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SUMMARY:Homologous recombination is very rare or absent in human influenza
  virus. - Maciej Boni\, Oxford University Clinical Research Unit\, Vietnam
DTSTART:20081010T150000Z
DTEND:20081010T160000Z
UID:TALK13907@talks.cam.ac.uk
CONTACT:Olivier Restif
DESCRIPTION:To determine the extent of homologous recombination in human i
 nfluenza A virus\, we assembled a data set of 13\,852 sequences representi
 ng all eight segments and both major circulating subtypes\, H3N2 and H1N1.
 \nUsing an exhaustive search and a nonparametric test for mosaic structure
 \, we identified 315 sequences (about 2%) in five different RNA segments t
 hat\, after a multiple-comparison correction\, had statistically significa
 nt mosaic signals compatible with homologous recombination. Of these\, onl
 y two contained recombinant regions of sufficient length (>100 nucleotides
  [nt]) that the occurrence of homologous recombination could be verified u
 sing phylogenetic methods\, with the rest involving very short sequence re
 gions (15 to 30 nt). Although this secondary analysis revealed patterns of
  phylogenetic incongruence compatible with the action of recombination\, n
 either candidate recombinant was strongly supported. Given our inability t
 o exclude the occurrence of mixed infection and template switching during 
 amplification\, laboratory artifacts provide an alternative and likely exp
 lanation for the occurrence of phylogenetic incongruence in these two case
 s. We therefore conclude that\, if it occurs at all\, homologous recombina
 tion plays only a very minor role in the evolution of human influenza A vi
 rus. 
LOCATION:Meeting room 4\, Centre for Mathematical Sciences
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