Saturday, March 12, 2016

ECDC Influenza Virus Characterization Report - February 2016

Credit NIAID


We talk about seasonal flu strains (H1N1, H3N2, Influenza B) as if they were individual entities – when in truth within each subtype there are many clades and variants - and these are constantly evolving. Geographically, these viruses can vary widely, and so the dominate subtypes and variants in Europe may differ from those circulating in North America or Asia.

Over time, new, more biologically `fit’ viruses replace older strains as community immunity drives them closer to obsolesce.

All which makes the flu world dynamic and ever-changing, and presents a genuine challenge for vaccine manufacturers to keep step. NIAID has a terrific 3-minute video that shows how influenza viruses drift over time, and why the flu shot must be frequently updated, which you can view at this link

To keep track of the changes to the flu strains in circulation, labs around the world send samples to the WHO Collaborating Centre in London for classification, and the ECDC publishes reports every couple of months.

The last report was issued in January for December  2015. Below you'll find the summary and a link to the full report for February 2016. I'll have a brief comment about the Russian H1N1 reports when you return.

Influenza virus characterisation, Summary Europe, February 2016

11 Mar 2016
PDF Document

From week 40/2015, the start of weekly reporting on influenza activity in the WHO European Region, to week 07/2016 over 70 000 influenza detections across the Region have been reported. Influenza type A viruses are prevailing over type B but, unlike the situation in the 2014–15 season, A(H1N1)pdm09 viruses are prevailing over A(H3N2), and the proportion of B/Victoria-lineage detections has risen substantially, representing ~92% of those ascribed to a B virus lineage.

To date, 23 EU/EEA countries have shared 424 influenza-positive specimens with the Francis Crick Institute, London, for detailed characterisation: 16 additional countries and 330 specimens since the December 2015 report. Since the latter report, 230 viruses have been characterised antigenically and genetic analyses are ongoing.

The 166 A(H1N1)pdm09 viruses characterised antigenically were similar to the vaccine virus A/California/7/2009. Worldwide new genetic sub-clusters of viruses within the 6B clade have emerged, with two being designated as subclades: 6B.1 defined by HA1 amino acid substitutions S162N and I216T and 6B.2 defined by HA1 amino acid substitutions V152T and V173I. Of the 123 viruses characterised genetically, 18 (14%) were clade 6B, 98 (80%) were subclade 6B.1 and seven (6%) were subclade 6B.2.

The 26 A(H3N2) test viruses characterised by haemagglutination inhibition (HI) assay were poorly recognised by reference antiserum raised against egg-propagated A/Switzerland/9715293/2013, the vaccine virus recommended for use in the 2015–2016 northern hemisphere influenza season, despite over 75% of the test viruses falling in the same genetic subclade (3C.3a) as the vaccine virus. The test viruses were recognised somewhat better by antisera raised against egg-propagated A/Hong Kong/4801/2014, the virus recommended for use in 2016 southern hemisphere and 2016–2017 northern hemisphere influenza vaccines. Of 40 A(H3N2) viruses characterised genetically: one (2%) was clade 3C.3, 23 (58%) were subclade 3C.2a and 16 (40%) were subclade 3C.3a.

The 33 B/Victoria-lineage viruses were antigenically similar to B/Brisbane/60/2008 and fell in genetic clade 1A as do recently collected viruses worldwide.

The five B/Yamagata viruses characterised fell in genetic clade 3 and reacted well with post-infection ferret antiserum raised against egg-propagated B/Phuket/3073/2013, the recommended vaccine virus for the northern hemisphere 2015–16 influenza season and for use in quadrivalent vaccines in the 2016 southern hemisphere and 2016–17 northern hemisphere influenza seasons.

In January and into February Russia reported very heavy influenza activity, and their Epidemic Surveillance centre reported a new subclade of the H1N1 virus (see A Russian Influenza Epidemiology Report To Ponder). Follow up reports (see here and here) indicated that a small number of samples taken in January showed reduced titers against the current vaccine strain.

In February, the ECDC issued a Risk Assessment : Reports Of Severe A(H1N1)pdm09 In Europe where they wrote it was `unclear if the emergence of a new genetic subgroup of A(H1N1) virus might compromise vaccine effectiveness.'

Today's ECDC virus characterization report includes H1N1 samples collected from 13 EU countries during January and February, but not from Russia.  Of the 95 flu samples submitted during this time, only 34 have been propagated for HI testing. 

Meaning it may be a few months before we know whether reduced titer (i.e. Low reactor) H1N1 viruses have turned up in Europe.

Despite growing diversity in the H1N1 flu virus, for now all indications are that the vast majority of H1N1 viruses in circulation continue to be a good antigenic match the 2009 H1N1 vaccine strain.

Which explains why - for the 7th year running - the H1N1 component in the vaccine remains unchanged (see WHO: Recommended Composition Of 2016-2017 Northern Hemisphere Flu Vaccine).

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