Search Results (161)

In this study, we investigated the long-term evolutionary dynamics of human norovirus GII.17[P17] using the RNA-dependent RNA polymerase (RdRp) region and the VP1 capsid gene, integrating phylogenetics, time-scaled inference, phylodynamics, and structure-based analyses. Maximum-likelihood phylogenies of both genomic regions consistently resolved four major clades (Clades 1–4). VP1 patristic-distance distributions indicated higher within-clade diversity in the phylogenetically basal Clades 1 and 3, whereas Clades 2 and 4 showed lower diversity, consistent with recent demographic expansion. Similarity-plot analysis identified pronounced variability in the VP1 P2 domain, while the S and P1 domains remained comparatively conserved, supporting P2 as the primary hotspot of diversification. Bayesian time-scaled analyses estimated the most recent common ancestor around 1993 (VP1) and 2000 (RdRp) and revealed two major lineages (Clade 1/2 and Clade 3/4), with the split between Clades 3 and 4 occurring around 2016–2017. Bayesian skyline plots showed a marked increase in effective population size after 2013, and substitution-rate estimates indicated faster evolution in VP1 than in RdRp, with higher VP1 rates in the Clade 3/4 lineage than in Clade 1/2. Capsid dimer modeling further mapped high-confidence conformational B-cell epitopes and positively selected residues predominantly to the distal surface of P2, with broadly conserved spatial patterns across clades. Compared with the Clade 1 reference (Kawasaki323), Clade 2 accumulated numerous P2 substitutions, whereas Clades 3 and 4 retained fewer changes and remained closer to Clade 1 at the amino-acid level. Together, these results suggest lineage turnover within GII.17[P17] driven by constrained diversification at the P2 surface, potentially contributing to the recent predominance of the Clade 3/4 lineage. Full article

Background/Objectives: We analyzed the whole-genome sequences of ciprofloxacin-resistant (CIP-R) enteropathogenic Escherichia coli (EPEC) ST752 isolates in South Korea to characterize their molecular epidemiology. This lineage has emerged as the predominant CIP-R EPEC clone in South Korea, accounting for 28.8% of human clinical isolates and circulating within the One Health interface. Methods: We performed whole-genome sequencing (WGS) and reference-based core-genome single-nucleotide polymorphism (SNP) analysis on 26 CIP-R EPEC ST752 isolates (19 human clinical and 7 poultry-derived isolates). To elucidate their evolutionary history and transmission dynamics, Bayesian phylodynamic and phylogeographic reconstructions were implemented by integrating domestic isolates with a global genome dataset (n = 508). Results: Isolates from human and poultry sources clustered together with an identical virulence profile and minimal genetic distance. The Bayesian molecular clock analysis estimated that the time to the most recent common ancestor of the South Korean clade was 2000.65. Moreover, the phylogeographic analysis supported statistical evidence (Bayes factor 32.16) for the introduction of this lineage into South Korea from Denmark and revealed a strongly supported host transition from humans to poultry (Bayes factor > 10,000), although this requires cautious interpretation due to limited temporal sampling of poultry isolates. Conclusions: Continued integrated One Health surveillance across human, animal, and environmental reservoirs is needed to monitor and prevent the spread of high-risk antimicrobial-resistant clones. Full article

Respiratory syncytial virus (RSV) is a leading cause of respiratory infections in infants and older adults, with epidemiological patterns shaped by viral evolution and diversity. To investigate the molecular epidemiology of RSV before and after the COVID-19 pandemic, we conducted genomic surveillance and phylodynamic analyses of RSV-A and RSV-B circulating in Maryland from 2018 to 2024. Whole-genome sequencing of RSV-positive samples (n = 451) was performed, and genomes were analyzed with phylogenetic and Bayesian methods to estimate evolutionary rates, population dynamics, selection pressures, and genetic diversity. RSV-A predominated in most seasons, while RSV-B showed episodic surges in 2018 and 2023. All RSV-A genomes belonged to the ON1 genotype, and RSV-B belonged to BA9, with sequential clade dominances including A.D.1, A.D.5.2, A.D.1.6, and B.D.E.1 across different epidemic seasons in Maryland. Bayesian analyses estimated evolutionary rates of 7.07 × 10⁻⁴ substitutions/site/year for RSV-A and 1.02 × 10⁻³ substitutions/site/year for RSV-B and temporal fluctuations in effective population size linked to pandemic-related disruptions. RSV-A displayed greater overall entropy, yet RSV-B evolved slightly faster. Genetic variability was concentrated in the G glycoprotein, with positively selected sites at codon 273 (RSV-A) and codon 217 (RSV-B). These findings demonstrate temporal fluctuations in RSV-A and RSV-B predominance, clade replacement, and ongoing viral adaptation throughout the COVID-19 era, underscoring the importance of integrated genomic and phylodynamic studies. Full article

Orf virus (ORFV), a member of the Parapoxvirus genus, is commonly associated with a highly infectious skin disease primarily affecting sheep and goats, with a reported zoonotic potential. Initially identified in the 18th century, ORFV has been sporadically reported in other species, including humans. The present study analyzed the genetic variability and phylodynamic patterns of ORFV using the highly variable VIR gene, focusing on global strains from multiple hosts, including various species of ruminants and humans. A dataset of 267 ORFV strains from around the world, including sequences from the understudied island of Cuba, was used for the analyses. Results revealed greater genetic variability for ORFV than previously reported. While the virus may be defined as a generalist pathogen, capable of infecting various ruminant species and less frequently humans, signs of host-specific specialization are emerging exclusively for sheep and goats. Other ruminant species and humans may be categorized as occasional hosts, with infections likely linked to habitat overlap with sheep and goats and sporadic transmission that appears influenced by specific risk factors. In conclusion, these findings contribute to a better understanding of the transmission risks posed by ORFV, highlighting the need for further investigations into its potential to infect a broader range of hosts, particularly humans. Full article

Human metapneumovirus genotype B (HMPV-B) is an important respiratory pathogen, requiring detailed elucidation of the evolutionary and antigenic features of its fusion (F) gene. Using 500 sequences collected between 1982 and 2024, we investigated the molecular evolution, phylodynamics, and structural epitope landscape of the HMPV-B F gene. Time-scaled phylogeny dated the divergence of sublineages B1 and B2 to around 1937, and Bayesian Skyline Plot analysis showed that these sublineages exhibited distinct demographic trajectories over time. The F gene evolved at a rate of 1.01 × 10⁻³ substitutions/site/year; however, amino acid variation remained limited, consistent with pervasive purifying selection, with 39% of codons under strong negative selection and little consensus evidence for positive selection. Conformational B-cell epitope prediction demonstrated a high degree of conservation across neutralizing antibody binding regions (sites Ø and I–V), and amino acid substitutions occurring within these sites were not predicted to substantially alter epitope architecture. Together, these findings indicate that the HMPV-B F gene evolves under strong evolutionary constraint while maintaining stable antigenic features, supporting the potential for antibody-based strategies that target neutralizing antibody binding regions of the F protein. Full article

Salmonella is a major foodborne pathogen, and its increasing antimicrobial resistance poses a significant public health challenge. In this study, we conducted a comprehensive genomic epidemiological investigation of Salmonella isolates recovered from meat products across multiple provinces in China. A total of 141 isolates were collected and subjected to antimicrobial susceptibility testing and whole-genome sequencing. Core genome MLST and hierarchical clustering (HierCC) were performed using EnteroBase, while SNP phylogeny and phylodynamic analyses were conducted to characterize the evolutionary dynamics of Salmonella populations. The predominant serovars were Enteritidis and Infantis, with a high proportion of multidrug-resistant isolates. Potentially transferable plasmids carrying ARGs, such as bla_CTX-M, qnrS1, sul2, and mcr-1.1, were frequently detected, indicating a risk of horizontal transfer during transmission. Genomic epidemiological investigation of our sequenced strains and their associated cgMLST HierCC clusters revealed both persistent Salmonella lineages, such as Enteritidis HC50-87 and Agona HC20-419, and emerging China-specific lineages, including Enteritidis HC20-10145 and Typhimurium HC50-2304. The estimated divergence times of these lineages mostly dated to the late mid-20th century, coinciding with the intensification of poultry farming in China. These findings highlight the power of genomic epidemiology in uncovering antimicrobial resistance patterns and transmission dynamics, underscoring the need for strengthened Salmonella surveillance. Full article

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Previous studies have reported the propagation of diverse HIV-1 CRFs of South American origin in Europe. Here, through protease-reverse transcriptase (Pr-RT) and integrase sequence analyses, we identify a Spanish cluster (BC3) branching with a Brazilian virus (10BR_RJ009) previously classified as CRF146_BC. In Pr-RT, BC3 comprised 14 viruses and was nested within a larger cluster, comprising 22 Brazilian viruses and 1 Spanish virus branching outside of BC3. Near full-length genome analyses of five BC3 viruses revealed mosaic structures identical to 10BR_RJ009, with two breakpoints delimiting a ~0.3 kb subtype B fragment within an otherwise subtype C genome. Two other Brazilian viruses previously classified as CRF146_BC (10BR_RJ039 and 01_BR_RGS69) had one and two additional short subtype B fragments, respectively, and failed to group with the 10BR_RJ009/BC3 cluster in subtype C fragments. Based on these results, we contend that 10BR_RJ009 and BC3 viruses, but not 10BR_RJ039 and 01_BR_RGS69, should be classified as CRF146_BC. Bayesian analyses estimated the CRF146_BC emergence in Brazil to be around 1999 and its introduction in Europe around 2011. CRF146_BC is the 10th CRF of South American origin reported to circulate in Europe, reflecting the relationship between South American and European HIV-1 epidemics. Full article

Influenza D virus (IDV), an emerging orthomyxovirus with zoonotic potential, infects diverse hosts, causes respiratory disease, and remains poorly characterized in China despite its global expansion. From October 2023 to January 2025, we collected 563 nasal swabs from cattle across 28 farms in Jilin Province, Northeast China, and identified seven IDV-positive samples (1.2%), recovering two viable isolates (JL/YB2024 and JL/CC2024). Full-genome sequencing revealed complete, stable seven-segment genomes with high nucleotide identity (up to 99.9%) to contemporary Chinese D/Yamagata/2019 strains and no evidence of reassortment. Maximum-likelihood and time-resolved Bayesian phylogenies of 231 global hemagglutinin-esterase-fusion (HEF) sequences placed the Jilin isolates within the East Asian D/Yamagata/2019 clade and traced their most recent common ancestor to approximately 2017 (95% highest posterior density: 2016–2018), suggesting a cross-border introduction likely associated with regional cattle movement. No IDV was detected in parallel surveillance of swine, underscoring cattle as the principal reservoir and amplifying host. Bayesian skyline analysis demonstrated a marked decline in global IDV genetic diversity during 2020–2022, coinciding with livestock-movement restrictions imposed during the COVID-19 pandemic. Collectively, these findings indicate that IDV circulation in China is sporadic and geographically localized, dominated by the D/Yamagata/2019 lineage, and shaped by multiple independent incursions rather than a single emergence. Both the incorporation of IDV diagnostics into routine bovine respiratory disease surveillance and cattle-import quarantine programs, and the adoption of a One Health framework to monitor potential human spillover and future viral evolution, were recommend. Full article

Infectious bronchitis virus (IBV) remains a common pathogen in poultry production. Although its clinical and economic impact in Europe has markedly declined in recent decades due to extensive vaccination, ongoing viral circulation continues to pose risks to animal health and provides opportunities for viral evolution. In this study, we investigated the molecular epidemiology of GI-19 and related strains in Spain using samples collected between 2008 and 2025. Partial S1 sequencing revealed a complex scenario involving three major clades and several minor ones, the latter likely resulting from independent introduction events from north-western Europe, particularly Denmark. Six distinct recombination events involving GI-13 and GI-19 parental strains—some apparently vaccine derived—were also identified, several of which showed wide geographical spread and long-term persistence. Both recombinant and non-recombinant variants were detected across multiple regions and production systems, indicating strong epidemiological connectivity among broilers, layers, and breeders. Although overall viral population size appeared stable over time, shifts in the predominance of specific clades and recombinant groups were observed, possibly reflecting fitness advantages of newly introduced or evolved variants and reduced cross-protection from existing immunity. These findings highlight the susceptibility of the poultry sector to repeated introductions, mixing, and the dissemination of IBV variants. Strengthened molecular surveillance and tailored control strategies, together with the periodic evaluation of vaccination practices and population immunity, are needed to limit viral circulation, reduce recombination opportunities, and mitigate the impact of IBV. Full article

Foot-and-mouth disease virus (FMDV) serotype SAT3 is a rarely studied serotype primarily circulating in southern Africa, with African buffalo (Syncerus caffer) serving as its key reservoir. In this study, we performed a comprehensive phylogenetic and phylodynamic analysis of SAT3 based on 81 full-length VP1 gene sequences collected between 1934 and 2018. Maximum likelihood and Bayesian analyses revealed five distinct topotypes, each with clear geographic and host associations. Notably, topotypes I, II and III were observed in both African buffalo and cattle (Bos taurus), while topotype IV appeared restricted to African buffalo. Likelihood mapping indicated moderate to strong phylogenetic signal, and the mean substitution rate was estimated at 3.709 × 10⁻³ substitutions/site/year under a relaxed molecular clock. The time to the most recent common ancestor (TMRCA) was traced back to 1875. Discrete phylogeographic reconstruction identified Zimbabwe as a major center, with multiple supported cross-border transmission routes. Host transition analysis further confirmed strong directional flow from buffalo to cattle (BF = 1631.09, pp = 1.0), highlighting the wildlife–livestock interface as a key driver of SAT3 persistence. Together, these results underscore the evolutionary complexity of SAT3 and the importance of integrating molecular epidemiology, spatial modeling, and host ecology to inform FMD control strategies in endemic regions. Full article

Background: The early months of the COVID-19 pandemic were characterized by high transmission rates and mortality, compounded by the emergence of multiple SARS-CoV-2 lineages, including Variants of Concern (VOCs). This study investigates the phylodynamic and spatio-temporal trends of VOCs during the peak of the pandemic in Nigeria. Methods: Whole-genome sequencing (WGS) data from three major VOCs circulating in Nigeria, B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.529 (Omicron), were analyzed using tools such as Nextclade, R Studio v 4.2.3, and BEAST X v 10.5.0. The spatial distribution, evolutionary history, viral ancestral introductions, and geographic dispersal patterns were characterized. Results: Three major lineages following WHO nomenclature were identified: Alpha, Delta, and Omicron. The Delta variant exhibited the widest geographic spread, detected in 14 states, while the Alpha variant was the least distributed, identified in only eight states but present across most epidemiological weeks studied. Evolutionary rates varied slightly, with Alpha exhibiting the slowest rate (2.66 × 10⁻⁴ substitutions/site/year). Viral population analyses showed distinct patterns: Omicron sustained elevated population growth over time, while Delta declined after initial expansion. The earliest Times to Most Recent Common Ancestor (TMRCA) were consistent with the earliest outbreaks of SARS-CoV-2 globally. Geographic transmission analysis indicated a predominant coastal-to-inland spread for all variants, with Omicron showing the most diffuse dispersal, highlighting commercial routes as significant drivers of viral diffusion. Conclusion: The SARS-CoV-2 epidemic in Nigeria was characterized by multiple variant introductions and a dominant coastal-to-inland spread, emphasizing that despite lockdown measures, commercial trade routes played a critical role in viral dissemination. These findings provide insights into pandemic control strategies and future outbreak preparedness. Full article

G8 rotaviruses are primarily associated with animals and infrequently cause infections in humans. The first detection of G8 strains in humans occurred around 1979, and since then, their presence has been sporadic, particularly in the United States (U.S.). During the 2016–2017 rotavirus surveillance season, the New Vaccine Surveillance Network (NVSN) identified 36 G8P[8] rotavirus strains across four sites in the U.S. This study presents the whole-genome characterization of these G8P[8] strains, along with comparative sequence analyses against the current vaccine strains, Rotarix and RotaTeq. Each strain exhibited a DS-1-like backbone with a consensus genotype constellation of G8P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and exhibited high genetic similarities to G8P[8] strains previously detected in Europe and Asia. Clinical analysis revealed no significant differences in hospitalization rates, length of stay, or severity scores between G8P[8] RVA-positive and non-G8P[8] RVA-positive subjects. Additionally, phylodynamic analysis determined the evolutionary rates and the most recent common ancestor for these strains, highlighting the importance of ongoing monitoring of rotavirus genotypes to assess the spread of these emerging G8P[8] strains. Full article

Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021 to assess the long-term impacts of live-attenuated vaccines (Massachusetts and 4/91) on viral evolution. Phylogenetic analysis of the S1 and N genes revealed four major lineages circulating in Chile—GI-1, GI-13, GI-16, and a novel monophyletic clade we propose as GI-31. The latter, identified in isolates from 1986 to 1988, is highly divergent (22–24%) from other known lineages, representing a previously unreported South American IBV variant. Despite widespread Mass vaccination, genetically distinct field strains circulated during the 1980s, facilitating potential recombination with GI-1 vaccine-derived strains, including evidence of shared ancestry with GI-11, an endemic lineage from Brazil. Non-recombinant GI-16, likely introduced from Asia, was detected in isolates from 2009. Notably, a recombinant strain emerged in 2015, four years after 4/91 vaccine introduction, indicating vaccine–field-strain genetic exchange. By 2017, isolates with >99% identity to the 4/91 strain were recovered, suggesting vaccine-derived variants. In 2021, GI-1 re-emerged, showing recombination signatures between GI-1 and GI-13 (4/91-derived) strains, likely reflecting suboptimal or inconsistent vaccination strategies. Selection analyses showed strong purifying selection across most of the S1 gene, with limited sites under positive selection in the receptor-binding domain. Phylodynamic reconstruction revealed time-structured evolution and multiple introduction events over 35 years, with lineage-specific tMRCA estimates. Collectively, these findings highlight the emergence of a novel lineage in South America and demonstrate that vaccine use, while mitigating disease, has significantly shaped the evolution of IBV in Chile. Our results underscore the importance of continuous genomic surveillance to inform vaccine strategies and limit recombinant emergence. Full article

 Porcine epidemic diarrhea virus (PEDV) continues to circulate globally, causing substantial economic losses to the swine industry. Historically, PEDV strains are classified into the classical G1, epidemic G2, and S-INDEL genotypes. Among these genotypes, the highly virulent and prevalent G2 genotype has been extensively studied. However, recent clinical outbreaks in China necessitate a reevaluation of the epidemiological and evolutionary dynamics of circulating strains. This study analyzed 37 newly sequenced S genes and public sequences to characterize the genetic variations of S-INDEL strains. Our analysis revealed that S-INDEL strains are endemic throughout China, with a phylogenetic analysis identifying two distinct clades: clade 1, comprising early endemic strains, and clade 2, representing a recently dominant, geographically restricted lineage in China. While inter-genotypic recombination has been documented, our findings also demonstrate that intra-genotypic and intra-clade recombination events contributed significantly to the emergence of clade 2, distinguishing its evolutionary pattern from clade 1. A comparative analysis identified 22 clade-specific amino acid changes, 11 of which occurred in the D0 domain. Notably, mutations at positively selected sites—113 and 114 within the D0 domain, a domain associated with pathogenicity—were specific to clade 2. A phylodynamic analysis indicated Germany as the epicenter of S-INDEL dispersal, with China acting as a sink population characterized by localized transmission networks and frequent recombination events. These results demonstrate that contemporary S-INDEL strains, specifically clade 2, exhibit unique recombination patterns and mutations potentially impacting virulence. Continuous surveillance is essential to assess the pathogenic potential of these evolving recombinant variants and the efficacy of vaccines against them.  Full article

Regional HIV-1 epidemics are evolving with distinct patterns in transmission routes, subtype distribution, and molecular transmission cluster (MTCs) characteristics. We analyzed 9500 HIV-1 cases diagnosed over 30 years using phylogenetic and network methods, integrating molecular, epidemiological, demographic, and behavioral data. Subtype A6 remains dominant nationally (80.6%), followed by 63_02A6 (7.9%), subtype B (5.6%), 02_AG_FSU (1.2%), 03_A6B (0.7%), and 14/73_BG (0.6%). Non-A6 infections were more common among males (OR 1.51) and men who have sex with men (OR 7.33). Network analysis identified 421 MTCs, with 256 active clusters. Clustering was more likely among young individuals (OR: 1.31), those not receiving antiretroviral therapy (OR: 2.70), and injecting drug users (OR: 1.28). Non-A6 subtypes showed a higher likelihood of clustering. Phylogenetic analysis revealed that local clusters of the major subtypes originated between the late 1970s (subtype B) and the mid-2000s (63_02A6) with links to populations in Eastern Europe, Central Asia (subtypes A6, 63_02A6, 02_AG_FSU, 03_A6B), and Western Europe and the Americas (subtype B, 14/73_BG). These findings indicate a complex, evolving regional epidemic transitioning from subtype A6 dominance to a more diverse mix of subtypes. The ability of non-A6 subtypes to form active MTCs suggests their establishment in the local population. Full article