Influenza A
Influenza A viruses have segmented genomes consisting of eight negative-sense, single-stranded RNA segments.
Influenza A subtypes are determined by the two viral envelope proteins HA and NA, on segments 4 and 6 respectively. The two main influenza A subtypes circulating in humans are H1N1 and H3N2. The primary host for most influenza A subtypes is birds, but they can also infect other animal species such as pigs and cattle. For the major subtypes, more fine grained clades are also determined based on the HA (and sometimes NA) segments.
The HA protein (on segment 4) is the primary target of neutralizing antibodies, and NA is often used as an antiviral drug target
How We Process Influenza Data
Genspectrum uses all open influenza A data that is available on the INSDC (taxonid: 197911). To classify influenza segments and subtypes we use nextclade sort (using half of all k-mers for each subtype defined in https://github.com/anna-parker/InfluenzaAReferenceDB ) to improve classification). 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: PB2 protein (part of the RNA polymerase subunit).
- Segment 2: PB1 protein (part of the RNA polymerase subunit).
- Segment 3: PA protein (part of the RNA polymerase subunit).
- Segment 4: HA protein (hemagglutinin, part of the envelope, 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, part of the envelope, 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 subtype you can view the CDS of each protein in the genome data viewer.