A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems

BMC Vet Res. 2016 Dec 19;12(1):287. doi: 10.1186/s12917-016-0902-6.

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.

Keywords: 3-peptides LSD repeat insert (LSD+); Deep sequencing; Infectious ecosystem; Subgroup J avian leukosis virus.

MeSH terms

  • Animals
  • Avian Leukosis / virology*
  • Avian Leukosis Virus / genetics*
  • Biological Evolution
  • Cell Line
  • Chickens
  • Ecosystem*
  • Genetic Variation*
  • Molecular Epidemiology
  • Mutation / genetics
  • Poultry Diseases / virology*
  • Specific Pathogen-Free Organisms