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Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae. 新西兰蝙蝠的病毒组分析揭示了冠状病毒科之间的跨物种病毒传播。
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2024-01-27 eCollection Date: 2024-01-01 DOI: 10.1093/ve/veae008
Stephanie J Waller, Pablo Tortosa, Tertia Thurley, Colin F J O'Donnell, Rebecca Jackson, Gillian Dennis, Rebecca M Grimwood, Edward C Holmes, Kate McInnes, Jemma L Geoghegan

The lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus) are Aotearoa New Zealand's only native extant terrestrial mammals and are believed to have migrated from Australia. Long-tailed bats arrived in New Zealand an estimated two million years ago and are closely related to other Australian bat species. Lesser short-tailed bats, in contrast, are the only extant species within the Mystacinidae and are estimated to have been living in isolation in New Zealand for the past 16-18 million years. Throughout this period of isolation, lesser short-tailed bats have become one of the most terrestrial bats in the world. Through a metatranscriptomic analysis of guano samples from eight locations across New Zealand, we aimed to characterise the viromes of New Zealand's bats and determine whether viruses have jumped between these species over the past two million years. High viral richness was observed among long-tailed bats with viruses spanning seven different viral families. In contrast, no bat-specific viruses were identified in lesser short-tailed bats. Both bat species harboured an abundance of likely dietary- and environment-associated viruses. We also identified alphacoronaviruses in long-tailed bat guano that had previously been identified in lesser short-tailed bats, suggesting that these viruses had jumped the species barrier after long-tailed bats migrated to New Zealand. Of note, an alphacoronavirus species discovered here possessed a complete genome of only 22,416 nucleotides with entire deletions or truncations of several non-structural proteins, thereby representing what may be the shortest genome within the Coronaviridae identified to date. Overall, this study has revealed a diverse range of novel viruses harboured by New Zealand's only native terrestrial mammals, in turn expanding our understanding of bat viral dynamics and evolution globally.

小短尾蝙蝠(Mystacina tuberculata)和长尾蝙蝠(Chalinolobus tuberculatus)是新西兰奥特亚罗瓦现存的唯一本土陆生哺乳动物,据信是从澳大利亚迁徙而来。据估计,长尾蝙蝠是在 200 万年前到达新西兰的,与澳大利亚的其他蝙蝠物种亲缘关系密切。相比之下,小短尾蝙蝠是蝙蝠科(Mystacinidae)中唯一现存的物种,据估计,在过去的 1600 万到 1800 万年间,它们一直与世隔绝地生活在新西兰。在这段与世隔绝的岁月里,小短尾蝙蝠已成为世界上最陆生的蝙蝠之一。通过对新西兰八个地方的鸟粪样本进行元转录本组分析,我们旨在描述新西兰蝙蝠病毒组的特征,并确定在过去的两百万年里,病毒是否在这些物种之间发生了跳跃。在长尾蝙蝠中观察到了丰富的病毒,病毒跨越了七个不同的病毒科。相比之下,在小短尾蝠中没有发现蝙蝠特有的病毒。这两种蝙蝠都携带大量可能与食物和环境相关的病毒。我们还在长尾蝙蝠的鸟粪中发现了以前在小短尾蝙蝠中发现的阿尔法短尾蝙蝠病毒,这表明这些病毒在长尾蝙蝠迁徙到新西兰后跨越了物种屏障。值得注意的是,这里发现的一种α-冠状病毒的完整基因组只有22,416个核苷酸,其中有几种非结构蛋白被整个缺失或截断,因此可能是迄今为止发现的冠状病毒科中基因组最短的病毒。总之,这项研究揭示了新西兰唯一的本土陆生哺乳动物所携带的多种新型病毒,从而扩大了我们对全球蝙蝠病毒动态和进化的了解。
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引用次数: 0
The untapped potential of phage model systems as therapeutic agents 噬菌体模型系统作为治疗剂的潜力尚待开发
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2024-01-16 DOI: 10.1093/ve/veae007
Jordan Romeyer Dherbey, Frederic Bertels
With the emergence of widespread antibiotic resistance, phages are an appealing alternative to antibiotics in the fight against multidrug-resistant bacteria. Over the past few years, many phages have been isolated from various environments to treat bacterial pathogens. While isolating novel phages for treatment has had some success for compassionate use, developing novel phages into a general therapeutic will require considerable time and financial resource investments. These investments may be less significant for well-established phage model systems. The knowledge acquired from decades of research on their structure, life cycle, and evolution ensures safe application and efficient handling. However, one major downside of established phage model systems is their inability to infect pathogenic bacteria. This problem is not insurmountable, phage host range can be extended through genetic engineering or evolution experiments. In the future, breeding model phages to infect pathogens could provide a new avenue to develop phage therapeutic agents.
随着抗生素耐药性的广泛出现,噬菌体成为抗生素的一种有吸引力的替代品,可用于对抗具有多重耐药性的细菌。在过去几年中,人们从各种环境中分离出许多噬菌体来治疗细菌病原体。虽然分离出新型噬菌体用于治疗在同情性使用方面取得了一些成功,但将新型噬菌体开发成通用疗法需要投入大量的时间和财力。对于成熟的噬菌体模型系统来说,这些投资可能不那么重要。通过数十年对噬菌体结构、生命周期和进化的研究而获得的知识可确保安全应用和高效处理。不过,成熟的噬菌体模型系统的一个主要缺点是无法感染病原菌。这个问题并非无法解决,噬菌体的宿主范围可以通过基因工程或进化实验来扩大。未来,培育能感染病原体的模式噬菌体将为开发噬菌体治疗药物提供新的途径。
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引用次数: 0
Conserved Untranslated Regions of Multipartite Viruses: Natural Markers of Novel Viral Genomic Components and Tags of Viral Evolution 多分化病毒的保守非翻译区:新型病毒基因组成分的天然标记和病毒进化的标签
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2024-01-13 DOI: 10.1093/ve/veae004
Song Zhang, Caixia Yang, Yuanjian Qiu, Ruiling Liao, Zhiyou Xuan, Fang Ren, Yafeng Dong, Xiaoying Xie, Yanhong Han, Di Wu, Pedro Luis Ramos-González, Juliana Freitas-Astúa, Huadong Yang, Changyong Zhou, Mengji Cao
Viruses with split genomes are classified as being either segmented or multipartite based on whether their genomic segments occur within a single virion or across different virions. Despite variations in number and sequence during evolution, the genomic segments of many viruses are conserved within the untranslated regions (UTRs). In this study, we present a methodology that combines RNA sequencing with iterative BLASTn of UTRs (UTR-iBLASTn) (https://github.com/qq371260/Iterative-blast-v.1.0) to identify new viral genomic segments. Some novel multipartite-like viruses related to the phylum Kitrinoviricota were annotated using sequencing data from field plant samples and public databases. We identified potentially plant-infecting jingmen-related viruses (order Amarillovirales) and jivi-related viruses (order Martellivirales) with at least six genomic components. The number of RNA molecules associated with a genome of the novel viruses in the families Closteroviridae, Kitaviridae, and Virgaviridae within the order Martellivirales reached five. Several of these viruses seem to represent new taxa at the subgenus, genus, and family levels. The diversity of novel genomic components and the multiple duplication of proteins or protein domains within single or multiple genomic components emphasize the evolutionary roles of reassortment and recombination (horizontal gene transfer), and genetic deletion. The relatively conserved UTRs at the genome level might explain the relationships between monopartite and multipartite viruses, as well as how subviral agents such as defective RNAs and satellite viruses can coexist with their helper viruses.
根据病毒的基因组片段是出现在单个病毒体中还是跨不同病毒体,具有分裂基因组的病毒被分为片段病毒和多片段病毒。尽管在进化过程中基因组片段的数量和序列发生了变化,但许多病毒的基因组片段在非翻译区(UTR)内是保守的。在这项研究中,我们提出了一种将 RNA 测序与 UTRs 的迭代 BLASTn(UTR-iBLASTn)(https://github.com/qq371260/Iterative-blast-v.1.0)相结合来识别新病毒基因组片段的方法。我们利用田间植物样本和公共数据库中的测序数据,对一些与Kitrinoviricota门相关的新型多位点类病毒进行了注释。我们发现了可能感染植物的荆门相关病毒(Amarillovirales目)和麻风相关病毒(Martellivirales目),它们至少有六个基因组片段。在Martellivirales目中的Closteroviridae科、Kitaviridae科和Virgaviridae科的新型病毒中,与一个基因组相关的RNA分子数量达到了5个。其中一些病毒似乎代表了亚属、属和科一级的新类群。新基因组成分的多样性以及单个或多个基因组成分中蛋白质或蛋白质结构域的多重复制,强调了重配和重组(水平基因转移)以及基因缺失在进化中的作用。基因组水平上相对保守的 UTR 可解释单分化病毒和多分化病毒之间的关系,以及缺陷 RNA 和卫星病毒等亚病毒介质如何与其辅助病毒共存。
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引用次数: 0
Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago 马疱疹病毒 4 感染了大约 4000 年前与辛塔什塔辐轮战车有关的家马
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2024-01-13 DOI: 10.1093/ve/vead087
Ophélie Lebrasseur, Kuldeep Dilip More, Ludovic Orlando
Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century, and continue to be of major concern to the horse industry today. With a seroprevalence of 60-80%, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological horse remains to detect the presence of EHV-4. We recover the first ancient EHV-4 genome with 4.2X average depth-of-coverage from a specimen excavated in the Southeastern Urals and dated to the Early Bronze Age period, approximately 3,900 years ago. The recovery of an EHV-4 virus outside of the upper respiratory tract not only points to an animal particularly infected, but also highlights the importance of post-cranial bones in pathogen characterisation. Bayesian phylogenetic reconstruction provides a minimal time estimate for EHV-4 diversification to around 4,000 years ago, a time when modern domestic horses spread across the Central Asian steppes together with spoke-wheeled Sintashta chariots, or earlier. The analyses also considerably revise the diversification time of the two EHV-4 subclades from the 16th century based solely on modern data to nearly a thousand years ago. Our study paves the way for a robust reconstruction of the history of non-human pathogens and their impact on animal health.
直到 19 世纪末,马病毒爆发一直扰乱着过去人类社会的社会经济生活,如今仍是马业关注的焦点。马疱疹病毒 4(EHV-4)的血清阳性率高达 60-80%,是全球最常见的马病原体。然而,对其进化史的研究仍然不足。在这里,我们筛选了 264 具考古马遗骸的测序数据,以检测 EHV-4 的存在。我们从出土于乌拉尔东南部、年代为青铜时代早期(距今约 3900 年)的一具标本中,首次发现了平均覆盖深度为 4.2 倍的古代 EHV-4 基因组。在上呼吸道之外发现的 EHV-4 病毒不仅表明该动物受到了特别的感染,而且突出了颅骨后骨骼在病原体特征描述中的重要性。贝叶斯系统发育重建提供了 EHV-4 多样化的最小时间估计,即大约 4000 年前,现代家马与带轮辐的辛塔什塔战车一起在中亚草原上传播的时间,或者更早。这些分析还大大修正了两个 EHV-4 亚支系的分化时间,即从 16 世纪仅根据现代数据分化到近千年前。我们的研究为重建非人类病原体的历史及其对动物健康的影响铺平了道路。
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引用次数: 0
SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method 使用系统进化定位/UShER 进行 SARS-CoV-2 世系分配优于 pangoLEARN 机器学习方法
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2024-01-13 DOI: 10.1093/ve/vead085
Adriano de Bernardi Schneider, Michelle Su, Angie S Hinrichs, Jade Wang, Helly Amin, John Bell, Debra A Wadford, Áine O’Toole, Emily Scher, Marc D Perry, Yatish Turakhia, Nicola De Maio, Scott Hughes, Russ Corbett-Detig
With the rapid spread and evolution of SARS-CoV-2, the ability to monitor its transmission and distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software for the lineage assignment of newly isolated SARS-CoV-2 genomes is pangolin, which offers two methods of assignment, pangoLEARN and pUShER. PangoLEARN rapidly assigns lineages using a machine learning algorithm, while pUShER performs a phylogenetic placement to identify the lineage corresponding to a newly sequenced genome. In a preliminary study, we observed that pangoLEARN (decision tree model), while substantially faster than pUShER, offered less consistency across different versions of pangolin v3. Here, we expand upon this analysis to include v3 and v4 of pangolin, which moved the default algorithm for lineage assignment from pangoLEARN in v3 to pUShER in v4, and perform a thorough analysis confirming that pUShER is not only more stable across versions but also more accurate. Our findings suggest that future lineage assignment algorithms for various pathogens should consider the value of phylogenetic placement.
随着 SARS-CoV-2 的快速传播和进化,监测其传播和区分病毒系谱的能力对于大流行病应对工作至关重要。对新分离到的 SARS-CoV-2 基因组进行系谱分配的最常用软件是 pangolin,它提供两种分配方法:pangoLEARN 和 pUShER。PangoLEARN 使用机器学习算法快速分配世系,而 pUShER 则进行系统发育排序,以确定与新测序基因组相对应的世系。在一项初步研究中,我们发现 pangoLEARN(决策树模型)虽然比 pUShER 快得多,但在不同版本的 pangolin v3 中的一致性较差。 在此,我们将这一分析扩展到 pangolin v3 和 v4,在 v4 中将世系分配的默认算法从 v3 中的 pangoLEARN 改为 pUShER,并进行了全面分析,证实 pUShER 在不同版本中不仅更稳定,而且更准确。我们的研究结果表明,未来针对各种病原体的世系分配算法应考虑系统发生学位置的价值。
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引用次数: 0
Human immunodeficiency virus (HIV) dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte (CTL) escape mutants 次级淋巴组织中人体免疫缺陷病毒(HIV)的动态变化和细胞毒性 T 淋巴细胞(CTL)逃逸突变体的进化
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2024-01-13 DOI: 10.1093/ve/vead084
Wen-Jian Chung, Elizabeth Connick, Dominik Wodarz
In the secondary lymphoid tissues, human immunodeficiency virus (HIV) can replicate both in the follicular and the extrafollicular compartments. Yet, virus is concentrated in the follicular compartment in the absence of antiretroviral therapy, in part due to the lack of cytotoxic T lymphocyte (CTL)-mediated activity there. CTL home to the extrafollicular compartment, where they can suppress virus load to relatively low levels. We use mathematical models to show that this compartmentalization can explain seemingly counterintuitive observations. First, it can explain the observed constancy of the viral decline slope during antiviral therapy in the peripheral blood, irrespective of the presence of CTL in SIV-infected macaques, under the assumption that CTL-mediated lysis significantly contributes to virus suppression. Second, it can account for the relatively long times it takes for CTL escape mutants to emerge during chronic infection even if CTL-mediated lysis is responsible for virus suppression. The reason is the heterogeneity in CTL activity, and the consequent heterogeneity in selection pressure between the follicular and extrafollicular compartments. Hence, to understand HIV dynamics more thoroughly, this analysis highlights the importance of measuring virus populations separately in the extrafollicular and follicular compartments rather than using virus load in peripheral blood as an observable; this hides the heterogeneity between compartments that might be responsible for the particular patterns seen in the dynamics and evolution of the HIV in vivo.
在次级淋巴组织中,人类免疫缺陷病毒(HIV)可以在滤泡和滤泡外区域复制。然而,在没有抗逆转录病毒疗法的情况下,病毒会集中在滤泡区,部分原因是滤泡区缺乏细胞毒性 T 淋巴细胞(CTL)介导的活性。细胞毒性 T 淋巴细胞(CTL)会回到滤泡外区,在那里它们可以将病毒载量抑制到相对较低的水平。我们利用数学模型证明,这种区隔可以解释看似违背直觉的观察结果。首先,它可以解释在外周血抗病毒治疗过程中观察到的病毒下降斜率的恒定性,无论 SIV 感染猕猴体内是否存在 CTL,假设 CTL 介导的裂解对病毒抑制有显著作用。其次,即使 CTL 介导的裂解对病毒抑制起作用,它也能解释为什么在慢性感染过程中 CTL 逃逸突变体的出现需要相对较长的时间。原因在于 CTL 活性的异质性,以及随之而来的滤泡和滤泡外区之间选择压力的异质性。因此,为了更透彻地了解 HIV 的动态变化,这项分析强调了分别测量滤泡外和滤泡内病毒数量的重要性,而不是将外周血中的病毒载量作为观测指标;这样做掩盖了滤泡外和滤泡内病毒数量之间的异质性,而这种异质性可能是造成体内 HIV 动态变化和演化的特殊模式的原因。
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引用次数: 0
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection 在仓鼠 SARS-CoV-2 感染模型中使用致突变药物的有效剂量和次优剂量的遗传后果
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2024-01-05 DOI: 10.1093/ve/veae001
Christopher J. R Illingworth, Jose A Guerra-Assuncao, Samuel Gregg, Oscar Charles, Juanita Pang, Sunando Roy, Rana Abdelnabi, Johan Neyts, Judith Breuer
Mutagenic antiviral drugs have shown promise against multiple viruses, but concerns have been raised about whether their use might promote the emergence of new and harmful viral variants. Recently, genetic signatures associated with molnupiravir use have been identified in the global SARS-COV-2 population. Here, we examine the consequences of using favipiravir and molnupiravir to treat SARS-CoV-2 infection in a hamster model, comparing viral genome sequence data collected from (i) untreated hamsters, and (ii) from hamsters receiving effective and suboptimal doses of treatment. We identify a broadly linear relationship between drug dose and the extent of variation in treated viral populations, with a high proportion of this variation being composed of variants at frequencies of less than one per cent, below typical thresholds for variant calling. Treatment with an effective dose of antiviral drug was associated with a gain of between 7 and 10 variants per viral genome relative to drug-free controls: Even after a short period of treatment a population founded by a transmitted virus could contain multiple sequence differences to that of the original host. Treatment with a suboptimal dose of drug showed intermediate gains of variants. No dose-dependent signal was identified in the numbers of single nucleotide variants reaching frequencies in excess of 5%. We did not find evidence to support the emergence of drug resistance or of novel immune phenotypes. Our study suggests that where onward transmission occurs, a short period of treatment with mutagenic drugs may be sufficient to generate a significant increase in the number of viral variants transmitted.
突变性抗病毒药物对多种病毒都有很好的疗效,但也有人担心使用这些药物是否会促进新的有害病毒变种的出现。最近,在全球 SARS-COV-2 群体中发现了与使用莫仑吡韦相关的基因特征。在这里,我们研究了在仓鼠模型中使用法非吡韦和莫仑吡韦治疗 SARS-CoV-2 感染的后果,比较了从(i)未接受治疗的仓鼠和(ii)接受有效和次优剂量治疗的仓鼠收集的病毒基因组序列数据。我们发现药物剂量与治疗后病毒群体的变异程度之间存在广泛的线性关系,其中很大一部分变异是由频率低于百分之一的变异组成的,低于变异调用的典型阈值。与无药对照组相比,使用有效剂量的抗病毒药物治疗会使每个病毒基因组增加 7 到 10 个变体:即使经过短期治疗,由传播病毒建立的群体也可能包含与原宿主不同的多个序列。使用次优剂量的药物治疗显示出中等程度的变体增加。在频率超过 5%的单核苷酸变体数量中,没有发现与剂量相关的信号。我们没有发现支持出现耐药性或新型免疫表型的证据。我们的研究表明,在发生向后传播的情况下,短时间的诱变药物治疗可能足以使传播的病毒变体数量显著增加。
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引用次数: 0
Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage 全基因组范围支持单一啮齿动物宿主系中的图拉汉坦病毒新物种
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2024-01-04 DOI: 10.1093/ve/veae002
Anton Labutin, Gerald Heckel
Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host-shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from 42 locations in the contact region between clades for TULV infection by RT-PCR. Sequencing yielded 23 TULV Central North and 21 TULV Central South genomes which differed by 14.9-18.5% at the nucleotide and 2.2-3.7% at the amino acid level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (&lt;1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis and genomic SNPs showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating of the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.
病毒的进化分化最常见的驱动因素是与宿主的共同分化或宿主转移后的传播隔离。然而,在已命名的病毒种类中,不同的系统发育支系是代表高进化率下功能等同的副产品,还是代表新出现的病毒种类,目前仍是个未知数。在这里,我们利用图拉正泛病毒(TULV)在其天然啮齿动物宿主--普通田鼠(Microtus arvalis)--的单一进化系中的两个广泛的系统发育支系的基因组数据,对这些替代方案进行了检验。我们通过 RT-PCR 检测了各支系之间接触区 42 个地点的田鼠的 TULV 感染情况。测序结果显示,23个TULV中北基因组和21个TULV中南基因组在核苷酸水平上的差异为14.9%-18.5%,在氨基酸水平上的差异为2.2%-3.7%,没有证据表明两个支系之间存在重组或重配。地理线性分析表明,在连续的地形中,同域的 TULV 支系之间有一个突然的过渡(宽 1 千米)。这一过渡位于 M. arvalis 的线粒体中央系,基因组 SNPs 显示宿主种群在过渡期间逐渐混合。与宿主两个进化系之间的杂交区相比,宿主在 TULV 中部南北过渡区的基因组分化要弱得多。我们认为,这些同域TULV支系代表了功能上不同的新生物种,它们很可能受到宿主基因多态性的不同影响。这凸显了天然病毒接触区作为研究遗传和进化因素促进或限制 RNA 病毒传播系统的潜力。
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引用次数: 0
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes 感染强制性生物营养体 Bremia lactucae 的病毒新支系代表了感染卵菌的病毒的独特进化轨迹
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2024-01-04 DOI: 10.1093/ve/veae003
Forgia Marco, Daghino Stefania, Chiapello Marco, Ciuffo Marina, Turina Massimo
Recent advances on NGS approaches allowed a broad exploration of viromes from different fungal hosts, unveiling a great diversity of mycoviruses with interesting evolutionary features. The word mycovirus historically applies also to viruses infecting oomycetes but most studies are on viruses infecting fungi, with less mycoviruses found and characterized in oomycetes, particularly in the obligatory biotrophs. We here describe the first virome associated to Bremia lactucae the causal agent of lettuce downy mildew, which is an important biotrophic pathogen for lettuce production and a model system for the molecular aspects of the plant-oomycetes interactions. Among the identified viruses, we could detect i) two new negative sense ssRNA viruses related to the yueviruses, ii) the first example of permuted RdRp in a virus infecting fungi/oomycetes, iii) a new group of bi-segmentd dsRNA viruses showing evidence of recent bi-segmentation and concomitantly, a possible duplication event bringing a bi-segmented genome to three-segmented, iv) a first representative of a clade of viruses with evidence of recombination between distantly related viruses and v) a new ORFan virus encoding for an RdRp with low homology to known RNA viruses, vi) a new virus, belonging to riboviria but not conserved enough to provide a conclusive phylogenetic placement, that shows evidence of a recombination event between a kitrinoviricota-like and a pisuviricota-like sequence. The results obtained show a great diversity of viruses and evolutionary mechanisms previously unreported for oomycetes-infecting viruses supporting the existence of a large diversity of oomycetes-specific viral clades ancestral of many fungal and insect virus clades.
近来,NGS 方法的进步使人们得以广泛探索不同真菌宿主的病毒体,发现了具有有趣进化特征的多种多样的真菌病毒。霉菌病毒一词在历史上也适用于感染卵菌的病毒,但大多数研究都是针对感染真菌的病毒,在卵菌中发现的霉菌病毒较少,特别是在强制性生物营养体中。我们在此描述了首个与莴苣霜霉病病原菌乳霉(Bremia lactucae)相关的病毒组,乳霉是莴苣生产中的重要生物营养型病原体,也是植物与卵菌相互作用分子方面的模型系统。在已鉴定的病毒中,我们发现了 i) 两种新的负感 ssRNA 病毒,它们与 yueviruses 病毒有关;ii) 第一个在感染真菌/木霉菌的病毒中出现包覆 RdRp 的例子;iii) 一组新的双片段 dsRNA 病毒,它们显示了最近发生双片段化的证据,同时可能发生了将双片段基因组变为三片段基因组的复制事件、v) 一种新的 ORFan 病毒,编码一种与已知 RNA 病毒同源性较低的 RdRp;vi) 一种新病毒,属于核糖核酸病毒属,但其保守性不足以提供确定的系统发育位置,它显示了 kitrinoviricota 样序列和 pisuviricota 样序列之间重组事件的证据。研究结果表明,卵菌感染病毒的多样性和进化机制以前从未报道过,这支持了许多真菌和昆虫病毒支系祖先的卵菌特异病毒支系的多样性。
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引用次数: 0
Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market 华南海鲜市场环境样本元基因组测序中病毒读数数量量化的重要性
IF 5.3 2区 医学 Q1 VIROLOGY Pub Date : 2023-12-30 DOI: 10.1093/ve/vead089
Jesse D Bloom
In March 2023, the Chinese CDC publicly released raw metagenomic sequencing data for environmental samples collected in early 2020 from the Huanan Seafood Market. Prior to that data release, some scientists had suggested that these samples could be informative for establishing if animals such as raccoon dogs had been infected with SARS-CoV-2. However, no one had analyzed how much SARS-CoV-2 was actually present in the metagenomic sequencing data. After the raw data became available, I fully analyzed the abundance of both viral and animal genetic material in the samples. That analysis, which was published in Virus Evolution, found that the SARS-CoV-2 content of most samples was very low and that the abundance of SARS-CoV-2 was most strongly associated with animals such as largemouth bass that are not plausible candidates for having been infected. Based on these results, I concluded that the metagenomic content of the samples was not informative for determining if any non-human animals in the market had been infected with SARS-CoV-2. One of the authors of an earlier study of these samples, Florence Débarre, recently submitted a response to my paper. Here, I reply in turn to explain why it is important to quantify the abundance of viral material before drawing conclusions from metagenomic sequencing. I also report new analyses of other animal coronaviruses in the samples and show that material from some other animal coronaviruses is much more abundant than SARS-CoV-2 in samples collected on the date when most wildlife stall sampling was performed. I further show that material from some of these animal coronaviruses is associated with the animals they probably infect but that no such association exists for SARS-CoV-2. Overall, these new analyses further emphasize the importance of quantifying the actual amount of viral material in metagenomic samples and underscore why the environmental samples from the Huanan Seafood Market are not informative for determining if any non-human animals were infected with SARS-CoV-2.
2023 年 3 月,中国疾控中心公开发布了 2020 年初从华南海鲜市场采集的环境样本的原始元基因组测序数据。在数据发布之前,一些科学家认为,这些样本对于确定浣熊犬等动物是否感染了 SARS-CoV-2 有参考价值。但是,没有人分析过元基因组测序数据中到底有多少 SARS-CoV-2 病毒。在获得原始数据后,我全面分析了样本中病毒和动物遗传物质的丰度。这项分析结果发表在《病毒进化》(Virus Evolution)上,它发现大多数样本中的 SARS-CoV-2 含量都很低,而且 SARS-CoV-2 的丰度与大嘴鲈鱼等动物的关系最为密切,而这些动物并不可能感染 SARS-CoV-2。基于这些结果,我得出结论,样本中的元基因组含量对于确定市场上是否有非人类动物感染了 SARS-CoV-2 没有参考价值。对这些样本进行早期研究的作者之一 Florence Débarre 最近对我的论文提交了一份答复。在此,我将依次回复,解释为什么在从元基因组测序得出结论之前,对病毒物质的丰度进行量化非常重要。我还报告了对样本中其他动物冠状病毒的新分析,结果表明,在大多数野生动物滞留地采样当日采集的样本中,来自其他一些动物冠状病毒的物质要比 SARS-CoV-2 多得多。我还进一步表明,其中一些动物冠状病毒的材料与它们可能感染的动物有关,但 SARS-CoV-2 则没有这种关联。总之,这些新的分析进一步强调了对元基因组样本中病毒物质的实际数量进行量化的重要性,并强调了为什么来自华南海鲜市场的环境样本对于确定是否有非人类动物感染了 SARS-CoV-2 没有参考价值。
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Virus Evolution
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