A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems.
A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems.
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深度测序揭示了两个传染性生态系统中禽白血病病毒的显着变异和进化动态
DOI：
10.1186/s12917-016-0902-6
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发表时间：
2016-12-19
影响因子：
2.6
通讯作者：
Cui Z
中科院分区：
文献类型：
--
作者：
Meng F;Dong X;Hu T;Chang S;Fan J;Zhao P;Cui Z
研究背景作为一种典型的逆转录病毒，J亚群禽白血病病毒（Avian leukosis virus subgroup J，ALV-J）在不同的感染生态系统中的进化并不完全一致，而是存在大量的变异株，即具有相当遗传多样性的准种。本研究旨在探讨J型ALV-J在DF 1细胞和SPF鸡间的感染生态系统对优势变异株的选择及其进化动态。高通量测序平台为更全面地检测准种多样性提供了一种方法。结果从不同感染生态系统的每个样本中获得的gp 85基因和LTR-U3区的两个可变区平均约20，000个有效读段。鸡血浆、DF 1细胞和肝肿瘤ALV-J的前10位优势变异株完全不同。不同感染生态系统的Shannon熵和整体选择压力值（ω）也存在差异。在两只鸡的血浆中，大部分准种含有3-肽“LSD”重复插入，其在DF 1细胞培养上清液中仅小于0.01%。在平行的研究中，theLTR-U3区的ALV-J从鸡血浆中表现出更多的变异，其转录调控元件的突变比那些从DF 1 cells.ConclusionsOur数据一起表明，分子流行病学的基础上分离的ALV-J在细胞培养可能不代表病毒在鸡群在该领域的真实演变。LTR-U3中“LSD”插入和突变的生物学意义有待进一步研究。
BackgroundAs 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.ResultsAn average of about 20,000 valid reads were obtained from two variable regions ofgp85gene andLTR-U3region 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, theLTR-U3region of ALV-J from the chicken plasmas demonstrated more variants with mutations in their transcription regulatory elements than those from DF1 cells.ConclusionsOur 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 inLTR-U3needs to be further studied.
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