Influenza virus characterisation - Summary Europe, September 2020

Surveillance report
19 Oct 2020
Publication series: Influenza Virus Characterisation
Time period covered: Week 40/2019 - week 39/2020

European Centre for Disease Prevention and Control. Influenza virus characterisation, summary Europe, September
2020. Stockholm: ECDC; 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 10th and final report for the 2019–2020 influenza season. As of week 39/2020, 164 917 influenza detections across the WHO European Region had been reported; 73% type A viruses, with A(H1N1)pdm09 prevailing over A(H3N2), and 27% type B viruses, with 4 480 (98%) of 4 569 ascribed to a lineage being B/Victoria.

Since the July 2020 characterisation report1, two shipments of influenza-positive specimens 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). In total (since week 40/2019), 1 719 virus specimens, with collection dates after 31 August 2019, have been received.

Of the 33 A(H1N1)pdm09 viruses from EU/EEA countries characterised antigenically since the July report, 23 were well recognised by antisera raised against the 2019–20 vaccine virus, A/Brisbane/02/2018. The 10 viruses that showed poor reactivity generally carried amino acid substitutions (notably N156K) in the HA1 150-loop region. The 498 EU/EEA test viruses with collection dates from week 40/2019 genetically characterised at the WIC have fallen within subclades of clade 6B.1A: 455 6B.1A5A, 30 6B.1A5B, 1 6B.1A6 and 12 6B.1A7.

The majority (7) of the 10 A(H3N2) viruses from EU/EEA countries characterised antigenically since the July report 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 viruses in clade 3C.3a and subclade 3C.2a1b subgroups have been detected, but for viruses detected since 1 February 2020, subclade 3c.2a1b subgroup viruses have prevailed in many countries worldwide while those of clade 3C.3a and subgroup 3C.2a1b+T131K have dominated in Europe. In total, 512 viruses from EU/EEA countries have been characterised genetically at the WIC: 288 clade 3C.3a, 139 3C.2a1b+T131K, 64 3C.2a1b+T135K-A and 21 3C.2a1b+T135K-B.

Thirty-two B/Victoria-lineage viruses from EU/EEA countries were antigenically characterised since the July report. All but one were subclade 1A(Δ3)B and four of these viruses were not recognised well by antiserum raised against the vaccine virus for the 2020–2021 northern hemisphere influenza season, B/Washington/02/2019. Poor recognition was associated with HA1 amino acid substitutions of either N126K (n = 3) or N150K (n = 1). In total, 333 EU/EEA viruses have been characterised genetically at the WIC: 316 subclade 1A(Δ3)B and 17 subclade 1A(Δ2).

A single B/Yamagata-lineage virus from Norway, with a collection date in February 2020, was antigenically characterised in August. All nine EU/EEA viruses characterised genetically at the WIC since week 40/2019, as for all recently circulating B/Yamagata-lineage viruses, 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.