Influenza virus characterization - Summary Europe, June 2022
This is the seventh report for the 2021-2022 influenza season. The May 2022 characterization report1, gave a breakdown of influenza detections across the World Health Organization (WHO) European Region reported to TESSy up to week 20/2022. As of week 25/2022, 138 352 detections had been reported (a rise of over 5 000 since week 20/2022) resulting from extended late season influenza activity. Of these 138 352 detections, 98% were type A viruses, with A(H3N2) (92%) dominating over A(H1N1)pdm09 (8%), and 2% type B of which only 125 were ascribed to a lineage, with all but two being B/Victoria. This represents a large increase (137 418, 148-fold ) in detections compared to the 2020-2021 season, on the back of a great increase (1 900 146, 200%) in the number of samples tested. However, while there have been clear indications of an influenza epidemic in 2021-2022 with the epidemic threshold of 10% positivity within sentinel specimens having been crossed for 17 weeks as of week 25/2022 (unlike in 2020-2021), numbers of detections are reduced compared to earlier seasons (e.g., 16% reduced compared to 2019-2020). The increased testing but reduced number of influenza detections is undoubtedly related to the emergence of SARS-CoV-2 and measures introduced to combat it.
Eleven shipments from countries within the WHO European Region were received at the London WHO Collaborating Centre, the Francis Crick Worldwide Influenza Centre (WIC) since the May report. This report focuses on viruses with collection dates after 31 December 2021 for which HA gene sequences were submitted to, and released in, the EpiFluTM database of the Global Initiative on Sharing All Influenza Data (GISAID) after April 2022 for influenza type A viruses and 31 December 2021 for influenza type B viruses, together with sequences generated and antigenic data determined at the WIC.
Globally relatively few A(H1N1)pdm09 viruses have been detected in the course of the 2021-2022 season. 6B.1A.5a.1 and 6B.1A.5a.2 genetic subgroups have been detected which are clearly antigenically different, as shown by viruses from seven WHO Region countries (6B.1A.5a.1) and Austria/Norway (6B.1A.5a.2) characterized here. 6B.1A.5a.1 viruses have been most numerous in Europe but 6B.1A.5a.2 viruses are currently dominant in some southern hemisphere countries, notably Australia, and greater numbers have recently been detected in Europe. An emergent 6B.1A.5a.1 genetic group showing antigenic drift, defined by HA1 P137S and G155E amino acid substitutions, has been detected. At the February 2022 WHO influenza vaccine composition meeting (VCM) the recommendation was to retain A/Victoria/2570/2019-like viruses (6B.1A.5a.2) as the vaccine component for the northern hemisphere 2022-2023 influenza season.
In Europe and across the world A(H3N2) viruses have been dominant with the vast majority of recently detected viruses falling in the ‘Bangladesh-like’ (3C.2a1b.2a.2) subgroup, except in China where 3C.2a1b.2a.1 viruses are circulating. While small clusters of viruses showing antigenic drift have emerged among the ‘Bangladesh-like’ viruses, the great majority of these viruses retained good recognition by post-infection ferret antisera raised against A/Darwin/9/2021-like and A/Darwin/6/2021-like (3C.2a1b.2a.2) viruses which were recommended for egg- and cell-based vaccines to be used in the 2022 southern hemisphere season. Antisera raised against viruses in two of the emergent antigenically drifted clusters gave poorer recognition of 3C.2a1b.2a.2 viruses than the antisera raised against the Darwin vaccine viruses. At the February 2022 WHO VCM the recommendation was to change the A(H3N2) vaccine components for the northern hemisphere 2022-2023 influenza season to match those being in the 2022 southern hemisphere season.
In Europe and across the world few B/Victoria-lineage viruses have been detected during the 2021-2022 influenza season. All fall within subclade V1A.3 represented by B/Washington/02/2019 the vaccine virus recommended for inclusion in influenza vaccines for the 2021-2022 northern hemisphere season. A large majority of HA sequences from recently detected viruses, in geographically dispersed countries, have fallen in the V1A.3a group defined by a series of HA1 amino acid substitutions including N150K, with most falling in the V1A.3a.2 subgroup with defining HA1 A127T, P144L and K203R amino acid substitutions. However, at least three virus genetic clusters have emerged among B/Washington/02/2019-like (V1A.3) viruses, one of which was recently been detected in the Netherlands but has not yet undergone detailed antigenic analysis. Post-infection ferret antisera raised against B/Washington/02/2019-like viruses do not recognise V1A.3a.2 viruses well and B/Austria/1359417/2021-like (V1A.3a.2) viruses were recommended for use in the southern hemisphere 2022 and the northern hemisphere 2022-2023 influenza seasons.
No cases of infection with circulating B/Yamagata-lineage viruses have been confirmed since March of 2020. All HA gene sequences from the 77 viruses detected in 2020, inclusive of 16 from the WHO European Region, belonged to genetic clade Y3 and had three HA1 amino acid substitutions (L172Q, D229N and M251V) compared to B/Phuket/3073/2013-like viruses which are still recommended for use quadrivalent influenza vaccines. There is need to share all B/Yamagata-lineage viruses detected recently for detailed characterization to determine if there are any in circulation that are not related to Live Attenuated Influenza Vaccines.