On the origin of the gene coding for an influenze A virus nucleocapsid protein

Homologous recombination in negative sense RNA viruses

Recombination is an important process that influences biological evolution at many different levels. More and more homologous recombination events have been reported among negative sense RNA viruses recently. While sporadic authentic examples indicate that homologous recombination does occur, recombination seems to be generally rare or even absent in most negative sense RNA viruses, and most of the homologous recombination events reported in the literature were likely generated artificially due to lab contamination or inappropriate bioinformatics methods. Homologous recombination in negative sense RNA viruses should be reported with caution in the future, and only after stringent quality control efforts. Moreover, co-infection experiments should be performed to confirm whether recombination can occur.

Genetics of influenza viruses

Influenza A viruses contain genomes composed of eight separate segments of negative-sense RNA. Circulating human strains are notorious for their tendency to accumulate mutations from one year to the next and cause recurrent epidemics. However, the segmented nature of the genome also allows for the exchange of entire genes between different viral strains. The ability to manipulate influenza gene segments in various combinations in the laboratory has contributed to its being one of the best characterized viruses, and studies on influenza have provided key contributions toward the understanding of various aspects of virology in general. However, the genetic plasticity of influenza viruses also has serious potential implications regarding vaccine design, pathogenicity, and the capacity for novel viruses to emerge from natural reservoirs and cause global pandemics.

Sequence similarities and evolutionary relationships of influenza virus A hemagglutinins

This study brings the analysis of amino acid sequences of hemagglutinin (HA) from the influenza virus A that can infect a wide variety of birds and mammals. 191 sequences belonging to all known 15 HA subtypes were compared. The emphasis was given on functional sites (receptor-binding cavity with its right and left edges) and degree of their conservation in each subtype. Three evolutionary trees of 15 avian HA representatives were constructed: one tree based on the alignment of the entire HA sequences and two trees based on the alignment of HA1 and HA2 chains, respectively. The results have shown that, despite low degree of sequence similarity among the 191 sequences of HA1 subunit, the active site is well conserved, and that there are only marginal differences in the clustering of the individual HA subtypes between the two subunit trees. In this respect, the subtype H9 seems to be the most fluctuating example. The proposals of the probable avian HAs that could be the closest relatives to human (mammalian) HAs were also provided for several HA subtypes.