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 03/2020, 6 357 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; 77% were type A and 23% were type B. The majority of viruses from non-sentinel specimens were not subtyped or assigned to a lineage; 72% of all subtyped A viruses were A(H1N1)pdm09 and 98% of all influenza type B viruses ascribed to a lineage were B/Victoria lineage.

For the season to date, more influenza type A (85%) than type B (15%) viruses have been detected. Relatively low numbers of the viruses have been ascribed to a subtype or lineage; 64% of all subtyped A viruses were A(H3N2) and 92% of influenza type B viruses ascribed to a lineage were B/Victoria lineage.


Genetic and antigenic characterization

For specimens collected since week 40/2019, genetic characterization of 901 viruses has been reported (Table 3):

  • 664 (74%) type A: 397 A(H3N2) and 267 A(H1N1)pdm09;
  • 237 (26%) type B: 220 B/Victoria and 17 B/Yamagata.

While the A(H1N1)pdm09 viruses fall within subgroups of subclade 6B.1A5 and subclade 6B.1A7 that are different to that of the vaccine virus A/Brisbane/02/2018 (6B.1A1), it is anticipated that the vaccine virus will be effective based on HI assays conducted with post-infection ferret antisera raised against the vaccine virus.

As seen elsewhere in the world, there is significant genetic diversity among circulating A(H3N2) viruses in the European region for the 2019–2020 influenza season to date, with 51% subclade 3C.2a. and 49% clade 3C.3a. All subclade 3C.2a1 viruses fall 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 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.

Table: Viruses attributed to genetic groups, cumulative for weeks 40/2019–03/2020

Phylogenetic group

Number of viruses

A(H1)pdm09 group 6B.1A5A representative A/Norway/3433/2018

239

A(H1)pdm09 group 6B.1A7 representative A/Slovenia/1489/2019

7

A(H1)pdm09 group 6B.1A5B representative A/Switzerland/3330/2018

20

A(H1)pdm09 attributed to recognised group in the guidance but not listed here

1

A(H3) clade 3C.3a representative A/Kansas/14/2017a

193

A(H3) clade 3C.2a1b+T135K-A representative A/La Rioja/2202/2018

16

A(H3) clade 3C.2a1b+T131K representative A/South Australia/34/2019

140

A(H3) clade 3C.2a1b+T135K-B representative A/Hong Kong/2675/2019

48

B(Vic)-lineage clade 1A (del162-164) representative B/Washington/02/2019

215

B(Vic)-lineage clade 1A (del162-163) representative B/Colorado/06/2017a

 4

B(Vic)-lineage clade 1A (del162-164) representative B/Hong Kong/269/2019

                                   1

B(Yam)-lineage clade representative B/Phuket/3073/2013b

17

a Vaccine component for 2019–2020 northern hemisphere.

b Vaccine component of quadrivalent vaccines for use in 2019–2020 northern hemisphere season.

ECDC published a report in January that largely focused on viruses from across the world, with collection dates after 31 August, that had full length HA gene sequence data deposited in GISAID by 2 January 2020. Since the November 2019 characterisation report, 12 shipments of influenza-positive specimens from European Union/European Economic Area (EU/EEA) countries were received by the WHO Collaborating Centre, London (the Francis Crick Institute). A total of 397 virus specimens had been received, with collection dates after 31 August. A summary of viruses from EU/EEA countries characterized in December is given below. Previously published influenza virus characterisation reports are also available on the ECDC website.

A(H1N1)pdm09 viruses

17 A(H1N1)pdm09 viruses from EU/EEA countries were characterized antigenically since the last report (for November, published in December),  with 16 showing good reactivity with antiserum raised against the 2019–20 vaccine virus, A/Brisbane/02/2018. The 21 viruses from EU/EEA countries characterized genetically fell within subclades of clade 6B.1A: 15 6B.1A5A, 3 6B.1A5B, 1 6B.1A6 and 2 6B.1A7.

A(H3N2) viruses

Antigenic characterization of A(H3N2) viruses remains technically difficult. 17 A(H3N2) viruses were characterized antigenically since the last characterization report. Of the 17, 12 were clade 3C.3a viruses that were antigenically similar to the vaccine virus, A/Kansas/14/2017. The remaining five were subgroup 3C.2a1b+T135K viruses that were poorly recognised by the vaccine virus. Of the 57 viruses characterized genetically, 38 were clade 3C.3a, 11 were subgroup 3C.2a1b+T131K, 3 were subgroup 3C.2a1b+T135K‑A and 5 were subgroup 3C.2a1b+T135K‑B.

B/Victoria viruses

14 B/Victoria-lineage viruses were characterised in December. All gave antigenic profiles characteristic of the triple deletion subgroup 1A(Δ3)B, represented by B/Washington/02/2019, the vaccine virus for the 2020 southern hemisphere season. The subgroup has been confirmed for nine of the viruses.

B/Yamagata viruses

B/Yamagata-lineage virus was characterised antigenically in December. It reacted poorly with antiserum raised against the vaccine virus B/Phuket/3073/2013 (clade 3) and only reacted well with an antiserum raised against a B/Yamagata-lineage virus carrying multiple unusual substitutions in HA1.

Vaccine composition

On 21 February 2019, WHO published recommendations for the components of influenza vaccines for use in the 2019–2020 northern hemisphere influenza season; the recommendations were finalized on 21 March. Vaccines should 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 decision and the 21 March addendum are available on the WHO website.

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

Antiviral susceptibility testing

Since the beginning of the season, 429 influenza viruses have been tested for susceptibility to neuraminidase inhibitors: 189 A(H1N1)pdm09, 178 A(H3N2) and 62 type B viruses. All showed normal inhibition (NI) by both oseltamivir and zanamivir.