Infection Genetics and Evolution最新文献

{"title":"Analysis of novel African swine fever variants circulating in wild boars in South Korea isolated in 2021 by deep sequencing","authors":"Van Dam Lai ,&nbsp;Yong-kwan Kim ,&nbsp;Min-Ho Kim ,&nbsp;Yeeun Moon ,&nbsp;Hyeok-Il Kwon ,&nbsp;Weon-hwa Jheong ,&nbsp;Jong-Soo Lee ,&nbsp;Sung-Sik Yoo ,&nbsp;In Pil Mo","doi":"10.1016/j.meegid.2025.105833","DOIUrl":"10.1016/j.meegid.2025.105833","url":null,"abstract":"<div><div>African swine fever (ASF) is major infectious disease of concern currently circulating in swine species, causing high mortality and significant economic damage on the global scale. Since the first incident of ASF outbreak in Korea in 2019, the disease has continued to spread throughout the country despite enhanced biosecurity measures, with wild boars playing a key role. Thus, characterizing the domestic African swine fever virus (ASFV) strains including its genetic variants is crucial for both monitoring and diagnostic purposes. In this study, we sequenced and analyzed the full genome of seven Korean ASFV strains isolated from ASFV positive wild boar samples collected in 2021 from various regions. The sequences were compared with previously isolated ASFV strains to track the origin and the evolutionary trend of the ASFV variants residing in the wild boar population in Korea. A total of thirty single-nucleotide polymorphisms (SNPs) were detected which consists of ten synonymous and eighteen non-synonymous mutations, a single mutation at intergenic region (IGR), and a truncation mutation which led to a premature stop codon. Out of the mutations, thirteen were present in the MGF 505-9R gene. All seven strains contained an additional ten-nucleotides (nt) long tandem repeat sequence (TRS) between the I73R and I179L gene, similar to strains previously studied in Korea. Additionally, a new seventeen-nt long tandem repeat sequence insertion, adjacent to the MGF 505-10R, has been observed at the IGR between the MGF 505-9R and 10R genes. The results of the study provide extra insight for characterizing the ASFV virus in Korea and suggesting new molecular genetic markers for epidemiological monitoring, thus minimizing the risk of new ASF outbreaks in Korea.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105833"},"PeriodicalIF":2.6,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145121163","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":"Targeted next-generation sequencing reveals pathogen mono- and co-detection patterns in pediatric Mycoplasma pneumoniae pneumonia","authors":"Genfeng Wu ,&nbsp;Yuejie Zheng ,&nbsp;Kangyan Yuan ,&nbsp;Yanmin Bao ,&nbsp;Li Li ,&nbsp;Yuzheng Li ,&nbsp;Wenjian Wang ,&nbsp;Heping Wang","doi":"10.1016/j.meegid.2025.105832","DOIUrl":"10.1016/j.meegid.2025.105832","url":null,"abstract":"<div><h3>Background</h3><div>Following pandemic control optimization, <em>Mycoplasma pneumoniae</em> (MP) has emerged as a predominant pediatric respiratory pathogen in Shenzhen. Understanding its epidemiological patterns and drug resistance is critical for managing severe MP-associated pneumonia.</div></div><div><h3>Methods</h3><div>This retrospective study analyzed 607 hospitalized children (February–November 2023) using targeted next-generation sequencing (tNGS) of bronchoalveolar lavage fluid. MP-positive cases were stratified by age, gender, clinical features, drug resistance genes, and co-detection profiles.</div></div><div><h3>Results</h3><div>Pathogens were identified in 605 cases (99.7 %), with MP constituting 85.0 % of detected pathogens. Among 209 cases with resistance genes, A2063G mutation predominated (98.1 %). Patients were categorized into: MP-positive (<em>n</em> = 444), MP-carriage (<em>n</em> = 72), and MP-negative (<em>n</em> = 91) groups. Age stratification revealed significantly older MP-positive patients (median 72 months, IQR 48–96) versus carriages (29.5 months, IQR 14–60) and negatives (36 months, IQR 16–60) (<em>P</em> <em>&lt;</em> 0.001). Gender distribution showed no significant intergroup differences (χ² = 2.619, <em>p</em> = 0.270). The MP-positive group demonstrated lower co-detection rates of <em>Haemophilus influenzae</em> (12.2 % vs 37.5 %/31.5 %) and <em>Moraxella catarrhalis</em> (10.6 % vs 25.0 %/20.2 %) compared to carriages and negatives (<em>P</em> &lt; 0.001). tNGS uncovered atypical pathogens including <em>Tropheryma whipplei</em> (13.3 %) and <em>Fusobacterium nucleatum</em> (6.3 %).</div></div><div><h3>Conclusion</h3><div>Post-pandemic MP resurgence correlates with increased severe pediatric pneumonia despite declining macrolide resistance rates (23.2 % in 2023 vs historical 80–90 %). MP primarily manifests as monoinfections, while <em>M. catarrhalis</em> and <em>H. influenzae</em> co-detection may confer observed co-detection pattern. These findings underscore tNGS's clinical utility in identifying atypical pathogens and guiding antimicrobial stewardship in pediatric pneumonia management.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105832"},"PeriodicalIF":2.6,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093088","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":"Unravelling ecological factors influencing phylodynamics of Kyasanur Forest Disease in India","authors":"Sahal Paladan ,&nbsp;Bhimanagoud Kumbar ,&nbsp;Dharani Govindasamy ,&nbsp;Shweta Patil ,&nbsp;H.B. Chethan Kumar ,&nbsp;Revanaiah Yogisharadhya ,&nbsp;Pragya Yadav ,&nbsp;T. Jeromie Wesley Vivian ,&nbsp;Sathish S. Gaekwad ,&nbsp;Naveen Kumar ,&nbsp;Baldev Raj Gulati ,&nbsp;Sathish Bhadravati Shivachandra ,&nbsp;Mohammed Mudassar Chanda","doi":"10.1016/j.meegid.2025.105831","DOIUrl":"10.1016/j.meegid.2025.105831","url":null,"abstract":"<div><div>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 <em>E</em>-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.</div><div>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.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105831"},"PeriodicalIF":2.6,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093098","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 insights of two Acinetobacter non-baumannii strains with uncommon mechanisms of resistance leading to cefiderocol resistance","authors":"Usman Akhtar ,&nbsp;Samyar Moheb ,&nbsp;Carol Davies-Sala ,&nbsp;Joshua Gutierrez ,&nbsp;Fernando Pasteran ,&nbsp;Marisel R. Tuttobene ,&nbsp;Tomás Subils ,&nbsp;Chun Fu Cheng ,&nbsp;Quentin Valle ,&nbsp;Rajnikant Sharma ,&nbsp;Marcelo E. Tolmasky ,&nbsp;Gauri Rao ,&nbsp;Robert A. Bonomo ,&nbsp;German M. Traglia ,&nbsp;María Soledad Ramírez","doi":"10.1016/j.meegid.2025.105820","DOIUrl":"10.1016/j.meegid.2025.105820","url":null,"abstract":"<div><div>The emergence of antimicrobial resistance in <em>Acinetobacter</em> species poses a significant clinical challenge, particularly in non<em>-baumannii</em> species, which are often overlooked in healthcare settings. In this study, we characterized two <em>Acinetobacter</em> clinical isolates, AMA204 and AMA207—identified as <em>A. junii</em> and <em>A. haemolyticus</em>, respectively—which exhibit uncommon resistance mechanisms that enable survival in the presence of cefiderocol, regardless of their initial minimum inhibitory concentration values. Whole-genome sequencing and comparative genomic analyses were performed to investigate the genetic determinants associated with their resistance profiles. Antimicrobial susceptibility testing confirmed multidrug resistance, with both isolates harboring key β-lactamase genes, including <em>bla</em>_OXA-58, and <em>bla</em>_NDM-1 in AMA204, and <em>bla</em>_OXA-58 and <em>bla</em>_PER-2 in AMA207. Phylogenomic analyses revealed genetic relatedness to geographically diverse isolates, suggesting possible evolutionary trends and transmission dynamics. Additionally, iron uptake systems were analysed, highlighting potential mechanisms contributing to cefiderocol resistance together with the presence of listed β-lactamase. This study underscores the clinical relevance of non-<em>baumannii Acinetobacter</em> species in antimicrobial resistance and emphasizes the need for continued surveillance and novel therapeutic strategies to combat these emerging threats.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105820"},"PeriodicalIF":2.6,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145088376","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":"Modeling and sensitivity analysis of cholera dynamics under fuzzy imprecision","authors":"Sara Riaz ,&nbsp;Asghar Ali ,&nbsp;Muhammad Munir","doi":"10.1016/j.meegid.2025.105821","DOIUrl":"10.1016/j.meegid.2025.105821","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105821"},"PeriodicalIF":2.6,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145088474","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":"Characterization of genes involved in hemoglobin degradation in Plasmodium vivax isolates from Chennai, India, and species of non-human primate malaria","authors":"Sneh Shalini ,&nbsp;Neelima Mishra ,&nbsp;Sonia Verma ,&nbsp;Sonal Kale ,&nbsp;Prashant K. Mallick ,&nbsp;Surendra K. Prajapati ,&nbsp;Anil Kumar ,&nbsp;Nalini Srivastava ,&nbsp;Hema Joshi ,&nbsp;Alex Eapen ,&nbsp;Om P. Singh","doi":"10.1016/j.meegid.2025.105823","DOIUrl":"10.1016/j.meegid.2025.105823","url":null,"abstract":"<div><h3>Background</h3><div><em>Plasmodium vivax</em> poses a persistent obstacle to global malaria elimination efforts. While no detectable chloroquine (CQ) resistance has been found in patient samples from India, this observation awaits confirmation. The mechanism of action of CQ continues to be debated. Hemoglobin degradation within the parasite's food vacuole (FV) is integral to its survival and serves as a promising target for antimalarial drug development.</div></div><div><h3>Methods</h3><div>This study investigates the molecular and structural characteristics of three key FV enzymes—plasmepsin IV (PM_IV), heme detoxification protein (HDP), and falcilysin (FLN)—in <em>P. vivax</em> isolates from India. Genomic DNA from 30 clinical isolates and three chloroquine (CQ)-resistant reference strains was analyzed to identify mutations and assess structural implications through homology modelling.</div></div><div><h3>Results</h3><div>Several nonsynonymous mutations were detected, including c.493G&gt;A (Val165Ile) in PM_IV, c.1537A&gt;G (Asn513Asp), and c.2027G&gt;A (Gly676Asp) in FLN, and a novel in-frame duplication c.28_33dup (ATCGCC) in HDP. Structural modelling revealed that these mutations did not affect the active binding sites of the enzymes.</div></div><div><h3>Conclusions</h3><div>The genes were highly conserved across isolates, underscoring their important (essential) roles in parasite survival and their potential as drug targets. These are the first findings from the Indian subcontinent that provide critical insights into the mechanisms of chloroquine (CQ) action and resistance, paving the way for novel therapeutic strategies against <em>Plasmodium vivax</em> malaria.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105823"},"PeriodicalIF":2.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058789","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":"Exploratory interaction of Chionis alba (snowy sheathbill) with the amatoxin-producing mushroom Galerina marginata in Antarctica","authors":"Fernando Augusto Bertazzo-Silva ,&nbsp;Alice Lemos Costa ,&nbsp;Jorge Renato Pinheiro Velloso ,&nbsp;Flavia Helena Aires Sousa ,&nbsp;Carlos Ernesto Gonçalves Reynaud Schaefer ,&nbsp;Jair Putzke","doi":"10.1016/j.meegid.2025.105822","DOIUrl":"10.1016/j.meegid.2025.105822","url":null,"abstract":"<div><div>We report a rare behavioral observation involving an individual of <em>Chionis alba</em> (snowy sheathbill) attempting to consume a basidiome of the toxic mushroom <em>Galerina marginata</em> on Livingston Island, Antarctica. The bird briefly picked up the basidiome before rejecting it. This event, to our knowledge, represents the first recorded interaction between an Antarctic bird and this deadly fungus, suggesting possible chemical or gustatory deterrence mechanisms. Such interactions, though anecdotal, contribute to the understanding of trophic dynamics and fungal ecology in polar environments.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105822"},"PeriodicalIF":2.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058782","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":"Early plasma cytokines associated with multi-drug resistant ventilator-associated pneumonia after neurosurgery: A retrospective cohort study","authors":"Yuanrun Zhu ,&nbsp;Zhaodi Liao ,&nbsp;Jianan Su ,&nbsp;Feng Zhang ,&nbsp;Jin Huang ,&nbsp;Ping He ,&nbsp;Zhifeng Wu ,&nbsp;Kangli Xu ,&nbsp;Xiaofeng Yang ,&nbsp;Chen Jiang ,&nbsp;Yadong Wang","doi":"10.1016/j.meegid.2025.105824","DOIUrl":"10.1016/j.meegid.2025.105824","url":null,"abstract":"<div><div>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 (&gt;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, <em>p</em> = 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.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105824"},"PeriodicalIF":2.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058778","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":"Whole genome characterisation of DS-1-like G8P[4] rotavirus A strains circulating in South Africa between 2009 and 2021 reveals endemic sub-lineages and evidence of radical epitope changes","authors":"Nkosazana D. Shange ,&nbsp;Milton T. Mogotsi ,&nbsp;Ayodeji E. Ogunbayo ,&nbsp;Nicola Page ,&nbsp;Hlengiwe Sondlane ,&nbsp;Matthew D. Esona ,&nbsp;Benjamin Kumwenda ,&nbsp;Chimwemwe Mhango ,&nbsp;Flywell Kawonga ,&nbsp;Ernest Matambo ,&nbsp;Samuel N.K. Mingle ,&nbsp;Francis E. Dennis ,&nbsp;Jere C. Khuzwayo ,&nbsp;Nigel A. Makoah ,&nbsp;Celeste M. Donato ,&nbsp;Martin M. Nyaga","doi":"10.1016/j.meegid.2025.105818","DOIUrl":"10.1016/j.meegid.2025.105818","url":null,"abstract":"<div><div>The sub-Saharan African region bears the highest burden of rotavirus-associated morbidity and mortality, with substantial genetic diversity observed in circulating strains despite vaccine introduction. The G8 genotype, originally predominant in bovine strains, has increasingly become prevalent in humans, suggesting a possible interface of animal-to-human transmission and highlighting its role in African strain diversity. In this study, we performed whole genome sequencing and evolutionary analysis of 21 archival G8P[4] strains collected through gastroenteritis surveillance in South Africa between 2009 and 2021 from children under five years of age. All strains exhibited DS-1-like genome constellations and phylogenetically clustered closely with sub-Saharan African G8P[4] strains across all 11 genome segments. A time-resolved phylogeny indicated the co-circulation of multiple G8 sub-lineages, with specific variants persisting for nearly a decade. The mean evolutionary rate for the G8 lineage V sequences was estimated at 1.49 × 10⁻³ substitutions per site per year, with a time to most common recent ancestor of 1981.8, suggesting long-term endemic divergence. Radical amino acid substitutions were identified in neutralising epitopes of VP4 (11 variations) and VP7 (18 variations) relative to the Rotarix® vaccine strain. These changes may impact antigenicity and immune recognition. These findings within the key antigenic sites of G8P[4] strains may reflect ongoing viral adaptation with potential implications for infectivity and sustained circulation in African regions. Taken together, the findings underscore the significance of continued genomic surveillance to monitor evolution and guide the reassessment, optimisation of current vaccines and the development of future vaccines with broader protective efficacy.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105818"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145010089","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":"Epidemiological and molecular retrospective analysis of porcine circovirus 3 in the US grower-finisher herd","authors":"Molly Kroeger ,&nbsp;Christopher James Stott ,&nbsp;Huigang Shen ,&nbsp;Ganwu Li ,&nbsp;Rodger Main ,&nbsp;Eric Bush ,&nbsp;Margaret Parker ,&nbsp;Dachrit Nilubo ,&nbsp;Jean Paul Cano ,&nbsp;Jack Creel ,&nbsp;Pablo Piñeyro","doi":"10.1016/j.meegid.2025.105819","DOIUrl":"10.1016/j.meegid.2025.105819","url":null,"abstract":"<div><div>Porcine circovirus type 3 (PCV3) was identified in 2016 and has since been associated with reproductive failure, multisystemic inflammation, and subclinical infection in swine. Numerous countries have retrospectively detected the presence of PCV3 before its first clinical description in 2016. The reported detection rate of PCV3 has varied from 6.5 to 84 % in pigs with various coinfections. Today, PCV3/PCV2 coinfection is commonly observed. However, the PCV3 prevalence and coinfection rate with PCV2 in the US swine industry had not been reported before 2016. The present study used serum samples from US grower finisher farms from 2000, 2006, and 2012 to determine the PCV3 and PCV3/PCV2 farm prevalence and geographical distribution, to evaluate the PCV3 evolutionary rate and selection pressure forces, and to identify structural and morphological changes in the Cap protein. Our findings revealed that PCV3 was endemic in the US swine industry before its first description in 2016. The PCV3 farm prevalence decreased from 47 % in 2000 to 22 % in 2012. The PCV3/PCV2 coinfection rate at the farm level was 47 % in 2000 and 39 % in 2006. After the introduction of PCV2 vaccines in 2006, the PCV3/PCV2 coinfection rate drastically declined to 3 % and 59 % of farms were negative for both PCV3 and PCV2 in 2012. From 13 PCV3 whole genome sequences, 12 sequences were clustered with PCV3a reference strain and one with the PCV3c subtype. From 28 PCV3 ORF2 sequences, PCV3a1 (1/28), PCV3a2 (4/28), PCV3a3 (19/28), PCV3b (2/28), and PCV3c (2/28) subtypes were obtained. ORF2 nucleotide identity ranged from 97.8 to 100 %. Diversifying selection occurred at amino acids 24 and 150 in 2006 and at amino acids 24 and 27 in 2012. Mutations A24V and R27K were common among all PCV3 subtypes in sequences identified in the present study and in reference sequences. Both the S77T and I150L mutation was common among sequences within the PCV3a2 subtype. The F104Y mutation lies within a predicted T-cell epitope and was present in sequences of the PCV3c, PCV3b, and PCV3a3 subtypes. Cap molecular modeling revealed that the structural folding of amino acids 24 and 27 changed from alpha helix to coiled in 2012 sequences. Thus, this study broadens current knowledge of PCV3's prevalence and molecular evolution in the US swine herd from 2000 to 2012.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105819"},"PeriodicalIF":2.6,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144996763","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}