Influenza virus characterisation - Summary Europe, May 2020

Surveillance report
Publication series: Influenza Virus Characterisation
Time period covered: Week 40/2019 - 20/2020

European Centre for Disease Prevention and Control. Influenza virus characterisation, summary Europe, May 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 seventh report for the 2019 2019–20 influenza season. As of week 20 /2020, 16 4 868 influenza detections across the WHO European Region ha have been reported; 73% type A viruses, with A(H1N1)pdm09 prevailing over A(H3N2), and 27% type B viruses, with 4 4 479 (98%) of 4 5 568 ascribed to a lineage being B/Victoria.

Since the April 2020 characterisation report report, eight shipments of influenza influenza-positive specimens from EU/EEA countries have been received at the London WHO CC, the Francis Crick Worldwide Influenza Centre (WIC). In total, 1 362 virus specimens, with collection dates after 31 August 2019, have been received. No influenza antigenic characterisation has been conducted during this reporting period.

Previous analyses have shown the great majority of test viruses to be well recognised by antisera raised against the 2019 –20 vaccine virus, A/Brisbane/02/2018. Those viruses showing poor reactivity generally carried amino acid substitutions (notably N156K) in the HA1 150 150-loop region. The 2 296 EU/EEA test viruses with collection dates from week 40/2019 genetically characterised at the WIC have fallen within subclades of clade 6B.1A: 2 263 6B.1A5A, 2 23 6B.1A5B, 1 6B.1A6 and 9 6B.1A7.

Previous analyses have shown clade 3C.3a 3a-specific recognition by antisera raised against egg egg-propagated A/Kansas/14/2017, the current vaccine virus. Globally Globally, approximately equal proportions of clade 3C.3a and subgroups 3C.2a1b+T131K and 3C.2a1b+T135K viruses have been detected , but for viruses detected since 1 February 2020, subgroups 3c.2a1b+T135KA/B have prevaled in the USA while those of clade 3C.3a and subgroup 3C .2a1b+T131K T131K.2a1b+T131K have dominated in Europe. In total, 35 355 viruses from EU/EEA countries have been characterised genetically at the WIC: 18 185 clade 3C.3a, 11 112 3C.2a1b+T131K, 4 43 3C.2a1b+T135K T135K-A and 15 3C.2a1b+T135K T135K-B.

Viruses detected in EU/EEA countries during February and March 2020, based on sequences available in GISAID, have all fallen in the 1A(Δ3)B subgroup. Viruses in this subgroup have been antigenically similar to B/Washington/02/2019, the vaccine virus for the 2020 2020–2021 northern hemisphere influenza seas on. In total, 2 221 EU/EEA viruses have been characterised genetically at the WIC: 208 subgroup 1A(Δ3)B and 13 subclade 1A(Δ2).

All eight EU/EEA viruses characterised genetically at the WIC since week 40/2019, as for all recently circulating B/Yamagata 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/3 073/2013, the antigenic effects of which have been minimal as assessed in earlier reports.