In Vivo Generation of BK and JC Polyomavirus Defective Viral Genomes in Human Urine Samples Associated with Higher Viral Loads.
In Vivo Generation of BK and JC Polyomavirus Defective Viral Genomes in Human Urine Samples Associated with Higher Viral Loads.
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DOI：
10.1128/jvi.00250-21
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发表时间：
2021-05-24
影响因子：
5.4
通讯作者：
Greninger AL
中科院分区：
文献类型：
--
作者：
Addetia A;Phung Q;Bradley BT;Lin MJ;Zhu H;Xie H;Huang ML;Greninger AL
有缺陷的病毒基因组 (DVG) 是含有可能干扰复制的点突变、缺失或重复的寄生病毒序列。 DVG 通常与培养系统中高感染复数时的病毒传代有关，但在临床标本中的报道也越来越多。然而迄今为止，只有 RNA 病毒被证明在临床标本中含有 DVG。在这里，我们使用多种文库制备策略的直接深度测序以及对免疫抑制个体的尿液样本进行验证性数字液滴 PCR (ddPCR)，表明临床 BK 多瘤病毒 (BKPyV) 和 JC 多瘤病毒 (JCPyV) 毒株在多个位点上存在广泛的基因组重排，这些重排可能会干扰病毒复制。 BKPyV DVG 源自 BKPyV 基因型 Ia、Ib-1 和 Ic。 DVG 的存在与含有较高病毒载量的样本相关，但从未达到克隆性，这与寄生复制模型一致。这些 DVG 在临床感染期间持续存在，从同一个人采集的两对含有 BK 病毒的样本（相隔长达 302 天）即可证明这一点。在一个单独的个体中，我们观察到病毒载量增加 57.5 倍后 DVG 的产生。总之，通过将临床标本中 DVG 的存在扩展到 DNA 病毒，我们证明了 DVG 在临床病毒学中的普遍存在。重要性 缺陷病毒基因组 (DVG) 会对传染性病毒颗粒的产生产生重大影响。仅在以高感染复数传代的培养病毒和从临床标本中收集的 RNA 病毒中发现了 DVG；野生 DNA 病毒尚未被证明含有 DVG。在这里，我们在临床尿液标本中鉴定出了 BK 和 JC 多瘤病毒 DVG，并证明这些 DVG 在病毒载量较高的样本中更常见。含有 DVG 的菌株的整个基因组发生了重排，其中大多数影响了病毒复制所需的基因。纵向分析表明，这些 DVG 可以在感染期间持续存在，但不会在慢性感染宿主体内达到克隆性。我们对多瘤病毒 DVG 的鉴定表明，这些寄生序列存在于能够引起人类疾病的许多类别的病毒中。
Defective viral genomes (DVGs) are parasitic viral sequences containing point mutations, deletions, or duplications that might interfere with replication. DVGs are often associated with viral passage at high multiplicities of infection in culture systems but have been increasingly reported in clinical specimens. To date however, only RNA viruses have been shown to contain DVGs in clinical specimens. Here, using direct deep sequencing with multiple library preparation strategies and confirmatory digital droplet PCR (ddPCR) of urine samples taken from immunosuppressed individuals, we show that clinical BK polyomavirus (BKPyV) and JC polyomavirus (JCPyV) strains contain widespread genomic rearrangements across multiple loci that likely interfere with viral replication. BKPyV DVGs were derived from BKPyV genotypes Ia, Ib-1, and Ic. The presence of DVGs was associated with specimens containing higher viral loads but never reached clonality, consistent with a model of parasitized replication. These DVGs persisted during clinical infection as evidenced in two separate pairs of samples containing BK virus collected from the same individual up to 302 days apart. In a separate individual, we observed the generation of DVGs after a 57.5-fold increase in viral load. In summary, by extending the presence of DVGs in clinical specimens to DNA viruses, we demonstrate the ubiquity of DVGs in clinical virology. IMPORTANCE Defective viral genomes (DVGs) can have a significant impact on the production of infectious virus particles. DVGs have only been identified in cultured viruses passaged at high multiplicities of infection and RNA viruses collected from clinical specimens; no DNA virus in the wild has been shown to contain DVGs. Here, we identified BK and JC polyomavirus DVGs in clinical urine specimens and demonstrated that these DVGs are more frequently identified in samples with higher viral loads. The strains containing DVGs had rearrangements throughout their genomes, with the majority affecting genes required for viral replication. Longitudinal analysis showed that these DVGs can persist during an infection but do not reach clonality within the chronically infected host. Our identification of polyomavirus DVGs suggests that these parasitic sequences exist across the many classes of viruses capable of causing human disease.