A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems
文献类型: 外文期刊
第一作者: Meng, Fanfeng
作者: Meng, Fanfeng;Dong, Xuan;Chang, Shuang;Zhao, Peng;Cui, Zhizhong;Hu, Tao;Fan, Jianhua
作者机构:
关键词: Subgroup J avian leukosis virus;Infectious ecosystem;3-peptides LSD repeat insert (LSD+);Deep sequencing
期刊名称:BMC VETERINARY RESEARCH ( 影响因子:2.741; 五年影响因子:2.955 )
ISSN: 1746-6148
年卷期: 2016 年 12 卷
页码:
收录情况: SCI
摘要: 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 (omega) 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.
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