Influenza virus characterisation, May 2019

Surveillance report
Publication series: Influenza Virus Characterisation
Time period covered: May 2019

This is the seventh report for the 2018–19 influenza season. As of week 20 in 2019, 204 512 influenza detections across the WHO European Region have been reported. Ninety-nine per cent were type A viruses, with A(H1N1)pdm09 prevailing over A(H3N2), and 1% type B viruses, with 83 (60%) of 139 ascribed to a B/Yamagata-lineage.

Executive summary

Since the April 2019 characterisation report1, an additional four shipments of influenza-positive specimens from EU/EEA countries were received at the London WHO CC, the Francis Crick Worldwide Influenza Centre (WIC). A total of 1 184 virus specimens with collection dates after 31 August 2018 have been received.

Nine A(H1N1)pdm09 test viruses from Slovenia characterised antigenically since the April 2019 characterisation report all showed good reactivity with antiserum raised against the 2018–19 vaccine virus, A/Michigan/45/2015 (clade 6B.1). Four hundred test viruses with collection dates from week 40 of 2018 genetically characterised at the WIC, including an H1N2 reassortant, all fell in a 6B.1 subclade designated 6B.1A, defined by HA1 amino acid substitutions of S74R, S164T and I295V. Of these recently circulating viruses, 365 also had HA1 S183P substitution, often with additional substitutions in HA1 and/or HA2.

Since the last report, only one successfully recovered A(H3N2) virus had sufficient haemagglutinin (HA) titre to allow antigenic characterisation by haemagglutination inhibition (HI) assay in the presence of oseltamivir. The virus was poorly recognised by antisera raised against the currently used vaccine virus, egg-propagated A/Singapore/INFIMH-16-0019/2016, in HI assays. Of the 337 viruses with collection dates from week 40 of 2018 genetically characterised at the WIC, 273 were clade 3C.2a (with 32 3C.2a2, 13 3C.2a3, six 3C.2a4 and 222 3C.2a1b) and 64 were clade 3C.3a. 

No B/Victoria-lineage viruses have been characterised in this reporting period. All recent viruses carry HA genes that fall in clade 1A, but encode HA1 amino acid substitutions of I117V, N129D and V146I compared to a previous vaccine virus, B/Brisbane/60/2008. Groups of viruses defined by deletions of two [Δ162–163, 1A(Δ2)] or three [Δ162–164, 1A(Δ3)] amino acids in HA1 have emerged, with the triple deletion group having subgroups of Asian and African origin. HI analyses with panels of post-infection ferret antisera have shown these virus groups to be antigenically distinguishable. Of the five viruses characterised from EU/EEA countries this season, one has been Δ162–163 and four Δ162–164 (three African and one Asian subgroup). 

No B/Yamagata-lineage viruses have been characterised in the reporting period. Eleven from the 2018–19 season have been characterised. All have HA genes that fall in clade 3 and encode HA1 amino acid substitutions of L172Q and M251V compared to the vaccine virus B/Phuket/3073/2013, but remain antigenically similar to the vaccine virus that is recommended for use in quadrivalent vaccines for current and subsequent northern hemisphere influenza seasons.