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 40/2019, 64 of 8 159 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; 84% were type A and 16% were type B. Of 18 A viruses subtyped, 94% were A(H3N2), and both B viruses ascribed to a lineage were B/Victoria.
Genetic and antigenic characterization
One A(H3N2) influenza virus from week 40/2019 has been characterized genetically and it belonged to the 3C.2a1b subclade.
ECDC published a report in September detailing influenza virus characterizations conducted in July 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.
All 103 test viruses characterized antigenically since the June 2019 characterization report were similar to the vaccine virus for use in the 2018–2019 northern hemisphere (A/Michigan/45/2015, clade 6B.1) The 539 test viruses with collection dates from week 40/2018 genetically characterized at the WHO Collaborating Centre, including two A(H1N2) reassortants, all fell in a 6B.1 subclade, designated 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, 493 also have an HA1 S183P substitution, often with additional substitutions in HA1 and/or HA2 that define several emerging genetic subgroups.
Antigenic characterization of A(H3N2) viruses remains technically difficult. Since the June 2019 characterization report, 21 A(H3N2) viruses 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 clade 3C.2a1 vaccine virus, egg-propagated A/Singapore/INFIMH-16-0019/2016, in HI assays. Of the 446 viruses with collection dates from week 40/2018 genetically characterized at the WHO Collaborating Centre, 363 were clade 3C.2a with many falling in subclades (32 3C.2a2, 13 3C.2a3, 6 3C.2a4 and 216 3C.2a1b) and 83 were clade 3C.3a.
Four B/Victoria lineage viruses had been tested by HI since the June 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 4 virus groups to be antigenically distinguishable. Of a total of 12 viruses characterized from EU/EEA countries this season, 1 has been Δ162-163 and 11 Δ162-164 (10 African and 1 Asian subgroup).
Two B/Yamagata lineage viruses had been characterized antigenically since the June characterization report and a total of 15 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 northern hemisphere influenza seasons, B/Phuket/3073/2013. However, all 15 viruses remained antigenically similar to the vaccine virus.
The recommended composition of the trivalent influenza vaccine for the 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 (Clade 6B.1A-S183P);
- 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 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 for the 21 February decision and the 21 March addendum are available on the WHO website. The WHO meeting on the composition of influenza vaccines for the 2020 southern hemisphere influenza season was held in Geneva on 23–26 September.
Antiviral susceptibility testing
Neuraminidase inhibitor susceptibility has not been assessed on viruses with collection dates in week 40/2019.