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 20/2019, 360 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; 87% were type A and 13% were type B. Of 69 A viruses subtyped, 17% were A(H1N1)pdm09 and 83% were A(H3N2).

For the season to date, the vast majority of viruses detected have been influenza type A (99%). Of A viruses subtyped, 58% were A(H1N1)pdm09 and 42% were A(H3N2). Of 76 influenza type B viruses ascribed to a lineage, 57% were B/Victoria (97% of type B viruses were reported without a lineage).

Genetic and antigenic characterization

Genetic characterization of influenza viruses is routinely performed to understand how similar currently circulating influenza viruses are to the viruses used in influenza vaccines for an ongoing season.

Since week 40/2018, genetic characterizations of 4 102 viruses have been reported by the network laboratories.

Of the genetically characterized viruses, 1 882 were A(H1)pdm09 viruses belonging to the A/Michigan/45/2015 (6B.1) clade with a further 3 attributed to a subgroup not listed; 2 163 were A(H3) viruses, with 1 435 belonging to the A/Alsace/1746/2018 (3C.2a1b) subgroup, 70 to the A/Switzerland/8060/2017 (3C.2a2) subclade, 33 to the A/Cote d'Ivoire/544/2016 (3C.2a3) subclade, 57 to the A/Singapore-16-0019/2016 (3C.2a1) subclade, 9 to the A/Greece/4/2017 (3C.2a1a) subgroup, 5 to the A/Hong Kong/4801/2014 (3C.2a) clade, 548 to the A/England/538/2018 (3C.3a) clade and 6 attributed to a subgroup not listed.

Of the 54 genetically characterized influenza B viruses, 29 were B/Yamagata viruses belonging to the B/Phuket/3073/2013 clade (clade 3). All 25 B/Victoria viruses characterized belonged to clade 1A (represented by B/Brisbane/60/2008); but of these, 5 fell in a subclade with a two amino acid deletion in HA (1A.Δ2; represented by B/Colorado/06/2017) and 15 fell in a subclade with a three amino acid deletion in HA (1A.Δ3; represented by B/Hong Kong/269/2017).

Table. Viruses attributed to genetic groups, cumulative for weeks 40/2018–20/2019

Phylogenetic group

Number of viruses

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

1 882

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

3

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

1 435

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

70

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

33

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

548

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

57

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

5

A(H3) attributed to recognized group in current guidance but not listed here

6

A(H3) clade 3C.2a1a representative A/Greece/4/2017 subgroup

9

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

5

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

5

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

15

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

29

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

b. Vaccine component for 2019 southern hemisphere season.

c. Vaccine component of quadrivalen vaccines for us in 2018-2019 northern hemisphere and 2019 southern hemisphere seasons.

d. Vaccine component for 2018-2019 northern hemisphere season.

 

ECDC recently published a report detailing influenza virus characterizations conducted in April 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

The vast majority (126/129) of A(H1N1)pdm09 viruses characterized overall and all 59 test viruses characterized antigenically since the March 2019 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 391 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, 355 also have 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 previous report published in March 2019, only 26 A(H3N2) viruses successfully recovered had sufficient HA titre to allow antigenic characterization by HI assay in the presence of oseltamivir. These viruses were poorly recognized by antisera raised against the currently used vaccine virus, egg-propagated A/Singapore/INFIMH-16-0019/2016, in HI assays. Of the 321 viruses with collection dates from week 40/2018 genetically characterized at the WHO Collaborating Centre, 267 were clade 3C.2a (with 32 3C.2a2, 13 3C.2a3, six 3C.2a4 and 216 3C.2a1b) and 54 were clade 3C.3a.

B/Victoria viruses

No B/Victoria lineage virus has been tested by HI since the March 2019 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

Only 2 B/Yamagata lineage viruses have been characterized antigenically since the March report and a total of 11 from the 2018–19 season. All have 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 remain antigenically similar to the vaccine virus recommended for use in quadrivalent vaccines for 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.

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 was assessed for 2 824 viruses with collection dates since week 40/2018 [1 668 A(H1N1)pdm09, 1 121 A(H3N2), and 35 type B]. 8 A(H1N1)pdm09 viruses carried amino acid substitution H275Y in NA indicative of highly reduced inhibition (HRI) by oseltamivir and 3 of them were confirmed by phenotypic testing, additional 3 showed evidence of reduced inhibition by oseltamivir in phenotypic assays. 2 A(H3N2) viruses showed reduced inhibition by phenotypic testing. 1 type B virus showed evidence of reduced inhibition (RI) by oseltamivir and zanamivir.