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PubMed2026

Molecular Epidemiology of Non-Polio Enterovirus: Insights From L20B Cell Line Adaptation From Children With Acute Flaccid Paralysis in Pakistan.

BACKGROUND: Non-polio enteroviruses (NPEVs) are increasingly implicated in acute flaccid paralysis (AFP), often resembling poliomyelitis and complicating eradication efforts. In Pakistan, limited molecular surveillance has hindered comprehensive characterization. The L20B cell line, designed for poliovirus detection, occasionally supports NPEV replication, challenging AFP case interpretation. METHODS: Between January 2021 and December 2022, 4615 stool samples from AFP cases in children ≤15 years were analyzed. Of these, 435 were identified as NPEVs via L20B cytopathic effects and intertypic differentiation reverse transcription-polymerase chain reaction. VP1 sequencing was performed on 218 representative isolates, yielding 153 high-quality sequences (70.2%). The 224/222 primer set showed superior amplification. Phylogenetic analysis used MUSCLE alignment and the Neighbor-Joining method in MEGA X, with statistical evaluation of epidemiological data. RESULTS: NPEVs were frequently found in L20B-positive AFP cases, highlighting the cell line's limited specificity. Most cases involved children under 5, with a slight male bias. Enterovirus B was predominant (98.0%), especially Echovirus 7 (20.3%) and Echovirus 11 (10.5%), followed by Coxsackievirus B1 and Echovirus 33 (5.9% each). Geographic clustering was noted in Punjab (45.1%), Khyber Pakhtunkhwa (30.7%) and Sindh (20.3%), with seasonal peaks in late summer and early autumn. Phylogenetic data revealed localized Enterovirus B circulation with minimal genetic variation. CONCLUSIONS: The detection of diverse NPEVs in L20B-positive AFP cases emphasizes their relevance in post-polio surveillance. Incorporating routine VP1 sequencing, optimized primer use, and targeted seasonal and regional monitoring is vital to reduce diagnostic uncertainty and inform public health strategies.

Humans↗

PubMed2025

Molecular Epidemiology of Coxsackievirus A10 Associated With Hand, Foot and Mouth Disease From 2021 to 2024 in Shenzhen, China.

The study aimed to investigate epidemiological profile and molecular characteristics of coxsackievirus A10 (CVA10) associated with hand, foot and mouth disease (HFMD) in Shenzhen, China and comparatively analyze genomes of CVA10 strains related to differential clinical phenotypes. A total of 3170 clinical specimens collected between 2021 and 2024 were examined for CVA10 using real-time RT-PCR. Complete VP1 sequences and near-complete genome sequences of CVA10 were determined by RT-PCR methods and sequencing. Sequences were analyzed using a series of bioinformatics programs. Two (33.33%) out of 6 severe cases were infected with CVA10. The detection rate of CVA10 associated with mild HFMD ranged from 1.21% to 6.11% in 2021-2024, with an overall detection rate of 3.73%. There was no significant difference in the infection rate of CVA10 between males and females or different age groups. The CVA10 infections mainly occurred in Spring (March to May) and Summer (June to August) in Shenzhen. Of the 74 VP1 sequences determined, 71 (95.95%) of them were detected in the sub-genotype C2, 3 (4.05%) were assigned to the genotype D. Genomic sequence analysis indicated that the genotype D of CVA10 of this study derived from genetic recombination between CVA10 and CVA16 in 3A-3D coding region (nucleotide position: 5075-6896). Different variable sites were observed in the two CVA10 strains associated with different severe complications when compared to CVA10 strains associated with mild diseases. In conclusion, CVA10 associated with HFMD circulated at a low level in Shenzhen in 2021-2024, with C2 as the predominant genotype. Recombinant genotype D of CVA10 was introduced first to Shenzhen in 2024. The study emphasizes the importance of continuous molecular surveillance of CVA10.

Humans↗

PubMed2025

Global Evolution and Transmission Dynamics of Enterovirus D68.

Enterovirus D68 (EV-D68), a serotype of the enterovirus species D, has garnered significant attention due to outbreaks reported in 2014, 2016, and 2018. In this study, 36 Chinese EV-D68 strains were isolated, sequenced, and combined with all EV-D68 VP1 sequences from GenBank to form a data set of 1679 sequences. This data set served as the basis for phylogenetic, evolutionary dynamics, phylogeographic, and key amino acid site mutation analyses of EV-D68. Based on the VP1 region, EV-D68 is classified into four genotypes (A-D), and seven subgenotypes (B1-B3, D1-D4), with B3 and D3 being the predominant subgenotypes. Bayesian skyline plots indicated that genotypes B and D experienced multiple population expansions, aligning with reported EV-D68 outbreaks. Phylogeographic analyses of the B3 subgenotypes revealed sequences from Europe and North America clustering into a single evolutionary branch, suggesting significant transmission between these regions. Additionally, mutation analysis identified VP1-98 as a high-frequency mutation site, differing significantly between the previously prevalent A and C genotypes and the currently prevalent B and D genotypes. However, the functional implications of this mutation require further investigation. This study provides a solid theoretical basis for epidemiological research, disease surveillance, and prevention efforts related to EV-D68.

Enterovirus Infections↗

PubMed2026

Evaluation of amplicon-based nanopore sequencing for foot-and-mouth disease viruses in clinical and environmental samples.

Foot-and-mouth disease (FMD) causes severe global economic loss, necessitating rapid viral characterization. Nanopore sequencing provides a simple, real-time workflow suitable for on-site outbreak response, addressing the limitations of conventional methods. In this study, we optimized a previously published amplicon-based protocol and used this method to characterize a diverse range of samples (vesicular fluid, epithelium, serum, nasal/oral swabs, and environmental samples) collected during FMD outbreaks in 2025 in the Republic of Korea. Of the 129 samples collected, we successfully recovered complete genomes from 37 samples and VP1 sequences from 85 samples. Amplifying the S-fragment in isolation and separately barcoding each pool of PCR amplicons markedly improved sequence recovery. Furthermore, sequencing success depended on viral load and sample type. Based on comparisons with real-time RT-PCR results, whole-genome sequence (WGS) recovery exceeded 77.3% at cycle threshold (Ct) values ≤25 across all clinical samples. In the Ct > 30 category, serum samples yielded the highest WGS recovery rates (44.4%). This rate was markedly higher than the success rates observed for epithelium (20.0%) and nasal swabs (9.1%), whereas oral swabs and environmental samples failed to yield any sequences (0%). However, VP1 recovery from environmental samples reached 80% at Ct ≤ 30 (8/10), providing an approach to enable non-invasive monitoring. These findings demonstrate that amplicon-based nanopore sequencing is a practical method for the rapid generation of genomic data during FMD outbreaks.IMPORTANCEAlthough rapid detection and genomic data analysis are crucial for effective foot-and-mouth disease (FMD) control, the collection of these data can be challenging for certain sample types and impacted by reduced viral loads that result from nationwide FMD vaccination. This study provides a practical solution through large-scale evaluation of an optimized amplicon-based nanopore sequencing protocol to enhance the sequencing success rates for both clinical and environmental samples. Using a modified protocol to enhance genome recovery, we demonstrated that sequence data could be retrieved from diverse sample types (even with high real-time RT-PCR cycle threshold values). We identified serum as the most suitable sample, with environmental sample sequencing allowing for non-invasive monitoring during outbreaks. These results support the use of nanopore sequencing for rapid genomic analysis, particularly in outbreak responses, such as rapid surveillance, emergency vaccine selection, and epidemiological monitoring.

Foot-and-Mouth Disease↗

PubMed2026

Molecular Epidemiology and Pathogenicity Evaluation of Porcine Teschovirus in Tibetan Pigs on the Qinghai-Tibet Plateau of China.

Porcine teschovirus (PTV) is the causative agent of porcine diarrhea and multisystem disorder and poses a global threat to the health of domestic pigs. However, its epidemic and pathogenic characteristics in Tibetan pigs, which are a unique indigenous breed in the Qinghai-Tibet Plateau of China, remain largely unexplored. Here, we conducted a comprehensive investigation during 2024-2025, in which 303 diarrheic fecal samples were collected from 21 farms across eight counties in Ganzi Tibetan Autonomous Prefecture, with an average altitude of 3433 m. RT-PCR testing identified 141 PTV-positive samples, yielding a high positivity rate of 46.5% (141/303). From these positives, 27 VP1 sequences were cloned and sequenced; phylogenetic analysis revealed that 16 strains belonged to Teschovirus A, three strains were divided into Teschovirus B, and three strains formed the interspecies recombinant genotypes (PTV-15/16). Interestingly, five novel strains were classified as undefined genotypes, indicating an extensive genetic diversity among PTV strains circulating in Tibetan pigs. Furthermore, a PTV strain, designated PTV-SCgz-01, was successfully isolated in PK-15 cells, with a near-complete genomic sequence of 7081 nucleotides. Phylogenetic analysis based on the polyprotein and the VP1 genes indicated that it belonged to genotype PTV-4, whereas recombination analysis revealed that PTV-SCgz-01 is a natural recombinant with parental strains derived from HNMY (PTV-4) and China/SWU-ZG2/2018 (PTV-6). Experimental infection of 17-day-old Tibetan piglets demonstrated that this isolate induces severe watery diarrhea. Notably, the virus also caused severe pulmonary hemorrhage and mild cerebral hyperemia with neuronal degeneration, and it had a high mortality rate (40%), suggesting that strain PTV-SCgz-01 has strong pathogenic potential for 17-day-old Tibetan piglets. Our findings provide a more comprehensive molecular epidemiology of PTVs in Tibetan pigs and underscore the need for viral surveillance and control in this unique pig population.

Animals↗

PubMed2025

Molecular characterization of JC virus in progressive multifocal leukoencephalopathy cases from India.

Progressive Multifocal Leukoencephalopathy (PML) is a rare, often fatal demyelinating disease of the central nervous system caused by reactivation of the John Cunningham virus (JCV) in immunocompromised individuals. Despite an estimated 2.4 million people living with HIV in India, the reported incidence of PML remains lower than in Western countries, likely due to underdiagnosis, underreporting, and distinct host genetic and viral factors. The rising number of individuals on immunosuppressive therapies, including organ transplant recipients and those with autoimmune disorders, further emphasizes the need to study JC virus diversity in the Indian context. This study aimed to characterize the genetic diversity of JCV in India by sequencing the VP1 and non-coding control region (NCCR) from cerebrospinal fluid (n=30) of confirmed PML cases using Sanger sequencing. VP1 sequencing (n=23) revealed a predominance of genotypes 2 (subtypes 2D, 2A, 2B) and 3A. NCCR analysis (n=17) showed extensive rearrangements relative to the archetype form, with most sequences classified as Type II-R. Structural variations, including deletions, duplications, and insertions were common, particularly in blocks D, C, and F. Transcription factor binding sites (TFBS) were identified for TATA box, Tst-1, SP-1, p53, CEBPB, AP-1, NF-1, EGR-1, GF-1, CRE-TAR and NFkB. Additional TFBS were created due to rearrangements, often spanning two blocks. These findings underscore the genomic diversity of JCV in India and highlight the need for continued molecular surveillance to better understand its implications for high-risk populations.

Leukoencephalopathy, Progressive Multifocal↗

PubMed2026

Balancing under constraint: Structural insights into norovirus evolution and antigenic innovation.

Norovirus is the leading cause of acute viral gastroenteritis worldwide. While genomic studies have revealed its diversity and evolutionary patterns, the structural mechanisms driving viral adaptation remain poorly understood. Here, we establish a comprehensive structural database of norovirus VP1 P-domains across nine genogroups (GI-GIX) through large-scale AlphaFold2 predictions. By integrating phylogenetic analysis of VP1 sequences and structures, we demonstrate that sequence and structural evolution show overall concordance under purifying selection, yet significant local discrepancies reveal distinct patterns of convergent evolution shaped by structural constraints and functional divergence. Focusing on the predominant GII.4 genotype, we found that compared to near-full-genome and nucleotide trees, only the VP1 amino acid tree reliably clustered GII.4 variants in chronological order as monophyletic groups. We further identify a hierarchical evolutionary strategy: positive selection may drive structural hypervariability in major antigenic epitopes D and C for immune escape, with epitope D exhibiting pronounced structural flexibility that complicates its structural characterization, whereas coevolutionary analysis uncovers a broad network of compensatory interactions spanning multiple epitopes, with striking enrichment in epitope A. These epitopes exhibited a pattern of "sequence plasticity with structural conservation", maintained by coevolutionary constraints that preserve conformational integrity. Together, these findings suggest that norovirus vaccine strategies targeting the structurally conserved conformations of epitopes A and G could overcome the limitations of traditional strain-specific approaches, offering a pathway toward broad protection against evolving viral diversity.

Norovirus↗

PubMed2025

Opportunities for machine learning to predict cross-neutralization in FMDV serotype O.

Accurately estimating cross-neutralization between serotype O foot-and-mouth disease viruses (FMDVs) is critical for guiding vaccine selection and disease management. In this study, we developed a machine learning approach to estimate r1 values-an established measure of antigenic similarity-using VP1 sequence data and published virus neutralization titer (VNT) results. Our dataset comprised 108 serum-virus pairs representing 73 distinct FMDV strains. We applied Boruta feature selection and random forest classifiers, optimizing model performance through tenfold cross-validation and sub-sampling to address class imbalance. Predictors included pairwise amino acid distances, site-specific polymorphisms, and differences in potential N-glycosylation sites. Using a 0.3 r1 threshold to define cross-neutralization, the final model achieved high accuracy (0.96), sensitivity (0.93), and specificity (0.96) in training, and performed robustly on independent test sets - accuracy was 0.75 (95% CI 0.60 and 0.90), F1 score 0.86% and PPV 0.77. Importantly, key VP1 residues-positions 48, 100, 135, 150, and 151-emerged as strong predictors of antigenic relationships. Our results demonstrate the utility of integrating routinely generated genomic data with machine learning to inform vaccine candidate selection and anticipate immune interactions among circulating FMDV strains. This approach offers a practical tool for accelerating vaccine decision-making and can be adapted to other FMDV serotypes. The latest version of the r1 predictive model is available for access via a Shiny dashboard (https://dmakau.shinyapps.io/PredImmune-FMD/).

Foot-and-Mouth Disease Virus↗

PubMed2026

The prevalence and molecular characterization of Porcine teschoviruses in Guangdong Province, China.

Porcine teschoviruses (PTVs) are globally endemic and widely circulate within pig populations. This study aimed to investigate the prevalence and genetic characteristics of PTVs in Guangdong Province, China. A total of 341 fecal and 99 tissue mixture samples were collected from pigs in seven cities across the province. These samples were screened for PTVs using reverse transcription-polymerase chain reaction (RT-PCR). The overall PTV positivity rate was determined to be 19.32%. In this study, the PTV3 PTV/CN/GD/316 strain was successfully isolated from a tissue mixture sample obtained from a pig exhibiting diarrhea. The isolation was performed using swine testicular (ST) cells. The complete viral genome of this isolate measured 6,999 nucleotides (nt) and encoded a polyprotein of 2,205 amino acids. Phylogenetic analysis of the complete VP1 gene identified seven distinct PTV genotypes (PTV2, PTV3, PTV4, PTV9, PTV14, PTV17, and PTV19) among the 21 PTV isolates obtained, with PTV3 being the dominant genotype (38.10%), followed by PTV9 (19.05%). Furthermore, our findings revealed a significant co-infection of PTVs with other common swine pathogens, including PCV2, PEDV, PCV3, PRRSV, CSFV, and PDCoV. The co-infection rate with these viruses was remarkably high, reaching 97.65%. Collectively, these data demonstrate the widespread circulation of PTVs in pig farms in Guangdong Province and highlight the prevalence of co-infection scenarios with other viral agents. The genetic analyses of all available PTV VP1 sequences also underscore the considerable diversity of PTV genotypes circulating within the Guangdong region.IMPORTANCECurrently, PTVs are widespread globally, with their infection rates showing a rising trend. The prevalence and molecular characterization of PTVs help prevent and control the spread of diseases. The findings of this study indicate a high prevalence and considerable genetic diversity of PTVs in certain areas of Guangdong Province, China. The occurrence of co-infection with other pathogens is also relatively common. Based on these data, we can better safeguard swine health and mitigate the economic impact of these infections on the agricultural industry.

Guangdong Province↗

PubMed2026

Performance comparison of rapid and native barcoding methods for Oxford Nanopore sequencing of Poliovirus Viral Protein 1 (VP1) amplicons.

Accurate and timely sequencing of poliovirus is critical for global eradication efforts, particularly for molecular epidemiology based on the typing region of the genome, viral protein 1 (VP1). While Oxford Nanopore Technologies (ONT) sequencing has expanded capabilities for poliovirus surveillance, the relative performance of different ONT library preparation methods, including ligation-based (Native Barcoding) and transposase-based (Rapid Barcoding) approaches, has not been systematically evaluated. In this study, we compared rapid barcoding and native barcoding workflows for sequencing VP1 amplicons from 17 type 2 poliovirus-positive samples, each processed in triplicate. Native barcoding generated significantly more sequencing output, producing approximately 2.3-fold greater total read yield than rapid barcoding, and demonstrated higher run-to-run reproducibility (R2 = 0.979-0.998 vs. 0.847-0.929, respectively; p < 0.001). In addition, native barcoding generated 80% of the total yield achieved by rapid barcoding within approximately 7 h, whereas rapid barcoding required approximately 40 h to reach the same output. Despite these differences, both methods produced identical VP1 consensus sequences across all samples, with comparable read quality (median per-base Q-scores of approximately Q17-Q18). Rapid barcoding provided substantial practical advantages, reducing hands-on library preparation time (55 vs. 200 min) and per-sample cost ($12.82 vs. $16.54), while simplifying workflow and reducing technical complexity. These findings indicate that sequencing yield may not be a determinant of downstream analytical outcomes for poliovirus VP1 ONT sequencing. Rapid barcoding therefore represents a cost-effective and efficient approach for routine poliovirus surveillance, whereas native barcoding remains advantageous in applications requiring rapid data generation or maximal sequencing depth.

Poliovirus↗

PubMed1976

Location of the sequences coding for capsid proteins VP1 and VP2 on polyoma virus DNA.

The 19S and 16S polyoma virus late mRNAs have been separated on sucrose-formamide density gradients and translated in vitro. The 16S RNA codes only for polyoma capsid protein VP1, while the 19S RNA codes in addition for capsid protein VP2. Since the 19S and 16S species have been previously mapped on the viral genome, these results allow us to deduce the location of the sequences coding for VP1 and VP2. Comparison of the chain lengths of the capsid proteins with the size of the viral mRNAs coding for them suggests that VP1 and VP2 are entirely virus-coded. Purified polyoma 19S RNA directs the synthesis of very little VP1 in vitro, although it contains all the sequences required to code for the protein. The initiation site for VP1 synthesis which is located at an internal position on the messenger is probably inactive either because it is inaccessible or because it lacks an adjacent "capped" 5' terminus. Similar inactive internal initiation sites have been reported for other eucarotic viral mRNAs (for example, Semliki forest virus, Brome mosaic virus, and tobacco mosaic virus), suggesting that while eucaryotic mRNAs may have more than one initiation site for protein synthesis, only those sites nearer the 5' terminus of the mRNA are active.

Base Sequence↗

PubMed2019

Cold chain and virus-free oral polio booster vaccine made in lettuce chloroplasts confers protection against all three poliovirus serotypes.

To prevent vaccine-associated paralytic poliomyelitis, WHO recommended withdrawal of Oral Polio Vaccine (Serotype-2) and a single dose of Inactivated Poliovirus Vaccine (IPV). IPV however is expensive, requires cold chain, injections and offers limited intestinal mucosal immunity, essential to prevent polio reinfection in countries with open sewer system. To date, there is no virus-free and cold chain-free polio vaccine capable of inducing robust mucosal immunity. We report here a novel low-cost, cold chain/poliovirus-free, booster vaccine using poliovirus capsid protein (VP1, conserved in all serotypes) fused with cholera non-toxic B subunit (CTB) expressed in lettuce chloroplasts. PCR using unique primer sets confirmed site-specific integration of CTB-VP1 transgene cassettes. Absence of the native chloroplast genome in Southern blots confirmed homoplasmy. Codon optimization of the VP1 coding sequence enhanced its expression 9-15-fold in chloroplasts. GM1-ganglioside receptor-binding ELISA confirmed pentamer assembly of CTB-VP1 fusion protein, fulfilling a key requirement for oral antigen delivery through gut epithelium. Transmission Electron Microscope images and hydrodynamic radius analysis confirmed VP1-VLPs of 22.3 nm size. Mice primed with IPV and boosted three times with lyophilized plant cells expressing CTB-VP1co, formulated with plant-derived oral adjuvants, enhanced VP1-specific IgG1, VP1-IgA titres and neutralization (80%-100% seropositivity of Sabin-1, 2, 3). In contrast, IPV single dose resulted in <50% VP1-IgG1 and negligible VP1-IgA titres, poor neutralization and seropositivity (<20%, <40% Sabin 1,2). Mice orally boosted with CTB-VP1co, without IPV priming, failed to produce any protective neutralizing antibody. Because global population is receiving IPV single dose, booster vaccine free of poliovirus or cold chain offers a timely low-cost solution to eradicate polio.

Animals↗

PubMed1977

Nucleotide sequence of the restriction fragment Hind F-Eco RI2 of SV40 DNA.

The nucleotide sequence of the SV40 genome region between the Hind K fragment and the Eco RI cleavage site has been determined by a combination of three different approaches : analysis of RNA products obtained by transcription with Escherichia coli DNA dependent RNA polymerase, partial degradations with snake venom exonuclease and base-specific chemical degradation of 5'-terminal labeled restriction fragments. This nucleotide sequence shows only one open reading frame and allows the deduction of a small segment of the amino acid sequence of VP1, the major structural protein.

Alkaline Phosphatase↗

PubMed1976

The initiation region of the SV40 VP1 gene.

The sequence of 15 nucleotides located at the 5' terminus of the plus strand of the SV40 Hind K fragment has been determined as (5') A-G-C-T-T-A-T-G-A-A-G-A-T-G-G (3'). The 3' on OH terminal G of this segment is part of the G-C-C codeword for the N terminal alanine of the VP1 protein. This region therefore presumably corresponds to a ribosome binding site on the 16S late mRNA. Complementarily to the 3' OH of eucaryotic 18S ribosomal RNA and homology with the BMV coat ribosome binding site are discussed.

Bacterial Proteins↗

PubMed2026

Long-term clinical and genomic surveillance of rare respiratory enterovirus C types in France, 2013-2025.

INTRODUCTION: Rare enterovirus types assigned to species C (EV-C) display respiratory tropism and may be associated with neurological involvement, which display similarities to EV-D68 disease. PATIENTS AND METHODS: We conducted continuous enterovirus/rhinovirus (EV/RV) surveillance between 2013 and 2025, including systematic EV/RV screening of all respiratory samples and reflex VP4/VP2 sequencing (a total of 5855 samples). When an EV-C strain was detected, the VP1-coding and complete genome sequence was sequenced to investigate phylogenetic relationships and to identify any recombinant forms. RESULTS: Over the 13-year period, 30 EV-C infections were identified from respiratory samples, with 23 cases (77%) detected between 2013 and 2018. EV-C105 was the most frequent type (n = 11), followed by EV-C104 (n = 8), EV-C109 (n = 6), and EV-C117 (n = 5). We also document the first detection of EV-C117 in France and only the second case reported in Europe since its initial description in 2011 in Lithuania. Clinical data were available for 25 patients, of whom 19 (76%) were children. Respiratory symptoms predominated (17/25, 68%), and 7 patients presented with lower respiratory tract infections. Hospitalization was required in 18 cases (72%), including three with ICU admissions (12%). Nearly half of the patients (12/25, 48%) had at least one risk factor for severe respiratory disease. Across all respiratory EV-C types, recovered sequences clustered with contemporary global strains. CONCLUSIONS: This long-term surveillance highlights the sustained circulation of multiple respiratory EV-C types in France and underscores the need for continued clinical and genomic monitoring to assess the evolution and pathogenic potential of these enteroviruses.

Complete genome characterization↗

PubMed1975

N-terminal amino acid sequences in the major capsid proteins of foot-and-mouth disease virus types A, O, and C.

Sequences of amino acids at the N-termini of virus proteins VP1, VP2, and VP3 were determined for foot-and-mouth disease virus types A12 strain 119, O1Brugge and C3Resende. In the polyacrylamide gel electrophoresis system used to purify the proteins, VP3 migrated faster than VP1 or VP2; and in the virion, VP3 could be cleaved by trypsin into VP3a and VP3b. The N-terminal amino acids for each of the virus types were glycine in VP1, aspartic acid in VP2, and threonine in VP3. No divergences in sequence across the virus types were indicated until at least the fourth position in VP1, and the third in VP3. For virus types A12, O1 and C3, the sequences were, respectively: for VP1 (Gly-ile-phe,pro,val---), (Gly,ile,phe---) and Gly-ile-phe,ala---); for VP2 (Asp,X,met---), (Asp---) and Asp-leu---); and for VP3 (Thr-thr-ala-thr---), (Thr-thr-ser---) and (Thr-thr---). Unresolved mixtures of VP3a and VP3b, from either A12 or O1 viruses, appeared to have the N-terminal amino acids threonine, which is presumed to be the same threonine as in uncleaved VP3 and serine, which is generated by the tryptic cleavage.

Amino Acid Sequence↗

PubMed2025

Genomic Epidemiology of Resurgent Hepatitis A in Florida, 2018-2022.

During 2018-2022, a resurgence of hepatitis A occurred in Florida, with 5491 cases reported. Genotyping was performed on a convenience sample of cases through amplification and sequencing of the hepatitis A virus VP1-P2B junction region. Virus isolates from 1190 cases (22%) were genotyped; 69% were subgenotype IB, 30% were subgenotype IA, and 1% were subgenotype IIIA. Subgenotype IB was more common among patients reporting recent drug use or homelessness, whereas IA was more common among those reporting recent international travel and among men who have sex with men. Genotype IB infection was associated with a more than 4-fold greater odds of death compared to IA infection. A network analysis revealed 11 genomic clusters of ≥10 cases, with distinct temporal and spatial distributions. Case reports in 2023 decreased to below pre-2018 numbers, likely due to high population immunity following natural infection and extensive vaccination activities in the highest-risk groups.

Humans↗

PubMed2026

Novel avian calicivirus genome with type IV internal ribosomal entry site (IRES) in black-headed gull (Chroicocephalus ridibundus) in Hungary.

In this study, a taxonomically novel avian calicivirus detected and characterized by next generation sequencing, RT-PCR and Sanger sequencing methods in faecal specimen collected from black-headed gull (Chroicocephalus ridibundus) in Hungary. The complete genome length of the calicivirus strain gull/HA15097/HUN/2018 (PZ810127) is remarkably long, 8,845 nucleotides, which had type IV internal ribosomal entry site (IRES) at the 5', and a stem-loop-II-like (s2m) sequence motif at the 3' untranslated regions. The VP1 capsid protein had less than 26% aa identity to the members of the known calicivirus genera. Caliciviruses appear to be widespread not only in mammals including humans but also in various bird species.

Animals↗