine roll out (see The `Other' Vaccine Challenge This Fall).

Deploying a record number of flu vaccines in the middle of a COVID pandemic - when most people are practicing social distancing, and many doctor's offices are seeing fewer people - will prove challenging. 

Hopefully the lessons learned from this fall's flu vaccine campaign will make for a smoother roll out of the COVID-19 vaccine, if and when a safe and effective vaccine is made widely available.