I aligned my influenza virus sequence using NCBI BLAST. Some segments belong to H9 strains, while others are more similar to H5 and H7. Indeed, the results indicate similarity of PB1, for example, with certain H9, H5, and H7 sequences. How can I ensure that the names of the sub-genotypes available in NCBI have been submitted correctly?
Influenza viruses have 8 gene segments each. The serotype is based on hemagglutinin and neuraminidase genes (H1N1, H5N1, H3N2, etc) but the segments re-assort quite often.
The Influenza A serotypes that circulate in humans are less diverse than those that circulate in wild birds. For example, we don't see many H7 viruses in humans, we see more H3N2 and a few other prominent lineages in humans.
I downloaded over 5,000 PB1 gene segments from H7 Influenza A from GISAID database and aligned them and built a phylogenetic tree. Then I colored H7N2 orange, H7N3 blue, and H7N3 green leaving the rest black to make the attached figures. In Fig 1 you see a lineage of PB1 segments that seem to get around into various N virus serotypes (remember these are all H7 to begin with). While in Fig 2 you see a lineage of PB1 that has been associated almost exclusively with the N9 serotype.
Thank you Brian Thomas Foley for your invaluable response. I appreciate it a lot.
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