Virus characteristics

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

Viruses detected in non-sentinel source specimens 

For week 30/2020, no 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 influenza viruses.

Cumulatively, for weeks 21-30/2020, 10 influenza type A and 8 influenza type B viruses were detected. The 2 subtyped A viruses were A(H3N2).

Genetic and antigenic characterization

From weeks 21-30/2020, no influenza viruses were characterised genetically. Genetic data for the 2019-2020 season can be found in the FNE report for week 20/2020.

The great majority of A(H1N1)pdm09 viruses have fallen within subgroups of subclade 6B.1A5 and subclade 6B.1A7, with those of 6B.1A5A becoming dominant as the season progressed. While these viruses have 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 has been significant genetic diversity among circulating A(H3N2) viruses in the European region for the 2019–2020 influenza season to date, with 53% clade 3C.3a and 47% subclade 3C.2a. All subclade 3C.2a1 viruses have fallen 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 may be less well covered by human immune responses to the vaccine.

For the B/Victoria-lineage, viruses in the B/Colorado/06/2017 vaccine virus double deletion clade (1A (del 162-163)) have been in the great minority. However, there is 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 have been detected in low numbers worldwide and, despite some genetic drift with associated HA amino acid substitutions, retain good reactivity with post-infection ferret antisera raised against the B/Phuket/3073/2013 vaccine virus.

ECDC published a report in July relating to viruses circulating globally, with collection dates after 31 August, but focusing on those from European Union/European Economic Area (EU/EEA) countries. Since the May 2020 characterization report, 9 shipments of influenza-positive specimens from EU/EEA countries had been received by the WHO Collaborating Centre, London (the Francis Crick Institute, Worldwide Influenza Centre (WIC)). In total, 1 608 virus specimens had been received, with collection dates after 31 August. A summary of viruses from EU/EEA countries characterized in June is given below. Previously published influenza virus characterization reports are also available on the ECDC website.

A(H1N1)pdm09 viruses

Of the 99 A(H1N1)pdm09 viruses from EU/EEA countries characterised antigenically since the May report, 77 were well recognised by antisera raised against the 2019–20 vaccine virus, A/Brisbane/02/2018. The 22 viruses that showed poor reactivity generally carried amino acid substitutions (notably N156K) in the HA1 150-loop region. The 397 EU/EEA test viruses with collection dates from week 40/2019 genetically characterised at the WIC have fallen within subclades of clade 6B.1A: 358 6B.1A5A, 29 6B.1A5B, 1 6B.1A6 and 9 6B.1A7.

A(H3N2) viruses

The majority (52) of the 68 A(H3N2) viruses from EU/EEA countries characterised antigenically in June were clade 3C.3a and were well recognised by antiserum raised against egg-propagated A/Kansas/14/2017, the current vaccine virus. Globally, approximately equal proportions of clade 3C.3a and subgroups 3C.2a1b+T131K and 3C.2a1b+T135K viruses have been detected, but for viruses detected since 1 February 2020, subgroups 3c.2a1b+T135KA/B have prevailed in the USA while those of clade 3C.3a and subgroup 3C.2a1b+T131K have dominated in Europe. In total, 438 viruses from EU/EEA countries have been characterised genetically at the WIC: 245 clade 3C.3a, 126 3C.2a1b+T131K, 48 3C.2a1b+T135K-A and 19 3C.2a1b+T135K-B.

B/Victoria viruses

Sixty-nine B/Victoria-lineage viruses from EU/EEA countries were antigenically characterised in June, 63 subclade 1A(Δ3)B, one subclade 1A(Δ2) and five not sequenced. Approximately 25% of the subclade 1A(Δ3)B viruses were not recognised well by antiserum raised against B/Washington/02/2019, the vaccine virus for the 2020–2021 northern hemisphere influenza season. Poor recognition was generally associated with HA1 amino acid substitutions of either N126K or E128K. In total, 269 EU/EEA viruses have been characterised genetically at the WIC: 255 subclade 1A(Δ3)B and 14 subclade 1A(Δ2).

B/Yamagata viruses

No B/Yamagata-lineage viruses were characterised antigenically in June. All 8 EU/EEA viruses characterised genetically at the WIC since week 40/2019, as for all recently circulating B/Yamagata-lineage viruses, belong to genetic clade 3 and contain at least two HA amino acid substitutions (HA1 L172Q and M251V) compared to B/Phuket/3073/2013, the antigenic effects of which have been minimal as assessed in earlier reports.

Vaccine composition

Based on WHO published recommendations on 21 February 2019, the composition of influenza vaccines for use in the 2019–2020 northern hemisphere influenza season contain the following:

  • an A/Brisbane/02/2018 (H1N1)pdm09-like virus (Clade 6B.1A1);
  • an A/Kansas/14/2017 (H3N2)-like virus (Clade 3C.3a);
  • a B/Colorado/06/2017-like virus (B/Victoria/2/87 lineage) (Clade 1A(Δ2)); and
  • a B/Phuket/3073/2013-like virus (B/Yamagata/16/88 lineage) (Clade 3).

It was recommended that the influenza B virus component of trivalent vaccines for use in the 2019–2020 northern hemisphere influenza season be a B/Colorado/06/2017-like virus of the B/Victoria/2/87-lineage.

The full report and Frequently Asked Questions for the 21 February 2019 decision and the 21 March 2019 addendum are available on the WHO website.

The report from the Vaccine Composition Meeting for the southern hemisphere 2020 season can be found here.

On 28 February 2020, WHO published recommendations for the components of influenza vaccines for use in the 2020–2021 northern hemisphere influenza season.

Egg-based vaccines should contain following:

  • an A/Guangdong-Maonan/SWL1536/2019 (H1N1)pdm09-like virus (Clade 6B.1A5A);
  • an A/Hong Kong/2671/2019 (H3N2)-like virus (Clade 3C.2a1b+T135K-B);
  • a B/Washington/02/2019 (B/Victoria lineage)-like virus (Clade 1A(Δ3)B); and
  • a B/Phuket/3073/2013 (B/Yamagata lineage)-like virus (Clade 3).

Cell- or recombinant-based vaccines should contain following:

  • an A/Hawaii/70/2019 (H1N1)pdm09-like virus (Clade 6B.1A5A);
  • an A/Hong Kong/45/2019 (H3N2)-like virus (Clade 3C.2a1b+T135K-B);
  • a B/Washington/02/2019 (B/Victoria lineage)-like virus (Clade 1A(Δ3)B); and
  • a B/Phuket/3073/2013 (B/Yamagata lineage)-like virus (Clade 3).

It is recommended that the influenza B virus component of both trivalent vaccine types for use in the 2020–2021 northern hemisphere influenza season should be a B/Washington/02/2019-like virus of the B/Victoria-lineage.

The full report and Frequently Asked Questions for the 28 February 2020 decision are available on the WHO website.

Vaccine effectiveness

Interim estimates of 2019-2020 seasonal influenza vaccine effectiveness (VE) for the northern hemisphere have been published based on six European studies (see below) and independent studies conducted in Finland, Canada and the United States of America. Influenza vaccine effectiveness estimates can vary depending on several factors, for example, study methods, health facility type, population, disease outcome, influenza vaccine types, influenza activity and type/subtype/lineage of circulating viruses. Vaccination against influenza remains the best method for prevention of influenza infection and/or development of severe disease during the ongoing 2019-2020 influenza season.

Interim 2019-2020 influenza VE estimates from the six European studies for all ages ranged from 29% to 61% against any influenza in the primary care setting and 35% to 60% in hospitalized older adults (aged 65 years and over). The VE point estimates against influenza A(H1N1)pdm09 (all ages, both settings) was 48% to 75%, and against influenza A(H3N2) ranged from −58% to 57% (primary care) and −16% to 60% (hospital). Against influenza type B, VE for all ages was 62% to 83% (primary care only).

Antiviral susceptibility testing 

From week 40/2019 to week 25/2020, 1 789 influenza viruses, collected up to week 14, were tested for susceptibility to neuraminidase inhibitors: 758 A(H1N1)pdm09, 626 A(H3N2) and 405 type B viruses.

In total, 6 A(H1N1)pdm09 viruses showed highly reduced inhibition (HRI) or reduced inhibition (RI) to oseltamivir and/or zanamivir. Of these, 4 viruses carried amino acid substitution H275Y in NA, with one of them also having H295S substitution, both of which are indicative of HRI by oseltamivir. An additional 2 A(H1N1)pdm09 viruses showed RI by oseltamivir by phenotypic assay; 1 of these viruses also showed RI by zanamivir by phenotypic assay.

1 A(H3N2) virus carried amino acid substitution R292K in NA and showed evidence of HRI by oseltamivir and RI by zanamivir.

1 B/Victoria-lineage virus showed RI by zanamivir and highly reduced inhibition (HRI) by oseltamivir by phenotypic assay.