Varanda Carla M R, Machado Marco, Martel Paulo, Nolasco Gustavo, Clara Maria I E, Félix Maria R
Laboratório de Virologia Vegetal, Instituto de Ciências Agrárias e Ambientais Mediterrânicas Universidade de Évora, Évora, Portugal.
Departamento de Ciências Biológicas e Bioengenharia, Faculdade de Ciências e Tecnologia da Universidade do Algarve, Faro, Portugal.
PLoS One. 2014 Oct 28;9(10):e110941. doi: 10.1371/journal.pone.0110941. eCollection 2014.
The genetic variability among 13 isolates of Olive mild mosaic virus (OMMV) and of 11 isolates of Tobacco necrosis virus D (TNV-D) recovered from Olea europaea L. samples from various sites in Portugal, was assessed through the analysis of the coat protein (CP) gene sequences. This gene was amplified through reverse transcriptase polymerase chain reaction (RT-PCR), cloned, and 5 clone sequences of each virus isolate, were analysed and compared, including sequences from OMMV and TNV-D isolates originally recovered from different hosts and countries and available in the GenBank, totalling 131 sequences. The encoded CP sequences consisted of 269 amino acids (aa) in OMMV and 268 in TNV-D. Comparison of the CP genomic and amino acid sequences of the isolates showed a very low variability among OMMV isolates, 0.005 and 0.007, respectively, as well as among TNV-D isolates, 0.006 and 0.008. The maximum nucleotide distances of OMMV and TNV-D sequences within isolates were also low, 0.013 and 0.031, respectively, and close to that found between isolates, 0.018 and 0.034, respectively. In some cases, less variability was found in clone sequences between isolates than in clone sequences within isolates, as also shown through phylogenetic analysis. CP aa sequence identities among OMMV and TNV-D isolates ranged from 84.3% to 85.8%. Comparison between the CP genomic sequences of the two viruses, showed a relatively low variability, 0.199, and a maximum nucleotide distance between isolates of 0.411. Analysis of comparative models of OMMV and TNV-D CPs, showed that naturally occurring substitutions in their respective sequences do not seem to cause significant alterations in the virion structure. This is consistent with a high selective pressure to preserve the structure of viral capsid proteins.
通过分析外壳蛋白（CP）基因序列，评估了从葡萄牙不同地点的油橄榄样本中分离得到的13株油橄榄轻度花叶病毒（OMMV）和11株烟草坏死病毒D（TNV-D）的遗传变异性。该基因通过逆转录聚合酶链反应（RT-PCR）进行扩增、克隆，并对每个病毒分离株的5个克隆序列进行分析和比较，其中包括最初从不同宿主和国家分离得到并保存在GenBank中的OMMV和TNV-D分离株序列，共计131个序列。OMMV编码的CP序列由269个氨基酸（aa）组成，TNV-D由268个氨基酸组成。分离株CP基因组和氨基酸序列的比较显示，OMMV分离株之间的变异性非常低，分别为0.005和0.007，TNV-D分离株之间的变异性也很低，分别为0.006和0.008。分离株内OMMV和TNV-D序列的最大核苷酸距离也很低，分别为0.013和0.031，接近分离株之间的距离，分别为0.018和0.034。在某些情况下，分离株之间的克隆序列变异性低于分离株内的克隆序列变异性，系统发育分析也表明了这一点。OMMV和TNV-D分离株之间CP氨基酸序列同一性在84.3%至85.8%之间。两种病毒CP基因组序列的比较显示变异性相对较低，为0.199，分离株之间的最大核苷酸距离为0.411。对OMMV和TNV-D CP的比较模型分析表明，其各自序列中的自然发生取代似乎不会导致病毒粒子结构的显著改变。这与保留病毒衣壳蛋白结构的高选择压力一致。
