Influenza virus characterisation - Summary Europe, November 2021

This is the second influenza virus characterisation report for the 2021-2022 influenza season. As of week 47/2021, 2 707 influenza detections across the World Health Organization (WHO) European Region were reported to the European Surveillance System (TESSy); 93% type A viruses, with A(H3N2) (96%) dominating over A(H1N1)pdm09(4%), and 7% type B, with only two having been ascribed to a lineage (B/Victoria). This represents a large increase (2 627, 3384%) in detections compared to the 2020-2021 season, following a large increase (354 256, 519%) in the number of samples tested, and is closer to the more usual number of detections seen at this time in earlier seasons. The increased testing is probably related to the emergence of SARS-CoV-2 and measures introduced to combat it.

Since the October 2021 characterisation report, no shipments from EU/EEA countries were received at the London WHO Collaborating Centre, the Francis Crick Worldwide Influenza Centre (WIC). This report therefore focuses on genetic characterisation of HA genes of representative seasonal influenza viruses submitted and/or released in GISAID during November2021, with a focus on those viruses with collection dates after 31 August 2021, together with sequences recently determined at the WIC. The genetic clade nomenclature system adopted during the September 2021 vaccine composition meeting (VCM)is used throughout the document. The data continued to show low levels of influenza detections globally but with a predominance of A(H3N2) viruses.

Very low numbers of A(H1N1)pdm09 detections have been reported. The three with the most recent collection dates fell in the 6B.1A.5a.1 subgroup, represented by the vaccine virus for the northern hemisphere 2020-2021 season, A/Guangdong-Maonan/SWL1536/201960. A batch of viruses from Bangladesh with collection dates in September 2021 all fell in the 6B.1A.5a.2 subgroup, represented by A/Victoria/2570-like and A/Wisconsin/588/2019-like viruses which have been recommended respectively for egg-and cell-based vaccines in the 2021-2022 northern and 2022 southern hemisphere influenza seasons, but with additional HA amino acid substitutions seen previously in viruses from India.

All recently detected A(H3N2) viruses have fallen in subgroup 3C.2a1b.2a and been Bangladesh-like (3C.2a1b.2a.2), with a number of EU/EEA countries reporting detections. A/Cambodia/e0826360/2020-like (3C.2a1b.2a.1) viruses were recommended for use in the 2021-2022 northern hemisphere season, while A/Darwin/9/2021-like and A/Darwin/6/2021-like (3C.2a1b.2a.2) viruses were recommended for egg-and cell-based vaccines in the 2022 southern hemisphere season. Recently detected viruses in Croatia were Bangladesh-like genetically and antigenically.

While the vast majority of B/Victoria-lineage HA sequences derived from viruses collected after 31 January 2021 were subclade V.1A.3, represented by B /Washington/02/2019, the vaccine virus recommended for inclusion in influenza vaccines for the 2021-2022 northern hemisphere season, such viruses have only been detected in the US recently. The vast majority of sequences from recently detected viruses, in geographically dispersed countries, have fallen in the V.1A.3.2 subgroup with defining HA1 A127T, P144L and K203R amino acid substitutions. B/Austria/1359417/2021-like (V.1A.3.2) viruses have been recommended for use in the southern hemisphere 2022 influenza season. Antigenically, viruses in subgroups of the V.1A.3a group differ and show some loss of reactivity with post-infection ferret antisera raised against B/Washington/02/2019.

NoB/Yamagata-lineage HA sequences from clinical specimens collected in 2021, and none with collection dates after March 2020, were available. All of the 77 sequences from viruses detected in 2020, inclusive of 12 from EU/EEA countries, belong to genetic clade Y3 and carry three HA1 amino acid substitutions (L172Q, D229N and M251V) compared to B/Phuket/3073/2013-like viruses which have been recommended for use in quadrivalent influenza vaccines for the 2021-2022 northern hemisphere and 2022 southern hemisphere seasons. The antigenic effects of these amino acid substitutions have been minimal as assessed in earlier reports.