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 45/2019, 451 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; 82.7% were type A and 17.3% were type B. Of 78 subtyped A viruses, 23.1% were A(H1N1)pdm09 and 76.9% were A(H3N2). Both type B viruses ascribed to a lineage were B/Victoria.

For the season to date, more influenza type A (82%) than type B (18%) viruses have been detected. Of 411 subtyped A viruses, 91 (22%) were A(H1N1)pdm09 and 320 (78%) were A(H3N2). Of 31 influenza type B viruses ascribed to a lineage, 90% were B/Victoria lineage.

Genetic and antigenic characterization

Since the beginning of the season, there have been no reports of influenza virus genetic characterization.

ECDC published a report in October on detailed influenza virus characterizations conducted in September 2019 by the WHO Collaborating Centre, London (the Francis Crick Institute), on influenza-positive specimens received from European Union/European Economic Area countries. A summary is given below.

A(H1N1)pdm09 viruses

All 85 test viruses characterized antigenically since the July 2019 characterization report were antigenically similar to the vaccine viruses used in the 2018–2019 (A/Michigan/45/2015, clade 6B.1) and 2019–2020 (A/Brisbane/02/2018, clade 6B.1A1) northern hemisphere seasons. All 613 viruses with collection dates from week 40/2018 that were genetically characterized at the WHO Collaborating Centre, including two A(H1N2) reassortants, fell in a 6B.1 subclade, designated as 6B.1A, defined by HA1 amino acid substitutions of S74R, S164T and I295V. Within this subclade there has been increasing genetic diversity of the HA genes and, of these recently circulating viruses, 564 also have an HA1 S183P substitution, often with additional substitutions in HA1 and/or HA2, that define several emerging genetic subgroups.

A(H3N2) viruses

Antigenic characterization of A(H3N2) viruses remains technically difficult. Since the last characterization report, 37 A(H3N2) viruses had sufficient HA titre to allow antigenic characterization by HI assay in the presence of oseltamivir. All these viruses were poorly recognized by antisera raised against the currently used clade 3C.2a1 vaccine virus, egg-propagated A/Singapore/INFIMH-16-0019/2016. Of the 505 viruses with collection dates from week 40/2018 that were genetically characterized at the WHO Collaborating Centre, 399 were in clade 3C.2a with many falling in subclades (43 in 3C.2a2, 17 in 3C.2a3, 8 in 3C.2a4 and 331 in 3C.2a1b) and 106 were clade 3C.3a.

B/Victoria viruses

Ten B/Victoria lineage viruses had been tested by HI since the last characterization report. All recent viruses carry HA genes that fall in clade 1A but encode HA1 amino acid substitutions of I117V, N129D and V146I when compared to B/Brisbane/60/2008. Groups of viruses defined by deletions of 2 (Δ162-163, 1A(Δ2)) or 3 (Δ162-164, 1A(Δ3)) amino acids in HA1 have emerged, with the triple deletion group having subgroups of Asian [1A(Δ3A)] and African [1A(Δ3B)] origin. HI analyses with panels of post-infection ferret antisera have shown these 4 virus groups to be antigenically distinguishable. Of a total of 20 viruses genetically characterized from EU/EEA countries this season, 1 has been 1A(Δ2) and 17 1A(Δ3) [16 1A(Δ3B) and 1 1A(Δ3A) subgroup].

B/Yamagata viruses

Nine B/Yamagata lineage viruses have been characterized antigenically since the last characterization report and a total of 23 have been characterized from the 2018–2019 season. All had HA genes that fell into clade 3 and encoded 2 HA amino acid substitutions not present in the virus recommended for inclusion in quadrivalent vaccines for the 2018–2019 and 2019–2020 northern hemisphere influenza seasons, B/Phuket/3073/2013. However, all 23 viruses remained antigenically similar to the vaccine virus.

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

One A(H3N2) virus, collected in the weeks 40–45/2019 period, tested for susceptibility to neuraminidase inhibitors showed normal inhibition (NI).