title: A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems.
abstract: BACKGROUND
  As a typical retrovirus, the evolution of Avian leukosis virus subgroup J (ALV-J) in different infectious ecosystems is not characterized, what we know is there are a cloud of diverse variants, namely quasispecies with considerable genetic diversity. This study is to explore the selection of infectious ecosystems on dominant variants and their evolutionary dynamics of ALV-J between DF1 cells and specific-pathogen-free (SPF) chickens. High-throughput sequencing platforms provide an approach for detecting quasispecies diversity more fully.
  
  
  RESULTS
  An average of about 20,000 valid reads were obtained from two variable regions of gp85 gene and LTR-U3 region from each sample in different infectious ecosystems. The top 10 dominant variants among ALV-J from chicken plasmas, DF1 cells and liver tumor were completely different from each other. Also there was a difference of shannon entropy and global selection pressure values (ω) in different infectious ecosystems. In the plasmas of two chickens, a large portion of quasispecies contained a 3-peptides "LSD" repeat insertion that was only less than 0.01% in DF1 cell culture supernatants. In parallel studies, the LTR-U3 region of ALV-J from the chicken plasmas demonstrated more variants with mutations in their transcription regulatory elements than those from DF1 cells.
  
  
  CONCLUSIONS
  Our data taken together suggest that the molecular epidemiology based on isolated ALV-J in cell culture may not represent the true evolution of virus in chicken flocks in the field. The biological significance of the "LSD" insert and mutations in LTR-U3 needs to be further studied.
authors.affiliation: College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China.
authors.forename: Fanfeng
authors.initials: F
authors.lastname: Meng
authors.affiliation: College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China.
authors.forename: Xuan
authors.initials: X
authors.lastname: Dong
authors.affiliation: Institute of Pathogen Biology, Taishan Medical College, Taian, Shandong, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Hu
authors.affiliation: College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China.
authors.forename: Shuang
authors.initials: S
authors.lastname: Chang
authors.affiliation: Poultry lnstitute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Fan
authors.affiliation: College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China. zhaopeng@sdau.edu.cn.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhao
authors.affiliation: College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China. zzcui@sdau.edu.cn.
authors.forename: Zhizhong
authors.initials: Z
authors.lastname: Cui
mesh_terms: D000818:Animals; D001353:Avian Leukosis / Q000821:virology*; D001354:Avian Leukosis Virus / Q000235:genetics*; D005075:Biological Evolution; D002460:Cell Line; D002645:Chickens; D017753:Ecosystem; D014644:Genetic Variation; D017720:Molecular Epidemiology; D009154:Mutation / Q000235:genetics; D011201:Poultry Diseases / Q000821:virology*; D013047:Specific Pathogen-Free Organisms
keywords: 3-peptides LSD repeat insert (LSD+); Deep sequencing; Infectious ecosystem; Subgroup J avian leukosis virus