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 07/2020, 11 258 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; 67% were type A and 33% were type B. The majority of viruses from non-sentinel specimens were not subtyped or assigned to a lineage; 68% of all subtyped A viruses were A(H1N1)pdm09 and all influenza type B viruses ascribed to a lineage were B/Victoria.

For the season to date, more influenza type A (78%) than type B (22%) viruses have been detected. Relatively low numbers of the viruses have been ascribed to a subtype or lineage; of subtyped A viruses, half were A(H3N2) and half A(H1N1)pdm09, and 94% of influenza type B viruses ascribed to a lineage were B/Victoria.

Genetic and antigenic characterization

For specimens collected since week 40/2019, genetic characterization of 2 083 viruses has been reported:

  • 1 542 (74%) type A: 826 A(H3N2) and 716 A(H1N1)pdm09;
  • 541 (26%) type B: 513 B/Victoria and 28 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 2019–20 influenza season to date, with 53% clade 3C.3a and 47% subclade 3C.2a. 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 40/2019–06/2020Phylogenetic g

Phylogenetic group

Number of viruses

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

649

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

14

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

35

A(H1)pdm09 group 6B.1A1 representative A/Brisbane/02/2018 a

11

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

7

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

77

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

434

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

55

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

259

A(H3) attributed to recognised group in the guidance but not listed here

1

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

16

B(Vic)-lineage clade 1A (del162-164 subgroup) representative B/Hong Kong/269/2017

3

B(Vic) attributed to recognised group in the guidance but not listed here

13

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

481

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

26

B(Yam) attributed to recognised group in the guidance but not listed here

2

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 had been 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 2019–2020 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

1 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.

The WHO consultation on the composition of influenza virus vaccines for use in the 2020–2021 northern hemisphere influenza season will be held in Geneva, Switzerland 24–27 February 2020.

Vaccine effectiveness

Interim estimates of 2019–20 seasonal influenza vaccine effectiveness (VE) in the United States have been published. Overall, VE against any influenza virus associated with medically attended ARI was 45% (95% CI: 36%–53%). VE was estimated to be 50% (95% CI: 39%–59%) against influenza B/Victoria viruses and 37% (95% CI: 19%–52%) against influenza A(H1N1)pdm09. VE among children and adolescents aged 6 months–17 years was 55% (95% CI: 42%–65%).

Interim influenza VE estimates for the 2019/20 season in Canada have also been published. Overall VE was 58% (95% CI: 47%–66%), with higher point estimates among children 1–19 years (74%; 95% CI: 59%–84%) but lower among adults aged ≥65 years (18%; 95% CI: −59%–58%). VE against influenza A(H1N1)pdm09 was 44% (95% CI: 26%–58%) overall; VE against influenza A(H3N2) was 62% (95% CI: 37%–77%) overall; and VE against influenza B was 69% (95% CI: 57%–77%)

Preliminary influenza VE estimates from Sweden and Finland suggest that overall 2019-2020 VE 39% and 41% (adjusted VE CI 95%: 29%–50%) respectively among adults 65 years and older, and 70% (adjusted VE CI 95%: 47%–70%) among children from 6 months to 6 years of age for both influenza virus types.

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 circulating viruses.

Antiviral susceptibility testing

Since the beginning of the season, 867 influenza viruses have been tested for susceptibility to neuraminidase inhibitors: 362 A(H3N2), 332 A(H1N1)pdm09 and 173 type B viruses. One A(H3N2) virus carried amino acid substitution R292K in neuraminidase and showed evidence of highly reduced inhibition by oseltamivir and reduced inhibition by zanamivir. One A(H1N1)pdm09 virus carried amino acid substitution H275Y in NA indicative of highly reduced inhibition by oseltamivir. One type B virus showed evidence of reduced inhibition by oseltamivir.