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H5N1

Sequencing efforts

Explore sequencing efforts and basic information around all sequences.

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Analyze a single variant

Analyze a single variant regarding to its prevalence over time, relative growth advantage, mutations and many more.

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Compare variants

Compare the prevalence and mutation changes between two variants.

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Compare to baseline

Investigate the prevalence of a variant compared to a baseline variant.

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Compare variants side‑by‑side

Compare two or more variants directly next to each other.

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Browse data

Browse the underlying data in the Loculus database.

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The H5N1 influenza subtype is enzootic in birds and can also infect other animals. Since 2018 the highly pathogenic subtype HPAI A(H5N1) has become the dominant strain in bird populations worldwide and has also caused widespread disease in cattle.

We assign clades based on the AF144305.1 HA segment, as defined in the community dataset: community/moncla-lab/iav-h5/ha/all-clades. For the other segments we use our own custom dataset based the GCF_000864105.1 assembly: genspectrum/flu/h5n1.

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.

Genome Data Viewer

PB2 (seg1)

PB1 (seg2)

PA (seg3)

HA (seg4)

NP (seg5)

NA (seg6)

MP (seg7)

NS (seg8)