Identification and evolution of avian endogenous foamy viruses

Yicong Chen; Xiaoman Wei; Guojie Zhang; Edward C Holmes; Jie Cui

doi:10.1093/ve/vez049

Identification and evolution of avian endogenous foamy viruses

Virus Evol. 2019 Nov 25;5(2):vez049. doi: 10.1093/ve/vez049. eCollection 2019 Jul.

Authors

Yicong Chen^{1

2

3}, Xiaoman Wei^{1

2

3}, Guojie Zhang^{4

5

6

7}, Edward C Holmes⁸, Jie Cui^{1

2}

Affiliations

¹ Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
² Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
³ University of Chinese Academy of Sciences, Beijing, China.
⁴ State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
⁵ China National GeneBank, BGI-Shenzhen, Shenzhen, China.
⁶ Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
⁷ Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
⁸ Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.

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 (Ciconia 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.

Keywords: birds; cross-species transmission; endogenous foamy viruses; incongruence.