Preprint open access publication

Identification and evolution of avian endogenous foamy viruses

bioRxiv, Cold Spring Harbor Laboratory,


DOI:10.1101/707083, Dimensions: pub.1118090545,


Chen, Yicong (1) (2) (3)
Wei, Xiaoman (1) (2) (3)
Zhang, Guojie (4) (5) (6) (7)
Cui, Jie * (2) (3)

* Corresponding author



  1. (1) University of Chinese Academy of Sciences, grid.410726.6
  2. (2) Institut Pasteur of Shanghai, grid.429007.8
  3. (3) Wuhan Institute Of Virology, grid.439104.b
  4. (4) Beijing Genomics Institute, grid.21155.32
  5. (5) Chinese Academy of Sciences, grid.9227.e
  6. (6) Kunming Institute of Zoology, grid.419010.d
  7. (7) University of Copenhagen, grid.5254.6, KU
  8. (8) University of Sydney, grid.1013.3


Abstract A history of long-term co-divergence means that foamy viruses (family Retroviridae ) provide an ideal framework to understanding virus-host evolution over extended time periods. Endogenous foamy viruses (EndFVs) are rare, and to date have only been described in a limited number of mammals, amphibians, reptiles and fish genomes. By screening 414 avian genomes we identified EndFVs in two bird species: the Maguari Stork ( Ciconia maguari ) and the Oriental Stork ( C. boyciana ). Analyses of phylogenetic relationships, genome structures and flanking sequences revealed a single origin of EndFVs in Ciconia species. In addition, the marked incongruence between the virus and host phylogenies suggested that this integration event occurred independently in birds. In sum, by providing evidence that birds can be infected with foamy viruses, we fill the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.


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