Influenza virus characterisation, December 2020

This is the third report for the 2020–2021 influenza season. As of week 53/2020, only 415 influenza detections across the WHO European Region had been reported; 50% type A viruses, with A(H3N2) prevailing over A(H1N1)pdm09, and 50% type B viruses with only four having been ascribed to a lineage, three B/Victoria and one B/Yamagata. This represents a 98% drop in detections compared to the same period in 2019, probably due to the COVID-19 pandemic and measures introduced to combat it.

Since the November 2020 characterisation report1, no shipments of influenza-positive specimens from European Union/European Economic Area (EU/EEA) countries have been received at the London WHO Collaborating Centre, the Francis Crick Worldwide Influenza Centre (WIC). Therefore, this report focuses on genetic characterisation of influenza viruses, the majority of which have collection dates prior to the start (week 40) of weekly influenza surveillance reporting for the 2020-2021 influenza season, based on HA sequences deposited in GISAID during December.

All 39 A(H1N1)pdm09 HA sequences deposited in GISAID in December were from viruses detected before April 2020 and fell in the 6B.1A5A group. 6B.1A5A viruses have continued to evolve and two subgroups have emerged designated 6B.1A5A+187V/A, representatives of which are recommended for use in the northern hemisphere 2020-2021 season, and 6B.1A5A+156K, an antigenically distinct group representatives of which are recommended for use in the southern hemisphere 2021 season. Following a rise in the number of 6B.1A5A+156K viruses detected, the two subgroups appear to be circulating in approximately equal proportions currently, based on low numbers of viruses with collection dates after March 2020 having been detected and characterised genetically.

Recently circulating A(H3N2) viruses have continued to fall in clades 3C.2a and 3C.3a, with the vast majority of clade 3C.2a viruses being in the 3C.2a1b group, which splits into four subgroups designated 3C.2a1b+T131K-A, 3C.2a1b+T131K-B, 3C.2a1b+T135K-A and 3C.2a1b+T135K-B. Antisera raised in ferrets show high levels of clade/group specificity, although there is some subgroup cross-reactivity. Viruses representative of subgroup 3C.2a1b+T135K-B have been recommended for use in influenza vaccines for the 2020-2021 northern hemisphere and 2021 southern hemisphere influenza seasons. The most recently detected viruses, with collection dates in September through November, have been reported from Bangladesh, Cambodia and India; all have subgroup 3C.2a1b+T131K-AHA genes that encode amino acid substitutions at positions in HA1 that are likely to affect antigenic properties of the viruses.

Of four antigenically distinct groups of viruses in the B/Victoria-lineage, all sequences deposited in GISAID in December were derived from subclade 1A(3)B viruses with a three amino acid deletion in HA1. The four viruses with collection dates in October and November, all detected in France, contain a series of HA1 amino acid substitutions that are likely to affect antigenic properties of the viruses. Viruses representative of subclade 1A(3)B have been recommended for use in influenza vaccines for the 2020-2021 northern hemisphere and 2021 southern hemisphere influenza seasons.

Six additional sequences for B/Yamagata-lineage viruses were deposited and/or released in GISAID during December (since the November report), but all had collection dates in January through March as has been the case throughout 2020. All HA sequences belong to genetic clade 3 and contain at least two HA amino acid substitutions (HA1 L172Q and M251V) compared to B/Phuket/3073/2013-like viruses which have been recommended for use in quadrivalent influenza vaccines for the northern hemisphere 2020-2021 and southern hemisphere 2021 seasons. The antigenic effects of these amino acid substitutions have been minimal as assessed in earlier reports.