Tuesday, June 05, 2018

ECDC: Influenza Virus Characterisation, March 2018


The ECDC  periodically publishes a review of recently isolated seasonal flu viruses in the EU they call an Influenza Virus Characterization Report.  Yesterday they published their 4th review of the 2017-18 influenza season, with data as of March of this year.
As we've discussed before, although there are currently 4 main categories of seasonal flu viruses (A/H1N1, A/H3N2, B/Yamagata and  B/Victoria), within each of these subtype/lineages there can be multiple variants and/or clades.
While influenza viruses are always evolving, in recent years - particularly with H3N2 subtype - we've seen the emergence of a number of new subclades, and (often subtle) amino acid changes that can make antigenic changes in the virus.

This not only complicates future vaccine virus selection - it can lower the effectiveness of the current vaccine - an all too familiar outcome over the past few years (see last October's ECDC: H3N2 Flu Vaccine Component Likely `Suboptimal').

While H1N1 has remained remarkably stable the past 9 years, requiring only one vaccine virus change since the 2009 pandemic - and influenza B viruses are typically slower to evolve than influenza A -  the same cannot be said for H3N2.

In February of 2017, in Eurosurveillance: Emergence Of A Novel Subclade Of Seasonal A/H3N2 - London, we saw a report of new subclade (3C.2a2) which followed the emergence of three earlier subclades in 2014'; one in subdivision 3C.2, 3C.2a, and two in 3C.3, 3C.3a and 3C.3b.
Today, via the ECDC's lastest characterization report, we learn that additional H3N2 subclades and genetic subgroups have now been identified, further complicating the field.
First the Executive summary, and then I'll have some specifics on the new subclades.

Influenza virus characterisation, March 2018
surveillance report
4 Jun 2018
Publication series: Influenza Virus Characterisation
Time period covered: 2017-2018 influenza season

European Centre for Disease Prevention and Control. Influenza virus characterisation, summary Europe, March 2018. Stockholm: ECDC; 2018.

This is the fourth report of the 2017–18 influenza season. The ECDC Influenza Virus Characterisations Reports are published periodically. The report provides an overview of the technical details of the circulating influenza viruses, such as antigenic and genetic properties, with a reference to the current vaccine strains. It also summaries the developments of the viruses since the last report, as well as the main developments for the ongoing season. The report is of special interest for influenza virologists and epidemiologists interested in the in-depth characterisation of influenza viruses.
Executive summary

This is the fourth report of the 2017–18 influenza season. As of week 13/2018, over 217 000 influenza detections across the WHO European Region have been reported. Types A and B viruses have been detected in the proportions 42% and 58%, respectively, with A(H1N1)pdm09 viruses now being slightly more prevalent than A(H3N2) (1:0.96), and B/Yamagata being significantly more prevalent than B/Victoria viruses (48.7:1). 

Twenty-nine EU/EEA countries have shared influenza-positive specimens with the London WHO CC, Crick Worldwide Influenza Centre (WIC), since week 40/2017, with 984 specimens having collection dates after August 2017. 

The 36 A(H1N1)pdm09 test viruses characterised antigenically showed good reactivity with antiserum raised against the 2017–18 vaccine virus, A/Michigan/45/2015. The 133 test viruses with collection dates from week 40/2017 genetically characterised at the WIC, as others from the WHO European Region with collection dates after 31 August 2017 deposited in GISAID (Global Initiative on Sharing All Influenza Data), all fell in subclade 6B.1, defined by HA1 amino acid substitutions S162N and I216T, the great majority with additional substitutions of S74R, S164T and I295V. 

Of 191 A(H3N2) viruses successfully recovered to date, only 32 (17%) had sufficient HA titre to allow antigenic characterisation by HI assay in the presence of oseltamivir. The majority of these 32 viruses were poorly recognised by antisera raised against the currently used vaccine virus, egg-propagated A/Hong Kong/4801/2014, in HI assays. Of the 225 viruses with collection dates from week 40/2017 genetically characterised at the WIC, 154 were clade 3C.2a (with 129 3C.2a2, 21 3C.2a3 and four 3C.2a4), 68 fell within clade 3C.2a1 (with two 3C.2a1a and 65 3C.2a1b) and three were clade 3C.3a. 

A single B/Victoria-lineage viruses was tested by HI and it reacted well with only one of the panel of post-infection ferret antisera; this antiserum was raised against tissue culture-propagated B/Norway/2409/2017, a virus with a deletion of two amino acids in HA1 (Δ162-163). Of the 29 viruses characterised genetically at the WIC with a collection date after week 40/2017, ten fell within clade 1A, and 19 fell within the subgroup carrying the HA1 double amino acid deletion.
A total of 45 B/Yamagata viruses were characterised antigenically and 98% reacted well (within fourfold of the homologous titre) with post-infection ferret antiserum raised against egg-propagated B/Phuket/3073/2013, the recommended vaccine virus for use in quadrivalent vaccines for the northern hemisphere 2017–18 and 2018–2019 seasons and for trivalent vaccines in the southern hemisphere 2018 season. The 180 viruses with collection dates from week 40/2017 genetically characterised

H3N2 viruses continue to be difficult to analyze antigenically due to variable agglutination of RBCs in laboratory testing, a problem we've been seeing for the past 4 years. From the PDF,  we've an excerpt on their characterization of the H3N2 subtype, including the addition of new subclades and new genetic subgroups.

Influenza A(H3N2) virus analyses

As described in many previous reports 2 , influenza A(H3N2) viruses have continued to be difficult to characterise antigenically by HI assay due to variable agglutination of red blood cells (RBCs) from guinea pigs, turkeys and humans, often with the loss of ability to agglutinate any of these RBCs. As was highlighted first in the November 2014 report 3 , this is a particular problem for most viruses that fall in genetic clade 3C.2a.

A number of the 278 A(H3N2) virus specimens with collection dates after week 40/2017, 24 of which were lysed specimens, are in process for antigenic and genetic characterisation (Table 2). However, of those successfully isolated to date (n = 191), as shown by positive neuraminidase activity, only 32 (17%) had sufficient HA activity in the presence of 20nM oseltamivir to allow antigenic analysis by HI assay.
Since the February 2018 report, no virus recovered, based on positive neuraminidase activity, retained sufficient HA activity to allow antigenic analysis by HI.

Phylogenetic analysis of the HA genes of representative A(H3N2) viruses from Europe with recent collection dates, after 31 August 2017 as available in GISAID, is shown in Figure 2.
Viruses in clades 3C.2a and 3C.3a have been in circulation since the 2013–14 northern hemisphere influenza season, with clade 3C.2a viruses predominating since the 2014–15 influenza season and continuing to predominate in recent months (Figure 2), but the HA gene sequences continue to diverge. New subclades and new genetic subgroups have been adopted. Amino acid substitutions that define these subdivisions and subclades are:
  • 3C.2a: L3I, N144S (resulting in the loss of a potential glycosylation site), F159Y, K160T (in the majority of viruses, resulting in the gain of a potential glycosylation site) and Q311H in HA1, and D160N in HA2, e.g. A/Hong Kong/4801/2014;
  • 3C.2a1: Those in clade 3C.2a plus: N171K in HA1 and I77V and G155E in HA2, most also carry N121K in HA1, e.g. A/Singapore/INFIMH-16-0019/2016;
  • 3C.2a1a: Those in subclade 3C.2a1 plus T135K in HA1, resulting in the loss of a potential glycosylation site, and also G150E in HA2, e.g. A/Greece/4/2017;
  • 3C.2a1b: Those in subclade 3C.2a1 plus K92R and H311K in HA1, e.g. A/England/74560298/2017;
  • 3C.2a2: Those in clade 3C.2a plus T131K, R142K and R261Q in HA1, e.g. A/Norway/4465/2016;
  • 3C.2a3: Those in clade 3C.2a plus N121K and S144K in HA1, e.g. A/Norway/4849/2016;
  • 3C.2a4: Those in clade 3C.2a plus N31S, D53N, R142G, S144R, N171K, I192T, Q197H and A304T in HA1 and S113A in HA2, e.g. A/Valladolid/182/2017;
  • 3C.3a: T128A (resulting in the loss of a potential glycosylation site), R142G and N145S in HA1 which defined clade 3C.3 plus A138S, F159S and N225D in HA1, many with K326R, e.g. A/Switzerland/9715293/2013.
The currently circulating viruses have HA genes that fall into genetic groups within clade 3C.2a, with the majority of recently circulating viruses in EU/EEA countries falling in subclade 3C.2a2. A sizable proportion had HA genes that fell into genetic group 3C.2a1b, and some also had HA genes that fell into other genetic subgroups. 

The location of A/Singapore/INFIMH-16-0019/2016 (3C.2a1), the A(H3N2) virus recommended for inclusion in vaccines for the southern hemisphere 2018 [2] and the northern hemisphere 2018–2019 influenza seasons [3], is indicated in Figure 2.
Although Europe saw more of a mixed bag of flu subtypes last winter (H1N1, H3N2, and Influenza B), North America has just come off its second H3N2 dominant flu season in a row. 
Normally, one would assume the odds now favor a switch back to H1N1 next fall due to an increased level of community immunity to H3N2 - and perhaps it will - but the emergence and continued spread  of so many H3N2 subclades makes things less certain.
Influenza has always been unpredictable, but as the number of viral players continues to grow, second guessing the flu has become increasingly difficult. All of which makes the development of a `universal flu shot' - even if it only covers seasonal strains - all the more important in the years to come.

For more on the challenges involved, you may wish to revisit J.I.D.: NIAID's Strategic Plan To Develop A Universal Flu Vaccine.

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