Homologous Recombination is Very Rare or Absent in Human Influenza A Virus

Resources for the Future, Washington, DC 20036, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544; Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, State College, PA, 16802; Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892. USA; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892. USA

^* To whom correspondence should be addressed. Email: boni{at}rff.org.

	Abstract

To determine the extent of homologous recombination in human influenza A virus we assembled a data set of 13,852 sequences representing all eight segments and of both major circulating subtypes, H3N2 and H1N1. Using an exhaustive search and a nonparametric test for mosaic structure, we identified 315 sequences (2%) in five different RNA segments that, after a multiple comparisons correction, had statistically significant mosaic signals compatible with homologous recombination. Of these, only two contained recombinant regions of sufficient length (>100 nt) that the occurrence of homologous recombination could be verified using phylogenetic methods, with the rest involving very short sequence regions (15–30 nt). Although this secondary analysis revealed patterns of phylogenetic incongruence compatible with the action of recombination, neither candidate recombinant was strongly supported. Given our inability to exclude the occurrence of mixed infection and template switching during amplification, laboratory artifact provides an alternative and likely explanation for the occurrence of phylogenetic incongruence in these two cases. We therefore conclude that, if it occurs at all, homologous recombination plays only a very minor role in the evolution of human influenza A virus.