Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan.
Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
BMC Bioinformatics. 2019 May 1;20(Suppl 7):192. doi: 10.1186/s12859-019-2736-2.
The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily RESULTS: The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of antigenicity and cross antigenicity. The conserved LEs for Iridoviridae family reflected high antigenicity responses for the two subfamilies, while exclusive LEs reflected high antigenicity responses only for the host-specific subfamily CONCLUSIONS: Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.
虹彩病毒科分为五个属，并聚类为两个亚科：α虹彩病毒亚科包括淋巴囊肿病毒、蛙病毒（GIV）和巨型囊泡病毒（TGIV），它们感染脊椎动物宿主；β虹彩病毒亚科包括虹彩病毒和噬藻体病毒，它们感染无脊椎动物宿主。聚类的虹彩病毒亚科具有宿主特异性特征，可被视为用于疫苗开发的有效表位的计算预测的特有特征。基于投票机制的线性表位（LE）预测系统被应用于识别和支持聚类亚科的 LE 候选者，每个亚科都有最小长度要求。结果：实验结果表明，从虹彩病毒科家族中预测出四个保守表位、一个无脊椎亚科特有的表位和两个脊椎动物家族特有的表位。这些预测的 LE 候选者通过 ELISA 测定进一步验证了它们的抗原性和交叉抗原性强度。虹彩病毒科家族的保守 LE 对两个亚科均表现出较高的抗原反应性，而特有 LE 仅对特定宿主的亚科表现出较高的抗原反应性。结论：宿主特异性特征是有效表位预测的重要特征和限制。我们提出的基于投票机制的系统为疫苗开发前的计算 LE 预测提供了一种新方法，对于分析两个聚类群之间具有特有特征的抗原序列尤其有效。
