Parapoxvirus species revisited by whole genome sequencing: A retrospective analysis of bovine virus isolates

IF 2.5 4区医学 Q3 VIROLOGY

Virus research Pub Date : 2024-05-25 DOI:10.1016/j.virusres.2024.199404

Graf Alexander , Rziha Hanns-Joachim , Krebs Stefan , Wolf Eckhard , Blum Helmut , Büttner Mathias

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引用次数: 0

Abstract

Parapoxviruses (PPV) of animals are spread worldwide. While the Orf virus (ORFV) species is a molecularly well-characterized prototype pathogen of small ruminants, the genomes of virus species affecting large ruminants, namely Bovine papular stomatitis virus (BPSV) and Pseudocowpox virus (PCPV), are less well known. Using Nanopore sequencing we retrospectively show the whole genome sequences (WGS) of six BPSV, three PCPV isolates and an attenuated ORFV strain, originating from different geographic locations. A phylogenetic tree shows that the de novo assembled genomes belong to PPV species including WGS of reference PPV. Remarkably, Nanopore sequencing allowed the molecular resolution of inverted terminal repeats (ITR) and the hairpin loop within the de novo assembled WGS. Additionally, peculiarities regarding map location of two genes and the heterogeneity of a genomic region were noted. Details for the molecular variability of an interferon response modulatory gene (ORF116) and the PCPV specificity of gene 073.5 are reported. In summary, WGS gained by Nanopore sequencing allowed analysis of complete PPV genomes and confident virus species attribution within a phylogenetic tree avoiding uncertainty of limited gene-based diagnostics. Nanopore-based WGS provides robust comparison of PPV genomes and reliable identity determination of new Poxviruses.

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通过全基因组测序重新审视副痘病毒物种：对牛病毒分离物的回顾性分析。

动物副痘病毒（PPV）遍布全球。奥尔夫病毒（ORFV）是小反刍动物的原型病原体，具有良好的分子特征，而影响大型反刍动物的病毒物种，即牛乳头状口炎病毒（BPSV）和假牛痘病毒（PCPV）的基因组则鲜为人知。利用 Nanopore 测序技术，我们回顾性地展示了源自不同地理位置的六株 BPSV、三株 PCPV 分离物和一株 ORFV 减毒株的全基因组序列（WGS）。系统发生树显示，从头组装的基因组属于 PPV 物种，包括参考 PPV 的 WGS。值得注意的是，通过 Nanopore 测序技术，从分子上解析了从头组装的 WGS 中的倒置末端重复序列（ITR）和发夹环。此外，还发现了两个基因的图谱位置和一个基因组区域的异质性。报告了干扰素反应调节基因（ORF116）的分子变异性和基因 073.5 的 PCPV 特异性。总之，通过 Nanopore 测序获得的 WGS 可以分析完整的 PPV 基因组，并在系统发生树中确定病毒的物种归属，避免了基于基因的有限诊断的不确定性。基于纳米孔的 WGS 可对 PPV 基因组进行稳健的比较，并可靠地确定新痘病毒的身份。

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来源期刊

Virus research 医学-病毒学

CiteScore

9.50

自引率

2.00%

发文量

239

审稿时长

43 days

期刊介绍： Virus Research provides a means of fast publication for original papers on fundamental research in virology. Contributions on new developments concerning virus structure, replication, pathogenesis and evolution are encouraged. These include reports describing virus morphology, the function and antigenic analysis of virus structural components, virus genome structure and expression, analysis on virus replication processes, virus evolution in connection with antiviral interventions, effects of viruses on their host cells, particularly on the immune system, and the pathogenesis of virus infections, including oncogene activation and transduction.