# Human seasonal Influenza A(H3N2) haemagglutination inhibition data 1990-2021 from the WHO Collaborating Centre for Reference and Research on Influenza, London, UK

Data upload associated with research article:
Citation [1]: Harvey WT, Davies V, Daniels RS, Whittaker L, Gregory V, Hay AJ, Husmeier D, McCauley JW and Reeve R (2023). A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses. PLOS Computational Biology. DOI:[10.1371/journal.pcbi.1010885](https://dx.doi.org/10.1371/journal.pcbi.1010885)

This dataset has been extended to include all available seasonal Influenza A(H3N2) haemagglutination inhibition data by the [Worldwide Influenza Centre](https://www.crick.ac.uk/research/platforms-and-facilities/worldwide-influenza-centre), the WHO Collaborating Centre for Reference and Research on Influenza, London, UK.

Additional citation for full dataset [2]: Whittaker L, Gregory V, Harvey WT, Daniels RS, Reeve R, Halai C, Douglas A, Gonsalves R, Skehel JJ, Hay AJ and McCauley JW (2023). Human seasonal Influenza A(H3N2) haemagglutination inhibition data 1990-2021 from the WHO Collaborating Centre for Reference and Research on Influenza, London, UK. doi:[10.5525/gla.researchdata.1405](https://dx.doi.org/10.5525/gla.researchdata.1405)

## WIC-HI-H3N2.csv [1,2]


Haemagglutination inhibition (HI) assays performed on dates between 1990 and 2021 on viruses collected between 1961 and 2021. The dataset includes HI titres measured between 16,213 viruses and antisera raised against 381 reference viruses. It includes 124,434 combinations of virus and reference virus if passage histories are ignored and 129,182 combinations accounting for differences in passage. Data columns are as follows:

- virus: test virus in HI assay.
- reference: reference virus used to raise antisera used in HI assay.
- virus_passage: Information on the passage history (CELL or EGG) of the test virus (where applicable and available). A virus passaged in cells then eggs is denoted CELL|EGG etc.
- virus_passage: Information on the passage history (CELL or EGG) of the reference virus (where applicable and available). A reference virus passaged in cells then eggs is denoted CELL|EGG etc.
- antiserum: The type of post-infection antiserum used (ferret except for a small number of assays were performed with chick antiserum). Assays for which this information is not available (marked NA) can generally be assumed to be post-infection ferret antiserum.
- RBC: The type of red blood cells used in the assay where information is available. In addition to the species (e.g. human, guinea pig, turkey), information on the presence or absence of Oseltamivir is included for some data points. Oseltamivir is an antiviral drug sometimes added to HI assays to prevent neuraminidase-mediated agglutination of red blood cells.
- date: The date on which assays were performed. In earlier years, day and month are often unknown. In such cases, unique identifiers (e.g. '1990-aaa', '1990-aab') that indicate assays carried out on different (but unknown) dates are used.
- titre: HI titre, the reciprocal of the maximum dilution of antisera that inhibited haemagglutinin agglutination. Some titres indicate the test virus was not inhibited by the minimal dilution of antisera tested (e.g. '<40' or just '<' when the minimal dilution used is unknown). 

For further information on the subset of titres used in [1], generating unique identifiers for branches of a phylogenetic tree separating virus and reference virus and models to perform Bayesian statistical analysis, please see the associated [GitHub repository](https://github.com/will-harvey/Flu_g2p_mapping).