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 weeks 21–32/2019, 821 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 an influenza virus; 86% were type A and 14% were type B. Of 369 A viruses subtyped, 18% were A(H1N1)pdm09 and 82% were A(H3N2).

Genetic and antigenic characterization

A total of 22 influenza viruses from weeks 21–32/2019 have been characterised genetically, 16 influenza A and 6 influenza B viruses. Genetic data from the 2018/2019 season can been found in the FNE report from week 20/2019 (see Archives page).

 Viruses attributed to genetic groups, cumulative for weeks 21/2019–32/2019

Phylogenetic group

Number of viruses

A(H1)pdm09 group 6B.1 representative A/Michigan/45/2015a

5

A(H3) clade 3C.2a1b representative A/Alsace/1746/2018 subgroup

10

A(H3) clade 3C.2a2 representative A/Switzerland/8060/2017 subgroupb

0

A(H3) clade 3C.2a3 representative A/Cote d'Ivoire/544/2016 subgroup

0

A(H3) clade 3C.3a representative A/England/538/2018 subgroup

1

A(H3) clade 3c.2a1 representative   A/Singapore-16-0019/2016 subgroupd

0

A(H3) clade 3c.2a representative A/Hong Kong/4801/2014 subgroup

0

B(Vic)-lineage clade 1A representative B/Brisbane/60/2008

1

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

0

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

3

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

2

a   Vaccine component for 2018–2019 northern hemisphere and 2019 southern hemisphere seasons.

Vaccine component for 2019 southern hemisphere season.

c   Vaccine component of quadrivalent vaccines for use in 2018–2019 northern hemisphere and 2019 southern hemisphere seasons.

d Vaccine component for 2018-2019 northern hemisphere season.

 

 

ECDC published a report in June detailing influenza virus characterizations conducted in May 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 9 test viruses characterized antigenically since the April 2019 characterization report were similar to the vaccine virus for use in the 2018–2019 northern hemisphere (A/Michigan/45/2015, clade 6B.1) and all fell in subclade 6B.1A. Within this subclade, there has been increasing genetic diversity of the HA genes with several emerging genetic subgroups. The 400 test viruses with collection dates from week 40/2018 genetically characterized at the WHO Collaborating Centre, including an A(H1N2) reassortant, all fell in a 6B.1 subclade, designated 6B.1A, defined by HA1 amino acid substitutions of S74R, S164T and I295V. Of these recently circulating viruses, 365 also have an HA1 S183P substitution, often with additional substitutions in HA1 and/or HA2.

A(H3N2) viruses

Antigenic characterization of A(H3N2) viruses remains technically difficult. Since the April 2019 characterization report, only 1 A(H3N2) virus had sufficient HA titre to allow antigenic characterization by HI assay in the presence of oseltamivir. This virus was poorly recognized by antisera raised against the currently used clade 3C.2a1 vaccine virus, egg-propagated A/Singapore/INFIMH-16-0019/2016, in HI assays. Of the 337 viruses with collection dates from week 40/2018 genetically characterized at the WHO Collaborating Centre, 273 were clade 3C.2a (including 32 3C.2a2, 13 3C.2a3, 6 3C.2a4 and 216 3C.2a1b) and 64 were clade 3C.3a.

B/Victoria viruses

No B/Victoria lineage virus had been tested by HI since the April 2019 characterization report. All recent viruses carry HA genes that fall in clade 1A but encode HA1 amino acid substitutions of I117V, N129D and V146I compared to a previous vaccine virus, 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 and African origin. HI analyses with panels of post-infection ferret antisera have shown these virus groups to be antigenically distinguishable. Of a total of 5 viruses characterized from EU/EEA countries this season, 1 has been Δ162-163 and 4 Δ162-164 (3 African and 1 Asian subgroup).

B/Yamagata viruses

No B/Yamagata lineage viruses had been characterized antigenically since the April characterization report, a total of 11 had been characterized from the 2018–19 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 current and subsequent northerm hemisphere influenza seasons, B/Phuket/3073/2013. However, all remained antigenically similar to the vaccine virus recommended for use in quadrivalent vaccines for the current and subsequent northern hemisphere influenza seasons.

Vaccine composition

The recommended composition of the trivalent influenza vaccine for the current northern hemisphere 2018–2019 season included an A/Michigan/45/2015 (H1N1)pdm09-like virus, an A/Singapore/INFIMH-16-0019/2016 (H3N2)-like virus and a B/Colorado/06/2017-like virus (B/Victoria lineage). For quadrivalent vaccines, a B/Phuket/3073/2013-like virus (B/Yamagata lineage) was recommended. The full report can be found here.

On 21 February 2019, WHO published recommendations for the components of influenza vaccines for use in the 2019–2020 northern hemisphere influenza season, and on 21 March it was finalized. Vaccines should contain the following

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

It is 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”  are available for the 21 February decision and the 21 March addendum on the WHO website. The next WHO meeting on the composition of influenza vaccines for the 2020 southern hemisphere influenza season will be held in Geneva on 23-26 September.

Vaccine effectiveness

Current influenza vaccines tend to work better against influenza A(H1N1)pdm09 and influenza B viruses than against influenza A(H3N2) viruses. Preliminary vaccine effectiveness estimates continue to support the use of vaccines. Early data suggest that vaccines are moderately effective, with estimates varying depending on the population studied and the proportions of circulating influenza A virus subtypes. See data from a European study (6 countries), Canada, Finland, Hong Kong (China), Sweden, and the United States of America.

Antiviral susceptibility testing

Neuraminidase inhibitor susceptibility has not been assessed on viruses with collection dates from week 21/2019 through week 32/2019.