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Enterovirus D68 circulation between 2014 and 2022 in Slovenian children 2014 年至 2022 年期间斯洛文尼亚儿童中 D68 型肠道病毒的传播情况
Q4 VIROLOGY Pub Date : 2024-01-10 DOI: 10.3389/fviro.2024.1335752
Tina Uršič, Monika Jevšnik Virant, Rok Kogoj, Uros Krivec, Joanna Prusnik, Minca Mramor, Sara Lovšin, Miroslav Petrovec
Introduction

Enterovirus D68 (EV-D68) belongs to the Picornaviridae family, genus Enterovirus. It is mostly known as a respiratory virus causing upper and lower respiratory tract infections, but it is also rarely associated with a variety of central nervous system complications, with acute flaccid myelitis being reported most frequently. This study assesses the incidence, seasonality, clinical presentation, and molecular epidemiology of the EV-D68 strain in EV-positive children hospitalized between 2014 and 2022 at the largest pediatric medical center in Slovenia.

Methods

EV-D68 was detected using specific qRT-PCR, whereas partial VP1 sequences were obtained with Sanger sequencing, and further analyzed using the software CLC Main Workbench version 7 and MEGA version X.

Results

EV-D68 was detected in 154 out of 1,145 (13.4%) EV-positive children. In the two epidemic years, 2014 and 2016, EV-D68 was most frequently detected in the summer and early autumn, peaking in September. The median age of EV-D68–infected children was 3 years (IQR 1–3 years), with a female: male ratio of 1:1.17. Rhinorrhea was present in 74.0% of children, respiratory distress in 82.5%, and hypoxemia requiring supplemental oxygen in 44.1%. Out of 154 patients, 80.0% were hospitalized, with a median stay of 2 days (IQR 1–3 days). Lower respiratory tract infection was observed in 89.0% of EV-D68–positive patients, with bronchitis and bronchiolitis being most frequently diagnosed. No central nervous system manifestations of EV-D68 infection were observed in the study cohort. Phylogenetic analysis of partial VP1 sequences of EV-D68 revealed close similarity to the EV-D68 variants that were circulating in other European countries in these years.

Discussion

Slovenia faced two EV-D68 epidemics in 2014 and 2016; however, after 2016 only nine more cases were detected until the end of the study period. Based on the results of this study, EV-D68 was a frequent cause of lower respiratory tract infection among EV-positive patients. However, none of the patients we studied needed ICU treatment, and none developed acute flaccid paralysis. Our results indicate that EV-D68 is not present constantly, so additional monitoring studies should be conducted in the future to better understand the implications of this EV type in human disease.

导言肠道病毒 D68(EV-D68)属于细小病毒科肠道病毒属。它主要是一种呼吸道病毒,可引起上呼吸道和下呼吸道感染,但也极少与各种中枢神经系统并发症有关,其中以急性弛缓性脊髓炎最为常见。本研究评估了斯洛文尼亚最大的儿科医疗中心在2014年至2022年期间住院的EV阳性儿童中EV-D68毒株的发病率、季节性、临床表现和分子流行病学。在2014年和2016年这两个流行年中,EV-D68最常在夏季和初秋被检测到,9月份达到高峰。感染EV-D68的儿童年龄中位数为3岁(IQR 1-3岁),男女比例为1:1.17。74.0%的儿童出现鼻出血,82.5%出现呼吸困难,44.1%出现低氧血症,需要补充氧气。154 名患者中有 80.0% 住院治疗,住院时间中位数为 2 天(IQR 1-3 天)。89.0%的 EV-D68 阳性患者出现下呼吸道感染,其中以支气管炎和支气管炎最为常见。研究队列中未观察到 EV-D68 感染的中枢神经系统表现。对EV-D68的部分VP1序列进行的系统发育分析表明,这些变种与这几年在欧洲其他国家流行的EV-D68变种非常相似。根据这项研究的结果,EV-D68 是 EV 阳性患者下呼吸道感染的常见原因。然而,我们研究的患者中没有人需要接受重症监护治疗,也没有人出现急性弛缓性麻痹。我们的研究结果表明,EV-D68 并非持续存在,因此今后应开展更多监测研究,以更好地了解这种 EV 类型对人类疾病的影响。
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引用次数: 0
Analysis of Parvovirus B19 persistence and reactivation in human heart layers 分析 Parvovirus B19 在人体心脏层中的持续存在和再活化情况
Q4 VIROLOGY Pub Date : 2024-01-10 DOI: 10.3389/fviro.2024.1304779
Ashwin Badrinath, Anais Gardere, Samantha L. Palermo, Kenneth S. Campbell, Anna Kloc

Heart disease is the leading cause of death worldwide. Myocarditis, or inflammation of the cardiac muscle, is estimated to cause up to 1.5 million cases annually, with viral infection being the most common disease culprit. Past studies have shown that Parvovirus B19 is routinely detected in endomyocardial biopsies. This virus has been linked to acute heart inflammation, which can cause cardiac muscle damage. However, because Parvovirus B19 can be found in the heart tissues in the absence of disease symptoms, it is unclear if the long-term presence of the virus contributes to, or initiates, heart disease. Here, we utilized a PCR-based detection assay to assess the presence of the B19V genome and its mRNA intermediates in human heart tissues. The analysis was carried out in three heart layers derived from one individual: epicardium, endocardium and myocardium. We showed the Parvovirus B19 genome presence variability in different heart layers. Similarly, viral transcriptional activity, assessed by the mRNA presence, was detected only in a few of the analyzed samples. Our results suggest that localized sites of Parvovirus B19 infection may exist within individual heart layers, which may have implication for the cardiac muscle inflammation.

心脏病是导致全球死亡的主要原因。据估计,心肌炎或心肌发炎每年导致多达 150 万例病例,而病毒感染是最常见的致病元凶。过去的研究表明,在心内膜活检中经常能检测到 Parvovirus B19。这种病毒与急性心脏炎症有关,可导致心肌损伤。然而,由于在没有疾病症状的情况下也能在心脏组织中发现 Parvovirus B19,因此尚不清楚病毒的长期存在是否会导致或引发心脏病。在这里,我们利用一种基于 PCR 的检测方法来评估人类心脏组织中是否存在 B19V 基因组及其 mRNA 中间体。分析在一个人的三个心脏层中进行:心外膜、心内膜和心肌。我们发现 Parvovirus B19 基因组在不同的心脏层中存在差异。同样,通过 mRNA 评估的病毒转录活性也只在少数分析样本中检测到。我们的研究结果表明,在个别心脏层中可能存在帕罗病毒 B19 的局部感染点,这可能与心肌炎症有关。
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引用次数: 0
APOBEC3D excludes APOBEC3F from HIV-1 virions by competitive binding of RNA APOBEC3D 通过与 RNA 竞争性结合,将 APOBEC3F 从 HIV-1 病毒中分离出来
Q4 VIROLOGY Pub Date : 2024-01-04 DOI: 10.3389/fviro.2024.1343037
Shreoshri Bhattacharjee, Amit Gaba, Linda Chelico

The human family of APOBEC3 enzymes are primarily studied as single-stranded DNA deoxycytidine deaminases that act as host restriction factors for a number of viruses and retroelements. The deamination of deoxycytidine to deoxyuridine causes inactivating mutations in target DNA and the nucleic acid binding ability may also cause deamination independent restriction. There are seven APOBEC3 enzymes in humans, named A-H, excluding E, each of which has restriction activity against a subset of viruses or retroelements. There are primarily four, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H that have been found to restrict replication of HIV-1, however their restriction activity varies and they have primarily been studied individually despite co-expression in the cells that HIV-1 infects. It is known that APOBEC3F hetero-oligomerizes with APOBEC3G and APOBEC3H and that this influences host restriction outcomes during HIV-1 infection in tissue culture. Here, we examined if APOBEC3F interacts with APOBEC3D and the functional outcomes. We found that APOBEC3D mRNA expression was similar to or higher than APOBEC3F mRNA in multiple donors, suggesting that the proteins would be co-expressed, allowing for interactions to occur. We determined that APOBEC3F and APOBEC3D interacted primarily through an RNA intermediate; however, this interaction resulted in APOBEC3D competitively excluding APOBEC3F from virions. Although HIV-1 restriction still occurred when APOBEC3F and APOBEC3D were co-expressed, it was due to primarily APOBEC3D-mediated deamination-independent restriction. The APOBEC3D-mediated exclusion of APOBEC3F from HIV-1 encapsidation could be recapitulated in vitro through RNA capture experiments in which APOBEC3D decreased or abrogated the ability of APOBEC3F to bind to HIV-1 protease or 5’UTR RNA, respectively. Overall, the data suggest that there are mechanisms at the protein level that segregate APOBEC3s into different virus particles.

人类 APOBEC3 酶家族主要作为单链 DNA 脱氧胞苷脱氨酶进行研究,它们是一些病毒和逆转录病毒的宿主限制因子。脱氧胞苷脱氨成脱氧尿苷会导致靶 DNA 发生失活突变,核酸结合能力也会导致脱氨限制。人类有七种 APOBEC3 酶,分别命名为 A-H(不包括 E),每种酶都具有针对特定病毒或逆转录病毒的限制活性。已发现主要有四种(APOBEC3D、APOBEC3F、APOBEC3G 和 APOBEC3H)能限制 HIV-1 的复制,但它们的限制活性各不相同,而且尽管它们在 HIV-1 感染的细胞中共同表达,但主要是对它们进行单独研究。众所周知,APOBEC3F 与 APOBEC3G 和 APOBEC3H 异源配位,这影响了组织培养中 HIV-1 感染过程中宿主的限制结果。在这里,我们研究了 APOBEC3F 是否与 APOBEC3D 相互作用及其功能结果。我们发现,在多个供体中,APOBEC3D mRNA 的表达量与 APOBEC3F mRNA 的表达量相似或更高,这表明这两种蛋白质会共同表达,从而发生相互作用。我们确定 APOBEC3F 和 APOBEC3D 主要通过 RNA 中间体相互作用;然而,这种相互作用导致 APOBEC3D 竞争性地将 APOBEC3F 从病毒中排除。虽然当 APOBEC3F 和 APOBEC3D 共同表达时仍会出现 HIV-1 限制,但这主要是由于 APOBEC3D 介导的脱氨基限制。APOBEC3D 介导的 APOBEC3F 对 HIV-1 包囊化的排斥作用可以通过 RNA 捕获实验在体外重现,在这些实验中,APOBEC3D 分别降低或削弱了 APOBEC3F 与 HIV-1 蛋白酶或 5'UTR RNA 结合的能力。总之,这些数据表明,在蛋白质水平上存在着将 APOBEC3 分离成不同病毒颗粒的机制。
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引用次数: 0
Characterization of the evolutionary and virological aspects of mutations in the receptor binding motif of the SARS-CoV-2 spike protein SARS-CoV-2 穗状病毒蛋白受体结合基团突变的进化和病毒学特征
Q4 VIROLOGY Pub Date : 2023-12-22 DOI: 10.3389/fviro.2023.1328229
Yuuka Masuda, H. Nasser, Jiří Zahradník, Shuya Mitoma, Ryo Shimizu, Kayoko Nagata, A. Takaori-Kondo, Gideon Schreiber, Kotaro Shirakawa, Akatsuki Saito, Terumasa Ikeda, Jumpei Ito, Kei Sato
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has substantially diversified during the pandemic, resulting in the successive emergence of variants characterized by various mutations. It has been observed that several epidemic variants, including those classified as variants of concern, share mutations at four key residues (L452R, T478K, E484K, and N501Y) within the receptor binding motif (RBM) region of the spike protein. However, the processes through which these four specific RBM mutations were acquired during the evolution of SARS-CoV-2, as well as the degree to which they enhance viral fitness, remain unclear. Moreover, the effect of these mutations on the properties of the spike protein is not yet fully understood. In this study, we performed a comprehensive phylogenetic analysis and showed that the four RBM mutations have been convergently acquired across various lineages throughout the evolutionary history of SARS-CoV-2. We also found a specific pattern in the order of acquisition for some of these mutations. Additionally, our epidemic dynamic modeling demonstrated that acquiring these mutations leads to an increase in the effective reproduction number of the virus. Furthermore, we engineered mutant spike proteins with all feasible combinations of the four mutations, and examined their properties to uncover the influence that these mutations have on viral characteristics. Our results provide insights into the roles these four mutations play in shaping the viral characteristics, epidemic proliferation, and evolutionary pathway of SARS-CoV-2.
严重急性呼吸系统综合症冠状病毒 2(SARS-CoV-2)在大流行期间发生了重大变化,相继出现了以各种突变为特征的变种。据观察,几种流行变异株,包括那些被列为关注变异株的变异株,都在尖峰蛋白的受体结合基团(RBM)区域内的四个关键残基(L452R、T478K、E484K 和 N501Y)上发生了突变。然而,在 SARS-CoV-2 的进化过程中,这四个特定的 RBM 突变是如何获得的,以及它们在多大程度上增强了病毒的适应性,目前仍不清楚。此外,这些突变对尖峰蛋白特性的影响也尚未完全清楚。在这项研究中,我们进行了全面的系统发育分析,结果表明在整个 SARS-CoV-2 的进化史中,四种 RBM 突变在不同种系中趋同获得。我们还发现了其中一些突变获得顺序的特定模式。此外,我们的流行病动态模型表明,获得这些突变会导致病毒的有效繁殖数量增加。此外,我们还设计了具有四种突变的所有可行组合的突变尖峰蛋白,并研究了它们的特性,以揭示这些突变对病毒特性的影响。我们的研究结果为我们揭示了这四种突变在塑造 SARS-CoV-2 病毒特征、流行增殖和进化途径方面所起的作用。
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引用次数: 0
Trends in the enterovirus surveillance in Oslo, Norway before and during the COVID-19 pandemic COVID-19 大流行之前和期间挪威奥斯陆肠道病毒监测趋势
Q4 VIROLOGY Pub Date : 2023-12-20 DOI: 10.3389/fviro.2023.1343781
Susanne Dudman, Ingvild Klundby, Joakim Øverbø, Sanela Numanovic, Mariann Nilsen, Andreas Lind, Mona Holberg-Petersen, Elisabeth Toverud Landaas
Background

Enteroviruses have the potential to cause both high morbidity and mortality especially in children. High season in Norway is between August and November, but this seasonality was interrupted by the COVID-19 pandemic.

Methods

In this study, we describe the enterovirus surveillance in Norway before and during the COVID-19 pandemic including the years from the start of 2016 until the end of 2022. Screening of enterovirus was performed by both laboratory developed methods and FilmArray® ME Panel. Relevant samples were typed, mostly by VP1 sequencing.

Results

Seventy-four percent of all cases occurred in infants under five years of age. A significant reduction in positive cases was observed during the peak years of the COVID-19 pandemic compared to the years before. Pre-pandemic, a wide range of types from all four enterovirus species were detected. During the years with COVID-19 infection control measures, significantly fewer enterovirus types were found along with a substantial reduction in the detection rate.

Conclusion

Enterovirus surveillance discovered a large amount of different types mainly affecting infants. The positivity rate was markedly reduced during the pandemic in 2020-2022 and fewer types occurred.

背景肠道病毒有可能导致高发病率和高死亡率,尤其是在儿童中。方法在本研究中,我们介绍了 COVID-19 大流行之前和期间挪威的肠道病毒监测情况,包括从 2016 年开始到 2022 年年底。通过实验室开发的方法和 FilmArray® ME Panel 对肠道病毒进行了筛查。结果74%的病例发生在五岁以下的婴儿身上。在 COVID-19 大流行的高峰期,阳性病例与之前相比明显减少。大流行前,检测到的肠道病毒种类繁多,包括所有四种肠道病毒。结论 肠道病毒监测发现了大量主要影响婴儿的不同类型的肠道病毒。在 2020-2022 年大流行期间,阳性率明显降低,出现的类型也更少。
{"title":"Trends in the enterovirus surveillance in Oslo, Norway before and during the COVID-19 pandemic","authors":"Susanne Dudman, Ingvild Klundby, Joakim Øverbø, Sanela Numanovic, Mariann Nilsen, Andreas Lind, Mona Holberg-Petersen, Elisabeth Toverud Landaas","doi":"10.3389/fviro.2023.1343781","DOIUrl":"https://doi.org/10.3389/fviro.2023.1343781","url":null,"abstract":"<sec><title>Background</title><p>Enteroviruses have the potential to cause both high morbidity and mortality especially in children. High season in Norway is between August and November, but this seasonality was interrupted by the COVID-19 pandemic.</p></sec><sec><title>Methods</title><p>In this study, we describe the enterovirus surveillance in Norway before and during the COVID-19 pandemic including the years from the start of 2016 until the end of 2022. Screening of enterovirus was performed by both laboratory developed methods and FilmArray<sup>®</sup> ME Panel. Relevant samples were typed, mostly by VP1 sequencing.</p></sec><sec><title>Results</title><p>Seventy-four percent of all cases occurred in infants under five years of age. A significant reduction in positive cases was observed during the peak years of the COVID-19 pandemic compared to the years before. Pre-pandemic, a wide range of types from all four enterovirus species were detected. During the years with COVID-19 infection control measures, significantly fewer enterovirus types were found along with a substantial reduction in the detection rate.</p></sec><sec><title>Conclusion</title><p>Enterovirus surveillance discovered a large amount of different types mainly affecting infants. The positivity rate was markedly reduced during the pandemic in 2020-2022 and fewer types occurred.</p></sec>","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"58 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139396459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Differential susceptibility of human microglia HMC3 cells and brain microvascular endothelial HBEC-5i cells to Mayaro and Una virus infection 人类小胶质细胞 HMC3 和脑微血管内皮细胞 HBEC-5i 对 Mayaro 和 Una 病毒感染的易感性差异
Q4 VIROLOGY Pub Date : 2023-12-19 DOI: 10.3389/fviro.2023.1325282
Dalkiria Campos, Madelaine Sugasti-Salazar, Patricia Valdés-Torres, Paola Elaine Galán-Jurado, Dalel Zegarra, José González-Santamaría

Mayaro (MAYV) and Una (UNAV) are emerging alphaviruses circulating in the Americas. Earlier reports have revealed that MAYV infects different human cell lines, including synovial and dermal fibroblasts, chondrocytes, osteoblasts, astrocytes and pericytes, as well as neural progenitor cells. In this study we evaluated the susceptibility of immortalized human microglia HMC3 cells and brain microvascular endothelial HBEC-5i cells to MAYV and UNAV infection. Cytopathic effects, cell viability, viral progeny yields, and the presence of E1 and nsP1 proteins in HMC3 and HBEC-5i cells infected with several MAYV or UNAV strains were assessed using an inverted microscope, MTT assay, plaque-forming assays, and immunofluorescence or Western blot, respectively. Finally, the expression of immune response genes was analyzed using RT-qPCR. MAYV and UNAV demonstrated strong cytopathic effects and significantly reduced cell viability in HMC3 cells. Moreover, the HMC3 cells were efficiently infected regardless of the virus strain tested, and E1 and nsP1 viral proteins were detected. In contrast, only MAYV appeared to infect HBEC-5i cells, and minimal effects on cell morphology or viability were observed. Furthermore, the MAYV titer and viral protein levels were substantially lower in the infected HBEC-5i cells when compared to those of the infected microglia cells. Finally, unlike UNAV, MAYV elicited a strong expression of specific interferon-stimulated genes in microglia cells, along with pro-inflammatory cytokines implicated in the immune response. Collectively, these findings demonstrate that MAYV and UNAV are capable of infecting relevant human brain cells.

Mayaro (MAYV) 和 Una (UNAV) 是在美洲流行的新型阿尔巴病毒。早先的报告显示,MAYV 可感染不同的人体细胞系,包括滑膜和真皮成纤维细胞、软骨细胞、成骨细胞、星形胶质细胞和周细胞以及神经祖细胞。在这项研究中,我们评估了永生化人小胶质细胞 HMC3 和脑微血管内皮细胞 HBEC-5i 对 MAYV 和 UNAV 感染的敏感性。我们使用倒置显微镜、MTT 试验、斑块形成试验、免疫荧光或 Western 印迹技术分别评估了感染了 MAYV 或 UNAV 株系的 HMC3 和 HBEC-5i 细胞的细胞病理效应、细胞活力、病毒后代产量以及 E1 和 nsP1 蛋白的存在情况。最后,使用 RT-qPCR 分析了免疫反应基因的表达。MAYV 和 UNAV 对 HMC3 细胞有很强的细胞病理效应,能显著降低细胞活力。此外,无论测试的是哪种病毒株,HMC3 细胞都能被有效感染,并能检测到 E1 和 nsP1 病毒蛋白。相比之下,只有 MAYV 能感染 HBEC-5i 细胞,而且对细胞形态和活力的影响极小。此外,与受感染的小胶质细胞相比,受感染的 HBEC-5i 细胞中 MAYV 滴度和病毒蛋白水平要低得多。最后,与 UNAV 不同的是,MAYV 在小胶质细胞中引起了特定干扰素刺激基因的强烈表达,同时还引起了与免疫反应有关的促炎细胞因子的表达。总之,这些发现证明 MAYV 和 UNAV 能够感染相关的人类脑细胞。
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引用次数: 0
Processing of the Hepatitis E virus ORF1 nonstructural polyprotein 戊型肝炎病毒 ORF1 非结构多聚蛋白的加工过程
Q4 VIROLOGY Pub Date : 2023-12-08 DOI: 10.3389/fviro.2023.1327745
Yogesh A. Karpe

Hepatitis E viruses (HEV) Open Reading Frame 1 (ORF1) encodes a non-structural polyprotein. In most positive-sense RNA viruses found in animals, this non-structural polyprotein is cleaved by viral protease or host protease. However, the mechanism behind the processing of HEV polyprotein remains one of the most controversial questions in HEV biology. The role of putative HEV protease in processing is difficult to demonstrate. Recent studies have questioned the existence of HEV protease and suggested that pORF1 lacks protease activity. Conversely, studies also suggested the role of host proteases involved in the blood coagulation cascade, like thrombin, in processing the HEV pORF1 polyprotein. In summary, recent studies support the notion that pORF1 lacks protease activity and host proteases are responsible for processing pORF1. The present review compiles a thorough overview of contentious research on HEV’s papain-like cysteine protease (PCP) and highlights recent advancements in the field. We aim to discuss the challenges and opportunities in the field to focus on further research.

戊型肝炎病毒(HEV)开放阅读框 1(ORF1)编码一种非结构性多聚蛋白。在动物体内发现的大多数正义 RNA 病毒中,这种非结构性多聚蛋白都会被病毒蛋白酶或宿主蛋白酶裂解。然而,HEV 多聚蛋白的加工机制仍是 HEV 生物学中最具争议的问题之一。假定的 HEV 蛋白酶在加工过程中的作用难以证明。最近的研究质疑 HEV 蛋白酶的存在,并认为 pORF1 缺乏蛋白酶活性。相反,也有研究表明,参与血液凝固级联的宿主蛋白酶(如凝血酶)在处理 HEV pORF1 多聚蛋白中发挥作用。总之,最近的研究支持 pORF1 缺乏蛋白酶活性、宿主蛋白酶负责处理 pORF1 的观点。本综述全面概述了有关 HEV 的木瓜蛋白酶样半胱氨酸蛋白酶(PCP)的争议性研究,并重点介绍了该领域的最新进展。我们旨在讨论该领域的挑战和机遇,以聚焦于进一步的研究。
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引用次数: 0
APOBEC3 family proteins as drivers of virus evolution 驱动病毒进化的 APOBEC3 家族蛋白
Q4 VIROLOGY Pub Date : 2023-12-04 DOI: 10.3389/fviro.2023.1332010
Michael Jonathan, Terumasa Ikeda

The apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) family consists of cytosine deaminases implicated in diverse and important biological functions. APOBEC3 (A3) proteins belong to the APOBEC/AID family, and they catalyze the deamination of cytosine to uracil in single-stranded DNA and, to a lesser extent, in RNA substrates. In humans, seven A3 genes have been identified (A3A, A3B, A3C, A3D, A3F, A3G, and A3H). The introduction of lethal G-to-A or C-to-U mutations into certain viral genomes leads to virus inactivation. However, the mutagenic capability of A3 proteins could serve as a source of mutations to drive virus evolution. Therefore, recent studies have implied the role of A3 proteins in aiding the evolution of viruses, conferring them with severe manifestations such as drug resistance and/or immune evasion. In this review, we discuss in depth the interactions of A3 proteins with viruses that infect humans and our self-proteins.

载脂蛋白 B mRNA 编辑酶催化多肽样(APOBEC)家族由胞嘧啶脱氨酶组成,涉及多种重要的生物学功能。APOBEC3(A3)蛋白属于 APOBEC/AID 家族,它们催化单链 DNA 中的胞嘧啶脱氨为尿嘧啶,其次也催化 RNA 底物中的胞嘧啶脱氨为尿嘧啶。在人类中,已经发现了 7 个 A3 基因(A3A、A3B、A3C、A3D、A3F、A3G 和 A3H)。在某些病毒基因组中引入 G 到 A 或 C 到 U 的致命突变会导致病毒失活。然而,A3 蛋白的诱变能力可能成为推动病毒进化的突变源。因此,最近的研究暗示 A3 蛋白在帮助病毒进化中的作用,赋予病毒严重的表现,如耐药性和/或免疫逃避。在这篇综述中,我们将深入讨论 A3 蛋白与感染人类的病毒以及我们自身蛋白之间的相互作用。
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引用次数: 0
Beyond survival: unraveling the dynamics of Ebola virus resurgence in Sub-Saharan Africa and the remarkable journey of survivors 超越生存:揭示撒哈拉以南非洲埃博拉病毒死灰复燃的动态和幸存者的非凡旅程
Q4 VIROLOGY Pub Date : 2023-11-13 DOI: 10.3389/fviro.2023.1227314
Eric Asare Fenteng, Paul Poku Sampene Ossei, William Gilbert Ayibor, Tracy Narh-Bedu
Ebola virus disease (EVD) remains a significant public health threat, with sporadic outbreaks occurring in Sub-Saharan Africa. Survivors of EVD may experience various post-infection symptoms, collectively known as post-Ebola virus syndrome (PES), which include chronic arthralgia, uveitis, headache, and psychosocial stressors. In this review, we discuss the persistence of Ebola virus in survivors and its possible role in the reemergence of current outbreaks. We highlight that waning immunity of survivors enhances viral persistence and may lead to viral reactivation and recurrence of disease in previously affected tissues. The delicate equilibrium between diminished immune cell surveillance and limited viral replication may lead to enduring chronic inflammation. Our systematic review, based on an extensive survivor cohort, underscores the importance of continued research and preparedness efforts to combat future outbreaks through adequate surveillance and timely public health interventions. This review serves as a comprehensive guide to understanding the complexities of EVD survivorship, the challenges of PES, and the strategies to mitigate its impact.
埃博拉病毒病(EVD)仍然是一个重大的公共卫生威胁,在撒哈拉以南非洲发生零星疫情。埃博拉病毒病幸存者可能出现各种感染后症状,统称为埃博拉病毒后综合征,包括慢性关节痛、葡萄膜炎、头痛和社会心理压力。在这篇综述中,我们讨论了埃博拉病毒在幸存者中的持续存在及其在当前疫情再次出现中的可能作用。我们强调,幸存者免疫力的减弱增强了病毒的持久性,并可能导致病毒再激活和先前受影响组织中的疾病复发。免疫细胞监视功能减弱和病毒复制受限之间的微妙平衡可能导致持久的慢性炎症。我们的系统综述基于广泛的幸存者队列,强调了继续研究和准备工作的重要性,通过充分的监测和及时的公共卫生干预措施来对抗未来的疫情。这篇综述为理解EVD存活的复杂性、PES的挑战以及减轻其影响的策略提供了全面的指导。
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引用次数: 0
classLog: Logistic regression for the classification of genetic sequences 用于基因序列分类的逻辑回归
Q4 VIROLOGY Pub Date : 2023-11-06 DOI: 10.3389/fviro.2023.1215012
Michael A. Zeller, Zebulun W. Arendsee, Gavin J.D. Smith, Tavis K. Anderson
Introduction

Sequencing and phylogenetic classification have become a common task in human and animal diagnostic laboratories. It is routine to sequence pathogens to identify genetic variations of diagnostic significance and to use these data in realtime genomic contact tracing and surveillance. Under this paradigm, unprecedented volumes of data are generated that require rapid analysis to provide meaningful inference.

Methods

We present a machine learning logistic regression pipeline that can assign classifications to genetic sequence data. The pipeline implements an intuitive and customizable approach to developing a trained prediction model that runs in linear time complexity, generating accurate output rapidly, even with incomplete data. Our approach was benchmarked against porcine respiratory and reproductive syndrome virus (PRRSv) and swine H1 influenza A virus (IAV) datasets. Trained classifiers were tested against sequences and simulated datasets that artificially degraded sequence quality at 0, 10, 20, 30, and 40%.

Results

When applied to a poor-quality sequence data, the classifier achieved between >85% to 95% accuracy for the PRRSv and the swine H1 IAV HA dataset and this increased to near perfect accuracy when using the full dataset. The model also identifies amino acid positions used to determine genetic clade identity through a feature selection ranking within the model. These positions can be mapped onto a maximum-likelihood phylogenetic tree, allowing for the inference of clade defining mutations.

Discussion

Our approach is implemented as a python package with code available at https://github.com/flu-crew/classLog.

测序和系统发育分类已经成为人类和动物诊断实验室的共同任务。常规做法是对病原体进行测序,以确定具有诊断意义的遗传变异,并将这些数据用于实时基因组接触者追踪和监测。在这种模式下,产生了前所未有的数据量,需要快速分析以提供有意义的推理。方法提出了一种可以对基因序列数据进行分类的机器学习逻辑回归管道。该管道实现了一种直观和可定制的方法来开发一个训练有素的预测模型,该模型在线性时间复杂度下运行,即使数据不完整也能快速生成准确的输出。我们的方法以猪呼吸与生殖综合征病毒(PRRSv)和猪H1甲型流感病毒(IAV)数据集为基准。训练好的分类器针对序列和模拟数据集进行了测试,这些数据集人为地将序列质量降低了0、10、20、30和40%。结果当应用于低质量的序列数据时,分类器对PRRSv和猪H1 IAV HA数据集的准确率在85%到95%之间,当使用完整数据集时,这一准确率增加到接近完美。该模型还通过模型内的特征选择排序来确定用于确定遗传进化支身份的氨基酸位置。这些位置可以映射到最大似然系统发育树上,允许对进化枝定义突变的推断。我们的方法是作为python包实现的,其代码可在https://github.com/flu-crew/classLog上获得。
{"title":"classLog: Logistic regression for the classification of genetic sequences","authors":"Michael A. Zeller, Zebulun W. Arendsee, Gavin J.D. Smith, Tavis K. Anderson","doi":"10.3389/fviro.2023.1215012","DOIUrl":"https://doi.org/10.3389/fviro.2023.1215012","url":null,"abstract":"<sec><title>Introduction</title><p>Sequencing and phylogenetic classification have become a common task in human and animal diagnostic laboratories. It is routine to sequence pathogens to identify genetic variations of diagnostic significance and to use these data in realtime genomic contact tracing and surveillance. Under this paradigm, unprecedented volumes of data are generated that require rapid analysis to provide meaningful inference. </p></sec><sec><title>Methods</title><p>We present a machine learning logistic regression pipeline that can assign classifications to genetic sequence data. The pipeline implements an intuitive and customizable approach to developing a trained prediction model that runs in linear time complexity, generating accurate output rapidly, even with incomplete data. Our approach was benchmarked against porcine respiratory and reproductive syndrome virus (PRRSv) and swine H1 influenza A virus (IAV) datasets. Trained classifiers were tested against sequences and simulated datasets that artificially degraded sequence quality at 0, 10, 20, 30, and 40%. </p></sec><sec><title>Results</title><p>When applied to a poor-quality sequence data, the classifier achieved between &gt;85% to 95% accuracy for the PRRSv and the swine H1 IAV HA dataset and this increased to near perfect accuracy when using the full dataset. The model also identifies amino acid positions used to determine genetic clade identity through a feature selection ranking within the model. These positions can be mapped onto a maximum-likelihood phylogenetic tree, allowing for the inference of clade defining mutations. </p></sec><sec><title>Discussion</title><p>Our approach is implemented as a python package with code available at <uri xlink:href=\"https://github.com/flu-crew/classLog\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">https://github.com/flu-crew/classLog</uri>.</p></sec>","PeriodicalId":73114,"journal":{"name":"Frontiers in virology","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138531603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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Frontiers in virology
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