Infection Genetics and Evolution最新文献_第3页

Human polyomavirus 6 differentially infects healthy and tumor tissue in the colon: A case report 人类多瘤病毒6型在结肠健康组织和肿瘤组织中的差异感染：1例报告。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2026-01-01 DOI: 10.1016/j.meegid.2025.105865

Maria Dolci , Fabio Frosio , Lucia Signorini , Alessio Soggiu , Gabriele Meroni , Evaldo Favi , Estefania Calvo Alvarez , Pasquale Ferrante , Serena Delbue

Introduction

Human polyomavirus 6 (HPyV6) is part of the human skin virome. Like other HPyVs, it encodes proteins with oncogenic properties.

Materials and methods

A 73-year-old Italian female patient with stage II right-sided colon adenocarcinoma underwent hemicolectomy; she died one month later because of bacterial sepsis. Colon tumor (T), adjacent healthy (AH) tissue, and serum samples were collected. Total nucleic acids were subjected to next-generation sequencing, followed by metagenomics analysis. HPyV detection was confirmed by real-time PCR and Rolling Circle Amplification (RCA); HPyV6 transcripts and proteins were identified by means of PCR and Western blot/mass spectrometry, respectively.

Results

Viral metagenomics analysis revealed the presence of several viral genomes, mainly belonging to unclassified viruses and phages, in both AH and T tissues. HPyV6 DNA was detected in the T tissue, representing 7 % of the viral sequences, but not in the AH tissue. Subsequent molecular analysis confirmed the presence of the HPyV6 genomes (3.3x10⁶copies/ug) as episomes, infecting 19.8 % of the tumor cells; LT-Ag and VP1 transcripts were expressed in the T tissue, and the LT-Ag protein was expressed twice as highly in the T tissue as in the AH tissue.

Conclusions

This is the first report of the differential presence and expression of the HPyV6 genome in colon tumors but not in the AH tissue. These results are indicative of ongoing active replication of the virus, which might play a triggering role in malignant transformation.

人类多瘤病毒6 （HPyV6）是人类皮肤病毒组的一部分。像其他hpyv一样，它编码具有致癌特性的蛋白质。材料和方法：73岁意大利女性II期右侧结肠腺癌患者行半结肠切除术；一个月后，她死于细菌性败血症。收集结肠肿瘤(T)、邻近健康组织（AH）和血清样本。总核酸进行下一代测序，然后进行宏基因组学分析。real-time PCR和Rolling Circle Amplification （RCA）检测HPyV；分别用PCR和Western blot/质谱法鉴定HPyV6转录本和蛋白。结果：病毒宏基因组分析显示，AH和T组织中均存在多个病毒基因组，主要属于未分类的病毒和噬菌体。在T组织中检测到HPyV6 DNA，占7 %的病毒序列，但在AH组织中未检测到。随后的分子分析证实HPyV6基因组（3.3x106拷贝/ μ g）作为片段存在，感染19.8% %的肿瘤细胞；LT-Ag和VP1转录本在T组织中表达，LT-Ag蛋白在T组织中的表达量是AH组织的两倍。结论：这是首次报道HPyV6基因组在结肠肿瘤中存在和表达的差异，而在AH组织中没有。这些结果表明病毒正在进行积极的复制，这可能在恶性转化中起触发作用。

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引用次数: 0

Distribution of voltage-gated sodium channel and acetylcholinesterase mutations in Bemisia tabaci species from the Democratic Republic of the Congo 刚果民主共和国烟粉虱种电压门控钠通道和乙酰胆碱酯酶突变的分布。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2026-01-01 DOI: 10.1016/j.meegid.2025.105866

Olivier Likiti Kola , Christophe Simiand , Hadija Mussa Ally , Daniel Otron , Sharon L. van Brunschot , Justin S. Pita , John Colvin , Godefroid Monde Te-Kazangba , Hélène Delatte

The intensive use of insecticides can result in the emergence of resistant genotypes, as observed globally in the B. tabaci species complex. Two well-studied/known cases of resistance mechanisms in B. tabaci involve mutations in the voltage-gated sodium channel (Kdr) and acetylcholinesterase (Ace 1) genes. However, no studies have surveyed these resistance mechanisms in whitefly populations from Central Africa. To study the frequency of these mutations in whitefly species on cassava, 1315 individuals were collected from 60 fields across 12 provinces of the Democratic Republic of the Congo. Species were identified molecularly, and then the frequencies of Kdr and Ace 1 mutations were assessed. Four species were found: SSA1-SG1 ∪ SG2 (71.48 %); SSA1-SG3 (0.31 %); SSA2 ∪ SSA3 (15.51 %), and MED ASL (12.70 %). For the Kdr mutation, 9 % of individuals of SSA1-SG1 ∪ SG2, 6 % of MED ASL, and 3 % of SSA2USSA3 carried at least one resistant allele. For the Ace 1 mutation, resistance alleles were found in 0.1 % of SSA1-SG1 ∪ SG2, 6 % of MED ASL, and 1 % of SSA2 ∪ SSA3 individuals. The geographical distribution of resistant genotypes remains limited to certain regions. However, there is a long-term risk that resistance becomes established around areas where insecticides are used on cotton and vegetable crops. Appropriate strategies for the management of these vectors of phytoviruses are discussed.

大量使用杀虫剂可导致抗性基因型的出现，正如在全球范围内观察到的烟粉虱物种复合体一样。两个研究充分/已知的烟粉虱耐药机制案例涉及电压门控钠通道（Kdr）和乙酰胆碱酯酶（Ace 1）基因的突变。然而，没有研究调查过中非白蝇种群的这些抗性机制。为了研究木薯粉虱物种中这些突变的频率，从刚果民主共和国12个省的60个田间收集了1315个个体。分子鉴定物种，然后评估Kdr和Ace 1突变的频率。共发现4种：SSA1-SG1∪SG2(71.48 %)；SSA1-SG3(0.31 %);SSA2∪SSA3(15.51 %),MED ASL（12.70 %）。对于Kdr突变，9 %的SSA1-SG1∪SG2个体，6 %的MED ASL个体和3 %的SSA2USSA3个体携带至少一个耐药等位基因。对于Ace 1突变，抗性等位基因在SSA1-SG1∪SG2个体中占0.1% %，在MED ASL个体中占6% %，在SSA2∪SSA3个体中占1% %。耐药基因型的地理分布仍然局限于某些地区。然而，长期的风险是，在棉花和蔬菜作物使用杀虫剂的地区周围形成抗药性。讨论了管理这些植物病毒载体的适当策略。

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引用次数: 0

Genetic diversity and evolutionary relationships of porcine astroviruses from wild boars and domestic pigs in Japan 日本野猪和家猪星状病毒的遗传多样性和进化关系。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2026-01-01 DOI: 10.1016/j.meegid.2025.105875

Shuntaro Mizuno , Natsuko Teshima , Tomoko Yokota , Shwe Thiri Maung Maung Khin , Hitoshi Takemae , Toru Oi , Fujiko Fukuda , Tsuneyuki Masuda , Yasuhiro Kikkawa , Takanori Shiga , Naoyuki Aihara , Junichi Kamiie , Hiroho Ishida , Hironobu Murakami , Tetsuya Mizutani , Mami Oba , Makoto Nagai

Porcine astrovirus (PoAstV) is a viral pathogen associated with diarrhea and neurological disorders in piglets. In this study, we performed metatranscriptome analysis of fecal samples, and compared the full-length genomes of PoAstVs detected in Japanese wild boars and domestic pigs collected between 2017 and 2023 with astrovirus sequences from the GenBank database. Phylogenetic analyses of near-complete genomes from 12 wild boar and 67 pig PoAstVs, together with sequences from our previous study and the GenBank database, revealed that six, four, and two wild boar PoAstV sequences clustered with PoAstV-2, PoAstV-4, and PoAstV-5, respectively. Pig-derived PoAstVs comprised all five known genotypes, with PoAstV-2 (31/67) being predominant, followed by PoAstV-4 (18/67) and PoAstV-5 (12/67), similar to the pattern observed in wild boars. Some wild boar PoAstV strains showed high nucleotide identity with domestic Japanese strains, whereas others exhibited greater similarity to foreign porcine strains. Notably, two wild boar PoAstV-4 strains showed high identity with Chinese and Vietnamese PoAstV-4 in ORF1a and ORF1b, forming a distinct cluster, while no clustering was observed in ORF2, indicating possible recombination events. Intragenotype recombination was also detected among wild boar and domestic pig strains of PoAstV-2, −4, and − 5, implying wildlife-domestic interface. These findings suggest that PoAstVs are exchanged between wild boars and domestic pigs in Japan, promoting genetic diversification within each genotype through recombination. To our knowledge, this is the first detection and genomic characterization of PoAstV in Japanese wild boars.

猪星状病毒（PoAstV）是一种与仔猪腹泻和神经系统疾病相关的病毒性病原体。在本研究中，我们对粪便样本进行了亚转录组分析，并将2017年至2023年收集的日本野猪和家猪中检测到的poastv的全长基因组与GenBank数据库中的星状病毒序列进行了比较。对12个野猪和67个猪PoAstV的近完整基因组进行系统发育分析，结合我们之前的研究和GenBank数据库的序列，发现野猪PoAstV序列分别有6个、4个和2个与PoAstV-2、PoAstV-4和PoAstV-5聚集。猪源性poastv包括所有五种已知的基因型，其中PoAstV-2（31/67）占主导地位，其次是PoAstV-4（18/67）和PoAstV-5(12/67)，与在野猪中观察到的模式相似。一些野猪PoAstV毒株显示出与日本国内毒株的高核苷酸同源性，而另一些则显示出与外国猪毒株的高相似性。值得注意的是，两株野猪PoAstV-4在ORF1a和ORF1b中与中国和越南的PoAstV-4表现出高度的同源性，形成了一个明显的聚类，而在ORF2中没有发现聚类，表明可能存在重组事件。PoAstV-2、-4和 - 5在野猪和家猪株中也检测到基因型内重组，提示存在野生-家猪界面。这些发现表明，poastv在日本野猪和家猪之间进行了交换，通过重组促进了每种基因型的遗传多样化。据我们所知，这是首次在日本野猪中检测到PoAstV并进行基因组鉴定。

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引用次数: 0

Corrigendum to “Comparative study of rapid influenza antigen tests versus PCR in an influenza-like illness population: A real-world multicenter study in China” [Infection, Genetics and Evolution, volume 133, article 105794]. “快速流感抗原检测与PCR在流感样疾病人群中的比较研究：中国真实世界的多中心研究”[感染，遗传与进化，第133卷，第105794条]的勘误表。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2026-01-01 DOI: 10.1016/j.meegid.2025.105873

Tongyan Zhang , Jinghui Du , Ying Cao , Hongyan Han , Yajun Du , Yazhu Hou , Qian Du , Juan Song , Weidong Su , Jihong Feng

引用次数: 0

Molecular epidemiology of Pasteurella multocida in cats: First multilocus sequence typing (MLST)-based insights from Iran 猫多杀性巴氏杆菌的分子流行病学：来自伊朗的首次基于多位点序列分型（MLST）的见解。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2026-01-01 DOI: 10.1016/j.meegid.2025.105874

Baharak Mirzavand , Darioush Gharibi , Dolores Cid , Ana Isabel Vela , Mohammad Khosravi , Keyvan Tadayon

Pasteurella multocida is a zoonotic bacterium commonly found in the oropharyngeal microbiota of cats; despite its clinical relevance, molecular data on feline isolates in Iran remain limited. This study aimed to provide molecular and phenotypic characterization of P. multocida isolates obtained from feline sources in Iran. This study characterized 18 P. multocida isolates recovered from oral swabs of cats previously sampled in Ahvaz, Iran. After polymerase chain reaction (PCR) confirmation targeting the kmt1 gene, multilocus sequence typing (MLST) was performed using the Rural Industries Research and Development Corporation (RIRDC) scheme. The MLST analysis assigned the 18 isolates to 14 distinct sequence types (STs). High genetic diversity was observed, with no ST dominating the population. Our results identified several STs, including ST30, ST344, ST487, and ST551, that have been reported worldwide, highlighting their epidemiological relevance. This study provides the first MLST data for feline P. multocida in Iran and contributes to global understanding of the species' genetic diversity.

多杀性巴氏杆菌是一种常见于猫口咽菌群的人畜共患细菌；尽管具有临床意义，但伊朗猫分离物的分子数据仍然有限。本研究旨在提供从伊朗猫源中分离的多杀假单胞菌的分子和表型特征。本研究鉴定了从先前在伊朗阿瓦士取样的猫口腔拭子中分离出的18株多杀性假单胞菌。针对kmt1基因的聚合酶链反应（PCR）确认后，使用农村工业研究与发展公司（RIRDC）计划进行多位点序列分型（MLST）。MLST分析将18株分离物划分为14种不同的序列类型（STs）。群体遗传多样性高，无ST显性。我们的研究结果确定了几种STs，包括ST30、ST344、ST487和ST551，这些STs已在世界范围内报道，突出了它们的流行病学相关性。本研究首次提供了伊朗多杀猫的MLST数据，有助于全球对该物种遗传多样性的了解。

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引用次数: 0

A panel of five microsatellites as an alternative to mitogenome sequencing for investigating the genetic diversity of Echinococcus granulosus sensu stricto from global to farm scale 一个由5颗微卫星组成的小组，作为有丝分裂基因组测序的替代方案，用于研究从全球到农场规模的严格感细粒棘球蚴的遗传多样性。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2026-01-01 DOI: 10.1016/j.meegid.2025.105868

Gérald Umhang , Vanessa Bastid , Laura Rinaldi , Paola Pepe , Elena Ciccone , Smaragda Sotiraki , Panagiota Ligda , Myriam Oudni-M'rad , Selim M'rad , Samia Lahmar , Yousra Said , Kefiya Elmehatli , Haroon Ahmed , Tetiana Kuzmina , Valentyna Yevstafieva , Sargis A. Aghayan , Hasmik Gevorgyan , Sami Simsek , Francesco Ponce-Gordo , M.C. Benchikh El Fegoun , Jaime Aguayo

While the molecular identification of Echinococcus granulosus species is essential for surveillance, a detailed investigation of the parasite's genetic diversity would offer a more accurate understanding of its transmission. This may be done by partial or whole mitochondrial genome sequencing, but both cost and time requirements limit routine application. Microsatellites are an alternative approach as they are a rapid, simple, highly discriminative, and low-cost tool. Our research project was designed to obtain a panel of microsatellite targets for population genetic analyses to describe the genetic diversity of E. granulosus sensu stricto (s.s.) at the global to farm scale. A panel of five informative microsatellite loci for population genetic analysis of E. granulosus s.s. was developed and validated. A total of 145 isolates from 11 countries were used to evaluate the panel at the international level. Additionally, 131 samples from sheep and cattle across six regions in southern Italy were analyzed to assess the panel's usefulness at both the regional and farm scale. Population genetics showed high genotypic diversity. Simpson's index gave high values (0.94–0.98) for the expected heterozygosity (0.80 to 0.87). Discriminant analysis of principal components (DAPC) revealed the structure of populations for each country, with Greece distinctly distant from Algeria, Italy, and Tunisia. This was also confirmed by FST values. DAPC further revealed a genetic structure among the farms from the Italian regional sample set, with three different clusters explained by different farming practices. This microsatellite panel can provide data relevant for E. granulosus s.s. population genetics from global to farm scale, making it a low-cost, simple alternative to full mitochondrial genome sequencing for analyzing numerous samples and obtaining a detailed overview of genetic diversity, an input that is useful for cystic echinococcosis control programs.

虽然细粒棘球绦虫的分子鉴定对监测至关重要，但对寄生虫遗传多样性的详细调查将提供对其传播的更准确理解。这可以通过部分或整个线粒体基因组测序来完成，但成本和时间要求限制了常规应用。微型卫星是另一种方法，因为它们是一种快速、简单、高度判别和低成本的工具。我们的研究项目旨在获得一组微卫星靶点，用于群体遗传分析，以描述全球到农场规模的狭粒棘球绦虫（s.s.）的遗传多样性。建立了一个由5个微卫星基因座组成的群体遗传分析模型，并进行了验证。来自11个国家的145个分离株被用于在国际一级对该小组进行评估。此外，对意大利南部六个地区的131个羊和牛样本进行了分析，以评估该小组在区域和农场规模上的实用性。群体遗传表现出较高的基因型多样性。期望杂合度（0.80 ~ 0.87）的辛普森指数较高（0.94 ~ 0.98）。主成分判别分析（DAPC）揭示了每个国家的人口结构，希腊明显远离阿尔及利亚、意大利和突尼斯。FST值也证实了这一点。DAPC进一步揭示了来自意大利区域样本集的农场之间的遗传结构，不同的耕作方式解释了三个不同的集群。该微卫星面板可以提供从全球到农场规模的颗粒棘球蚴种群遗传学相关数据，使其成为一种低成本，简单的替代全线粒体基因组测序的方法，用于分析大量样本并获得遗传多样性的详细概述，这对囊性棘球蚴病控制计划是有用的输入。

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引用次数: 0

Comprehensive in silico genomic surveillance of β-lactam and methicillin resistance in Staphylococcus aureus: Machine learning–based analysis of lineage dynamics and global evolution 金黄色葡萄球菌β-内酰胺和甲氧西林耐药性的综合硅基因组监测：基于机器学习的谱系动力学和全球进化分析。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2026-01-01 DOI: 10.1016/j.meegid.2025.105862

Saeid Sadeghi Ghazi Chaki , Bilal Khaleel Midhin , Samer Saleem Alshkarchy , Mahshid Kalantar-Neyestanaki , Reham yahya albaz , Munthar Kadhim Abosaoda , Ali Kamil Kareem , Renu Sharma , Mohammad Sholeh , Masoumeh Beig

<div><h3>Background</h3><div>According to the World Health Organization, methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) is classified as a “High” priority pathogen on its Global Priority Pathogens List. The aim of this study is to perform a comprehensive genome-based in silico analysis of <em>S. aureus</em> to elucidate the evolutionary dynamics of β-lactam and methicillin resistance, focusing on resistance genes and minimum inhibitory concentration (MIC) phenotypes. This study analyzes all publicly available <em>S. aureus</em> genomes in NCBI to investigate β-lactam and methicillin resistance, including resistance genes and MIC phenotypes. The dataset covers isolates from multiple countries worldwide, representing global diversity.</div></div><div><h3>Methods</h3><div>A total of 111,350 <em>S. aureus</em> genomes (1880s–2020s) were retrieved from GenBank and rigorously quality-filtered. Antimicrobial resistance genes were identified with AMRFinderPlus, and phenotypic MIC data for key β-lactams were integrated via genome–BioSample linkage from the National Center for Biotechnology Information AST Browser. Multi-locus sequence typing was used to resolve sequence types (STs), while machine learning models (Random Forest, eXtreme Gradient Boosting, Elastic Net regularized regression, and Partial Least Squares) were trained on gene/mutation profiles to predict log₂ MICs under repeated 5-fold cross-validation. Temporal and lineage-specific trends were assessed with correlation and generalized linear models, and genotype–phenotype associations tested using chi-square or Fisher's exact test with Bonferroni correction. All genomic, clustering, and phylogenetic analyses were performed in R using fully reproducible pipelines.</div></div><div><h3>Results</h3><div>The dataset included 111,350 <em>S. aureus</em> genomes, 78 % clinical and 10 % environmental, spanning 1884–2025 from 137 countries. Core genome size remained stable (mean 2.87 Mb; ∼2874 genes), with modest increases in total genes (<em>r</em> = 0.15, <em>p</em> < 0.001) and pseudogenes (<em>r</em> = 0.09, p < 0.001), reflecting subtle genomic plasticity. MLST analysis identified >2000 STs, but ST8 (16.6 %), ST5 (13.8 %), and ST22 (6.9 %) together accounted for ∼37 % of isolates, illustrating epidemic clone dominance and temporal turnover from pre-1980 hospital lineages to modern polyclonal populations. β-lactam resistance showed a marked upward trend: the bla operon (<em>blaZ–blaI–blaR1</em>) increased from ∼60 % in the early 2000s to >95 % by 2024, while <em>blaPC1</em> declined from near ubiquity in the 1990s to <10 %. Methicillin resistance, driven by <em>mecA</em> (62.7 %), was accompanied by progressive loss of regulators <em>mecR1</em> (52.0 %) and <em>mecI</em> (13.8 %), reflecting evolutionary streamlining for constitutive PBP2a expression. Clinical isolates carried higher frequencies of <em>blaZ</em> (+17.4 %) and <em>mecA</em> (+15.5 %) than environmental str

背景：根据世界卫生组织，耐甲氧西林金黄色葡萄球菌（MRSA）在其全球优先病原体清单上被列为“高”优先病原体。本研究的目的是对金黄色葡萄球菌进行全面的基因组分析，以阐明β-内酰胺和甲氧西林耐药的进化动力学，重点关注耐药基因和最低抑制浓度（MIC）表型。本研究分析了NCBI中所有公开的金黄色葡萄球菌基因组，以研究β-内酰胺和甲氧西林耐药性，包括耐药基因和MIC表型。该数据集涵盖了来自全球多个国家的分离物，代表了全球多样性。方法：共111,350例 S。从GenBank中检索1880 -2020s的金黄色葡萄球菌基因组，并进行严格的质量过滤。利用AMRFinderPlus对耐药基因进行鉴定，并通过来自国家生物技术信息中心AST浏览器的基因组-生物样本链接整合关键β-内酰胺的表型MIC数据。多位点序列分型用于解决序列类型（STs），而机器学习模型（随机森林、极端梯度增强、弹性网络正则化回归和偏最小二乘）在基因/突变谱上进行训练，在重复的5倍交叉验证下预测log₂mic。通过相关和广义线性模型评估时间和谱系特异性趋势，并使用卡方检验或Fisher精确检验（Bonferroni校正）检验基因型-表型相关性。所有基因组、聚类和系统发育分析均在R中使用完全可重复的管道进行。结果：数据集包括111,350 S。金黄色葡萄球菌基因组，78 %临床和10 %环境，跨越1884年至2025年，来自137个国家。核心基因组规模保持稳定(平均2.87 Mb; ~ 2874个基因),与适度增加总基因(r = 0.15,p 2000 STs,但ST8(16.6 %),ST5(13.8 %),和ST22(6.9 %)一起占~ 37 %的隔离,说明流行克隆优势和时间营业额从1980年以前医院现代多克隆种群血统。β-内酰胺耐药性呈明显上升趋势：bla操纵子（blad - blai - blar1）从21世纪初的~ 60% %上升到2024年的~ 95% %，而blaPC1则从20世纪90年代的几乎无所不在下降到结论：金黄色葡萄球菌在bla和mecA卡带周围巩固β-内酰胺和甲氧西林耐药性的同时保持了稳定的核心基因组，流行谱系推动了全球传播。尽管对老的β-内酰胺类广泛耐药，碳青霉烯类和头孢他林仍然有效，强调了基于wgs的监测和管理的价值。

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引用次数: 0

Molecular epidemiology of Mycobacterium tuberculosis based on core-genome single nucleotide variant analysis and evaluation of variable-number tandem-repeat typing in Kanagawa, Japan 基于核心基因组单核苷酸变异分析的结核分枝杆菌分子流行病学及日本神奈川地区变数串联重复分型评价。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2026-01-01 DOI: 10.1016/j.meegid.2025.105870

Naoki Nakajima, Eriko Mitani, Aya Okamura

Studies applying whole-genome sequencing to Mycobacterium tuberculosis in Japan remain limited, particularly in non-urban regions. In this study, we analyzed 734 isolates collected between 2013 and 2025 in the central and western region of Kanagawa Prefecture using core-genome single nucleotide variant (cgSNV) analyses, including lineage classification and cluster detection, to elucidate transmission dynamics. Elderly patients accounted for 65.3 % of cases and were significantly enriched for the ancient sublineages L2.2.A and L4.9, both of which exhibited longer terminal branch lengths (TBLs), suggesting reactivation. In contrast, the modern Beijing sublineages L2.2.M2.2 and L2.2.M4 were enriched among younger patients and showed shorter TBLs, consistent with recent transmission. Lineage-based cgSNV analysis identified 39 clusters across 20 lineages, indicating intergenerational transmission. Separately, four clusters within the M strain reflected sustained transmission of this genotype. The presence of mixed cgSNV clusters involving Japan-born and foreign-born patients further extends nationwide observations and highlights the importance of continued genomic surveillance of imported lineages. To inform local TB control programs, we evaluated whether cgSNV analyses performed within variable-number tandem repeat (VNTR)-defined clusters could serve as a prescreening approach for identifying transmission clusters. This approach successfully captured all cgSNV clusters defined at ≤5 SNVs and demonstrated complete directional congruence from cgSNV to VNTR (Adjusted Wallace = 1.00). These findings indicate that VNTR-based grouping can efficiently prioritize isolates for WGS-based molecular epidemiological surveillance in routine public health settings.

在日本应用全基因组测序检测结核分枝杆菌的研究仍然有限，特别是在非城市地区。本研究采用核心基因组单核苷酸变异（cgSNV）分析方法，对2013 - 2025年在神奈川县中西部地区采集的734株分离株进行分析，包括谱系分类和聚类检测，以阐明其传播动力学。老年患者占65.3 %，古亚系L2.2显著富集。A和L4.9均表现出较长的末端分支长度（TBLs），提示再激活。相比之下，现代北京的子谱系是L2.2. m2.2和L2.2。M4在年轻患者中富集，表现出较短的tbl，与最近的传播一致。基于谱系的cgSNV分析在20个谱系中鉴定出39个集群，表明代际传播。另外，M株中的4个集群反映了该基因型的持续传播。涉及日本出生和外国出生患者的混合cgSNV集群的存在进一步扩大了全国范围内的观察，并强调了继续对输入谱系进行基因组监测的重要性。为了向当地结核病控制规划提供信息，我们评估了在可变数量串联重复（VNTR）定义的集群中进行的cgSNV分析是否可以作为识别传播集群的预筛选方法。该方法成功捕获了所有定义在≤5个snv的cgSNV簇，并证明了cgSNV到VNTR的完全方向同列（Adjusted Wallace = 1.00）。这些发现表明，在常规公共卫生环境中，基于vntr的分类可以有效地优先考虑基于wgs的分子流行病学监测分离株。

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引用次数: 0

In silico profiling of the plasmodium knowlesi 32 kDa antigen: Diversity, epitope prediction, and structural modeling 诺氏疟原虫32 kDa抗原的硅谱分析：多样性，表位预测和结构建模。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-31 DOI: 10.1016/j.meegid.2025.105871

Ahmed Saif , Pratisthita Baruah , Jawahir Marzouq Alghamdi , Rudraangsh Acharyya , Yee Ling Lau , Jin-Hee Han , Md Atique Ahmed

The emergence of Plasmodium knowlesi malaria in Southeast Asia, particularly Malaysia, necessitates effective interventions. However, high polymorphism often limits the utility of key merozoite surface proteins (MSPs) as viable vaccine candidates. Pk32, a predicted glycosylphosphatidylinositol (GPI)-anchored protein in P. knowlesi, shares homology with the relatively conserved Plasmodium vivax Pv32, suggesting it may be a promising vaccine candidate. We analyzed the genetic diversity, polymorphism, and signatures of natural selection and 3-D structure using 39 full-length Pk32 sequences, primarily from Malaysian Borneo. Sequence analysis showed low nucleotide diversity (π = 0.0061) and limited polymorphism. Phylogenetic analysis indicated no geographical clustering. Natural selection tests; codon-based Z-test, tajima's D, codon-based site-by-site analysis (FEL, MEME, FUBAR, SLAC) provided strong evidence of purifying selection acting on Pk32, suggesting functional constraint alongside population expansion. In silico B-cell epitope prediction identified three common epitomes. Crucially, two epitopes (145PKERES150 and 167DIGKKQNS174) were conserved in all sequences. Mapping these conserved epitopes onto the predicted and refined 3D structure of Pk32 highlights specific stable targets. The observed combination of limited genetic variation and the presence of stable, conserved B-cell epitopes strongly suggests that Pk32 is a compelling candidate for inclusion in a blood-stage vaccine against P. knowlesi.

东南亚，特别是马来西亚出现了诺氏疟原虫疟疾，需要采取有效的干预措施。然而，高多态性往往限制了关键的裂殖子表面蛋白（MSPs）作为可行的候选疫苗的效用。Pk32是诺氏疟原虫中预测的糖基磷脂酰肌醇（GPI）锚定蛋白，与相对保守的间日疟原虫Pv32具有同源性，这表明它可能是一种有希望的候选疫苗。我们分析了主要来自马来西亚婆罗洲的39个全长Pk32序列的遗传多样性、多态性、自然选择特征和3-D结构。序列分析显示核苷酸多样性低（π = 0.0061），多态性有限。系统发育分析未发现地理聚类。自然选择测试；基于密码子的z检验，tajima's D，基于密码子的逐点分析（FEL， MEME， FUBAR， SLAC）提供了强有力的证据，证明纯化选择作用于Pk32，表明随着种群扩张，功能受到限制。在硅b细胞表位预测鉴定了三个常见的表位。关键是，两个表位（145PKERES150和167DIGKKQNS174）在所有序列中都是保守的。将这些保守的表位映射到Pk32的预测和改进的3D结构上，突出了特定的稳定目标。观察到的有限遗传变异和存在稳定、保守的b细胞表位的结合强烈表明Pk32是包含在抗诺氏疟原虫血期疫苗中的令人注目的候选者。

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引用次数: 0

Natural syndemic infection between African swine fever virus (ASFV) and porcine reproductive and respiratory syndrome virus (PRRSV) leads to shifting of ASFV tissue tropism to lungs with exacerbated presentation of the disease 非洲猪瘟病毒（ASFV）和猪繁殖与呼吸综合征病毒（PRRSV）之间的自然综合征感染导致ASFV的组织向肺转移，并加剧疾病的表现。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-30 DOI: 10.1016/j.meegid.2025.105872

Charitha B. Balakrishna , Tridib Kumar Rajkhowa , Kiran Jayappa , Guillermo R. Risatti

African swine fever (ASF) and porcine reproductive and respiratory syndrome (PRRS) are two of the most devastating and economically important transboundary diseases of pig. The current epidemic-to-pandemic situation of ASF and the unavailability of broadly effective vaccine against PRRS raise the possibility of these highly pathogenic viruses circulating simultaneously in the same pig population. This study is reporting natural occurrence of syndemic infections of ASF and PRRS in pig population of Mizoram, India. The syndemic infections resulted in high mortality in the affected crossbred pigs, while the indigenous Zovawk pigs revealed some degree of tolerance. The symbiosis between the two viruses resulted in extensive tissue damage in wider range of body systems with multiple organ failure leading to more severe acute disease. The absolute quantification of both the viruses in various organs revealed distinct tissue tropism and suggested shifting of ASFV tissue tropism towards lungs tissues in the naturally occurring syndemic infection of PRRSV and ASFV. The phylogenetic analysis based on the B646L gene of ASFV and the ORF7 gene of PRRSV identified the circulating strains in genotype II ASFV and lineage 8 of PRRSV 2. Our findings underscore the complexity of co-infections in natural cases and emphasize the importance of integrated diagnostics and targeted disease management strategies for the swine population to combat this emerging situation.

非洲猪瘟（ASF）和猪繁殖与呼吸综合征（PRRS）是猪的两种最具破坏性和经济重要性的跨界疾病。目前非洲猪瘟从流行到大流行的情况以及无法获得广泛有效的抗PRRS疫苗，增加了这些高致病性病毒在同一猪群中同时传播的可能性。本研究报告了印度米佐拉姆邦猪群中ASF和PRRS合并症感染的自然发生。合群感染导致受影响杂交猪的高死亡率，而本地Zovawk猪显示出一定程度的耐受性。两种病毒之间的共生导致更广泛的身体系统的广泛组织损伤，多器官衰竭，导致更严重的急性疾病。两种病毒在不同器官中的绝对定量显示出明显的组织趋向性，提示在自然发生的PRRSV和ASFV合并症感染中，ASFV组织趋向性向肺组织转移。基于ASFV的B646L基因和PRRSV的ORF7基因进行系统发育分析，鉴定出基因型ASFV的循环株和基因型PRRSV 2的8系。我们的研究结果强调了自然病例中合并感染的复杂性，并强调了综合诊断和有针对性的疾病管理策略对猪群对抗这种新情况的重要性。

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引用次数: 0