Victoria
Victoria is only currently circulating influenza B lineage. Until 2020 both B/Yamagata and B/Victoria circled in the population but now only Victoria is circulating.
We use the official nextclade dataset for sequence alignment and HA and NA clade assignment: /nextstrain/flu/vic
How We Process Influenza Data
Genspectrum uses all open influenza B data that is available on the INSDC (taxonid: 11520). To classify influenza segments and lineages we use nextclade sort (using half off all k-mers for each lineage defined in https://github.com/anna-parker/InfluenzaAReferenceDB/blob/main/influenza-b/config/config.yaml). Where available we use the assembly information to group segments that are from the same sample/isolate. For all remaining segments we use a heuristic grouping algorithm to group all segments from the same sample/isolate using the metadata available from each segment.
Protein Functions Explained
- Segment 1: PB1 protein (part of the RNA polymerase subunit).
- Segment 2: PB2 protein (part of the RNA polymerase subunit).
- Segment 3: PA protein (part of the RNA polymerase subunit).
- Segment 4: HA protein (hemagglutinin, functions as an attachment factor and membrane fusion protein. It is responsible for binding influenza to sialic acid on the surface of target cells in the upper respiratory tract.)
- Segment 5: NP protein (nucleoprotein, at start of infection binds with RNA to enter host cell nucleus where it is transcribed and replicated).
- Segment 6: NA protein (Neuraminidase is an enzyme that breaks glycosidic bonds in molecules called neuraminic acids (often found as sialic acids). This helps the new virus particles leave the infected cell and spread to other cells).
- Segment 7: M1 and M2 proteins (M1 forms the capsid - a layer between the nucleoprotein and the envelope, M2 a proton channel protein).
- Segment 8: NS1 and NEP proteins (non-structural protein and nuclear export protein)
For each individual influenza lineage you can view the CDS of each protein in the genome data viewer.