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Complete genome sequence of a new member of the genus Badnavirus infecting nettle (Urtica dioica) 荨麻毒病毒属新成员的全基因组序列
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-12 DOI: 10.1007/s00705-024-06197-y
Elena Motsar, Anna Sheveleva, Svetlana Tsygankova, Fedor Sharko, Kristina Petrova, Irina Mitrofanova, Sergei Chirkov

A new badnavirus was discovered in nettle plants (Urtica dioica L., family Urticaceae) with vein banding symptoms using high-throughput sequencing. This virus was provisionally named "nettle badnavirus 1" (NBV 1). The complete NBV 1 genome consists of 7598 bp and contains three overlapping open reading frames. NBV 1 found to be was most closely related to green Sichuan pepper vein clearing-associated badnavirus, sharing 73.9% nucleotide sequence identity in the whole genome. These two viruses showed 76.3% nucleotide sequence identity in the region of the genome encoding RT-RNase H. This is lower than the species demarcation cutoff (80%) for the genus Badnavirus of the family Caulimoviridae, suggesting that NBV 1 is a new member of this genus. Phylogenetic analysis based on full-length badnavirus genome sequences showed that NBV 1 belongs to the same clade as a badnavirus whose genome was found to be integrated into chromosome 6 of the nettle genome, sharing 78% identity. Using PCR, NBV 1 was detected in a symptomless nettle plant growing next to symptomatic ones. It is therefore likely that the observed vein banding was due to an idaeovirus or a partitivirus, which were shown to be coinfecting the symptomatic plant. These findings expand the list of viruses infecting nettle.

利用高通量测序技术,在荨麻科荨麻植物中发现了一种新的具有静脉带状症状的坏病毒。该病毒暂时命名为“荨麻坏病毒1号”(NBV 1)。NBV 1的完整基因组由7598 bp组成,包含三个重叠的开放阅读框。nbv1与青椒清脉相关坏病毒亲缘关系最密切,全基因组同源性为73.9%。这两种病毒在编码RT-RNase h的基因组区域的核苷酸序列同源性为76.3%,低于Caulimoviridae的badnavvirus属的种划分界限(80%),表明NBV 1是该属的新成员。基于全基因组序列的系统发育分析表明,NBV - 1与被发现整合到荨麻基因组6号染色体上的一种坏病毒属于同一进化支,同源性为78%。利用PCR技术,在一株无症状荨麻植株中检测到NBV - 1。因此,观察到的静脉条带很可能是由一种观念病毒或一种局部病毒引起的,这两种病毒被证明同时感染了有症状的植物。这些发现扩大了感染荨麻的病毒名单。
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引用次数: 0
Circulatory microRNAs as potential biomarkers for different aspects of COVID-19 循环mirna作为COVID-19不同方面的潜在生物标志物
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-12 DOI: 10.1007/s00705-024-06184-3
Mahsan Zali, Mona Sadat Larijani, Anahita Bavand, Ladan Moradi, Fatemeh Ashrafian, Amitis Ramezani

The coronavirus disease of 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can alter the expression levels of host microRNAs (miRNAs). Increasing evidence suggests that circulating miRNAs can potentially play an important role in the diagnosis and prognosis of respiratory infectious diseases, especially COVID-19, and might serve as sensitive indicators of disease before the emergence of clinical symptoms. Here, we review the potential of circulatory microRNAs as novel biomarkers for different aspects of COVID-19. Recent studies have suggested that they can be useful not only for COVID‐19 prognosis but also for prediction of disease severity and mortality among intensive care unit (ICU) and ward patients. Moreover, extracellular vesicle (EV) miRNAs can be associated with antibody titer after COVID-19 vaccination. This review provides an overview of miRNA‐based biomarkers.

由新型严重急性呼吸综合征冠状病毒2 (SARS-CoV-2)引起的2019年冠状病毒病(COVID-19)可以改变宿主microrna (mirna)的表达水平。越来越多的证据表明,循环mirna可能在呼吸道传染病特别是COVID-19的诊断和预后中发挥重要作用,并可能在临床症状出现之前作为疾病的敏感指标。在这里,我们回顾了循环microrna作为COVID-19不同方面的新型生物标志物的潜力。最近的研究表明,它们不仅可用于预测COVID - 19的预后,还可用于预测重症监护病房(ICU)和病房患者的疾病严重程度和死亡率。此外,细胞外囊泡(EV) mirna可与COVID-19疫苗接种后的抗体滴度相关。本文综述了基于miRNA的生物标志物。
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引用次数: 0
Characterization and complete genome sequence of a novel zetapatitivirus from Penicillium exsudans isolate RCEF7900 exsudans青霉分离株RCEF7900新型zetapatitivirus的鉴定和全基因组序列分析
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-12 DOI: 10.1007/s00705-024-06205-1
Yanjie Zhao, Ping Wang, Lili He, Guogen Yang, Bo Huang

Penicillium exsudans strain RCEF7900, obtained from leaf litter, was found to harbor two double-stranded RNA (dsRNA) elements, designated as dsRNA1 and dsRNA2, with lengths of 1,816 bp and 1,625 bp, respectively. dsRNA1 encodes a 572-amino-acid RNA-dependent RNA polymerase (RdRp) protein (65.29 kDa), while dsRNA2 encodes a 503-amino-acid coat protein (CP) (56.73 kDa). A BLASTp search indicated that dsRNA1 and dsRNA 2 together constitute the genome of a novel partitivirus, which we have named "Penicillium exsudans partitivirus 1" (PePV1). Phylogenetic analysis based on RdRp amino acid sequences revealed that these genome segments belong to a member of a new species within the proposed genus “Zetapatitivirus” of the family Partitiviridae, with the RdRp showing the most sequence similarity (79.72% identity) to that of Sonifin virus. This is the first report of a zetapatitivirus from P. exsudans, expanding our understanding of mycoviral diversity in this fungal species.

从凋落叶中分离得到的外延青霉菌株RCEF7900含有两个双链RNA (dsRNA)元件,分别为dsRNA1和dsRNA2,长度分别为1816 bp和1625 bp。dsRNA1编码572个氨基酸的RNA依赖RNA聚合酶(RdRp)蛋白(65.29 kDa),而dsRNA2编码503个氨基酸的外壳蛋白(CP) (56.73 kDa)。BLASTp检索结果表明,dsRNA1和dsrna2共同构成了一种新型局部病毒的基因组,我们将其命名为“Penicillium exsudans partitivirus 1”(PePV1)。基于RdRp氨基酸序列的系统发育分析表明,这些基因组片段属于分病毒科“Zetapatitivirus”属的一个新种成员,RdRp与Sonifin病毒的序列相似性最高(同源性为79.72%)。这是首次报道来自埃及假单胞菌的zetapatitivirus,扩大了我们对该真菌物种中分枝病毒多样性的认识。
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引用次数: 0
Molecular characterization of a novel victorivirus isolated from Stagonosporopsis citrulli 瓜穗孢子虫分离的一种新型维多利亚病毒的分子特征
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-12 DOI: 10.1007/s00705-024-06185-2
Xiaofang Ma, Xing Zhang, Lifeng Zhai, Yingchun Jiang, Peter Moffett, Yu Zhang, Fang Song, Xin Song, Zhijing Wang, Ligang He, Shengmei Ji, Liming Wu

Members of the fungal genus Stagonosporopsis are important plant pathogens that can cause severe disease on a wide range of economically important plants and crops. Here, a novel victorivirus, tentatively named "Stagonosporopsis citrulli victorivirus 1" (SciVV1), was isolated from S. citrulli isolate HS2-8. The SciVV1 genome is 5,163 nucleotides in length, with a predicted GC content of 63.85%, and contains two open reading frames (ORF1 and ORF2), which overlap at an AUGA sequence. ORF1 and ORF2 are predicted to encode a coat protein (CP) and an RNA-dependent RNA polymerase (RdRp). A phylogenetic tree based on RdRp amino acid (aa) sequences showed that SciVV1 clustered together with members of the genus Victorivirus in the family Pseudototiviridae. Our results indicate that SciVV1 is a novel victorivirus. This is the first report of the complete genome sequence of SciVV1 infecting S. citrulli.

Stagonosporopsis真菌属的成员是重要的植物病原体,可以对广泛的重要经济植物和作物造成严重疾病。本文从瓜螺孢子虫HS2-8分离株中分离出一种新的维多利亚病毒,暂命名为“瓜螺孢子虫维多利亚病毒1号”(SciVV1)。SciVV1基因组全长5163个核苷酸,预测GC含量为63.85%,包含两个开放阅读框(ORF1和ORF2),在一个AUGA序列上重叠。预计ORF1和ORF2编码外壳蛋白(CP)和RNA依赖性RNA聚合酶(RdRp)。基于RdRp氨基酸(aa)序列的系统进化树显示,该病毒与假假病毒科维多利亚病毒属成员聚集在一起。我们的结果表明,SciVV1是一种新的维多利亚病毒。这是首次报道的感染柑橘S. citrulli的SciVV1全基因组序列。
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引用次数: 0
Direct TaqMan assay for the detection and genotyping of bovine viral diarrhea virus types 1 and 2 直接TaqMan法检测牛病毒性腹泻病毒1型和2型并进行基因分型
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-12 DOI: 10.1007/s00705-024-06207-z
Shakir Ullah, Kosuke Notsu, Akatsuki Saito, Tamaki Okabayashi, Hirohisa Mekata, Norikazu Isoda, Satoshi Sekiguchi

Bovine viral diarrhea (BVD), caused by bovine viral diarrhea virus (BVDV), has a significant economic impact on affected farms worldwide. For effective disease control, it is crucial to select an appropriate vaccine based on the specific genotype of BVDV. Therefore, developing a rapid and reliable assay to detect and genotype BVDV is imperative for controlling the spread of disease. In this study, we developed a TaqMan assay to detect and genotype BVDV types 1 and 2 directly in bovine serum without extraction of RNA. The direct BVDV TaqMan assay effectively detected both BVDV1 and BVDV2 with confirmed specificity and showed no cross-reactivity with any of the other viruses tested, including bovine respiratory syncytial virus, bovine coronavirus, Akabane virus, bovine herpesvirus 1, bovine parainfluenza virus 3, bovine immunodeficiency virus, and bovine leukemia virus. The assay could detect the virus in serum samples with a titer as low as 102 TCID50/mL in two out of three trials for BVDV1 and all three trials for BVDV2, indicating that its sensitivity is equivalent to that of virus isolation. Our findings represent a significant advancement in BVDV detection and typing directly from bovine serum.

牛病毒性腹泻(BVD)是由牛病毒性腹泻病毒(BVDV)引起的,对世界范围内受影响的农场具有重大的经济影响。为了有效控制疾病,根据BVDV的特定基因型选择合适的疫苗是至关重要的。因此,开发一种快速可靠的检测方法来检测和分型BVDV对于控制疾病的传播是必不可少的。在这项研究中,我们建立了一种TaqMan方法,直接在牛血清中检测BVDV 1型和2型并进行基因分型,而无需提取RNA。直接BVDV TaqMan试验有效地检测出BVDV1和BVDV2,并证实了特异性,并且与任何其他测试病毒无交叉反应性,包括牛呼吸道合胞病毒、牛冠状病毒、Akabane病毒、牛疱疹病毒1、牛副流感病毒3、牛免疫缺陷病毒和牛白血病病毒。该方法在BVDV1和BVDV2的三次试验中均能检测出低至102 TCID50/mL的血清样本中的病毒,表明其灵敏度与病毒分离相当。我们的发现代表了直接从牛血清中检测和分型BVDV的重大进展。
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引用次数: 0
Characterisation of the genetic diversity of citrus viroid VII using amplicon sequencing 柑橘类病毒VII遗传多样性的扩增子测序分析
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-12 DOI: 10.1007/s00705-024-06191-4
Grant A. Chambers, Andrew D.W. Geering, Daniel R. Bogema, Paul Holford, Georgios Vidalakis, Nerida J. Donovan

Viroids occur in plants as swarms of sequence variants clustered around a dominant variant, leading to adoption of the term ‘quasispecies’ to describe the viroid population in an individual host. The composition of the quasispecies can potentially change according to the age of the infection, the position of the leaf or branch in the canopy, and the host species. The primary aim of this study was to investigate the quasispecies concept for citrus viroid VII (CVd-VII), a recently discovered member of the family Pospiviroidae. Three experiments were conducted to determine factors affecting viroid variability (i) within different tissues of a lemon plant, (ii) among different plants of the same species (citron), and (iii) among different species and hybrids of citrus. Using two primer sets to produce amplicons for high-throughput sequencing, viroid population profiles were generated for each sample. The number of variants that were identified with both primer sets ranged from 2 to 13 per sample, and each sample comprised 1 to 4 major (> 10% sample) variants. The composition of variants differed in samples from different plants and among tissue types of a single plant. Single-nucleotide polymorphisms (SNPs), mostly in the form of substitutions, were the primary source of variation; in this study, SNPs were observed in approximately 10% of the viroid genome. The results of the three experiments indicate that CVd-VII follows the quasispecies model as reported for other viroids and that variability occurs in viroid populations in different tissue types and host species.

类病毒发生在植物中,是一群序列变异聚集在一个显性变异周围,导致采用术语“准种”来描述单个宿主中的类病毒种群。准种的组成可能会根据感染的年龄、叶片或树枝在冠层中的位置和宿主物种而发生变化。本研究的主要目的是探讨柑橘类病毒VII (CVd-VII)的准种概念,CVd-VII是最近发现的柑橘类病毒科成员。通过三个试验来确定影响类病毒变异的因素:(i)在柠檬植株的不同组织内,(ii)在同一物种(香橼)的不同植株之间,(iii)在柑橘的不同品种和杂交品种之间。使用两组引物产生高通量测序扩增子,生成每个样本的类病毒种群谱。两个引物组鉴定的变异数量在每个样本2到13个之间,每个样本包括1到4个主要变异(>; 10%样本)。变异的组成在来自不同植物的样品和单一植物的组织类型之间是不同的。单核苷酸多态性(SNPs)主要以取代的形式出现,是变异的主要来源;在这项研究中,在大约10%的类病毒基因组中观察到snp。这三个实验的结果表明,CVd-VII遵循其他类病毒的准种模型,并且在不同组织类型和宿主物种的类病毒群体中发生变异。
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引用次数: 0
Complete genome sequence of a novel bipartite begomovirus infecting butterfly pea (Clitoria ternatea L.) in India 一种感染印度蝴蝶豌豆(Clitoria ternatea L.)的新型双部begomavirus的全基因组序列。
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-11 DOI: 10.1007/s00705-024-06203-3
Mohammad Akram, Deepender Kumar, Naimuddin Kamaal

In India, plants from the non-cultivated, horticultural, and agricultural categories are commonly infected with various begomoviruses, most of which produce yellow mosaic, bright yellow mosaic, or curling symptoms on leaves. In this study, the complete genome of a new bipartite begomovirus causing yellow mosaic disease (YMD) in butterfly pea (Clitoria ternatea L.) was characterized using rolling-circle amplification followed by restriction digestion, cloning, and sequencing to obtain the full-length DNA-A (2727 nt) and DNA-B (2648 nt) sequences. The DNA-A and DNA-B components have a genome organization that is typical of the Old World bipartite begomoviruses, and the common regions (95 nt) of DNA-A and DNA-B share 91% nucleotide sequence identity, which is well above the threshold (>85%) for them to be considered cognate components. Both DNA molecules contain a begomovirus nonanucleotide motif, conserved iterons, and a putative stem-loop structure. The DNA-A of this virus was found to be most similar to that of Cajanus scarabaeoides yellow mosaic virus (CsYMV), with 82.61% nucleotide sequence identity, which is far below the species demarcation threshold (< 91%) for begomoviruses, whereas the DNA-B sequence showed the most similarity (77.16% identity) to that of Rhynchosia yellow mosaic virus (RhYMV). In phylogenetic analysis, both DNA-A and DNA-B were formed a clade with the corresponding genome segments of other YMD-causing begomoviruses. Based on these characteristics, this virus, for which the name “butterfly pea yellow mosaic virus” (BpYMV) is proposed, should be considered a member of a new species in the genus Begomovirus.

在印度,来自非栽培、园艺和农业类别的植物通常感染各种begomovirus,其中大多数在叶子上产生黄色马赛克、亮黄色马赛克或卷曲症状。本研究采用滚圈扩增、限制性酶切、克隆、测序等方法,对一种新的引起蝴蝶豌豆黄花叶病(YMD)的双部begomvirus (Clitoria ternatea L.)的全基因组进行了鉴定,获得了全长DNA-A (2727 nt)和DNA-B (2648 nt)序列。DNA-A和DNA-B组分具有典型的东半球双部begomovirus的基因组组织,并且DNA-A和DNA-B的共同区域(95 nt)具有91%的核苷酸序列同一性,这远远高于将它们视为同源组分的阈值(>85%)。这两种DNA分子都含有一个begomvirus非核苷酸基序、保守的内含子和一个假定的茎环结构。该病毒的DNA-A序列与圣甲虫黄花叶病毒(Cajanus scarabaeoides yellow mosaic virus, CsYMV)最相似,核苷酸序列同源性为82.61%,远低于begomovirus的种界阈值(< 91%),而DNA-B序列与黄花叶病毒(RhYMV)最相似,同源性为77.16%。在系统发育分析中,DNA-A和DNA-B与其他引起ymd的begomovirus的相应基因组片段形成一个进化支。基于这些特征,这种病毒被命名为“蝴蝶豌豆黄花叶病毒”(BpYMV),应该被认为是Begomovirus属一个新种的成员。
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引用次数: 0
Resolving viral structural complexity by super-resolution microscopy 用超分辨率显微镜分析病毒结构的复杂性
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-09 DOI: 10.1007/s00705-024-06192-3
Kevin Olaya-Bravo, Daniel Martínez-Flores, Aaron Pavel Rodríguez-Hernández, Ileana Tobías-Juárez, Jorge A. Castro-Rodríguez, Alicia Sampieri, Luis Vaca

In this review, we discuss different super-resolution microscopy (SRM) techniques employed to study viral structures and virus composition with nanometric resolution. We describe the basic principles of the different microscopy methods utilized to break the light diffraction limit, enabling the study of protein composition in viral structures. Finally, we demonstrate for the first time the differential spatial distribution of two structural proteins in an individual baculovirus using single-molecule super-resolution microscopy. We discuss the future of these powerful methods for virology, medicine, and biotechnology applications.

在这篇综述中,我们讨论了不同的超分辨率显微镜(SRM)技术用于研究纳米分辨率的病毒结构和病毒组成。我们描述了用于打破光衍射极限的不同显微镜方法的基本原理,使研究病毒结构中的蛋白质组成成为可能。最后,我们首次使用单分子超分辨率显微镜证明了两种结构蛋白在单个杆状病毒中的差异空间分布。我们将讨论这些强有力的方法在病毒学、医学和生物技术方面的应用前景。
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引用次数: 0
An epizootic of highly pathogenic avian influenza virus H7N3 in a Mexican ecological reserve 墨西哥某生态保护区发生H7N3型高致病性禽流感
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-09 DOI: 10.1007/s00705-024-06200-6
Roberto Navarro-López, Héctor Enrique Valdez-Gómez, Mitzunari Zalapa-Hernández, Mario Solís-Hernández, Miguel Ángel Márquez-Ruiz, Abel Rosas-Tellez, Carlos Guichard-Romero, Gerardo Cartas-Heredia, Romeo Morales-Espinoza, Claudio L. Afonso, Ninnet Gómez-Romero

In this case study, we describe an outbreak of highly pathogenic avian influenza (HPAI) virus subtype H7N3 in an ecological reserve in Chiapas, Mexico, affecting captive and wild birds. The virus was detected mainly in plain chachalacas displaying respiratory and gastrointestinal clinical signs and death within 24 hours. Mortality in white-fronted parrots and a clay-colored thrush was also recorded. We describe control strategies implemented to prevent virus dissemination and active surveillance within the risk area. Phylogenetic analysis revealed that the HPAI H7N3 virus detected in affected birds shared a close genetic relationship with Mexican H7N3 isolates from 2012.

在本案例研究中,我们描述了墨西哥恰帕斯州一个生态保护区爆发的H7N3型高致病性禽流感(HPAI)病毒,影响了圈养和野生鸟类。该病毒主要在查恰拉卡斯平原发现,表现为呼吸和胃肠道临床症状,24小时内死亡。白额鹦鹉和一种粘土色画眉的死亡率也有记录。我们描述了在风险区域内为防止病毒传播和主动监测而实施的控制策略。系统发育分析显示,在病禽中检测到的HPAI H7N3病毒与2012年墨西哥H7N3分离株具有密切的遗传关系。
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引用次数: 0
Molecular and ultrastructural characteristics of virulent and attenuated vaccine strains of goose parvovirus LIV-22 鹅细小病毒LIV-22强毒株和弱毒株的分子和超微结构特征
IF 2.5 4区 医学 Q3 VIROLOGY Pub Date : 2024-12-08 DOI: 10.1007/s00705-024-06188-z
Ezekiel S. Oloruntimehin, Sofya I. Volodina, Ivan V. Patraman, Grigory A. Nadtochey, Alexander S. Malogolovkin

The disease caused by goose parvovirus (GPV) affects young goslings and ducks and leads to substantial losses for farmers due to high mortality rates, reaching 70-100% in naive flocks. Here, we present the results of a study focusing on the historical virulent GPV LIV-22 strain, which was isolated in the USSR in 1972. An attenuated GPV LIV-22 vaccine strain that was generated by continuous passaging in goose embryonic fibroblasts was also studied. Phylogenetic analysis placed both GPV LIV-22 strains in the classical GPV group, close to the vaccine and low-pathogenic strains. However, several individual changes in the GPV LIV-22 VP1 gene highlight the uniqueness of the evolution and adaptation mechanism of GPV LIV-22 strains. Transmission electron microscopy (TEM) revealed severe ultrastructural changes in goose hepatocytes and enterocytes as early as 24-48 h postinfection, confirming abrupt GPV pathogenesis. This description of some of the essential characteristics of the GPV LIV-22 virulent and vaccine strain will be useful for studying GPV evolution and molecular pathogenesis.

鹅细小病毒(GPV)引起的疾病影响雏鹅和鸭,由于高死亡率给农民造成重大损失,在未成熟的鸡群中达到70-100%。在这里,我们介绍了对1972年在苏联分离的历史毒性GPV LIV-22株的研究结果。对鹅胚成纤维细胞连续传代产生的GPV减毒株LIV-22进行了研究。系统发育分析表明,这两种GPV LIV-22菌株均属于经典GPV组,接近疫苗和低致病性菌株。然而,GPV LIV-22 VP1基因的几个个体变化凸显了GPV LIV-22菌株进化和适应机制的独特性。透射电镜(TEM)显示,早在感染后24-48 h,鹅肝细胞和肠细胞就发生了严重的超微结构变化,证实了GPV的突变发病。对GPV LIV-22毒力株和疫苗株的一些基本特征的描述将有助于研究GPV的进化和分子发病机制。
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引用次数: 0
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