The influenza A virus genome comprises eight individual RNP complexes
each with a single-stranded negative-sense RNA segment encoding one or more
proteins. The segmented nature of the viral genome allows it to undergo
reassortment when 2 or more strains co-infect the same cell and this process is
a major contributing factor to the emergence of novel pandemic strains. Despite
this, the factors that govern gene selection during reassortment are not well
understood. Co-infection with A/Puerto Rico/8/34 (PR8, H1N1) and A/Udorn/307/72
(Udorn, H3N2) viruses and selection for the H3N2 surface glycoproteins (HA and
NA) yields progeny virus that also contain Udorn’s polymerase subunit PB1. Using
a competitive transfection model where plasmids encoding the PR8 and Udorn PB1 gene
segments are competed in the presence of plasmids encoding Udorn HA or Udorn NA
and the remaining 6 gene segments of PR8 we showed that the Udorn PB1 gene
segment is preferentially packaged into progeny virions with the Udorn NA gene
segment. Analysis of chimeric PB1 in which the 3’ and 5’ packaging sequences were
swapped between the two parental viruses revealed that the co-selection of NA
and PB1 segments was not directed by these terminal packaging sequences but rather
through interactions involving the internal coding region of the PB1 gene.
Here, we have created additional chimeric PB1 genes to further define the location
within the central coding region in the Udorn PB1 gene that interacts with the
NA gene. This work has identified associations between viral genes that can
direct selection during reassortment and may potentially highlight key regions
involved in RNP-RNP interactions in the supra-molecular complex that is
predicted to form prior to budding to allow one of each segment to be packaged
in the viral progeny.