{"title":"Genomic analysis of peste des petits ruminants virus in Europe: Common origin for emergence in Greece, Romania, and Bulgaria","authors":"Samia Guendouz , Olivier Kwiatek , Aikaterini Kirtzalidou , Angeliki Katsifa , Maria Gianniou , Corina Ancuceanu , Mona Ghiță , Cristian Laurențiu Mortasivu , Anna Zdravkova , Iliyan Kostov , Emilia Ivanova , Florica Bărbuceanu , Konstantia E. Tasioudi , Arnaud Bataille","doi":"10.1016/j.meegid.2025.105774","DOIUrl":"10.1016/j.meegid.2025.105774","url":null,"abstract":"<div><div>Outbreaks of the highly pathogenic small ruminant disease peste des petits ruminants (PPR) were reported in Greece and Romania in July 2024, and central Bulgaria in November 2024. The origin and the link between these outbreaks are not clear. In this study, genome sequences of PPR virus were obtained from samples collected by veterinary authorities in the first farms notified as infected in the three European countries. Genomic analyses confirmed that the emergence of PPR across Europe has a common origin, pointing towards an introduction from Northern Africa, although additional sequencing from the virus currently circulating globally is needed to confirm this hypothesis. More sequencing from the different outbreaks in Europe could also help to resolve the pathway of PPR transmission between and within European countries. Multiple nucleotide and amino acid differences separate the genomes from Europe from other sequences, with potential impact on the functionality of viral proteins to be investigated.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105774"},"PeriodicalIF":2.6,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144167631","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}
Yulian Kuryliak , Michael T.M. Emmerich , Dmytro Dosyn
{"title":"Simulating epidemic peak dynamics on complex networks using efficient Gillespie algorithms","authors":"Yulian Kuryliak , Michael T.M. Emmerich , Dmytro Dosyn","doi":"10.1016/j.meegid.2025.105768","DOIUrl":"10.1016/j.meegid.2025.105768","url":null,"abstract":"<div><div>We present an integrated study of epidemic spreading on complex networks that (i) reveals how network structure and targeted interventions shape the peak count of infected nodes (PCIN) and its timing, (ii) supplies an open-source dashboard that lets researchers explore these effects with realistic model extensions, and (iii) delivers a high-performance simulation engine which improves the time complexity of existing sparse network implementations of Gillespie's algorithm by multiplicative factors. Continuous-time SI/SIS/SIR dynamics are analyzed with respect to two intervention knobs: edge-specific infection rate reduction and node-level recovery acceleration, yielding explicit bounds on peak height and delay across heterogeneous topologies. To test scenarios interactively, we extend the dashboard simulator to include non-exponential recovery times, temporal rewiring, weighted and multi-type contacts, simulation of antigenically equivalent mutant strains, and a novel visual aggregation of likely infection routes. Moreover, we redesign Gillespie's algorithm for sparse graphs at its core by succinctly and incrementally updating the (sums of the) transition rate and maintaining a sorted infected node list, achieving speed increases with a multiplicative factor compared to the state-of-the-art implementation of the adjacency list. Additional speed gains can be achieved by our new algorithm when infection is in its early stage and only a few nodes of a large network are infected; a complementary dense matrix variant covers non-sparse cases. Benchmarks on Barabási–Albert networks confirm up-to-order-of-magnitude gains over the standard adjacency-list implementation of Gillespie's algorithm.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105768"},"PeriodicalIF":2.6,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144167630","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}
Zeinab H Helal, Nina Francesca Soriano, David H Chung, Dong-Hun Lee, Natalie Tocco, Fatma Gazeyoglu, Ji-Yeon Hyeon, Guillermo R Risatti
{"title":"Molecular epidemiology of West Nile Virus in Raptors, Connecticut, USA, 2022: A case series with whole genome sequencing and phylogenetic analysis.","authors":"Zeinab H Helal, Nina Francesca Soriano, David H Chung, Dong-Hun Lee, Natalie Tocco, Fatma Gazeyoglu, Ji-Yeon Hyeon, Guillermo R Risatti","doi":"10.1016/j.meegid.2025.105769","DOIUrl":"https://doi.org/10.1016/j.meegid.2025.105769","url":null,"abstract":"<p><p>West Nile virus (WNV), a mosquito-borne flavivirus, circulates in an enzootic cycle between birds and mosquitoes, with raptors serving as key amplifying hosts. Despite their importance in WNV surveillance, complete genome sequences from raptors remain limited. This study aimed to investigate the genetic diversity and evolutionary history of WNV in raptors from Connecticut, USA. Samples were collected in 2022 from the brain tissue of deceased red-tailed hawks, red-shouldered hawks, Cooper's hawks, a peregrine falcon, and American crows. Complete protein-coding sequences (CDSs) of 19 WNV isolates were obtained using multiplex tiling reverse transcription polymerase chain reaction (RT-PCR) developed in this study and Illumina iSeq100 sequencing. Phylogenetic analyses revealed our sequences were grouped into two monophyletic clusters and two singletons within lineage 1, showing genetic similarities to WNV strains detected in mosquitoes in New York (2012-2015) rather than earlier strains from Connecticut (1999-2008). Bayesian analysis indicated at least four independent introductions, with the estimated time to the most recent common ancestor (tMRCA) for Clusters 1 and 2 in April 2009 and February 2010, respectively. The mean substitution rate was 4.30 × 10<sup>-4</sup> substitutions/site/year. All sequences contained the T249P mutation in NS3, which has been linked to reduced virulence in avian models. These findings provide valuable reference data for future WNV genomic surveillance studies, emphasizing the role of raptors as sentinel species and the need for ongoing genomic surveillance to monitor WNV evolution, transmission, and potential public health risks.</p>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":" ","pages":"105769"},"PeriodicalIF":2.6,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163951","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}
Natasha Edwards, Andrew E Shaw, Antonello Di Nardo, Amy Sowood, Hayley M Hicks, Jemma Wadsworth, Krupali Parekh, Amy Mccarron, Pradeep Lakpriya Kumarawadu, Yassir Mohammed Eltahir, Meera Saeed Mohamed, Lekh Raj Dahal, Krishna Raj Pandey, Nisha Paudel, Emma Taylor, Daniel L Horton, Valerie Mioulet, Anna Ludi, Nick J Knowles, Donald P King, Lidia Lasecka-Dykes
{"title":"Foot-and-mouth disease virus O/ME-SA/SA-2018: A new emerging threat posed by viruses circulating in Asia?","authors":"Natasha Edwards, Andrew E Shaw, Antonello Di Nardo, Amy Sowood, Hayley M Hicks, Jemma Wadsworth, Krupali Parekh, Amy Mccarron, Pradeep Lakpriya Kumarawadu, Yassir Mohammed Eltahir, Meera Saeed Mohamed, Lekh Raj Dahal, Krishna Raj Pandey, Nisha Paudel, Emma Taylor, Daniel L Horton, Valerie Mioulet, Anna Ludi, Nick J Knowles, Donald P King, Lidia Lasecka-Dykes","doi":"10.1016/j.meegid.2025.105771","DOIUrl":"https://doi.org/10.1016/j.meegid.2025.105771","url":null,"abstract":"<p><p>In 2018, a novel lineage of foot-and-mouth disease virus (FMDV) termed O/ME-SA/SA-2018 was identified in India, which subsequently spread into neighbouring countries (Nepal, Bangladesh and Sri Lanka). Since then, incursions of this lineage have occurred in the Middle East, beyond its usual epidemiological distribution. Using sequence data derived from field cases, this paper reconstructs the evolutionary history of the O/ME-SA/SA-2018 lineage, presents vaccine matching data for six commercially available FMD vaccines, and describes a novel lineage-specific RT-PCR assay which can be used to help detect field cases due this emerging lineage. Further surveillance studies are warranted to understand the distribution of this virus in Asian countries.</p>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":" ","pages":"105771"},"PeriodicalIF":2.6,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144152790","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}
Spenser J. Babb-Biernacki , Li Peng , Claire M. Jardine , Jamie L. Rothenburger , Mark T. Swanson , Joseph A. Kovacs , Jacob A. Esselstyn , Vinson P. Doyle , Liang Ma
{"title":"Three distinct forms of Pneumocystis coexist in individuals of two species of deer mice (genus Peromyscus)","authors":"Spenser J. Babb-Biernacki , Li Peng , Claire M. Jardine , Jamie L. Rothenburger , Mark T. Swanson , Joseph A. Kovacs , Jacob A. Esselstyn , Vinson P. Doyle , Liang Ma","doi":"10.1016/j.meegid.2025.105767","DOIUrl":"10.1016/j.meegid.2025.105767","url":null,"abstract":"<div><div>As emerging zoonoses represent a significant public health threat, understanding how pathogens' host ranges evolve is critical to protect human and wildlife health. Closely related hosts infected with host-specific pathogens provide valuable opportunities for clear inferences of host range evolution, as they allow for the examination of early diversification patterns in their resident pathogens. <em>Pneumocystis</em>, an obligate lung symbiont that is believed to be ubiquitous in mammals, exemplifies such a model. To explore the early stages of divergence in <em>Pneumocystis,</em> we collected geographically dispersed samples from two sister species of deer mice: <em>Peromyscus leucopus</em> (white-footed mice) and <em>Peromyscus gossypinus</em> (cotton mice<em>).</em> We sequenced two nuclear and two mitochondrial loci of <em>Pneumocystis</em> sampled from the lungs of these mice. These sequences revealed three distinct <em>Pneumocystis</em> taxa, two of which were found to cross-infect both host species and were often found coexisting within the same individual. Genetic diversity and phylogenetic analysis suggest that the three <em>Pneumocystis</em> taxa represent separate species. Further analysis of the mitochondrial large subunit rRNA gene from the most common taxon of these three revealed that host geographic origins influenced <em>Pneumocystis</em> genetic structure more than host species identity. Nevertheless, the results also suggest an overall interconnectedness of the symbiont metapopulation.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105767"},"PeriodicalIF":2.6,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144133194","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":"The impact of infections and genetics on secondary sex ratio","authors":"Iasonas Dermitzakis , Paschalis Theotokis , Efthymia Delilampou , Evangelos Axarloglou , Chrysoula Gouta , Maria Eleni Manthou , Soultana Meditskou , Dimosthenis Miliaras","doi":"10.1016/j.meegid.2025.105770","DOIUrl":"10.1016/j.meegid.2025.105770","url":null,"abstract":"<div><div>The secondary sex ratio (SSR), which reflects the proportion of male to female offspring at birth, is influenced by a complex interplay of multiple factors. This review delves into the current understanding of how infections and genetics contribute to variations in the SSR. The effects of infections on the SSR represent an intriguing intersection of biology and epidemiology. Research indicates that several infectious diseases, such as toxoplasmosis, coronavirus disease 2019, Spanish flu, acquired immunodeficiency syndrome and tuberculosis, can impact the SSR through mechanisms that are only partially understood. Genetics are also scrutinized in this review. Although their involvement in determining the SSR is debatable, various genetic factors have been studied. The influences of the Rhesus D heterozygous phenotype, major histocompatibility complex, corticosteroid-binding globulin deficiency, ethnicity, and consanguinity on SSR have been delineated. By amalgamating findings from diverse disciplines, this review aims to offer a comprehensive overview of the multifaceted impact of infections and genetics on SSR, pinpointing potential implications for reproductive biology and public health.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105770"},"PeriodicalIF":2.6,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144123994","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}
Hina Fatima , Muhammad Salman , Zunera Jamal , Rabia Hakim , Massab Umair , Javaria Qazi
{"title":"Molecular characterization and genetic diversity of mumps virus genotype G in Pakistan during the 2023 outbreaks","authors":"Hina Fatima , Muhammad Salman , Zunera Jamal , Rabia Hakim , Massab Umair , Javaria Qazi","doi":"10.1016/j.meegid.2025.105766","DOIUrl":"10.1016/j.meegid.2025.105766","url":null,"abstract":"<div><div>Mumps, despite being a vaccine-preventable disease, poses a significant public health challenge globally. In Pakistan, the absence of mumps vaccination in the national immunization program, coupled with limited epidemiological and surveillance data, presents a concerning scenario. This study investigates the molecular epidemiology of the Mumps virus (MuV) during the 2023 outbreaks, focusing on the genetic variability of the small hydrophobic (SH) gene, a key determinant for viral evolution and genotyping. Buccal swabs were collected from suspected patients presenting swollen parotid glands during the outbreak periods. Out of 62 mumps suspects, 40 (64.5 %) samples tested positive for MuV through RT-PCR. The incidence rate of positive cases was higher in males (70 %) than in females (30 %), with the highest incidence observed in early childhood (0–5 year-old) infants. Phylogenetic analysis revealed that all the specimens belonged to genotype G, with 97.4 % homology with genotype G of MuV isolates from Spain and up to 98.73 % with Japan, and UK. This research study underscores Pakistan's vulnerability to mumps outbreaks due to the absence of mumps vaccine in the national immunization program and highlights the need for effective surveillance systems for Mumps in the country.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105766"},"PeriodicalIF":2.6,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112980","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}
Pimlapas Leekitcharoenphon , Valeria Bortolaia , Viktor Karl Wilhelm Tornblom , Achiraya Siriphap , Orasa Suthienkul , Jednipit Borthong , Kaknokrat Chonsin , Frederik Duus Møller , Baptiste Avot , Saria Otani , Frank M. Aarestrup
{"title":"Effect of large-scale population-based dietary change to vegetarianism on antimicrobial resistance and bacterial composition of sewage in Thailand","authors":"Pimlapas Leekitcharoenphon , Valeria Bortolaia , Viktor Karl Wilhelm Tornblom , Achiraya Siriphap , Orasa Suthienkul , Jednipit Borthong , Kaknokrat Chonsin , Frederik Duus Møller , Baptiste Avot , Saria Otani , Frank M. Aarestrup","doi":"10.1016/j.meegid.2025.105765","DOIUrl":"10.1016/j.meegid.2025.105765","url":null,"abstract":"<div><div>Antimicrobial resistance (AMR) is on one of the global priority challenges. This study explored the impact of diet alteration on AMR bacteria through metagenomic analysis during the annual vegetarian festival in Thailand in October 2019. The study investigated the effects of a 10-day shift from a regular to a vegetarian diet by collecting urban sewage from Nakhon Sawan, Surat Thani, and Bangkok before, during, and after the festival. Additionally, faecal samples from individuals in the northern city were analyzed. Using shotgun metagenomic sequencing, the samples were mapped against bacterial, AMR genes, and carbohydrate-active enzymes databases.</div><div>The results revealed significant changes in AMR gene abundance and increased carbohydrate metabolism genes in sewage samples from all three cities during the festival. There was also a notable shift in the composition and diversity of bacterial species, particularly in the northern city. The total abundance of AMR genes increased during the vegetarian festival across all locations. This study highlights the correlation between a population's vegetarian diet and increased AMR in Thailand. It also demonstrates that metagenomic analysis of sewage can effectively assess the impact of dietary changes on bacterial communities and AMR at a population level, providing valuable insights for public health strategies.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105765"},"PeriodicalIF":2.6,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103210","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":"Genome-based alert on a clinical Plesiomonas shigelloides PSU59 from Thailand: Resistance and virulence features","authors":"Thunchanok Yaikhan , Kamonnut Singkhamanan , Thitaporn Dechathai , Arnon Chukamnerd , Sarunyou Chusri , Rattanaruji Pomwised , Monwadee Wonglapsuwan , Komwit Surachat","doi":"10.1016/j.meegid.2025.105764","DOIUrl":"10.1016/j.meegid.2025.105764","url":null,"abstract":"<div><div><em>Plesiomonas shigelloides</em>, an aquatic Gram-negative bacterium, is increasingly recognized as an emerging pathogen with antimicrobial resistance (AMR) potential. This study provides a genome-based alert on <em>P. shigelloides</em> PSU59, isolated from a patient in Thailand. Whole-genome sequencing (WGS) revealed a 3.6 Mb draft genome (38 contigs, 51.9 % GC) encoding 3265 coding sequences and 129 RNA genes. Thirteen AMR genes were identified, including efflux pumps (<em>adeF</em>, <em>tet(A)</em>), target modifiers (<em>dfrA1</em>, <em>sul2</em>), and aminoglycoside-inactivating enzymes. Mobile genetic elements (MGEs) flanking resistance genes suggest horizontal gene transfer (HGT). Virulence analysis revealed 48 factors, notably flagellar genes (<em>fliM</em>, <em>fliN</em>, <em>flhA</em>) linked to motility. Phylogenetic comparison placed PSU59 in Clade 3, closely related to a food-derived strain. These results highlight the pathogenic and drug-resistant potential of <em>P. shigelloides</em> PSU59 and underscore the importance of genomic surveillance in tracking emerging threats among under-recognized pathogens.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105764"},"PeriodicalIF":2.6,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144089364","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}
Dandan Niu , Yankun Ke , Qiuying Lv , Zhen Zhang , Tengyingzi Liu , Zhongyao Xu , Tong Li , Yingluan Zhang , Renli Zhang , Xiaomin Zhang , Shunping Cai , Xiaonan You , Yuqing Chen , Hanguang Wu , Yingxin Li , Chan Yin , Danzhu Wang , Xinhua Duan , Yongchao Guo , Rongqi Liu , Tiejian Feng
{"title":"Corrigendum to “Pathogens and drug resistance or virulence genes from animals and surrounding environment in Shenzhen, 2023 using targeted next-generation sequencing” [Infection, Genetics and Evolution, volume 131, 105755].","authors":"Dandan Niu , Yankun Ke , Qiuying Lv , Zhen Zhang , Tengyingzi Liu , Zhongyao Xu , Tong Li , Yingluan Zhang , Renli Zhang , Xiaomin Zhang , Shunping Cai , Xiaonan You , Yuqing Chen , Hanguang Wu , Yingxin Li , Chan Yin , Danzhu Wang , Xinhua Duan , Yongchao Guo , Rongqi Liu , Tiejian Feng","doi":"10.1016/j.meegid.2025.105759","DOIUrl":"10.1016/j.meegid.2025.105759","url":null,"abstract":"","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"131 ","pages":"Article 105759"},"PeriodicalIF":2.6,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144071219","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}