Infection Genetics and Evolution最新文献_第7页

Early plasma cytokines associated with multi-drug resistant ventilator-associated pneumonia after neurosurgery: A retrospective cohort study 神经外科术后早期血浆细胞因子与多药耐药呼吸机相关肺炎相关：一项回顾性队列研究

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-11 DOI: 10.1016/j.meegid.2025.105824

Yuanrun Zhu , Zhaodi Liao , Jianan Su , Feng Zhang , Jin Huang , Ping He , Zhifeng Wu , Kangli Xu , Xiaofeng Yang , Chen Jiang , Yadong Wang

Ventilator-associated pneumonia (VAP) is a major infectious complication in the neurologic intensive care unit (NICU). VAP caused by multi-drug resistant (MDR) pathogens is related to poor clinical outcomes. This study investigates the relationship between early plasma cytokine profiles and the development of MDR VAP following neurosurgery. We retrospectively analyzed neurosurgical patients admitted to the NICU who developed VAP between January 2021 and January 2024. A receiver operating characteristic (ROC) curve was used to determine the predictive value of the cytokines. Among 67 VAP patients, MDR VAP cases exhibited lower Glasgow Coma Scale (GCS) scores on admission and a higher incidence of prolonged hospitalization (>5 days) before infection. Significantly elevated levels of IL-2, IL-6, IL-10 and IL-17a were observed in MDR VAP patients, while IL-4, TNFα and IFNγ presented no statistical difference. ROC curves revealed that IL-2 (AUC: 0.722, 95 % CI: 0.599–0.845) and IL-10 (AUC: 0.798, 95 % CI: 0.687–0.909) had the strongest predictive value, with optimal cut-off values of 2.635 pg/mL (IL-2, sensitivity 57.1 %, specificity 84.4 %) and 8.495 pg/mL (IL-10, sensitivity 77.1 %, specificity 84.4 %), respectively. A combined IL-2 + IL-10 model further improved predictive performance (AUC: 0.827, 95 % CI: 0.726–0.927). This was confirmed by a multivariate analysis (OR: 23.1, p = 0.007). In conclusion, early elevations in plasma IL-2, IL-6, IL-10 and IL-17a (at 24 h of admission to the NICU) are associated with MDR VAP in NICU patients. The combined measurement of IL-2 and IL-10 may serve as a useful adjunctive tool for predicting post-neurosurgery MDR VAP risk, aiding in early clinical intervention.

呼吸机相关性肺炎（VAP）是神经重症监护病房（NICU）的主要感染性并发症。多药耐药（MDR）病原菌引起的VAP与临床预后差有关。本研究探讨了早期血浆细胞因子谱与神经外科术后MDR VAP发生的关系。我们回顾性分析了2021年1月至2024年1月期间入住NICU的发生VAP的神经外科患者。采用受试者工作特征（ROC）曲线确定细胞因子的预测价值。在67例VAP患者中，MDR VAP患者入院时格拉斯哥昏迷评分（GCS）较低，感染前住院时间延长（bbb50 天）的发生率较高。MDR VAP患者IL-2、IL-6、IL-10、IL-17a水平显著升高，IL-4、TNFα、IFNγ水平差异无统计学意义。ROC曲线显示，IL-2 （AUC: 0.722, 95 % CI: 0.599-0.845）和IL-10 （AUC: 0.798, 95 % CI: 0.687-0.909）具有最强的预测价值，最佳临界值分别为2.635 pg/mL （IL-2，敏感性57.1 %，特异性84.4 %）和8.495 pg/mL （IL-10，敏感性77.1 %，特异性84.4 %）。联合IL-2 + IL-10模型进一步提高了预测性能（AUC: 0.827, 95 % CI: 0.726-0.927）。多变量分析证实了这一点（OR: 23.1, p = 0.007）。综上所述，NICU患者早期血浆IL-2、IL-6、IL-10和IL-17a升高（入院24 h）与MDR VAP相关。联合测量IL-2和IL-10可作为预测术后MDR VAP风险的有用辅助工具，有助于早期临床干预。

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引用次数: 0

Modeling and sensitivity analysis of cholera dynamics under fuzzy imprecision 模糊不精确条件下霍乱动力学建模及敏感性分析。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-16 DOI: 10.1016/j.meegid.2025.105821

Sara Riaz , Asghar Ali , Muhammad Munir

This article presents a sensitivity analysis of the cholera transmission model, in which all parameters related to disease dynamics are considered as fuzzy numbers. Classical and system sensitivities of this fuzzy system have been analyzed to provide a real world approximation to cholera outbreaks. Graphical results indicate that the susceptible population is most sensitive to the new recruitment and disease-induced mortality rates of the infected and treated populations, whereas the infected population is found to be more sensitive to immune loss and disease transmission rate. The treated individuals have proven sensitivity towards the contact rate, while the recovered ones are more sensitive to the recovery and disease-induced death rates. The cumulative effect of these sensitivities with respect to induced fuzzy parameters on the model output has been reflected in the system sensitivities. As a consequence of this analysis, treatment and the disease transmission rate are identified as the most influential parameters for this newly structured model.

本文提出了霍乱传播模型的敏感性分析，其中所有与疾病动力学有关的参数都被认为是模糊数。分析了该模糊系统的经典灵敏度和系统灵敏度，以提供一个真实世界的近似霍乱暴发。图形结果表明，易感人群对感染和治疗人群的新招募率和疾病引起的死亡率最为敏感，而感染人群对免疫丧失和疾病传播率更为敏感。经治疗的个体已证实对接触率敏感，而康复的个体对康复率和疾病引起的死亡率更为敏感。这些灵敏度相对于诱导模糊参数对模型输出的累积效应已反映在系统灵敏度中。作为分析的结果，治疗和疾病传播率被确定为这个新结构模型中最具影响力的参数。

引用次数: 0

Unravelling ecological factors influencing phylodynamics of Kyasanur Forest Disease in India 揭示影响印度Kyasanur森林病害系统动力学的生态因素。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-17 DOI: 10.1016/j.meegid.2025.105831

Sahal Paladan , Bhimanagoud Kumbar , Dharani Govindasamy , Shweta Patil , H.B. Chethan Kumar , Revanaiah Yogisharadhya , Pragya Yadav , T. Jeromie Wesley Vivian , Sathish S. Gaekwad , Naveen Kumar , Baldev Raj Gulati , Sathish Bhadravati Shivachandra , Mohammed Mudassar Chanda

Kyasanur Forest Disease Virus (KFDV) is a tick-borne flavivirus endemic to the Western Ghats region of India, with increasing reports of geographic expansion. This study employs phylogenetic analysis and spatial diffusion modeling to understand the evolutionary dynamics and transmission patterns of KFDV. Whole genome and E-gene sequences were analysed to identify major phylogenetic clusters, transmission velocity, and environmental factors influencing viral spread. The analysis revealed two primary phylogenetic clusters: Cluster A, originating in Karnataka, and linked to initial outbreaks (1957–1972) and subsequent re-emergence post-2010 in Karnataka, Kerala, and Goa; and Cluster B, which expanded from Maharashtra in the late 1970s into Tamil Nadu, Karnataka, and Kerala. Phylogenetic findings indicated a slow mutation rate, indicative of long-term viral persistence in sylvatic reservoirs rather than sustained human-human transmission.

Spatial diffusion analysis estimated a median transmission velocity of 59.67 km/year. Environmental factors such as deforestation, land cover change, and livestock density acted as facilitators of viral spread, while urbanization, open water bodies, and precipitation served as resistance factors. The findings underscore the need for enhanced surveillance, ecological monitoring, and public health interventions to mitigate the increasing risk of KFD outbreaks. This study provides a comprehensive framework for understanding KFDV transmission and evolution, integrating phylogenetic and ecological data to improve risk assessment and guide control strategies in both endemic and emerging regions.

喀萨努尔森林病病毒（KFDV）是印度西高止山脉地区的一种地方性蜱传黄病毒，有越来越多的地理扩展报告。本研究采用系统发育分析和空间扩散模型来了解KFDV的进化动力学和传播模式。分析全基因组和e基因序列，以确定主要的系统发育集群、传播速度和影响病毒传播的环境因素。分析揭示了两个主要的系统发育聚集性：聚集性A，起源于卡纳塔克邦，与卡纳塔克邦、喀拉拉邦和果阿邦的最初暴发（1957-1972年）和2010年后的再次暴发有关；B集群在20世纪70年代末从马哈拉施特拉邦扩展到泰米尔纳德邦、卡纳塔克邦和喀拉拉邦。系统发育结果表明突变率缓慢，表明病毒在森林水库中长期存在，而不是持续的人类传播。空间扩散分析估计中位传播速度为59.67 km/年。森林砍伐、土地覆盖变化和牲畜密度等环境因素是病毒传播的促进因素，而城市化、开放水体和降水是病毒传播的阻力因素。研究结果强调需要加强监测、生态监测和公共卫生干预，以减轻口蹄疫爆发日益增加的风险。该研究为了解KFDV的传播和进化提供了一个全面的框架，整合了系统发育和生态数据，以改善流行地区和新兴地区的风险评估和指导控制策略。

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引用次数: 0

Meta-analysis of genetic diversity of VP1 gene of foot and mouth disease virus serotypes prevalent in Bangladesh from 2010 to 2024 2010 - 2024年孟加拉国流行口蹄疫病毒血清型VP1基因遗传多样性的meta分析

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-10-01 DOI: 10.1016/j.meegid.2025.105835

Md. Abdur Rahman , Farah Zereen , Md. Al-Amin , Md. Golzar Hossain , Jahangir Alam , Masaru Shimada , Md. Tanvir Rahman , Sukumar Saha

Foot and Mouth Disease (FMD) is a transboundary viral disease caused by the Foot and Mouth Disease Virus (FMDV), which is classified into seven serotypes (A, O, C, Asia 1, SAT 1, SAT 2 and SAT 3) within the Picornaviridae family and Aphthovirus genus that affects both wild and domesticated cloven-hoofed animals, leading to high morbidity and substantial economic losses. In Bangladesh, three serotypes of FMDV: O, A, and Asia 1 predominantly affect cattle, remarkably more than one serotype in each year. Disease prevention relies on vaccination against the prevalent serotypes. However, despite extensive vaccination efforts, FMD outbreaks continue to occur due to high variability in FMDV, particularly of the VP1 gene, which gives rise to new variants and complicates control strategies. This review aims to Meta-analyze the epidemiological characteristics and functional divergence of prevalent FMDV serotypes in Bangladesh from 2010 to 2024 by examining their evolutionary history and dynamics based on partial VP1 gene sequences retrieved from NCBI GenBank database. It explores the FMDV serotypes, host, ecology, annual prevalence, sequence length, antigenic regions, evolutionary relationships, genotypes, and divergence, as well as amino acid variables in the BC loop, G-H loop and C-terminus region of the VP1 gene of prevalent FMDV serotypes. Additionally, the study addresses the similarity of currently used FMDV vaccine strains` VP1 amino acid sequences compare to VP1 amino acid sequence of prevalent FMDV serotypes, underscoring the need for updated vaccines that target circulating strains for effective disease control.

口蹄疫（FMD）是由口蹄疫病毒（FMDV）引起的一种跨界病毒性疾病，该病毒分为小核糖核酸病毒科和Aphthovirus属的七种血清型（a、O、C、Asia 1、SAT 1、SAT 2和SAT 3），可影响野生和家养的分蹄动物，导致高发病率和重大经济损失。在孟加拉国，三种血清型口蹄疫病毒：O型、A型和亚洲1型主要影响牛，每年明显不止一种血清型。疾病预防依赖于针对流行血清型的疫苗接种。然而，尽管开展了广泛的疫苗接种工作，但由于口蹄疫病毒，特别是VP1基因的高度变异，导致新的变异和控制策略复杂化，口蹄疫疫情继续发生。本文基于NCBI GenBank数据库检索的部分VP1基因序列，对2010 - 2024年孟加拉国流行FMDV血清型的进化历史和动态进行meta分析。探讨流行FMDV血清型、宿主、生态、年流行率、序列长度、抗原区、进化关系、基因型、分化，以及VP1基因BC环、G-H环和c端区的氨基酸变化。此外，该研究解决了目前使用的FMDV疫苗株的VP1氨基酸序列与流行的FMDV血清型的VP1氨基酸序列的相似性，强调需要更新针对流行菌株的疫苗以有效控制疾病。

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引用次数: 0

Genomic insights into persistent infections, reinfections, and subspecies diversity of Mycobacteroides abscessus: A whole-genome sequencing study of Thai and global isolates 持续感染、再感染和脓肿分枝杆菌亚种多样性的基因组研究：泰国和全球分离株的全基因组测序研究。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-10-09 DOI: 10.1016/j.meegid.2025.105838

Kanwara Trisakul , Auttawit Sirichoat , Arnone Nithichanon , Suwatchareeporn Rotcheewaphan , Jody Phelan , Taane G. Clark , Kiatichai Faksri

Mycobacteroides abscessus is a highly resistant pathogen with significant genetic diversity and complicating clinical management. This study used whole-genome sequencing to analyze genomic variations in seven serially collected isolates from three Thai patients, distinguishing between persistent infections and reinfections. Comparative analysis with 43 global isolates revealed subspecies-specific genetic diversity and distribution patterns. Among Thai isolates, two paired samples (P7.1-P7.2 and P15.1-P15.2) were persistent infections (same clone), while two (P8.1-P8.2 and P15.2-P15.3) were reinfections (different clones). Genome-wide comparisons revealed depth distribution patterns and gene cluster variations among different clones, whereas minimal divergence was observed within persistent infections. Although initial pan-genome analysis identified unique genes in same-clone pairs (P7.1 vs. P7.2 and P15.1 vs. P15.2), further validation using raw read mapping confirmed these genes were not truly unique. Analysis of global isolates showed subspecies-specific genetic variations. M. abscessus subsp. abscessus (MAB) and M. abscessus subsp. massiliense (MMAS) exhibited distinct genotypically drug resistance profiles, with unique core genes linked to adaptation and resistance mechanisms. STRING analysis identified 42 unique core genes in MAB, with 11 gene interactions—truB, prmC_2, and aguA_2 showing the highest interaction scores. In contrast, MMAS had 11 unique core genes with a single interaction between lgrD_4 and rnc. Subsequent validation using NCBI BLAST showed only fmt_2 and aguA_2 were truly unique to MAB. This study provides new insights into the genomic evolution of M. abscessus during persistent and reinfections and genetic variation among subspecies. The findings enhance understanding of M. abscessus epidemiology and may inform therapeutic and infection control.

脓肿分枝杆菌是一种高度耐药的病原体，具有显著的遗传多样性和复杂的临床管理。该研究使用全基因组测序分析了从3名泰国患者连续收集的7株分离株的基因组变异，区分了持续感染和再感染。与43个全球分离株的比较分析揭示了亚种特异性遗传多样性和分布格局。在泰国分离株中，2对样本（p7.1 ~ p7.2和p15.1 ~ p15.2）为持续感染（同一克隆），2对样本（p8.1 ~ p8.2和p15.2 ~ p15.3）为再感染（不同克隆）。全基因组比较揭示了不同克隆之间的深度分布模式和基因簇变异，而在持续感染中观察到的差异很小。虽然最初的泛基因组分析确定了相同克隆对中的独特基因（P7.1 vs. P7.2和P15.1 vs. P15.2），但使用原始读取图谱进一步验证证实这些基因并非真正独特。全球分离株分析显示亚种特异性遗传变异。脓肿支原体脓疡芽孢杆菌（MAB）和脓疡芽孢杆菌。马尾蛇（MMAS）表现出独特的基因典型耐药谱，具有与适应和耐药机制相关的独特核心基因。字符串分析鉴定出42个独特的MAB核心基因，其中trub、prmC_2和aguA_2等11个基因互作得分最高。相比之下，MMAS有11个独特的核心基因，lgrD_4和rnc之间存在单一的相互作用。随后使用NCBI BLAST验证表明，只有fmt_2和aguA_2是MAB真正独特的。本研究为脓疡分枝杆菌在持续感染和再感染期间的基因组进化以及亚种间的遗传变异提供了新的见解。研究结果增强了对脓疡分枝杆菌流行病学的认识，并可能为治疗和感染控制提供信息。

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引用次数: 0

Genetic diversity of Echinococcus multilocularis from red foxes and humans in northern and northeastern Poland investigated using the microsatellite EmsB 用微卫星EmsB对波兰北部和东北部地区红狐和人多房棘球蚴的遗传多样性进行了研究。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-10-12 DOI: 10.1016/j.meegid.2025.105843

Paweł Gładysz , Małgorzata Samorek-Pieróg , Jacek Karamon , Krzysztof Rębała , Małgorzata Sulima , Dariusz Zadrożny , Anna Lass

Background

Echinococcus multilocularis is the causative agent of alveolar echinococcosis (AE). We explored the diversity of EmsB profiles of E. multilocularis from red foxes and humans in northern and northeastern Poland, with a particular focus on autochthonous Asian variants.

Methods

We investigated 263 adult tapeworms from 59 red foxes hunted in selected districts of three voivodships and ten metacestodes extracted from AE patients who never visited Asia. We conducted hierarchical clustering of the obtained EmsB profiles combined with a custom Asian reference dataset and interpreted the resulting phenogram by applying the standard genetic distance threshold (GDT) of 0.08 and Dynamic Tree Cut (DTC).

Results

The GDT divided the 273 profiles into six units, with Pol-B being the most frequent (220/273, 81 %) and widespread variant. DTC grouped the profiles into three phenons (PH). Eight out of ten people got infected with the predominant variant, PH-2/Pol-B. Among the 273 samples, thirty-six (13 %) matched the Asian reference set, including metacestodes from a Lithuanian patient and a Polish patient.

Conclusions

Genetically extra-European variants reach as far north as Pomorskie Voivodship. They likely come from East Asia. The autochthonous AE case with an Asian profile confirms that such tapeworms have penetrated the synanthropic cycle.

背景：多房棘球蚴是肺泡棘球蚴病（AE）的病原体。我们探索了波兰北部和东北部红狐和人类多房棘猴EmsB谱的多样性，特别关注亚洲本土变异。方法：从3个省选定地区捕获的59只红狐中提取263条成虫，并从从未去过亚洲的AE患者中提取10种囊绦虫。我们结合自定义的亚洲参考数据集对获得的EmsB谱进行了分层聚类，并通过0.08的标准遗传距离阈值（GDT）和动态树切（DTC）来解释得到的表型图。结果：GDT将273个基因型分为6个单位，其中Pol-B是最常见的（220/273,81 %）和广泛变异。DTC将这些剖面分为三个表型（pH）。10人中有8人感染了主要变种PH-2/Pol-B。在273个样本中，36个（13 %）与亚洲参考集匹配，包括来自立陶宛患者和波兰患者的元跖骨。结论：基因上的非欧洲变异最远可到达波莫尔斯基省北部。他们可能来自东亚。具有亚洲特征的本土AE病例证实，这种绦虫已经穿透了共胞循环。

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引用次数: 0

Postbiotics and extracellular vesicles: Mechanisms of action and clinical promise in respiratory infections and inflammation 生物后制剂和细胞外囊泡：呼吸道感染和炎症的作用机制和临床前景。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-10-03 DOI: 10.1016/j.meegid.2025.105837

Manouchehr Fadaee , Danial Mahrooghi , Masoud Lahouty , Shahram Abdoli Oskouei , Javad Nezhadi

Postbiotics are bioactive metabolites and structural components derived from probiotic microorganisms that exert health benefits without the requirement for live bacteria. These include short-chain fatty acids, peptides, polysaccharides, and bacterial cell wall fragments, all of which demonstrate immunomodulatory, anti-inflammatory, and antimicrobial properties. Compared with probiotics, postbiotics are more stable, safer, and increasingly recognized as potential therapeutic agents. Extracellular vesicles (EVs) released by probiotics have likewise emerged as important mediators of host–microbe interactions. In respiratory diseases such as pneumonia, influenza, coronavirus disease 2019 (COVID-19), asthma, cystic fibrosis, tuberculosis, and allergic rhinitis, postbiotics strengthen epithelial barriers, regulate immune responses, disrupt pathogenic biofilms, and enhance the effectiveness of conventional therapies. Their capacity to influence the gut–lung axis further extends their benefits beyond the respiratory system, contributing to systemic immune balance and microbiota homeostasis. Moreover, postbiotics show potential in mitigating antimicrobial resistance by selectively targeting pathogens while preserving commensal microbes. Taken together, the safety, versatility, and therapeutic promise of postbiotics highlight their potential as adjuncts to standard treatments and as innovative strategies for infection control and respiratory health management.

后生物制剂是从益生菌微生物中提取的生物活性代谢物和结构成分，在不需要活菌的情况下发挥健康益处。这些物质包括短链脂肪酸、多肽、多糖和细菌细胞壁片段，它们都具有免疫调节、抗炎和抗菌特性。与益生菌相比，后益生菌更稳定、更安全，越来越被认为是潜在的治疗药物。由益生菌释放的细胞外囊泡（EVs）也同样成为宿主-微生物相互作用的重要介质。在肺炎、流感、2019冠状病毒病（COVID-19）、哮喘、囊性纤维化、结核病和变应性鼻炎等呼吸道疾病中，后生物制剂可增强上皮屏障，调节免疫反应，破坏致病性生物膜，并增强常规疗法的有效性。它们影响肠-肺轴的能力进一步将其益处扩展到呼吸系统之外，有助于系统免疫平衡和微生物群稳态。此外，后生物制剂显示出通过选择性靶向病原体同时保存共生微生物来减轻抗菌素耐药性的潜力。综上所述，后生物制剂的安全性、多功能性和治疗前景突出了它们作为标准治疗的辅助手段以及作为感染控制和呼吸健康管理的创新策略的潜力。

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引用次数: 0

Long-term circulation and molecular evolution of rat hepatitis E virus in wild Norway rat populations from Berlin, Germany 德国柏林野生挪威大鼠种群中戊型肝炎病毒的长期循环和分子进化。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-10-16 DOI: 10.1016/j.meegid.2025.105841

Jessica Panajotov , Katja Schilling-Loeffler , Calvin Mehl , Dorina Meneghini , Jörns Fickel , Janina Beyer , Thomas von Graffenried , Gerald Heckel , Rainer G. Ulrich , Reimar Johne

Rat hepatitis E virus (ratHEV, Rocahepevirus ratti) is an emerging zoonotic pathogen which was recently identified in several human hepatitis patients. The virus has been demonstrated in its primary reservoir hosts, rats, in many countries of the world. However, little is known about the persistence and molecular evolution of ratHEV in a host population over time. Here, wild Norway rats (Rattus norvegicus) from Berlin, Germany, were screened for ratHEV, and virus strains and rats were genetically characterized. The ratHEV detection rate in 2023 (8.3 %, 11/131) was similar to that of 2009/2010 (11.5 %, 7/61). Generated virus genome sequences showed 89.3 % to 100 % nucleotide sequence similarity to each other. Phylogenetic analysis indicated clustering of the sequences from the rats and a human patient from Berlin, irrespective of year and separate from sequences from other parts of Germany. Strains from Berlin formed subclades according to sampling districts, and rivers were identified as possible barriers between subclades. Rat population genetics analysis indicated a stable rat population with a dominant genetic cluster containing most ratHEV-infected rats at both time-points, and the presence of closely related virus strains within a genetic subcluster. Analysis of all ratHEV strains identified variable amino acid positions in all four virus-encoded proteins. The results indicate long-term persistence of ratHEV in wild rat populations, which is mainly driven by local transmission of virus strains in small geographic areas. Environmental and rat surveillance for ratHEV, along with effective pest control, should be considered to reduce the risk of human infections in future.

大鼠戊型肝炎病毒（ratHEV）是一种新出现的人畜共患病原体，最近在一些人类肝炎患者中发现。在世界许多国家，该病毒已在其主要宿主大鼠中得到证实。然而，随着时间的推移，人们对ratHEV在宿主群体中的持久性和分子进化知之甚少。在这里，对来自德国柏林的野生挪威大鼠（褐家鼠）进行了ratHEV筛选，并对病毒株和大鼠进行了遗传表征。2023年ratHEV检出率（8.3 %,11/131）与2009/2010年（11.5 %,7/61）相似。生成的病毒基因组序列之间核苷酸序列相似性为89.3% % ~ 100% %。系统发育分析表明，来自柏林的大鼠和一名人类患者的序列聚类，不分年份，与来自德国其他地区的序列分离。来自柏林的菌株根据采样区形成亚支系，河流被确定为亚支系之间可能的屏障。大鼠群体遗传学分析表明，在两个时间点，大鼠群体稳定，优势遗传集群包含大多数感染rathev的大鼠，并且在遗传亚集群中存在密切相关的病毒株。对所有ratHEV菌株的分析发现，所有四种病毒编码蛋白的氨基酸位置都是可变的。结果表明，ratHEV在野生大鼠种群中长期存在，这主要是由于病毒株在小地理区域的局部传播所致。应考虑开展环境和鼠类监测，同时采取有效的害虫防治措施，以减少今后人类感染的风险。

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引用次数: 0

Single-cell RNA sequencing in high-burden viral respiratory infections: Decoding immune cell subsets and immune-related differential gene expression 高负荷病毒性呼吸道感染的单细胞RNA测序：解码免疫细胞亚群和免疫相关差异基因表达

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-23 DOI: 10.1016/j.meegid.2025.105834

Milad Sheervalilou, Mostafa Ghanei, Masoud Arabfard

Respiratory infections remain a major global health burden, ranking among the leading causes of mortality worldwide. Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology for dissecting the cellular and molecular complexity of these infections. This review focuses on recent scRNA-seq studies investigating the immune landscape of high-burden viral respiratory infections, particularly COVID-19 and influenza, which are characterized by high transmissibility and clinical impact. We provide an overview of publicly available scRNA-seq datasets derived from human peripheral blood and bronchoalveolar lavage fluid (BALF), as well as lung tissues and explants from murine models, emphasizing their value in profiling immune heterogeneity. scRNA-seq has revealed significant remodeling of immune cell populations during infection, including the identification of novel subsets such as CD4⁺ c13-MKI67⁺ CCL5^low T cells, CD8⁺ CXCR3^high GZMA⁺ T cells, and CD56^high CD16⁻ GZMB⁺ NK cells. These subsets are frequently associated with differential expression of cytokines, chemokines, and interferon-stimulated genes that reflect disease severity and progression. In addition, scRNA-seq has highlighted key pathogen-induced pathways, including type I interferon, NF-κB, and JAK/STAT signaling, and has identified emerging immune-related biomarkers—such as PTX3, MCEMP1, CXCR4, IFIT1, ISG15, and STAT1—with potential diagnostic and prognostic utility. While scRNA-seq applications in respiratory infections of other microbial origins are limited, its role in mapping immune responses and guiding biomarker discovery in viral infections is rapidly expanding. This review synthesizes these findings to inform future translational research and immunodiagnostic strategies.

呼吸道感染仍然是一个主要的全球健康负担，是全世界死亡的主要原因之一。单细胞RNA测序（scRNA-seq）已经成为一种革命性的技术，用于解剖这些感染的细胞和分子复杂性。本文综述了最近的scRNA-seq研究，研究了高负担病毒性呼吸道感染的免疫景观，特别是COVID-19和流感，这些疾病具有高传染性和临床影响。我们概述了来自人类外周血和支气管肺泡灌洗液（BALF）以及小鼠模型肺组织和外植体的公开可用scRNA-seq数据集，强调了它们在分析免疫异质性方面的价值。scRNA-seq揭示了感染期间免疫细胞群的显著重塑，包括鉴定出新的亚群，如CD4+ c13-MKI67+ CCL5low T细胞、CD8+ CXCR3high GZMA+ T细胞和cd56高CD16- GZMB+ NK细胞。这些亚群通常与反映疾病严重程度和进展的细胞因子、趋化因子和干扰素刺激基因的差异表达有关。此外，scRNA-seq还发现了关键的病原体诱导通路，包括I型干扰素、NF-κB和JAK/STAT信号，并发现了新兴的免疫相关生物标志物，如PTX3、MCEMP1、CXCR4、IFIT1、ISG15和stat1，具有潜在的诊断和预后价值。虽然scRNA-seq在其他微生物来源的呼吸道感染中的应用有限，但它在绘制免疫反应和指导病毒感染中生物标志物发现方面的作用正在迅速扩大。这篇综述综合了这些发现，为未来的转化研究和免疫诊断策略提供信息。

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引用次数: 0

Molecular characterization and clinical insights into feline chaphamaparvovirus (FeChPV) in cats from Thailand 泰国猫chaphamparvovirus （FeChPV）的分子特征和临床研究。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-29 DOI: 10.1016/j.meegid.2025.105836

Aisyah Nikmatuz Zahro , Panida Poonsin , Tanit Kasantikul , Chutchai Piewbang , Somporn Techangamsuwan

Feline chaphamaparvovirus (FeChPV) is a recently discovered parvovirus in cats that is linked to respiratory and enteric diseases. Notably, FeChPV is also detected in healthy cats, warranting further investigation into its clinical significance. This study aimed to assess the presence of FeChPV in cats across Thailand while also exploring its genetic characteristics through phylogenetic, recombination, and selective pressure analyses. Molecular investigations were performed on oropharyngeal swabs from both healthy (n = 165) and diseased (n = 167) cats. The findings revealed an FeChPV detection rate of 10.2 % (34/332), with the virus detected in both healthy (9.1 %, 15/165) and diseased cats (11.4 %, 19/167). However, no significant association was observed between these conditions and the presence of FeChPV (p = 0.5879). Among the FeChPV-positive cases, 61.8 % (21/34) exhibited concurrent detection with common feline viruses. Apart from oropharyngeal swab samples, FeChPV was also detected in additional clinical samples, including nasal swabs, auricular swabs, rectal swabs, and urine samples. Phylogenetic analysis of the complete coding sequence indicated that most FeChPV strains in this study clustered into a single clade, except for BKK052 and CB050. Two recombinant strains (C14 and HF2) from China were found, in which FeChPV CB050 Thai strain served as putative minor and major parents, respectively. The NS1 and VP1 codon sequences underwent negative selective pressure, with multiple positive selection sites observed. Although a specific disease associated with FeChPV infection could not be concluded, underlying health conditions may increase susceptibility to FeChPV infection. Further research is essential to comprehensively understand the role of this virus in feline health.

猫chaphamparvovirus （FeChPV）是最近在猫身上发现的一种与呼吸道和肠道疾病有关的细小病毒。值得注意的是，在健康猫中也检测到FeChPV，值得进一步研究其临床意义。本研究旨在评估泰国猫中FeChPV的存在，同时通过系统发育、重组和选择压力分析探索其遗传特征。对健康猫（n = 165）和患病猫（n = 167）的口咽拭子进行了分子调查。结果显示，FeChPV的检出率为10. %(34/332)，在健康猫（9.1 %,15/165）和病猫（11.4 %,19/167）中均检测到病毒。然而，这些情况与FeChPV的存在之间没有明显的关联（p = 0.5879）。在fechpv阳性病例中，61.8 %（21/34）与常见猫病毒同时检测。除了口咽拭子样本外，还在其他临床样本中检测到FeChPV，包括鼻拭子、耳拭子、直肠拭子和尿液样本。完整编码序列的系统发育分析表明，除BKK052和CB050外，本研究中大多数FeChPV株聚集在一个分支中。从中国分离到2株重组菌株（C14和HF2），其中泰国菌株FeChPV CB050分别推定为主要亲本和次要亲本。NS1和VP1密码子序列存在负选择压力，存在多个正选择位点。虽然与FeChPV感染相关的特定疾病尚未确定，但潜在的健康状况可能会增加对FeChPV感染的易感性。要全面了解这种病毒在猫科动物健康中的作用，进一步的研究是必不可少的。

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引用次数: 0