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 11/2019, 5 057 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; 98.4% were type A and 1.6% were type B. Of 2 053 A viruses subtyped, 47.4% were A(H1N1)pdm09 and 52.6% were A(H3N2) (Table).

For the season to date, more influenza type A (n=161 013, 99.2%) than type B viruses  (n= 1 300, 0.8%) have been detected. Of 54 046 A viruses subtyped, 32 929 (60.9%) were A(H1N1)pdm09 and 21 117 (39.1%) were A(H3N2). Of 41 influenza type B viruses ascribed to a lineage, 46.3% were B/Yamagata (96.8% of type B viruses were reported without a lineage) (Table).

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 2 737 viruses have been reported by the network laboratories.

Of the genetically characterized viruses, 1 399 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; 1 293 were A(H3) viruses, with 881 belonging to the A/Alsace/1746/2018 (3C.2a1b) subgroup, 58 to the A/Switzerland/8060/2017 (3C.2a2) subclade, 25 to the A/Cote d'Ivoire/544/2016 (3C.2a3) subclade, 306 to the A/England/538/2018 (3C.3a) clade, 12 to the A/Singapore-16-0019/2016 (3C.2a1) subclade, 4 to the A/Hong Kong/4801/2014 (3C.2a) clade, and 7 attributed to a subgroup not listed.

Of the 42 genetically characterized influenza B viruses, 22 were B/Yamagata viruses belonging to the B/Phuket/3073/2013 clade (clade 3). All 20 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 10 fell in a subclade with a three amino acid deletion in HA (1A.Δ3; represented by B/Hong Kong/269/2017) (Table).

Table. Viruses attributed to genetic groups, cumulative for weeks 40/2018–11/2019

Phylogenetic group

Number of viruses

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

1 399

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

881

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

58

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

25

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

306

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

12

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

4

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

7

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

10

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

22

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.

 

A report detailing influenza virus characterization data through Febrauary 2019 from the WHO European Region was published by the European centre for Disease Prevention and Control. A summary is given below.

A(H1N1pdm09) Viruses

The great majority (203/204) of A(H1N1)pdm09 viruses characterized this season were antigenically similar to the vaccine virus for use in the 2018-19 northern hemisphere (A/Michigan/45/2015, clade 6B.1) and fell in subclade 6B.1A. Within this subclade, there has been increasing genetic diversity of the HA genes with several emerging genetic subgroups.  Most viruses carried the HA1 amino acid substitution of S183P.

A(H3N2) Viruses

Antigenic characterisation of A(H3N2) viruses remains technically difficult. Since the previous report published in December 2018, only 33 A(H3N2) viruses have had a sufficient HA titre to allow antigenic characterisation by hemagluttinin inhibition (HI) assay. By HI assay, all viruses belonging to 3C.2a and 3C.3a subgroups were poorly recognized by antisera raised against egg-propagated A/Singaport/INFM-16-0019/2015, the current vaccine virus.

B/Victoria Viruses

Only 5 B/Victoria viruses were characterised antigenically during this season. Of these, two were antigenically similar to the current vaccine virus, B/Colorado/06/2017, which belongs to a subclade with a two amino acid deletion in HA (Δ 162-163, 1A.Δ2). The other three were antigenically similar to a virus of African origin with a three amino acid deletion in HA1 (Δ 162-164, 1A.Δ3).

B/Yamagata Viruses

Only 7 B/Yamagata viruses were characterised antigenically during this season. HI analyses with post-infection ferret antisera raised against B/Phuket/3072/2013, the virus recommended for inclusion in the quadrivalent virus for the current and subsequent northern hemisphere influenza seasons, indicated that all 7 viruses were antigenically similar to the vaccine virus.

 

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 updated. 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.

Antiviral susceptibility testing

Neuraminidase inhibitor susceptibility was assessed for 1 901 viruses with collection dates since week 40/2018 [1 154 A(H1N1)pdm09, 720 A(H3N2), and 27 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. 1 A(H3N2) virus showed evidence of reduced inhibition (RI) by oseltamivir only. 1 type B virus showed evidence of RI by zanamivir only.