Search Results (80)

Avian reovirus (ARV) has emerged as an important pathogen in turkeys, causing economic losses through tenosynovitis, necrotizing hepatitis, immunosuppression, and enteric disease. Despite its ubiquity, the evolutionary history of ARV cross-species transmission among chickens, turkeys, and wild birds remains poorly understood, hindering effective control and surveillance. This study investigates ARV temporal phylogenetics with an emphasis on interspecies transmission in turkeys. Whole genome sequences (WGSs) from seventy-seven turkey cases and one quail case at the Iowa State University Veterinary Diagnostic Laboratory, along with 74–136 segment sequences per gene from GenBank (1970–2023), were analyzed. Temporal phylogenetic analyses identified chickens as the ancestral host, with spillover into turkeys beginning in the mid-20th century, followed by stable transmission within turkey populations. Migration analyses revealed predominantly unidirectional transmission from chickens to turkeys. WGS analyses showed high variability in the M2 and σC-encoding region of the S1 segment, suggesting selective pressure on outer capsid proteins. M2, S1 σC, and L3 had the highest substitution rates, implicating their role in adaptation and antigenic diversity. These findings highlight the complexity of ARV evolution across hosts and underscore the need for robust genotyping schemes and surveillance strategies to mitigate outbreaks in poultry. Full article

Background: Since the massive outbreak of foot-and-mouth disease (FMD) in South Korea in 2010–2011, cloven-hoofed livestock have been immunized with serotype O and A vaccines across the country. Other serotypes of FMD vaccines were stockpiled in overseas FMD vaccine factories as antigen banks. Once a manufacturing facility has been established in South Korea, the overseas antigen banks will be replaced by domestic one. Therefore, this study aimed to evaluate the commercial potential of the previously developed SAT2 vaccine candidate (SAT2 ZIM-R). Methods: The optimal condition was determined at various virus concentrations, infection times, and pH levels, resulting in 0.01 MOI for SAT2 ZIM-R for 24 h infection at a pH of 7.5. Results: When the SAT2 ZIM-R virus was produced in flasks from 40 to 1000 mL in fivefold increments, all scales of production yielded > 7.0 µg/mL of antigens. Using a bioreactor, 5.6 µg/mL of antigens was recovered from a 1 L viral culture. The optimal conditions of viral inactivation kinetics were determined to be 1 mM of binary ethyleneimine (BEI) treatment at 26 °C for 24 h, with approximately 91% of the antigen being retained after virus inactivation. When the SAT2 ZIM-R experimental vaccine was administered twice to pigs, the neutralizing antibody titer increased approximately 500-fold after booster immunization. Conclusions: To the best of our knowledge, this is the first study to evaluate the antigen productivity, viral inactivation kinetics, and immunogenicity of the SAT vaccine strain in pigs. In the future, the SAT2 ZIM-R vaccine may be a useful candidate vaccine for a domestic antigen bank. Full article

Trypanosoma cruzi GenBank^® M21331 encodes for Antigen 36 (Ag 36), which is a tandemly repeated T. cruzi antigen. GenBank M21331 has a gene sequence similarity to human immune genes IFN-α, IFN-β, and IFN-γ, as well as to human TRIM genes. A BLAST-p search revealed that T. cruzi GenBank M21331 had seven gene sequences homologous to microtubule-associated protein (MAP) genes with a 100% amino acid sequence identity. There are 36 genes in the T. cruzi genome with >94% identity to GenBank M21331, and these genes encode proteins ranging in size from 38 to 2011 amino acids in length, the largest containing 20, 25, and 30 repeats of the Ag 36 thirty-eight-amino-acid-sequence motif. The purpose of this study was to perform a genetic and molecular comparative analysis of T. cruzi GenBank M21331 to determine if this gene sequence is unique to the T. cruzi clade, present in the T. brucei clade, and/or exists in other trypanosomatids. There are seven homologous genes to GenBank M21331 in T. cruzi, but only one homolog found of this gene in T. brucei. The MAP genes in T. cruzi appear to have expanded at least eleven-fold in number compared to similar MAP genes in T. brucei. The DNA sequences and functions of these MAP genes in their respective species and clades will be discussed and are a fascinating area for further scientific study. Full article

Virulence attributes and putative antibiotic resistance genes from enterococcal isolates from wastewater treatment facilities for sustainable reuse and the areas where they discharge treated water were assessed using phenotypic and molecular methods. This analysis was performed on 269 Enterococci, of which 202 were vancomycin-resistant Enterococcus (VRE). VRE strains show markedly higher resistance across multiple antibiotics, especially glycopeptides and beta-lactams, compared to the more susceptible profile observed in vancomycin-susceptible Enterococcus (VSE) strains. vanC was found in every instance of E. gallinarum among VRE and enterococci susceptible to vancomycin (VSE) isolates but not in VR E. faecium/faecalis. Among VRE, 127 (62.9%) possessed at least one of the tetK, tetL, tetM, or tetO, while 22 (17.3%) had two of these genes. The multidrug efflux pump gene emeA was detected in 27 out of 202 (13.4%) VRE isolates and 8 out of 67 (11.9%) VSE isolates. Exactly 69 (78.4%) possessed at least one of the virulence determinants tested, with 10 (11.4%) and seven (8%) positive for haemolysis and gelatinase activity respectively. The gelatinase gene, gelE, was detected in 16 (18.1%) isolates, while more isolates (n = 23; 26.1%) were positive for gelatinase activity. Cytolytic (cyl) genes (1.1%), Angiotensin-converting-enzyme genes (ace) (13.6%), endocarditis-specific antigen A genes (efaA) (25%), hyaluronidase (hyl) genes (9.1%), enterococcal surface protein (esp) genes (4.5%), among others, were detected. Gelatinase activity and the amplified virulence genes were further validated by sequencing the gel-positive amplicons, which were almost identical (98.97%), and the gelE gene of Enterococcus sp. strain SQ07C was deposited under the GenBank accession number PQ381122. Overall, our results showed that the enterococcal isolates were considered as potential pathogens of notable threat to human health via exposure through reuse, and there is a need for more stringent treatment protocols. Full article

Background and Objectives: The Rh blood group system is highly polymorphic, and accurate classification of Rh(D) variants is critical in transfusion medicine to prevent alloimmunization and optimize blood utilization. Despite the advances in conventional serologic testing, weak and partial Rh(D) phenotypes still remain challenges in Transfusion Medicine practice. The objective is to implement and assess the impact of RHD genotyping in classifying Rh(D) antigen status. Materials and Methods: We conducted a retrospective study at the University of South Alabama Medical Center and Children and Women’s Hospital between 1 January 2023 and 31 December 2024 to assess the impact of RHD genotyping in cases with discrepant Rh(D) typing, Rh(D)-positive patients with anti-Rh(D) antibodies, and neonates with positive weak Rh(D) tests. ABO and Rh(D) antigen typing was performed on 12,994 patients, including 3767 newly tested individuals. Weak Rh(D) testing was performed on newly tested individuals using automated microplate direct agglutination, followed by molecular genotyping. Results: Among the 25 patients with weak or discrepant Rh(D) phenotypes, weak Rh(D) variants were observed in 52% of cases, with Weak Type 2 being the most common, particularly in pediatric (age < 18 years old) patients. Partial Rh(D) phenotypes were identified in 40% of cases, predominantly among Black individuals. Three patients were reclassified as Rh(D)-positive based on genotyping and received 615 Rh(D)-positive RBC units without evidence of alloimmunization, while four patients were confirmed at risk of alloimmunization and remained classified as Rh(D)-negative. Fisher’s exact test demonstrated a significant association between ethnicity and Rh(D) classification (p < 0.01), and the McNemar exact test confirmed a significant reclassification of cases from Rh(D)-negative to Rh(D)-positive (p < 0.01). Conclusions: RHD genotyping enhances the accuracy of Rh(D) antigen classification, mitigating alloimmunization risks and the unnecessary use of Rh Immunoglobulin and optimizing blood product utilization. The reclassification of patients to Rh(D)-positive alleviates pressure on Rh(D)-negative blood supplies, particularly during critical shortages. These findings underscore the necessity of integrating molecular RHD testing into routine transfusion medicine practices to improve patient safety and resource management. Full article

Babesia bigemina is one of the most important etiological agents of bovine babesiosis, a tick-borne disease posing a major threat in the livestock industry globally, including South Africa. Despite the huge economic impact of cattle babesiosis in South Africa, antigenic variation observed among B. bigemina strains worldwide has impeded the successful development of a single vaccine with the potential to eliminate the disease. As such, there is still a dearth of information regarding the conservation of B. bigemina genes encoding functionally important proteins that play a crucial role during the invasion of bovine erythrocytes by merozoites. Fifty blood samples previously collected from cattle in eight provinces of South Africa were genetically tested for the presence of B. bigemina DNA fragments using four nested PCR-based assays. The genes targeted coded for SpeI-AvaI restriction fragment, rhoptry-associated protein 1 (BgRAP-1), apical membrane antigen 1 (BgAMA-1) and β-tubulin (BgβTUB). PCR-generated fragments of randomly selected samples were sequenced. BLAST searches in GenBank were performed with newly determined sequences to search for homologous sequences. Neighbor-joining phylogenies were inferred from aligned, contiguous sequences of BgRAP-1, BgAMA-1 and BgβTUB genes. Nested PCR assays generated single fragments of 170 bp, 472 bp, 765 bp and 302 bp for SpeI-AvaI, BgRAP-1, BgAMA-1 and BgβTUB fragments, respectively. Of the 50 bovine samples tested by nested PCR, 82% (42/50; 95% CI = 69.2–90.2%), 68% (34/50; 95% CI = 54.2–79.2%), 50% (25/50; 95% CI = 36.6–63.4%) and 46% (23/50; 95% CI = 33.0–59.6%) possessed B. bigemina-specific SpeI-AvaI, BgRAP-1, BgAMA-1 and BgβTUB DNA fragments, respectively. The BgRAP-1, BgAMA-1 and BgβTUB sequences of South African B. bigemina isolates shared 98–100% similarity with previously reported sequences of strains originating from cattle in countries other than South Africa. The high genetic conservation observed among geographical isolates of B. bigemina suggests the conserved functional role of BgRAP-1 and BgAMA-1 proteins as potential candidates that could be incorporated in recombinant subunit vaccines. Full article

The bacterium Bacillus anthracis secretes three protein exotoxins: Protective Antigen 83 (PA83), Lethal Factor (LF), and Edema Factor (EF). A cleaved form of PA83 (PA63) aids LF and EF entry into the cytoplasm, which leads to anthrax-induced cell death. The Protein Data Bank (PDB) has more than 25 structures of LF: the monomer alone, bound with inhibitors, or bound to PA63. The structures are all—with only minor shifts of a few Ångströms—nearly congruent. We have measured the structure of LF at equilibrium in D₂O solution by small-angle neutron scattering (SANS). The shape is modeled well by a parallelepiped (all angles 90°) with dimensions of 12 Å × 49 Å × 129 Å. For a protein with a typical density of 1.4, the molecular weight would be between 55 and 94 kDa, which is comparable to that of the 90.2 kDa monomer. However, the LF crystal structure PDB 1pwu (a generally V-shaped molecule with equal arm lengths ≈ 70 Å) with the same model fits the dimensions 30 Å × 48 Å × 104 Å. Given the large changes in the long and short dimensions, straightforward physical modeling of the solution structure from the crystal form is unable to match the SANS results. Full article

Background: Malaria remains a global health crisis, with the World Health Organization (WHO) reporting 241 million cases and 627,000 deaths worldwide in 2020, predominantly affecting Sub-Saharan Africa. The region accounted for 95% of cases and 96% of deaths, reflecting the immense challenges in malaria prevention and treatment. Plasmodium falciparum Schizont Egress Antigen-1 (PfSEA-1) is crucial in facilitating immune evasion and promoting the sequestration of infected red blood cells (RBCs), contributing to severe malaria symptoms, including cerebral malaria, and necessitates the urgent identification of novel or repurposed drugs targeting PfSEA1. Methods: The protein structure of PfSEA-1 (UniProt ID: A0A143ZXM2) was modelled in three dimensions, prepared, and subjected to a 50 ns molecular dynamics (MD) simulation to achieve a stable structure. The equilibrated structure was minimised for molecular docking against the DrugBank compound library. Docking analysis identified potential inhibitors, including Alparabinos, Dihycid, Ambenzyne, Amiflupipquamine, Ametchomine, and Chlobenethyzenol, with docking scores ranging from −8.107 to −4.481 kcal/mol. Advanced analyses such as interaction fingerprints, density functional theory (DFT), and pharmacokinetics evaluations were conducted. Finally, a 100 ns MD simulation in the NPT ensemble was performed to assess the stability of protein–ligand complexes, with binding free energy and total energy calculations derived from the simulation trajectories. Results and Discussion: The identified compounds exhibited satisfactory pharmacokinetic profiles and binding interactions with PfSEA-1. The MD simulations demonstrated overall stability, with minor fluctuations in some instances. Key intermolecular interactions were observed, supporting the binding stability of the identified compounds. Binding free energy calculations confirmed favourable interactions, underscoring their potential as therapeutic agents against Plasmodium falciparum. While the in silico results are promising, experimental validation is essential to confirm their efficacy and safety for clinical use. Conclusion: These findings highlight PfSEA-1 as a promising antimalarial target and identify potential inhibitors with strong binding affinities and favourable pharmacokinetics. While the computational results are encouraging, further in vitro and in vivo validation is necessary to confirm their therapeutic potential and facilitate future drug development. Full article

Feline infectious peritonitis virus (FIPV) remains as one of the leading causes of morbidity and mortality in young cats from shelters and catteries worldwide. Since little is known about the molecular characteristics of currently circulating FIPV strains in Long Island, New York, samples from two shelter cats submitted to the Pathology Diagnostic Services of the Long Island University College of Veterinary Medicine, with gross and microscopic lesions consistent with those of FIP were processed for virus isolation, molecular characterization and full-length genome decoding. The younger shelter cat, a 1-year-old male (A15) was found dead without previous signs of illness. Postmortem examination revealed gross and microscopic lesions characterized by vasculitis, necrosis, hemorrhage, and pyogranulomatous inflammation confined to the colon and associated lymph nodes. The second cat, a 7-year-old spayed female (A37) had an identical clinical history and similar but widespread lesions, including fibrinous peritoneal effusion, cecal, colonic, renal, and hepatic involvement. The gross and microscopic diagnosis of FIP in these cats was confirmed by immunohistochemistry (IHC) demonstration of feline coronavirus antigen using mouse anti-FIPV3-70 monoclonal antibody. Virus isolation from saved frozen kidney and colon tissue was performed through several subsequent blind passages in MDCK and Vero cell lines. Confirmation of the FIPV isolation was done through qRT-PCR, IFA, western blot using N protein antibodies, and NGS of the full-length genome sequencing. The full-length genome sequences of the virus isolate from the two cats were decoded using next-generation sequencing (NGS) and deposited in the GenBank as accession numbers PQ192636 and PQ202302. The genome size of these isolates was (29355 and 29321) nucleotides (nt) in length, respectively. While their genome organization was consistent with other FIPV genomes as follows (5’UTR-ORF1ab-S-3abc-M-E-7b-3’UTR-3’), marked differential mutations were observed in the ORF1a/b, S, 3Abc, and 7b protein genes of the two FIPV isolates. One notable deletion of 34 nucleotides was observed in the 7b genes of one of these isolates but was absent in the other. We confirmed the potential recombination events during the evolution of those two FIPV field isolates with the potential parent virus as FECoV-US isolated in 1970 and the potential minor parent as the Canine coronavirus. Our results provide a comprehensive molecular analysis of two novel FIPV isolates causing fatal disease in shelter cats from Long Island. Diagnostic surveillance with molecular characterization and sequencing analysis of circulating FIPV strains within animal shelters may help early detect unique emerging clinical and pathological manifestations of the disease and develop more targeted prophylactic and therapeutic approaches to control it. Full article

Citrullination, a post-translational modification (PTM), plays a critical role in rheumatoid arthritis (RA) by triggering immune responses to citrullinated self-antigens. Some HLA-DRB1 genes encode molecules with the shared epitope (QKRAA/QRRAA) sequence in the peptide-binding groove which preferentially presents citrulline-modified peptides, like vimentin, that intensifies the immune response in RA. In this study, we used computational approaches to evaluate intermolecular interactions between vimentin peptide-ligands (with/without PTM) and HLA-DRB1 alleles associated with a significantly increased risk for RA development. Crystal structures for HLA-DRB1*04:01, *04:04, and *04:05 bound to citrullinated peptides (PDB ID: 4MCY, 4MD5, 6BIR) were retrieved from the Protein Data Bank and non-citrullinated 3D structures were generated by mutating citrulline to arginine. The pHLA complexes were submitted to four rounds (50 ns each) of molecular dynamic simulations (MD) with Gromacs v.2022. Our results show that citrulline strengthens the interaction between vimentin and the HLA-DRB1 molecules, therefore impacting both the peptide affinity to the HLAs and pHLA stability; it also induces more intermolecular hydrogen bond formation during MD in the pHLA. Citrulline prevents repulsion between amino acid 71β and the P4-residue of native vimentin. Thus, vimentin citrullination seems to affect pHLA binding and dynamics, which may influence RA-related immune responses. Full article

Adenoviruses are important human pathogens that are widespread and mainly associated with respiratory and gastrointestinal infections. In a previous study on human adenovirus (HAdV) seroprevalence, we observed reduced binding antibody levels against a range of HAdV types in sera collected from students in 2021 compared to sera collected before the SARS-CoV-2 pandemic. In this follow-up study, we wanted to verify this observation in a cohort of regular blood donors for whom serial samples were available. Therefore, HAdV-specific binding antibody levels were analyzed in sera collected over a 5-year period from 2018 to 2022 in a cohort of 60 regular donors to the blood bank of the University Hospital in Greifswald, Germany. Using ELISA-based assays, we quantified the binding antibody responses against 39 HAdV types. On the cohort level, we found largely stable antibody levels over the analyzed time period, with the highest antibody responses against HAdV-C1, -D25, -D26, -E4, -D10, -D27, -C5, -D75, -C2, and -C6. Only minor but significant reductions in comparison to the first serum samples from 2018 were detected for antibody levels in 2021 and 2022 against the low-prevalent types HAdV-A31, -D8, -D20, -D37, -D65, and -D69. On the other hand, we detected fluctuations in antibody levels on the individual level, with strong increases in antibody levels indicative of novel antigen contact. Interestingly, we frequently found simultaneous changes in antibody responses against multiple HAdV types, resulting in strong correlations of antibody responses against distinct clusters of HAdVs suggesting extensive cross-reactivity of HAdV-specific antibodies. To our knowledge, this is the first study of antibodies against a broad range of HAdV types in serum samples collected from a cohort of individuals over a prolonged period, and our data provide important insight into the long-term stability of HAdV-specific antibody levels. In this cohort of regular blood donors, we did not observe any major impact of the SARS-CoV-2 pandemic on HAdV immunity. Correlations of changes in antibody levels against different types indicate cross-reactivity of HAdV-specific antibodies that are important to consider for HAdV vector development. Our data also reveal possible candidates for future development of HAdV-based vectors. Full article

Background: Variations in the fusion (F) protein of respiratory syncytial virus (RSV) with main antigenic sites I–V and Ø may affect the development of RSV vaccines and therapies. Methods: In the study, 30 respiratory specimens positive for RSV were randomly selected from children with acute lower respiratory infections (ALRI) in Beijing every year from 2012 to 2021 for F gene sequencing. Then, 300 F gene sequences and 508 uploaded to GenBank from China were subjected to phylogenetic analysis. Results: The results indicated the nucleotide identities were 95.4–100% among 446 sequences of RSV A, and 96.3–100% among 362 of RSV B. The most common variant loci were N80K (100.00%) and R213S (97.76%) for site Ø, and V384I/T (98.43%) for site I among sequences of RSV A, and M152I (100.00%), I185V (100.00%), and L172Q/H (94.48%) for site V, and R202Q (99.45%) for site Ø among sequences of RSV B. N276S appears in 95.29% sequences of RSV A, while S276N and N262 I/S appear in 1.38% and 0.55% sequences of RSV B, respectively. No variation was found in all sequences at the binding sites of 14N4 and motavizumab. Conclusions: There were cumulative variations of the RSV F gene, especially at some binding sites of antigenic sites. Full article

Critical blood shortages plague healthcare systems, particularly in lower-income and middle-income countries. This affects patients requiring regular transfusions and creates challenges during emergencies where universal blood is vital. To address these shortages and support blood banks during emergencies, this study reports a method for increasing the compatibility of blood group A red blood cells (RBCs) by blocking surface antigen-A using anti-A single chain fragment variable (scFv). To enhance stability, the scFv was first modified with the addition of interdomain disulfide bonds. The most effective location for this modification was found to be H44-L232 of mutant-1a scFv. ScFv was then produced from E.coli BL21(DE3) and purified using a three-step process. Purified scFvs were then used to block maximum number of antigens-A on RBCs, and it was found that only monomers were functional, while dimers formed through incorrect domain-swapping were non-functional. These antigen-blocked RBCs displayed no clumping in hemagglutination testing with incompatible blood plasma. The dissociation constant K_D was found to be 0.724 μM. Antigen-blocked RBCs have the potential to be given to other blood groups during emergencies. This innovative approach could significantly increase the pool of usable blood, potentially saving countless lives. Full article

The purpose of this study was to assess the efficacy, specificity, and predictive value of a newly discovered biomarker, Zinc finger-like1 protein (referred to as neuroendocrine marker, NEM) for the detection of prostate cancer (PCa). We retrospectively analyzed banked plasma samples from 508 men, with a median age of 67 years (range 48–97), to compare the performance of NEM and PSA in predicting subsequent histologic PCa. The cohort consisted of four groups of patients visiting a urology clinic: (1) patients not diagnosed with either benign prostatic disease or prostate cancer (PCa) were defined as normal; (2) patients diagnosed with benign hyperplasia (BPH) but not PCa; (3) patients with confirmed PCa; and (4) patients with cancer other than PCa. The normal men displayed a mean NEM plasma level of 0.948 ± 0.051 ng/mL, which increased to 1.813 ± 0.315 ng/mL in men with BPH, 86.49 ± 15.51 ng/mL in men with PCa, and 10.47 ± 1.029 ng/mL in men with other Ca. The corresponding concentrations of prostate-specific antigen (PSA) in these subjects were 1.787 ± 0.135, 5.405 ± 0.699, 35.77 ± 11.48 ng/mL, and 8.036 ± 0.518, respectively. Receiver operating characteristic (ROC) curve analysis was performed to compare NEM and PSA performance, and the Jouden Index for each biomarker was calculated to determine cut-off points for each biomarker. The area under the ROC curve to predict PCa was 0.99 for NEM and 0.81 for PSA (p < 0.0001). The cut-off for NEM was at 1.9 ng/mL, with sensitivity of 98% and specificity of 97%. The corresponding PSA values were 4.4 ng/mL, with sensitivity of 76% and specificity of 95%. The predictive value of each biomarker in a patient was matched with his pathologic data to determine the accuracy of each biomarker. NEM was more accurate than PSA in differentiating cancer from benign conditions, such as BPH or prostatitis. In conclusion, NEM was a better predictor of PCa than PSA in patients visiting urology clinics. NEM tests, either alone or in conjunction with other biomarkers, provide a reliable, non-invasive, and inexpensive test to remarkably reduce false positives and thereby reduce the number of diagnostic biopsies and associated painful procedures and the loss of quality of life. Full article

The SARS-CoV-2 pandemic and the emergence of novel virus variants have had a dramatic impact on public health and the world economy, underscoring the need for detailed studies that explore the high efficacy of additional vaccines in animal models. In this study, we confirm the pathogenicity of the SARS-CoV-2/Leiden_008 isolate (GenBank accession number MT705206.1) in K18-hACE2 transgenic mice. Using this isolate, we show that a vaccine consisting of capsid virus-like particles (cVLPs) displaying the receptor-binding domain (RBD) of SARS-CoV-2 (Wuhan strain) induces strong neutralizing antibody responses and sterilizing immunity in K18-hACE2 mice. Furthermore, we demonstrate that vaccination with the RBD-cVLP vaccine protects mice from both a lethal infection and symptomatic disease. Our data also indicate that immunization significantly reduces inflammation and lung pathology associated with severe disease in mice. Additionally, we show that the survival of naïve animals significantly increases when sera from animals vaccinated with RBD-cVLP are passively transferred, prior to a lethal virus dose. Finally, the RBD-cVLP vaccine has a similar antigen composition to the clinical ABNCOV2 vaccine, which has shown non-inferiority to the Comirnaty mRNA vaccine in phase I-III trials. Therefore, our study provides evidence that this vaccine design is highly immunogenic and confers full protection against severe disease in mice. Full article