Virus Characteristics

Details of the distribution of viruses detected in sentinel-source specimens can be found in the Primary care data section.

Non-sentinel virological data
  • For week 47/2020, 12 specimens from non-sentinel sources (such as hospitals, schools, primary care facilities not involved in sentinel surveillance, or nursing homes and other institutions) tested positive for an influenza virus: 8 type A and 4 type B viruses.
  • Since the beginning of the season, 79 of 80 027 non-sentinel specimens tested positive for influenza viruses, 42 (53.2%) were type A and 37 (46.8%) type B. Twenty-four of the type A viruses were subtyped: 18 (75.0%) as A(H3) and 6 (25.0%) as A(H1)pdm09. Only 2 (5.4%) of 37 type B viruses were ascribed to a lineage, both were B/Victoria.
Genetic characterization

No virus characterization data for viruses detected in weeks 40-47/2020 have been reported.  


Data from influenza season 2019-2020 

 

The great majority of A(H1N1)pdm09 viruses fell within subgroups of subclade 6B.1A5 and subclade 6B.1A7, with those of 6B.1A5A becoming dominant as the season progressed. While these viruses had HA amino acid substitutions compared to the vaccine virus A/Brisbane/02/2018 (6B.1A1), it was anticipated that the vaccine virus would still be effective based on HI assays conducted with post-infection ferret antisera raised against the vaccine virus, until emergence of a group of viruses with HA1 N156K substitution.

 

As seen elsewhere in the world, there was significant genetic diversity among circulating A(H3N2) viruses in the European region for the 2019–2020 influenza season, with 53% being clade 3C.3a and 47% subclade 3C.2a1. All subclade 3C.2a1 viruses fell in subgroup 3C.2a1b (with the latter splitting between 3 designated genetic clusters). The vaccine virus, A/Kansas/14/2017, falls within clade 3C.3a and viruses within this clade induce clade-specific antibodies in ferrets, so viruses falling in other clades/subclades were expected to be less well covered by human immune responses to the vaccine virus.

 

For the B/Victoria-lineage, viruses in the B/Colorado/06/2017 vaccine virus double deletion clade (1A (del 162-163)) were in the great minority. However, there was evidence of some cross-reactivity with viruses in the triple deletion clade (1A (del 162-164)) by post-infection ferret antisera raised against the egg-propagated vaccine virus.

 

B/Yamagata lineage viruses were detected in low numbers worldwide and, despite some genetic drift with associated HA amino acid substitutions, retained good reactivity with post-infection ferret antisera raised against the B/Phuket/3073/2013 vaccine virus.

 

ECDC published a report in October relating to viruses circulating globally, with collection dates after 31 August 2019, but focusing on those from European Union/European Economic Area (EU/EEA) countries. This was the final report for the 2019-2020 season.

 

ECDC published the first report for the 2020-2021 season in November. No antigenic data relating to viruses detected in the course of the 2020-2021 influenza season had been generated and the report was based on an analysis of seasonal influenza HA sequenced most recently submitted to GISAID. The following text is repeated from the Summary text of this report with minor modification. Previously published influenza virus characterization reports are also available on the ECDC website.

 

A(H1N1)pdm09 viruses

 

The vast majority of A(H1N1)pdm09 viruses had continued to fall in genetic subclade 6B.1A5, mostly in the 6B.1A5A group with few in the 6B.1A5B 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.

 

A(H3N2) viruses

 

Recently circulating A(H3N2) viruses had 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 has now been divided 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, though there is some subgroup cross-reactivity. Viruses representative of subgroup 3C.2a1b+T135K-B have been recommended for use in influenza vaccines for the northern hemisphere 2020-2021 and southern hemisphere 2021 seasons.

 

B/Victoria viruses

 

Of four antigenically distinct groups of viruses in the B/Victoria-lineage, only two had circulated recently, small numbers of that designated subclade 1A (Δ2) with a two amino acid deletion in HA1 and that designated subclade 1A(Δ3)B with a three amino acid deletion in HA1 being hugely dominant. Viruses representative of subclade 1A(Δ3)B have been recommended for use in influenza vaccines for the northern hemisphere 2020-2021 and southern hemisphere 2021 seasons.

 

B/Yamagata viruses

 

When the report published in November was written, genetic information for only 70 B/Yamagata-lineage viruses with collection dates in 2020 was available in GISAID. All 67 viruses for which full-length HA sequences were available belonged to genetic clade 3 and contained 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.

Antiviral susceptibility of seasonal influenza viruses

For week 47/2020 and since the beginning of the season, no influenza viruses were tested for susceptibility to neuraminidase inhibitors.