Infection Genetics and Evolution最新文献

{"title":"Taxonomic reassessment of genomes from a divergent population of Streptococcus suis by average nucleotide identity analysis","authors":"Wenbo Luo ,&nbsp;Xueli Yi ,&nbsp;Xiyan Zhang ,&nbsp;Chaoyuan Yuan ,&nbsp;Wenfei Wei ,&nbsp;Xuezhen Li ,&nbsp;Danna Pu ,&nbsp;Jing Yang ,&nbsp;Han Zheng","doi":"10.1016/j.meegid.2025.105753","DOIUrl":"10.1016/j.meegid.2025.105753","url":null,"abstract":"<div><div><em>Streptococcus</em> spp., including the emerging zoonotic pathogen <em>S. suis</em>, represent a dominant bacterial population in the porcine nasopharynx. Species identification within the <em>Streptococcus</em> genus remains challenging and frequently ambiguous, resulting in indistinct species boundaries. By employing comparative genomic analyses, a previous study categorized <em>S. suis</em> into a central population and divergent lineages, based on the single nucleotide polymorphisms (SNPs) within core genes and the presence or absence of accessory genes, indicating evolutionary divergence. The divergent lineages were designated as the “out population” in this study for clarity. The <em>16S rRNA</em> gene sequences of seven putative novel <em>Streptococcus</em> strains isolated from the throats of healthy pigs in China exhibited 100 % similarity to that of the 684_17B strain of <em>S. suis</em>, which clustered in the out population. This study established a threshold average nucleotide identity (ANI) value of 93.17 % for the identification of authentic <em>S. suis</em>. All the 645 genomes from the out population fell below this threshold, indicating that they did not belong to <em>S. suis</em>. Further taxonomic assessment of the 645 genomes from the out population revealed 18 clusters based on pairwise ANI comparisons, using a 92.33 % threshold, determined by pairwise ANI comparisons among the 2422 genomes from the central population of <em>S. suis</em>. These clusters were identified as 12 novel <em>Streptococcus</em> spp. (<em>Streptococcus</em> sp. nov-1–12) and six known <em>Streptococcus</em> spp. by ANI comparisons with type or reference genomes of 98 known <em>Streptococcus</em> spp. The study provides a useful framework for the identification of authentic <em>S. suis</em> and the determination of <em>Streptococcus</em> sp. nov.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"131 ","pages":"Article 105753"},"PeriodicalIF":2.6,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasmodium falciparum genetic diversity and multiplicity of infection in northern and southern Ghana assessed by amplicon sequencing","authors":"Xiaoyun Wei ,&nbsp;Awtum Brashear ,&nbsp;Faiza Siddiqui ,&nbsp;Georgina Agyekum ,&nbsp;Amuza Lucky ,&nbsp;Anongruk Chim-Ong ,&nbsp;Yaw Afrane ,&nbsp;Jun Miao ,&nbsp;Chengqi Wang ,&nbsp;Linda Amoah ,&nbsp;Liwang Cui","doi":"10.1016/j.meegid.2025.105754","DOIUrl":"10.1016/j.meegid.2025.105754","url":null,"abstract":"<div><div>Malaria is a significant public health challenge in Ghana, with <em>Plasmodium falciparum</em> accounting for 80–90 % of infections. This study aimed to determine whether different climatic conditions, demographics, transmission patterns, and control practices in northern and southern Ghana result in differences in the genetic diversity, population structure, and evolutionary dynamics of <em>P. falciparum</em>. A total of 354 clinical samples collected in 2018 and 2021 were analyzed using the amplicon sequencing approach, targeting the <em>CSP</em>, <em>AMA1</em>, <em>SERA2</em>, and <em>TRAP</em> genes. Parasite populations from both northern and southern Ghana exhibited high haplotype diversity (Hd = 0.93–0.98). More than 70 % of the patient samples contained multiclonal infections, and the multiplicity of infection was significantly higher in northern (2.91) than in southern Ghana (2.42). Despite such a difference, extensive haplotype sharing was observed. The haplotype network and phylogenetic analyses highlighted substantial genetic connectivity among the parasite populations, likely driven by multiple factors, including human movement and shared vectors. Predominant haplotypes were consistent across regions and years, reflecting a stable pool of core haplotypes, which was not significantly impacted by contemporary control measures. In conclusion, this study underscored the high genetic diversity and connectivity of <em>P. falciparum</em> populations in Ghana despite different transmission ecology and the implementation of divergent control measures.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"131 ","pages":"Article 105754"},"PeriodicalIF":2.6,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endemic transmission of a Mycobacterium tuberculosis L2.2.M3 sublineage of the L2 lineage within Colon, Panama: A prospective study","authors":"Fermín Acosta ,&nbsp;Daniela Candanedo ,&nbsp;Priya Patel ,&nbsp;Alejandro Llanes ,&nbsp;Johanna Elizabeth Ku ,&nbsp;Kharla Salazar ,&nbsp;Mitchelle Morán ,&nbsp;Dilcia Sambrano ,&nbsp;Julio Jurado ,&nbsp;Isolina Martínez ,&nbsp;Lizbeth Garibaldi ,&nbsp;Mariela Delgado ,&nbsp;Laura Solís ,&nbsp;Odemaris Luque ,&nbsp;Kesia Da Silva ,&nbsp;Jason Andrews ,&nbsp;Amador Goodridge","doi":"10.1016/j.meegid.2025.105749","DOIUrl":"10.1016/j.meegid.2025.105749","url":null,"abstract":"<div><div><em>Mycobacterium tuberculosis</em> lineage 2 (L2) remains a globally significant lineage associated with increased drug resistance and rapid transmission. The L2 lineage exhibits a hotspot for genetic diversity and evolution in Panama, requiring an in-depth analysis. We conducted a prospective analysis of 274 <em>Mycobacterium tuberculosis</em> L2 isolates from Colon City between January 2021 and October 2023. Drug resistance was determined using GeneXpert and MTBDRplus-Genotype assays, strain lineage was determined by strain-specific PCR (ASO-PCR), and whole-genome sequencing was conducted for phylogenetic analysis. Sequencing data were analyzed using the mtb-call2 pipeline and TB-gen tools to predict drug resistance and sublineage, respectively. Genome-wide single-nucleotide polymorphisms (SNPs) were used for phylogenetic and evolutionary analyses. ASO-PCR results identified all 31.7 % (86/271) isolates as Modern L2.2. WGS analysis of 66 strains confirmed all isolates belonged to the L2.2.1 sublineage. Sixty-four strains were analyzed in depth, with 96.9 % (62/64) classified as pan-susceptible and 3.1 % (2/64) as rifampicin/pyrazinamide-resistant. The sublineage analysis based on SNPs using the TB-gen tool identified a SNP at position 1219683G &gt; A, which genotyped all 64 strains as L2.2.M3 sublineage. Phylogenetic analysis revealed a correlation with geographical distribution compared to other Latin American L2 isolates. Transmission clusters (≤12 SNPs) were identified and used to determine recent transmission events or TB transmission clusters. These analyses also confirmed a relatively low evolutionary rate within Panama L2 isolates and a highly conserved common ancestor shared with L2 isolates from Peru, Colombia, and Guatemala. These findings suggest endemic transmission of the <em>Mycobacterium tuberculosis</em> L2.2.M3 sublineage in Colon, Panama. We recommend combining genomic information with epidemiological data to accurately track and identify the source hotspot for the L2.2.M3 sublineage and focus control measures.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"131 ","pages":"Article 105749"},"PeriodicalIF":2.6,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of tobacco necrosis virus A in a diseased Colombian Cannabis sativa plant","authors":"Juliana Lopez-Jimenez ,&nbsp;Herman D. Palacio-Torres ,&nbsp;Juan F. Alzate","doi":"10.1016/j.meegid.2025.105752","DOIUrl":"10.1016/j.meegid.2025.105752","url":null,"abstract":"<div><div>Plant viral infections pose a significant threat to global crop productivity. Despite their profound impact on agriculture, plant viruses have been relatively understudied, primarily due to technological limitations associated with classical molecular methods. However, the advent of RNA Next-Generation Sequencing (NGS) RNA-seq analysis has revolutionized virus characterization in environmental settings, overcoming previous limitations and providing a powerful tool for studying plant viruses.</div><div>In an RNA-seq experiment conducted on a diseased Colombian <em>Cannabis sativa</em> hemp plant, we identified a linear positive-sense single-stranded RNA genome belonging to Tobacco Necrosis Virus A (TNV-A), a common cause of necrotic lesions in plants such as tobacco and tulipa. The affected <em>Cannabis sativa</em> hemp plant exhibited severe symptoms, including alterations in pigmentation, leaf morphology such as chlorosis, necrotic tissue formation, and surface wear on the leaves. The complete genome sequence of the <em>Cannabis sativa</em> TNV-A was 3656 nucleotides long, containing five putative ORFs, and was classified in the family <em>Tombusviridae</em>, genus <em>Alphanecrovirus</em>, and belonging to the Necro-like clade based on RdRp protein phylogenetic analysis. Our analysis revealed a well-conserved RdRp protein among the Alphanecroviruses, with 89 % of the amino acid residues in the peptide being entirely conserved. In contrast, the coat protein exhibited significantly higher variability, with only 49.3 % of the residues being 100 % conserved. Regarding the viral genome expression of <em>Cannabis sativa</em> TNV-A, we observed that the virus was highly abundant in the leaves of the diseased plant, ranking among the topmost abundant transcripts, occupying the percentile position of 3 %. Overall, our study generated the first reference genome of TNV-A virus in the tropical region and reported the first case of this virus infecting a <em>Cannabis sativa</em> plant.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"131 ","pages":"Article 105752"},"PeriodicalIF":2.6,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting host-pathogen interactions with machine learning algorithms: A scoping review","authors":"Rasool Sahragard ,&nbsp;Masoud Arabfard ,&nbsp;Ali Najafi","doi":"10.1016/j.meegid.2025.105751","DOIUrl":"10.1016/j.meegid.2025.105751","url":null,"abstract":"<div><h3>Background</h3><div>Diseases caused by pathogenic microorganisms pose a persistent global health challenge. Pathogens exploit host mechanisms through intricate molecular interactions. Understanding these host-pathogen interactions (HPIs), particularly protein-protein interactions (PPIs), is crucial for developing therapeutic strategies. While experimental approaches are essential, they are often labor-intensive and costly. Researchers have been able to predict HPIs more efficiently due to recent advances in artificial intelligence and machine learning. However, existing reviews lack a systematic evaluation of different machine learning methodologies and their effectiveness.</div></div><div><h3>Methods</h3><div>This scoping review critically examines recent studies on machine learning-based Host-Pathogen Interaction (HPI) prediction, categorizing them by host and pathogen types, machine learning algorithms, and key evaluation metrics. The methodology is based on the study beginning with a preliminary search in reputable using key phrases related to host-pathogen interactions from 2019 to 2024. This process yielded 46 relevant articles, from which 30 were selected for review after evaluating titles and abstracts.</div></div><div><h3>Results</h3><div>Our findings indicate that tree-based algorithms, particularly Random Forest and Gradient Boosting, are the most prevalent in Host-Pathogen Interaction (HPI) prediction. The filter articles were categorized by host and pathogen type and further subdivided into four subcategories based on the prediction type and machine learning algorithms: classic, tree-based, vector-based, and neural network algorithms. Convolutional and recurrent neural networks are among the deep learning models that demonstrate promising accuracy, but they require a lot of labeled data for effective training. Additionally, the analysis uncovers significant gaps in dataset standardization and model interpretability, which pose challenges to the broader applicability of these predictive models.</div></div><div><h3>Conclusion</h3><div>In this review, we emphasize the potential of machine learning in HPI prediction and highlight the important challenges that must be addressed to improve predictive accuracy. Unlike previous reviews, our study systematically compares different computational approaches, offering a roadmap for future research. The findings emphasize the importance of dataset quality, feature selection, and model transparency in advancing AI-driven pathogen research.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105751"},"PeriodicalIF":2.6,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143821329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First detection and molecular characterization of Mycoplasma species in camels, cattle, buffalo, and their associated ticks from southern Egypt","authors":"Ahmed M. Soliman ,&nbsp;Hassan Y.A.H. Mahmoud ,&nbsp;Moaz M. Amer ,&nbsp;Samah Mohamed ,&nbsp;Tatsuro Hifumi ,&nbsp;Abdelrahman A. Rady ,&nbsp;Alsagher O. Ali ,&nbsp;Walaa F.A. Emeish ,&nbsp;Tetsuya Tanaka","doi":"10.1016/j.meegid.2025.105750","DOIUrl":"10.1016/j.meegid.2025.105750","url":null,"abstract":"<div><div><em>Mycoplasma</em> species are wall-less bacteria that infect multiple mammalian orders, including livestock, and are associated with economically significant diseases. In Egypt, molecular data on the presence and diversity of <em>Mycoplasma</em> spp. in camels, cattle, buffalo, and their associated ticks remain limited, despite their potential impact on livestock health and productivity. This study aimed to detect and genetically characterize <em>Mycoplasma</em> spp. in cattle, buffalo, camels, and their associated ticks in southern Egypt. A total of 571 samples (384 ticks, 50 buffalo, 68 cattle, and 69 camels) were screened using PCR targeting the 16S rRNA gene, followed by phylogenetic analysis of representative amplicons. <em>Hyalomma dromedarii</em>, <em>Hyalomma marginatum</em>, and <em>Rhipicephalus annulatus</em> were the tick species collected. Overall, <em>Mycoplasma</em> DNA was detected in 10.3 % of the samples. <em>Mycoplasma ovis</em>-like was identified in 2.9 % of camel blood, 9.4 % of <em>H. dromedarii</em>, 75 % of <em>H. marginatum</em>, and 13.8 % of <em>R. annulatus</em> ticks. <em>Candidatus</em> Mycoplasma haematovis was found in 0.4 % of <em>H. dromedarii</em>, and <em>Mycoplasma wenyonii</em>-like in 13.2 % of cattle and 4 % of buffalo blood. Remarkably, this is the first global detection of <em>M. ovis</em> in camel blood, as well as the detection of <em>M. ovis</em>-like and Ca. M. haematovis in ticks circulating on camels. This study also reports the first detection of <em>M. wenyonii</em>-like in bovines in Egypt and documents <em>M. ovis</em>-like in three tick species parasitizing cattle. The genetic similarities of <em>Mycoplasma</em> sequences from ticks and livestock suggest that these arthropods may serve as potential vectors. These findings highlight the need for additional studies on the zoonotic potential, infectivity, and vector competence of <em>Mycoplasma</em> spp. in Egypt.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105750"},"PeriodicalIF":2.6,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143829861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic stability of Mpox virus during in-vitro serial passaging: Insights from mutational analysis","authors":"J. Khurana ,&nbsp;Y. Joshi ,&nbsp;S. Yadav,&nbsp;P.D. Yadav,&nbsp;A.M. Shete","doi":"10.1016/j.meegid.2025.105748","DOIUrl":"10.1016/j.meegid.2025.105748","url":null,"abstract":"","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105748"},"PeriodicalIF":2.6,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143829862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic surveillance of SARS-CoV-2 variants in Guangzhou, China, from April 2023 to March 2024","authors":"Zhuoyun Li ,&nbsp;Liya Li ,&nbsp;Yuyi Min ,&nbsp;Yaqing Lin ,&nbsp;Yingfen Wen ,&nbsp;Ruiying He ,&nbsp;Jiaojiao Li ,&nbsp;Quanyang Gao ,&nbsp;Fengyu Hu ,&nbsp;Feng Li ,&nbsp;Yun Lan","doi":"10.1016/j.meegid.2025.105747","DOIUrl":"10.1016/j.meegid.2025.105747","url":null,"abstract":"<div><h3>Background</h3><div>After the relaxation of stringent control measures, nationwide large-scale SARS-CoV-2 surveillance was gradually phased out post-2023, transitioning to focused monitoring of Influenza-like Illness (ILI) through sentinel hospitals and laboratory networks. Nationally, surveillance of respiratory pathogens was performed via random sampling, resulting in a lack of microbial monitoring results in Guangzhou China. A crucial area of scientific inquiry is whether the current cases are attributable to the emergence of a novel SARS-CoV-2 variant.</div></div><div><h3>Methods</h3><div>Throat swab samples were obtained from 1478 outpatients and 337 hospitalized patients with fever (temperature ≥ 38 °C) and cough or sore throat to detect SARS-CoV-2. The positive samples were subjected to viral whole-genome sequencing and phylogenetic analysis. Respiratory pathogen multiplex PCR tests were performed on stratified random samples.</div></div><div><h3>Results</h3><div>SARS-CoV-2 was detected in 517 (28.48 %) patients. There were higher rates of SARS-CoV-2 infection among women, older patients and those who were hospitalized. A total of 299 high-quality SARS-CoV-2 sequences were obtained, including 12 clades and 71 pango lineages. The advantageous clades evolved over three peak periods of infection, from BA.5 (April 2023) to XBB (June to July 2023) and then to JN.1 (February 2024). A total of 590 distinct amino acid mutations were identified across the sequences. The highest prevalence of mutations was observed for spike protein mutations, with more than 50 % of the three epidemic peaks detected. Epidemiological profiles of interactions between SARS-CoV-2 and other respiratory pathogens exhibit considerable variation across different seasons, with a tendency toward suppression within each.</div></div><div><h3>Conclusion</h3><div>Surveillance by Guangzhou Eighth People's Hospital provides a snapshot of the epidemic in Guangzhou, which is consistent with the national epidemic and offers important data for understanding the spread of SARS-CoV-2 in southern China.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105747"},"PeriodicalIF":2.6,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Latitude-driven patterns and dynamics in Jingmen group viral lineages: Spatial correlation, recombination, and phylogeography","authors":"You Zhang ,&nbsp;LvYing Wu ,&nbsp;Jun Wang ,&nbsp;Yuan Bai ,&nbsp;Jian Xiao ,&nbsp;Burno Coutard ,&nbsp;Hua Pei ,&nbsp;Fei Deng ,&nbsp;Shu Shen","doi":"10.1016/j.meegid.2025.105744","DOIUrl":"10.1016/j.meegid.2025.105744","url":null,"abstract":"<div><div>The global emergence of Jingmen group viruses (JMVs), including Jingmen tick virus (JMTV), Alongshan virus (ALSV), and Yanggou tick virus (YGTV), has significantly broadened our perspective on the potential public health risks posed by segmented flaviviruses. However, the global evolutionary and genetic epidemiology of JMVs remains unclear. In this study, we conducted a comprehensive analysis of the spatial correlation, recombination, and phylogeography of JMVs. Our phylogenetic analysis identified three latitudinal lineages: (1) a mid–high-latitude group with YGTV and ALSV, prevalent in Europe and Asia; (2) a mid-latitude group with JMTV in Romania, Turkey, Kosovo, Trinidad, and Tobago; and (3) a mid–low-latitude group with JMTV and the Sichuan tick virus in Brazil, Japan, China, Kenya, and Uganda. The strong correlation between genetic distance and latitude also supports a latitude-dependent evolutionary pattern. Notably, concordance between the phylogenies of dominant tick species and JMVs underscores the pivotal role of tick species in the evolution of JMVs. Furthermore, the detection of frequent intra-lineage recombination and global migration events underscores the ecological pressures and tick-mediated evolutionary mechanisms that propel the global dissemination of emerging segmented flaviviruses. Additionally, the complex interplay of JMV recombination and migration events of JMVs identified here, particularly the recombination between JMTV and ALSV from disparate regions and viral migration across different regions and continents, complicates their evolutionary interrelationships and heightens potential health risks. Overall, our study provides valuable insights into ecological factors and tick species-mediated evolution and transmission that shape the global spread of emerging segmented flaviviruses.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105744"},"PeriodicalIF":2.6,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143797210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Viral integration and fusion transcript characteristics of possibly high-risk HPV in cervical cancer","authors":"Hong Liu ,&nbsp;Ruiyi Xu ,&nbsp;Jinglan Chen ,&nbsp;Shuyan Wang ,&nbsp;Lingfang Wang ,&nbsp;Min Wu ,&nbsp;Hui Wang","doi":"10.1016/j.meegid.2025.105746","DOIUrl":"10.1016/j.meegid.2025.105746","url":null,"abstract":"<div><div>HPV34, HPV66, HPV73, and HPV82 are classified by the International Agency for Research on Cancer as possibly high-risk HPV (pHR-HPV) types. Despite their relatively lower pathogenicity, some cervical cancer (CC) patients have been found to be infected with pHR-HPV, though the underlying pathogenic characteristics remain unclear. Using viral integration detection and RNA sequencing in 8 pHR-HPV⁺ CC samples, we identified that the integration of pHR-HPV into the human genome and the formation of pHR-HPV-human fusion transcripts are critical events in cervical carcinogenesis. These events disrupt normal gene expression and favor the stable expression of oncogenes. Additionally, we discovered that pHR-HPV undergoes alternative splicing from the AGGTA motif. Despite their lower pathogenicity, pHR-HPV integration may represent a significant risk factor for CC development. Our findings underscore the importance of considering pHR-HPV infections in future HPV screening strategies and clinical management of cervical lesions, especially those associated with HPV integration.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105746"},"PeriodicalIF":2.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143767952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}