Influenza virus characterization - Summary Europe, July 2022
This is the eighth report for the 2021-2022 influenza season. The June 2022 characterization report, gave a breakdown of influenza detections across the World Health Organization (WHO) European Region reported to TESSy up to week 25/2022. As of week 30/2022, 145 913 detections had been reported (a rise of nearly 13 000 since week 20/2022) resulting from extended late season influenza activity. Of these 145 913 detections, 98% were type A viruses, with A(H3N2) still dominating (84%) over A(H1N1)pdm09 (16%), but by a lower margin than in the June report (92%:8%), and 2% type B of which only 134 were ascribed to a lineage, with all but two being B/Victoria. This represents a large increase (144 903, 144-fold) in detections compared to the 2020-2021 season, on the back of a great increase (1 926 053, 176%) 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., 12% 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.
Executive Summary
Thirteen 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 June report. This report focuses on viruses with collection dates within 2022 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 June 2022 for influenza type A viruses and March for influenza B/Victoria-lineage 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 11 WHO Region countries (6B.1A.5a.1) and Croatia/Italy/the Netherlands (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 significant numbers of 3C.2a1b.2a.1 viruses have been detected. 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 egg-propagated A/Darwin/9/2021 (3C.2a1b.2a.2) which was recommended for egg-based vaccines to be used in the 2022 southern hemisphere season. Antisera raised against a range of cell culture- and egg-propagated 3C.2a1b.2a.2 viruses generally gave good recognition of 3C.2a1b.2a.2 test 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 used 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. At least three virus genetic clusters have emerged among B/Washington/02/2019-like (V1A.3) viruses, one of which was recently detected in the Netherlands and characterized by HA1 G184R amino acid substitution – here we show that such viruses are not well recognised by the entire panel of post-infection ferret antisera and a hyperimmune sheep antiserum raised against B/Brisbane/60/2008. 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 in 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.
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