Influenza virus characterisation, summary Europe, April 2020

This is the sixth report for the 2019–20 influenza season. As of week 18/2020,162 345 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 4 418 (98%) of 4 505 ascribed to a lineage being B/Victoria.

Since the March 2020 characterisation report1, no 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, 1 076 virus specimens, with collection dates after 31 August 2019, have been received.

Since the last report, no A(H1N1)pdm09 test viruses from EU/EEA countries were characterised antigenically but 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-loop region. The 267 EU/EEA test viruses with collection dates from week 40/2019 genetically characterised at the WIC have fallenwithin subclades of clade 6B.1A: 237 6B.1A5A, 20 6B.1A5B, 1 6B.1A6 and 9 6B.1A7.

Since the last report, no A(H3N2) viruses have been characterised antigenically, but previous analyses have shown clade3C.3a-specific recognition by antisera raised againstegg-propagated A/Kansas/14/2017, the current vaccine virus. Globally there have been approximately equal proportions of clade 3C.3a and subgroups 3C.2a1b+T131K and 3C.2a1b+T135K viruses detected. However, based on sequences available in GISAID from viruses detected since 1 February 2020, subgroups 3c.2a1b+T135KA/B are prevalent in the USA while those of clade 3C.3a and subgroup 3C.2a1b+T131K dominate in Europe. In total, 351 viruses from EU/EEA countries have been characterised genetically at the WIC: 183 clade 3C.3a, 111 3C.2a1b+T131K, 42 3C.2a1b+T135K-A and 15 3C.2a1b+T135K-B.

No B/Victoria-lineage viruses were characterised antigenically in this reporting period. 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 2020–2021 northern hemisphere influenza season. In total, 209 EU/EEA viruses have been characterised genetically at the WIC: 196 subgroup 1A(Δ3)B and 13 subclade 1A(Δ2).

No B/Yamagata-lineage viruses were characterised antigenically in this reporting period. All seven 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.