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 12/2020, 2 764 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; 68% were type A and 32% were type B. The majority of viruses from non-sentinel specimens were not subtyped or assigned to a lineage. Of 852 subtyped A viruses, 65% were A(H1N1)pdm09 and 35% were A(H3N2). All influenza type B viruses ascribed to a lineage were B/Victoria.

For the season to date, more influenza type A (n=105 386, 75%) than type B (n=35 558, 25%) viruses have been detected but relatively low numbers have been ascribed to a subtype or lineage. Of 35 436 subtyped A viruses, 54% were A(H1N1)pdm09 and 46% were A(H3N2). Of 2 020 influenza type B viruses ascribed to a lineage, 97% were B/Victoria.

Genetic and antigenic characterization

For specimens collected since week 40/2019, genetic characterization of 2 553 viruses has been reported:

  • 1 909 (75%) type A: 993 A(H3N2) and 916 A(H1N1)pdm09;
  • 644 (25%) type B: 616 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 from that of the vaccine virus A/Brisbane/02/2018 (6B.1A1), it is anticipated that the vaccine virus will still 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 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 40/2019–12/2020Phylogenetic g

Phylogenetic group

Number of viruses

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

839

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

18

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

41

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

81

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

528

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

63

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

320

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

19

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

5

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

552

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

40

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 March 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 December 2019 characterization report, 25 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)). A total of 954 virus specimens had been received, with collection dates after 31 August. A summary of viruses from EU/EEA countries characterized in the period January to February is given below. Previously published influenza virus characterization reports are also available on the ECDC website.

A(H1N1)pdm09 viruses

Of 151 A(H1N1)pdm09 viruses characterised antigenically from EU/EEA countries since the last report (for December, published in January 2020) 129 (85%) showed good reactivity with antiserum raised against the 2019–20 vaccine virus, A/Brisbane/02/2018, with those viruses showing poor reactivity carrying amino acid substitutions (notably N156K) in the HA1 150-loop region. The 159 test viruses with collection dates from week 40/2019 genetically characterised at the WIC have fallen within subclades of clade 6B.1A: 139 6B.1A5A, 12 6B.1A5B, 1 6B.1A6 and 7 6B.1A7.

A(H3N2) viruses

122 A(H3N2) viruses have been characterised antigenically, the majority of which showed reduced recognition by antiserum raised against the current vaccine virus, egg-propagated A/Kansas/14/2017. While circulation of A(H3N2) viruses has varied considerably between countries in terms of numbers and genetic clades, globally there have been approximately equal proportions of clade 3C.3a and subgroups 3C.2a1b+T131K and 3C.2a1b+T135K viruses detected. In total, 191 viruses have been characterised genetically at the WIC: 103 clade 3C.3a, 62 3C.2a1b+T131K, 19 3C.2a1b+T135K-A and seven 3C.2a1b+T135K-B.

B/Victoria viruses

The great majority of the 104 B/Victoria-lineage viruses characterised in this reporting period gave antigenic profiles characteristic of subgroup 1A(Δ3)B viruses represented by B/Washington/02/2019, the vaccine virus for the 2020 southern hemisphere season.  A minority of viruses gave a profile characteristic of 1A(Δ2) viruses represented by the 2019–20 northern hemisphere vaccine virus B/Colorado/06/2017. In total, 125 viruses have been characterised genetically at the WIC: 118 subgroup 1A(Δ3)B and seven 1A(Δ2).

B/Yamagata viruses

The five B/Yamagata-lineage virus characterised antigenically in this reporting period reacted well with antiserum raised against the vaccine virus B/Phuket/3073/2013 (clade 3). All five viruses characterised genetically at the WIC, 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_Δ3B); 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_Δ3B); 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

Since the beginning of the season, 1 382 influenza viruses have been tested for susceptibility to neuraminidase inhibitors: 603 A(H1N1)pdm09, 531 A(H3N2) and 248 type B viruses. Three A(H1N1)pdm09 viruses carried amino acid substitution H275Y in NA, with one of them also having H295S substitution, both of which are indicative of highly reduced inhibition (HRI) by oseltamivir. One A(H3N2) virus carried amino acid substitution R292K in NA and showed evidence of HRI by oseltamivir and reduced inhibition (RI) by zanamivir.