Influenza virus characterisation - Summary Europe, June 2020

This is the eighth report for the 2019–20 influenza season. As of week 25/2020, 164 883 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 4 479 (98%) of 4 568 ascribed to a lineage being B/Victoria.

Since the May 2020 characterisation report1, nine shipments of influenza-positive specimens from EU/EEA countries have been received at the London WHO CC, the Francis Crick Worldwide Influenza Centre (WIC). In total, 1 608 virus specimens, with collection dates after 31 August 2019, have been received.

Of the 99 A(H1N1)pdm09 viruses from EU/EEA countries characterised antigenically since the May report, 77 were well recognised by antisera raised against the 2019–20 vaccine virus, A/Brisbane/02/2018. Of those viruses, 22, that showed poor reactivity generally carried amino acid substitutions (notably N156K) in the HA1 150-loop region. The 397 EU/EEA test viruses with collection dates from week 40/2019 genetically characterised at the WIC have fallen within subclades of clade 6B.1A: 358 6B.1A5A, 29 6B.1A5B, 1 6B.1A6 and 9 6B.1A7.

The majority (52) of the 68 A(H3N2) viruses from EU/EEA countries characterised antigenically in June 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 been 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, 438 viruses from EU/EEA countries have been characterised genetically at the WIC: 245 clade 3C.3a, 126 3C.2a1b+T131K, 48 3C.2a1b+T135K-A and 19 3C.2a1b+T135K-B.

Sixty-nine B/Victoria-lineage viruses from EU/EEA countries were antigenically characterised in June, 63 subclade 1A(Δ3)B, one subclade 1A(Δ2) and five not sequenced. Approximately 25% of the subclade 1A(Δ3)B 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 generally associated with HA1 amino acid substitutions of either N126K or E128K. In total, 269 EU/EEA viruses have been characterised genetically at the WIC: 255 subclade 1A(Δ3)B and 14 subclade 1A(Δ2).