Mammalian orthoreoviruses exhibit rare genotype variability in genome constellations.
Mammalian orthoreoviruses exhibit rare genotype variability in genome constellations.
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DOI：
10.1016/j.meegid.2023.105421
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发表时间：
2023-06
影响因子：
3.2
通讯作者：
Ogden, Kristen M.
中科院分区：
文献类型：
--
作者：
Diller, Julia R.;Thoner Jr, Timothy W.;Ogden, Kristen M.
哺乳动物正呼肠孤病毒（呼肠孤病毒）目前基于附着蛋白σ 1的性质进行分类。已经鉴定了四种呼肠孤病毒血清型，其中三种由充分研究的原型人呼肠孤病毒株代表。呼肠孤病毒含有10个双链RNA片段，编码12种蛋白质，并在共同感染期间可以重新排列。为了了解呼肠孤病毒遗传多样性的广度及其对重配的潜在影响，应该考虑整个基因组的序列。虽然对原型毒株有很多了解，但以前没有对所有十种呼肠孤病毒基因组片段序列进行过彻底分析。我们分析了60多个完整或接近完整的呼肠孤病毒基因组序列的10个片段中的每一个的系统发育关系和核苷酸序列保守性，包括原型菌株。使用这些关系，我们定义了每个片段的基因型，对于包含几个代表性序列的大多数基因型，最小核苷酸同一性为77 - 88%。我们应用片段基因型来确定呼肠孤病毒基因组星座，我们建议实施一个更新的呼肠孤病毒基因组分类系统，将每个片段的基因型信息。对于大多数测序的呼肠孤病毒，编码σ 1的S1以外的片段聚类为少量基因型和有限的基因组星座阵列，这些基因组星座随时间或基于动物宿主没有很大差异。然而，少数呼肠孤病毒，包括原型菌株琼斯，具有其中片段基因型不同于大多数其他测序的呼肠孤病毒的片段基因型的星座。对于这些呼肠孤病毒，几乎没有证据表明与主要基因型重配。未来的基础研究集中在最具遗传差异的呼肠孤病毒上，可能会为呼肠孤病毒生物学提供新的见解。可用的部分序列和额外的完整呼肠孤病毒基因组测序的分析也可以揭示基于呼肠孤病毒基因型的重配偏倚、宿主偏好或感染结果。
Mammalian orthoreoviruses (reoviruses) are currently classified based on properties of the attachment protein, σ1. Four reovirus serotypes have been identified, three of which are represented by well-studied prototype human reovirus strains. Reoviruses contain ten segments of double-stranded RNA that encode 12 proteins and can reassort during coinfection. To understand the breadth of reovirus genetic diversity and its potential influence on reassortment, the sequence of the entire genome should be considered. While much is known about the prototype strains, a thorough analysis of all ten reovirus genome segment sequences has not previously been conducted. We analyzed phylogenetic relationships and nucleotide sequence conservation for each of the ten segments of more than 60 complete or nearly complete reovirus genome sequences, including those of the prototype strains. Using these relationships, we defined genotypes for each segment, with minimum nucleotide identities of 77–88% for most genotypes that contain several representative sequences. We applied segment genotypes to determine reovirus genome constellations, and we propose implementation of an updated reovirus genome classification system that incorporates genotype information for each segment. For most sequenced reoviruses, segments other than S1, which encodes σ1, cluster into a small number of genotypes and a limited array of genome constellations that do not differ greatly over time or based on animal host. However, a small number of reoviruses, including prototype strain Jones, have constellations in which segment genotypes differ from those of most other sequenced reoviruses. For these reoviruses, there is little evidence of reassortment with the major genotype. Future basic research studies that focus on the most genetically divergent reoviruses may provide new insights into reovirus biology. Analysis of available partial sequences and additional complete reovirus genome sequencing may also reveal reassortment biases, host preferences, or infection outcomes that are based on reovirus genotype.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
5.4
作者：
DERMODY, TS;NIBERT, ML;FIELDS, BN
通讯作者：
FIELDS, BN
DOI：
10.1006/bbrc.2001.5612
发表时间：
2001-09-21
影响因子：
3.1
作者：
Attoui, H;Biagini, P;de Lamballerie, X
通讯作者：
de Lamballerie, X
影响因子：
3.1
作者：
He, C;Pang, WY;Duan, Q
通讯作者：
Duan, Q
影响因子：
3.8
作者：
Anbalagan, Srivishnupriya;Cooper, Elyse;Hause, Ben M.
通讯作者：
Hause, Ben M.