VIROLOGY
impact of circulating influenza at a regional level, and is usually available nationally through health ministries, as shown for England on the
GOV.UK website.
Laboratory testing data. This comprises of between 50,000-150,000 clinical respiratory samples per week, year-round, tested for the detection of influenza, mainly through the use of RT-PCR. This work is mainly undertaken at national level through the WHO GISRS system. Data are comprised of counts of viruses typed typed and subtyped at national influenza centres around the world and is reported weekly to WHO through the FLUNET platform. The data at national level is
supplemented by sub-national laboratories which test for a range of respiratory pathogens, including influenza, for clinical diagnosis. In England, the surveillance system which provides the information about the results of testing in clinical laboratories is the Second Generation Surveillance System (SGSS) system. With the increasing use of PCR and commercial testing kits, the amount of testing for influenza A and B has more than doubled over a ten year period, but the majority of tests undertaken at subnational level do not provide subtype information, so that counts of viruses only distinguish influenza A or B. Specific surveillance schemes may be needed to provide an assessment of the proportions of different circulating virus strains. In England, this is obtained through primary care surveillance, organised by the RCGP linked to UKHSA, featured in Pathology in Practice in April 2025.
Genomic characterisation of circulating strains. This is undertaken on samples which are influenza positive (A or B) to provide information on subtype (H1 or H3) and sequence data on the viral HA. Increasingly, as sequencing technology has become higher throughput and more affordable, genetic analysis of circulating strains has expanded to become a whole genome analysis. This allows understanding of virus gene constellations and identification of any reassortment events, alongside recognition of paterns of parallel or convergent evolution. The analysis of HA and neuraminidase NA gene segments provides information about circulating virus clades (lineages) and sub-clades. This information is used to track which variants
Influenza subtype: 40,000 30,000 20,000 10,000
A (H1N1)pdm09 A (H3)
A (H5) A not subtyped
B (Victoria) B (lineage not determined)
0
Global respiratory virus activity: weekly update report for week 8, ending 22 February 2026. Showing weekly numbers of influenza virus positive specimens by type and subtype at the global level for the previous 12 months.
are predominating with growth or disappearance of individual different lineages. Increasingly, sequence data is used to determine the selection of material to atempt to make virus isolates, a pathway called ‘Sequence First’.
Antigenic characterisation of circulating viruses. Undertaken on a proportion of virus isolates to assess the level of divergence (antigenic drift) from progenitor or previous viruses, and/or vaccine reference strains. Typically, the methodology used involves post-infection antisera from an animal model, usually the ferret. Such antisera are used to compare the reactivity between different virus strains and prototype
or reference viruses. Analysis using animal antisera is supplemented by the analysis of human sera taken post-vaccination. Animal antisera may not always be a good measure of human immunity, in part because the animal antisera are raised to single infections, whereas the profile of antibody in human sera is much more complicated as a result of multiple natural exposures to influenza. Nevertheless, human antisera can highlight strains which have less antibody directed at them, indicative of gaps in immunity.
WHO Full Value of improved Influenza Vaccine Assessment (FVIVA).
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WWW.PATHOLOGYINPRACTICE.COM May 2026
Laboratory tests for assessment of antigenicity. Laboratory tests involve analysis of functional antibodies, otherwise known as neutralising antibodies. In addition to being the major viral antigen target of the immune response, viral HA is also the virus receptor protein which binds to target host cells, required to initiate infection. Antibodies which bind to HA may inhibit virus binding, otherwise known as neutralising viral infectivity. Interruption of this interaction prevents infection and provides immunity. The presence of neutralising antibodies is a correlate of protective immunity. Such functional antibodies are titrated either through virus neutralisation assays, or through a proxy measurement of virus binding. A useful property of influenza viruses is the ability of influenza viruses to bind to red cells, causing a haemagglutination reaction. This is mediated through the viral HA protein. Antibodies which interrupt the ability of influenza viruses to bind red cells, are called haemagglutinin inhibiting (HAI) antibodies. Such antibodies typically bind on the globular surface of HA
Influenze positive specimens
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