Data from: Reassortment patterns of avian influenza virus internal segments among different subtypes

Background: The segmented RNA genome of avian Influenza viruses (AIV)
allows genetic reassortment between co-infecting viruses, providing an
evolutionary pathway to generate genetic innovation. The genetic diversity
(16 haemagglutinin and 9 neuraminidase subtypes) of AIV indicates an
extensive reservoir of influenza viruses exists in bird populations, but
how frequently subtypes reassort with each other is still unknown. Here we
quantify the reassortment patterns among subtypes in the Eurasian avian
viral pool by reconstructing the ancestral states of the subtypes as
discrete states on time-scaled phylogenies with respect to the internal
protein coding segments. We further analyzed how host species, the
inferred evolutionary rates and the dN/dS ratio varied among segments and
between discrete subtypes, and whether these factors may be associated
with inter-subtype reassortment rate. Results: The general patterns of
reassortment are similar among five internal segments with the exception
of segment 8, encoding the Non-Structural genes, which has a more
divergent phylogeny. However, significant variation in rates between
subtypes was observed. In particular, hemagglutinin-encoding segments of
subtypes H5 to H9 reassort at a lower rate compared to those of H1 to H4,
and Neuraminidase-encoding segments of subtypes N1 and N2 reassort less
frequently than N3 to N9. Both host species and dN/dS ratio were
significantly associated with reassortment rate, while evolutionary rate
was not associated. The dN/dS ratio was negatively correlated with
reassortment rate, as was the number of negatively selected sites for all
segments. Conclusions: These results indicate that overall selective
constraint and host species are both associated with reassortment rate.
These results together identify the wild bird population as the major
source of new reassortants, rather than domestic poultry. The lower
reassortment rates observed for H5N1 and H9N2 may be explained by the
large proportion of strains derived from domestic poultry populations. In
contrast, the higher rates observed in the H1N1, H3N8 and H4N6 subtypes
could be due to their primary origin as infections of wild birds with
multiple low pathogenicity strains in the large avian reservoir.