Influenza virus characterization - Summary Europe, September 2022
This is the ninth and final report for the 2021-2022 influenza season. The July 2022 characterisation report, gave a breakdown of influenza detections across the World Health Organisation (WHO) European Region reported to TESSy up to week 30/2022. As of week 39/2022, 149 372 detections had been reported, resulting from extended late season influenza activity. Of these 149 372 detections, 98% were type A viruses, with A(H3N2) dominating (91%) over A(H1N1)pdm09 (9%), and 2% type B of which only 156 were ascribed to a lineage, with all but two being B/Victoria. This represents a large increase (148 096, 117-fold ) in detections compared to the 2020-2021 season, on the back of a great increase (1 957 744, 151%) 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 (unlike in 2020-2021), numbers of detections are reduced compared to earlier seasons (e.g., 9.4% reduced compared to 2019-2020, when the number of samples tested was over 3-fold lower). 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.
Five 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 July report. This report focuses on viruses with collection dates within 2022 for which HA gene sequences were submitted to, and released in, the EpiFlu database of the Global Initiative on Sharing All Influenza Data (GISAID) after July 2022, 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. 6B.1A.5a.1 viruses have been the most numerous in Europe but 6B.1A.5a.2 viruses have circulated globally and greater numbers of this subgroup have recently been detected in Europe. 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. At the September 2022 VCM the recommendation was to change the southern hemisphere A(H1N1)pdm09 vaccine virus for the 2023 season to an A/Sydney/5/2021-like virus as all recently circulating 6B.1A.5a.2 viruses carry HAI K54Q, A186T, Q189E, E224A, R259K and K308R amino acid substitutions compared to A/Victoria/2570/2019; while these viruses are well recognised by post-infection ferret antisera raised against A/Victoria/2570/2019, they are recognised less well by human post-vaccination sera.
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 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 has been recommended for egg-based vaccines to be used in the 2022 and 2023 southern hemisphere, and 2022-23 northern hemisphere seasons. 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
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.
B/Austria/1359417/2021-like (V1A.3a.2) viruses have been recommended for use in the southern hemisphere 2022 and 2023, and the northern hemisphere 2022-2023 influenza seasons. A B/Washington/02/2019-like (V1A.3) virus cluster that emerged and spread in the Netherlands, which showed poor recognition by the panel of post-infection ferret antisera used at the WIC, has now been detected in Spain.
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 characterisation to determine if there are any in circulation that are not related to Live Attenuated Influenza Vaccines.