Virologica Sinica
○ Elsevier BV
Preprints posted in the last 90 days, ranked by how well they match Virologica Sinica's content profile, based on 11 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.
Li, L.; Zhang, X.; Fan, J.; Fan, J.; Du, J.; Yan, H.; Dai, E.; Gao, H.; Feng, A.
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Purpose: To investigate the incidence, clinical features, and risk factors for SARS-CoV-2 nucleic acid re-positivity in recovered COVID-19 patients. Methods: We enrolled 441 convalescent COVID-19 patients from the rehabilitation ward of the Fifth Hospital of Shijiazhuang between January and April 2021. Based on nucleic acid test results, patients were categorized into repositive (n = 69) and non-repositive (n = 372) groups. Demographic, clinical, laboratory, and imaging data were compared between groups. Logistic regression was used to identify factors associated with re-positivity. Results: The overall re-positivity rate was 15.65%. Compared with the non-repositive group, the repositive group presented with a significantly higher proportion of moderate disease severity (72.46% vs. 50.54%) and a lower proportion of patients under 14 years old (7.25% vs. 23.66%). Additionally, multi-lobar involvement ([≥] 3 lobes) during the acute phase was more common in the repositive group (43.48% vs. 26.61%), with all differences being statistically significant (P < 0.001). Laboratory analysis revealed that repositive patients had significantly lower lymphocyte and eosinophil counts, as well as reduced albumin (ALB), aspartate aminotransferase/alanine aminotransferase (AST/ALT) ratio, and albumin/globulin (A/G) ratio. Furthermore, circulating CD3+, CD4+, and CD8+ T-cell counts were markedly decreased. In contrast, the neutrophil-to-lymphocyte ratio (NLR), immunoglobulin M (IgM), immunoglobulin A (IgA), and neutralizing antibody (NAb) levels were significantly elevated in re-positive patients (all P < 0.05). Multivariate logistic regression analysis identified the CD8+ as independent risk factors for re-positivity. Conclusion: In convalescent patients, SARS-CoV-2 RNA re-positivity correlates with distinct clinical and immunological characteristics. The CD8+ T-cell level is an independent predictor, highlighting that dysregulated immune and inflammatory responses contribute to delayed viral clearance.
Agrawal, A.; Kumar, S.; Vindal, V.
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A protein whose removal or deletion causes significant disruption or collapse of a protein-protein interaction (PPI) network is referred to as a vulnerable protein. Such proteins may serve as valuable therapeutic or diagnostic targets in disease-associated networks. In this study, two PPI networks were constructed, one for HPV-positive and the other for HPV-negative head and neck squamous cell carcinoma (HNSCC), and the vulnerable proteins of these networks were identified by the node deletion approach. After analyzing the networks, 27 unique vulnerable proteins in HPV-positive and 72 unique vulnerable proteins in HPV-negative HNSCC were identified. Among them, one HPV-positive and seven HPV-negative HNSCC vulnerable proteins were further chosen by integrating multi-omics data. To exploit the vulnerabilities of these proteins, candidate synthetic lethal (SL) partners were predicted whose inhibition may selectively impair tumor survival. Subsequently, drug-gene interaction analysis was performed to identify inhibitors targeting the SL partners of these vulnerable proteins. Notably, in HPV-positive HNSCC, TOP2A, CHEK1, and CHEK2 genes were identified as SL partners of TTN, and their inhibitors were already clinically approved. While in HPV-negative HNSCC, ADA and MMP19 were identified as an SL partner of LMO7; TMEM45B, CDH3, and ELF3 genes were identified as an SL partner of CGN; and ZNF433 was identified as an SL partner of FLNC. However, MMP19, ZNF433, and TMEM45B inhibitors were not reported. Thus, these vulnerable proteins, including their SL partners, provide novel avenues to explore and develop more efficient and precise therapeutic and diagnostic strategies.
Abuduwaili, M.; Makokha, G. N.; Naderi, M.; Sakai, H.; Yamamoto, A.; Sakaguchi, T.; Matsumoto, T.; Shirouzu, M.; Seishi, K.; Yamamoto, A.; Kubo, Y.; Matsushita, M.; Inoue, Y.; Shankhajit, D.; Hijikata, M.; Chayama, K.
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Chronic hepatitis B virus (HBV) infection remains a major global health challenge because current antiviral therapies rarely achieve complete viral clearance. We evaluated the antiviral activity of a newly developed monoclonal antibody, 7-4G mAb, directed against the hepatitis B surface antigen (HBsAg). The antibody showed specific binding to the p27 component of HBsAg and efficiently removed HBV-related particles from patient serum in vitro. Significant HBV neutralizing activity of 7-4G mAb was observed in primary human hepatocytes and in humanized mouse models. In persistently HBV-infected PXB mice, a single administration of 7-4G mAb, either alone or in combination with another monoclonal antibody, reduced serum HBsAg levels and HBV DNA levels by two orders magnitude for two weeks after the treatment. In half of the treated mice, suppression of both viral markers was maintained through the study period, whereas rebound occurred within three to four weeks in the remaining animals. In addition, 7-4G mAb enhanced the HBV DNA-lowering effect of entecavir, a known anti-HBV drug. These findings support the further development of 7-4G mAb as part of an innovative HBV treatment strategy, addressing limitations of existing therapies and advancing toward a more effective HBV management solution.
Espinosa-Parrilla, Y.; Fuentes-Guajardo, M.; Carvajal-Silva, L.; Aguilar-Valdes, K.; Signore, I. A.; Arevalo, T. V.; Zapata-Contreras, D.; Donoso, G.; Zuniga-Pacheco, P.; Valenzuela-Jorquera, H.; Rosso Villanelo, S. A.; Tobar-Calfucoy, E. A.; Yanez, C. E.; Carvajal, F.; Saez Hidalgo, J. M.; Sanhueza, S.; Quiroga, R. A.; Martinez, M. F.; Cerpa, L. C.; Varela, N. M.; Cappelli, C. L.; Campillay-Veliz, C. P.; Valdebenito-Maturana, B.; Garcia-Araya, J.; Santander, R. A.; Opazo, J.; Retamales-Ortega, R.; Bocchieri, P.; Alarcon, T. A.; Plaza, A.; Moraga, M.; Munoz, C. A.; Echeverria, C. A.; Dorador,
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Background: More than five years after the COVID-19 outbreak, the infection by the SARS-CoV-2 virus should still be considered as a global threat with highly heterogeneous clinical outcomes from asymptomatic to fatal depending on existing genetic and phenotypic inter-individual and inter-population variability. Our objective is to identify risk loci associated with COVID-19 in an admixed Latin American population. Methods: We performed a genome-wide association study in the framework of the Chilean C19-GenoNet team, analyzing a cohort of 3,417 individuals recruited from the northernmost to the southernmost regions of the country, who presented variations in the severity of their COVID-19 clinical manifestations. Results: Our investigation replicated the extensively reported association of several variants at the 3p21.31 locus with COVID-19 severity and found a suggestive association for a variant within the FOXP4 gene at 6p21.1 with COVID-19 hospitalization. Both associations appear to be shared with other populations. Importantly, our study identified three previously unreported loci associated with COVID-19 severity or hospitalization at 7q21.11, 16p13.12 and 6p25.3, and one additional locus at 4p13 associated with SARS-CoV-2 positivity, a proxy for infection susceptibility. Conclusions: these new risk loci may represent population-specific effects in Chilean and, potentially, other Latin American admixed groups. Our study highlights the importance of expanding efforts to study underrepresented and genetically different populations, which may provide new clues on the genetic basis of human diseases and may help to anticipate global responses to emerging viral infections and future pandemics.
Li, Y.-T.; Lin, Y.-T.; Chen, B.-S.; Kuo, C.-Y.; Huang, H.-Y.; Ko, H.-Y.; Huang, P.-Y.; Smith, G. J.; Lin, Y.-L.; Liu, M.-T.
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Low pathogenic avian influenza A(H7N7) virus detected in a poultry worker in Taiwan, 2026 was related to viruses circulating in Asian wild birds and possessed PB2 E627K, a mammalian adaptation marker. Enhanced surveillance for H7 viruses in poultry and rapid characterization of human cases are essential to assess pandemic potential.
Wang, Y.; VACCA, F.; Rountree, W.; Wiehe, K.; He, M. M.; Moody, T.
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MotivationInfluenza is an infectious disease associated with excess human deaths. For influenza A virus (IAV), the surface antigens hemagglutinin (HA) and neuraminidase (NA) define the specific subtype. The high mutation rate of IAV can make clinical testing and assigning subtype after sequencing challenging. Accurate subtype classification is important for tracking circulating IAV strains that may impact human health. ResultsWe analyzed a large IAV protein sequence dataset with known HA and NA subtypes. Using logistic regression and random forest approaches, we identified a small set of subtype-associated amino acids, which were then used to develop a subtype characterization method with near-optimal accuracy. Further analysis indicated that signal sequence peptide variation and indels in HA and NA explained the unique combination of subtype-associated amino acids.
Huang, F.; Nishiura, K.; Fujinaga, K.
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While many cellular and viral mechanisms are associated with proviral latency, the positive transcription factor b (P-TEFb), a cellular co-factor of the nuclear factor kappa B and viral transactiator proteins, plays a critical role in low viral transcription levels in resting infected cells. P-TEFb, comprised of CDK9 and Cyclin T1 (CycT1), is absent in quiescent CD4+T cells that represent the bulk of the viral latent reservoir. In these cells, the CycT1 subunit is dephosphorylated and dissociated from CDK9, leading to its rapid proteasomal degradation. Based on the knowledge of CycT1 phosphorylation and proteolysis, we designed a mutant CycT1 protein [constitutively active (CA)-CycT1] that is resistant to protein degradation and is stably expressed in resting CD4+ T cells. Interestingly, the expression of CA-CycT1 significantly delayed the establishment of viral latency in CD4+ T cells. This is the first example of expressing a high level of CycT1 proteins in resting CD4+ T cells, which modulates viral latency and T cell functions. This finding presents a significant therapeutic potential for the development of effective therapies for latent viral infections.
Cao, Y.; Long, Y.; Schleibinger, S.; von Heyl, T.; de Wit, J. J.; Kaufer, B.; Schusser, B.; Sid, H.
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Infectious bronchitis virus (IBV) is an economically important avian gammacoronavirus. IBV uses sialic acids and heparan sulfate for cellular attachment, but the host proteins governing its infection remain poorly defined. Here, we investigated the roles of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) during IBV Beaudette (IBV BD) infection. ACE2 knockout impaired IBV replication in DF-1 cells, whereas ACE2 reconstitution restored infection. Furthermore, ACE2 overexpression enhanced infection of DF-1 and primary chicken embryo kidney cells, supporting the role of chicken ACE2 as a proviral host factor. In contrast, TMPRSS2 exerted a restrictive function on IBV BD infection as demonstrated in TMPRSS2 KO DF-1 cells and upon pharmacological inhibition, which significantly increased IBV BD infection in DF-1 and Vero cells. RNA sequencing revealed significant changes in lipid metabolism and membrane-related processes following TMPRSS2 knockout and pharmacological inhibition. These findings highlight the opposing roles of ACE2 and TMPRSS2 in IBV BD infection, emphasizing the combined impact of proviral host factors, protease activity, and the cellular membrane environment during gammacoronavirus infections.
Hebert-Milette, I.; Mercier, V.; Paquette, J.; Boucher, G.; Levesque, C.; Goyette, P.; Rioux, J. D.
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Background Genome-wide association studies have identified >200 loci associated with IBD, yet the causal gene for most remains unknown. As multiple epithelial functions have been linked with susceptibility to IBD, there is a need to prioritize candidate causal genes for functional studies in this cellular context. Methods Using a standardized definition of regions implicated by index SNPs from three GWAS studies, we categorized regions as containing: (1) a known casual gene, (2) a single gene or (3) multiple genes. We then developed an IBD Priority Score to rank genes based on genetic, genomic and functional data. We next developed and applied an Epithelial Priority Score, based on expression patterns and quantitative traits, to prioritize genes for functional validation in epithelial models. Two candidate genes identified through this approach were tested for their impact on viral response pathways in HT-29 cells. Results The IBD Priority Score prioritized a single gene in 71 of the 104 regions containing multiple genes. The Epithelial Priority Score identified 31 epithelial candidates. Functional studies demonstrated that IRF6 enhanced, whereas IRF8 suppressed, antiviral responses in intestinal epithelial cells stimulated with Poly(I:C). Conclusions Combining multiple genetic, genomic, and functional data is a useful approach for prioritizing the most likely causal gene within IBD GWAS loci, and for prioritizing functional validation studies in epithelial cells and tissues. Moreover, we provide functional evidence for two IBD genes playing a role in the regulation of anti-viral responses in intestinal epithelial cells.
Kurumida, Y.; Saito, Y.
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Antibodies exhibit species-specific sequence and structural features that influence their antigen-recognition properties. Although several studies have investigated porcine antibodies, their repertoire and structural characteristics remain less well characterized than those of several other mammalian species. In this study, we analyzed public porcine heavy-chain repertoire sequencing data together with available antibody structural data to identify characteristic features of porcine antibodies. We found several residues enriched in porcine antibody framework regions, particularly at the base of heavy-chain complementarity-determining region 3 (CDR-H3). In particular, Arg101 and Glu123 were closely positioned in available structures and may influence CDR-H3 conformation at its base, whereas Pro120 may help constrain local backbone conformation. We also observed non-canonical cysteine usage in both framework region 1 and CDR-H3, which may contribute to structural diversity in the porcine repertoire. Finally, we evaluated the humanization potential of a porcine antibody using a human antibody language model and found that human-likeness increased after model-guided substitutions, although the resulting sequences did not exceed the T20 score threshold. Overall, these results indicate that porcine antibodies possess distinct sequence and structural features that may influence CDR-H3 properties and should be considered in future antibody analysis and engineering.
Singh, Y. J.; Sehrawat, S.
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Genetic ablation approaches are routinely used to establish gene function, but these are not beyond limitations. The intracellularly expressed camelid single-domain antibodies (sdAbs), or nanobodies, can specifically disrupt molecular interactions and, therefore, help ascertain their role in the process of cellular differentiation. The approach has not been evaluated in differentiating T cells or the stimulating DCs during viral infection. We modified the intracellular response of Galectin-3 (Gal-3) using an -Gal-3 intrabody (IB) in antigen-specific CD8+ T cells and assessed their differentiation patterns during a resolving Influenza A virus encoding SIINFEKL epitope (IAV: WSN-SIINFEKL). The -Gal-3 IB expressors, compared to the cells genetically depleted of Gal-3, exhibit a significantly prolonged activation, enhanced proliferation, and elevated cytokine production following in vitro stimulation. The -Gal-3 IB expressing cells show enhanced functionality and generate an efficient effector response, favoring the generation of memory precursor effector cells (MPECs: CD127hiKLRG1lo) over short-lived effector cells (SLECs: CD127loKLRG1hi) in IAV-infected animals. Such a differentiation pattern results in improved differentiation of effector memory (CD44hiCD62LloCCR7lo) cells amongst the -Gal-3 IB-expressing cells. The generated memory cells are efficiently recalled upon challenge infection with MHV68-SIINFEKL and help control the infection better. Therefore, modifying the intracellular response of Gal-3 using a sdAb could improve the primary and memory response of antigen-specific CD8+ T cells.
Muthuvel, s. k.; BALAKRISHNAN, S. S.; MANJINI, S.; DHAL, K.; DAS, S.; S, D.
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The Dengue virus (DENV), a major global health concern, causes dengue fever, predominantly affecting tropical and subtropical regions. The NS2B-NS3 protease complex of DENV is critical for viral replication, making it a promising target for antiviral drug development. This study investigates the structural dynamics of the NS2B-NS3 protease under varying pH conditions, integrating experimental and computational approaches. The recombinant NS2B-NS3 protease was expressed in E. coli, purified using affinity chromatography, and analysed for purity via SDS-PAGE. Circular dichroism (CD) spectroscopy revealed pH-dependent secondary structural changes, indicating stability at neutral to slightly basic pH and destabilization under acidic and highly basic conditions. Dynamic light scattering (DLS) analysis demonstrated protein aggregation and structural heterogeneity under extreme pH levels. Complementary in silico techniques, including homology modelling and molecular dynamics (MD) simulations, provided detailed insights into the conformational changes of the protease. The modelled structure, validated and refined through computational tools, revealed structural stability at physiological pH, with notable disruptions at pH extremes. DSSP (Dictionary of Secondary Structure of Proteins) and principal component analyses highlighted significant secondary structural transitions, especially at acidic pH where -helices and {beta}-sheets transformed into random coils Docking and MD simulation was carried out with the small molecule for therapeutic analysis between Dengue NS2bNS3 and small molecule. This study emphasizes the pH-dependent conformational plasticity of the NS2B-NS3 protease, contributing to the understanding of its functional mechanisms and providing a foundation for the rational design of pH-specific inhibitors. These findings underscore the importance of structural biology in advancing therapeutic strategies against dengue fever.
Tung, K. S.; Mahish, C.; Ghosh, S.; Mukherjee, K.; Singh, S.; Bhowmick, B.; Khamaru, S.; Borasi, H.; Gaur, M.; Subudhi, B. B.; Chattopadhyay, S.; Chattopadhyay, S.
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Neuropilin-1 (NRP1) is a transmembrane glycoprotein involved in angiogenesis, neurodevelopment, inflammation, cancer driven immune suppression, and immune homeostasis. However, its contribution to virus-induced immune responses is not explored. Chikungunya virus (CHIKV) is a re-emerging arthritogenic alphavirus that causes severe arthralgia, and myalgia, accompanied by heightened inflammatory cytokine responses. The host factors that drive these inflammatory responses, however, remain poorly defined. Here, in this current study, the role of NRP1 in CHIKV infection was investigated using in vitro, and in vivo model systems. Using genetic manipulation, pharmacological, and antibody blockade-mediated approaches in murine and human cellular infection models, it was demonstrated that NRP1 promotes CHIKV infection while restraining the production of proinflammatory cytokines. Furthermore, NRP1 inhibition selectively increased JNK phosphorylation. Hence, inhibiting JNK reduced the elevated cytokine production caused by NRP1 blockade. Moreover, NRP1 interacted with CHIKV-E1 and is involved in multiple phases of CHIKV infection. In addition, it was demonstrated that NRP1 inhibition using EG00229 trifluoroacetate can reduce viral infection in several CHIKV-susceptible cells, human peripheral blood macrophages, and in the in vivo mice model of infection. Together, these findings indicate that NRP1 is an important host factor and a probable therapeutic target during CHIKV infection. IMPORTANCEChikungunya virus (CHIKV) causes acute febrile illness that can progress to debilitating chronic musculoskeletal and occasional neurological complications. The absence of a globally available effective vaccine and the lack of specific antivirals underscore CHIKV as a major burden, especially in endemic tropical regions. There is a growing need to understand host factors that shape CHIKV-driven immune response. The importance of our study lies in understanding the immunoregulatory role of the host receptor Neuropilin-1 (NRP1) during CHIKV infection. We identify NRP1 as a novel host factor of CHIKV infection that also acts as a rheostat to restrict the inflammatory viral immune response. Moreover, we report anti-viral potential of the NRP1 antagonist EG00229 trifluoroacetate in multiple cell lines, primary cells, and mice model. Our findings indicate NRP1 as a probable therapeutic target in CHIKV pathogenesis.
Mimura, Y.; Hiono, T.; Arakawa, H.; Go, S.; Shigeno, A.; Ito, M.; Fujii, E.; Mizuma, K.; Nakao, R.; Orba, Y.; Kaji, H.; Matsuno, K.
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A growing number of emerging and re-emerging tick-borne orthonairoviruses belonging to the Sulina and Tamdy genogroups have recently been identified in association with febrile diseases in East Asia. Yezo virus (YEZV) is one such viruses and is genetically distinct from well-characterized Crimean-Congo hemorrhagic fever virus. Orthonairovirus glycoproteins (Gn and Gc) expressed from a single glycoprotein precursor (GPC) gene mediate interaction with host cells, yet the organization and functions of the YEZV glycoproteins remain largely undefined. To characterize YEZV glycoproteins in the context of infection, we developed a reverse genetics system that enables recovery of recombinant YEZV entirely from cloned cDNAs. The recombinant wild-type virus exhibited growth properties comparable to those of the parental isolate in vitro and maintained pathogenicity in vivo. Proteomic analysis of purified virus particles produced in mammalian cells showed that peptide coverage of GPC-derived products began at residue 69. We therefore used the reverse genetics system to examine the functional importance of the GPC subregion upstream of residue 69. A mutant with a deletion of GPC residues 28 to 68 (rYEZV GPC{Delta}28-68), which retained the predicted signal peptide, was successfully recovered, suggesting that this subregion is dispensable for producing infectious virus. rYEZV GPC{Delta}28-68 propagated at levels comparable to those of the wild-type virus in mammalian cells and exhibited similar pathogenicity in a mouse model. Interestingly, the mutant reached lower viral titers in tick-derived ISE6 cells and in ticks in vivo, suggesting that this N-terminal subregion may contribute to virus replication in ticks. Together, these findings demonstrate the utility of the newly established reverse genetics system for dissecting the functions of the YEZV glycoproteins in mammalian and tick systems.
Ma, E.; Tesi, N.; Salazar, A.; Hulsman, M.; Holstege, H.; Reinders, M.
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INTRODUCTION: Throughout history, viruses have been infecting humans, leaving genomic traces called endogenous viral elements (EVEs). This study explores the infectious hypothesis for Alzheimer's disease (AD) that suggests that viral infections may contribute to AD by analyzing EVEs in genomes of AD patients and cognitively healthy centenarians (CHCs) measured by long-read sequencing. METHODS: We implemented an EVE detection pipeline that screened the genomes of 248 AD patients and 240 CHCs. EVEs were measured based on EVE count, length, and chromosome location. RESULTS: The genomes of AD patients contain significantly more EVEs than those of CHCs (p=3.2x10-4). Moreover, certain chromosomal regions in AD patients show a higher EVE count, particularly of the Orthoherpesviridae family, near genes differentially expressed in AD brains. DISCUSSION: These findings suggest that viral infections may increase susceptibility to AD, highlighting that preventive measures against infections potentially reduce AD risk.
Khan Chowdhury, A. R.; Islam, S.; Farid, A.; Lamia, F.; Ahmad, T. F.; Hossain, N. J.; Paul, A. R.; Afrin, T.; Elias, S. M.
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Drug targets and vaccines for bacterial diseases are challenging to develop. Computational subtractive genomics and reverse vaccinology offer a viable substitute for conventional drug and vaccine development approaches. In recent years, Pasteurella multocida, a Gram-negative pathogen responsible for severe infections in humans along with major diseases in livestock and poultry, has developed resistance to multiple drugs. As a result, there is an urgent demand for research into reliable, efficient, highly potent, and cost-effective strategies to combat the rise of Pasteurella multocida infections. To address this, the present study integrated an in silico subtractive genomics and reverse vaccinology workflow to pinpoint proteins with potential value as both drug and vaccine targets. From the complete Pasteurella multocida Pm70 proteome, we identified 446 proteins that had no similarities with human proteins, out of which 129 were found to be essential for the pathogens survival. These 129 proteins are therefore potential candidates for drug development. Further metabolic pathway analysis, virulence potential, subcellular localization, and structural analyses revealed two outer membrane proteins, namely, 47 kDa outer membrane protein and lipopolysaccharide-assembly protein LptD, as promising candidates for therapeutic development. Subsequent antigenicity analysis revealed both outer membrane proteins as potential vaccine targets, exhibiting highly favorable antigenicity scores. Candidate B- and T-cell epitopes were systematically mapped from these two targets based on antigenicity, immunogenicity, toxicity, and allergenicity potential and only high-confidence epitopes were assembled using adjuvants and class-specific linkers to construct the final multi-epitope vaccine (MEV). The designed MEV construct was demonstrated to be highly antigenic, non-toxic and non-allergenic to humans, while possessing favorable structural and physicochemical properties, and exhibited strong binding interactions with human toll-like receptors with minimal molecular deformability. Although further experimental validation is recommended to fully assess their efficacy, the present study establishes a solid foundation for the development of novel therapeutics and vaccine candidates against P. multocida, ultimately contributing to the reduction of its rising infections.
Razmjooei, F.; Ashayeri, H.; Jafarzadeh, Z.; Dabbaghabdollahi, P.; Jafarizadeh, A.
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Background: Uveal melanoma (UM) and cutaneous melanoma (CM) both originate from the same cell line. This proposes the possibility of a shared mechanism between entities, requiring explicit investigation. Methods: Data from GWAS Catalog and DisGeNET were used to identify shared variation-disease associations (VDAs) between UM and CM. The results were validated using the Ensembl database. In the next step, the STRING database was used to identify the protein-protein interaction. Results: Subsequently, 109 unique VDAs were identified for UM and 880 for CM. However, only 2 VDAs were found to be shared among UM and CM in different ethnic groups. These shared VDAs were rs12203592 of the IRF4 gene, rs12913832 of the HECT and RLD domain-containing E3 ubiquitin protein ligase 2 (HERC2) gene. Notably, PPI network assessment through STRING showcased that OCA2 and IRF4 directly interacted with HERC2. Conclusion: While HERC2 acts as a poor prognostic factor in uveal melanoma, IRF4 status is a key prognostic indicator in both UM and CM. Identifying IRF4 allele contributions enables a better understanding of melanoma pathogenesis and fosters the development of disease-specific approaches.
Tamura, K.; Chang, B.; Shimbashi, R.; Gotoh, K.; Tanabe, Y.; Kuronuma, K.; Ohshima, K.; Maruyama, T.; Nakamatsu, M.; Abe, S.; Kasahara, K.; Ooka, T.; Arakawa, Y.; Kinjo, Y.; Akeda, Y.; Oishi, K.
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Aims: To estimate the preventable pneumococcal disease burden by 21-valent pneumococcal conjugate vaccine (PCV21) compared to PCV20 for the national immunization program for adults aged 65 years or older in Japan. Methods: Serotype distribution among isolates and the annual incidence of invasive pneumococcal disease (IPD) in adults were monitored. The numbers of IPD or pneumococcal community-acquired pneumonia (pCAP) cases preventable by immunization with PCV20 or PCV21 were estimated according to reported vaccine efficacy and duration of protection in older adults. Data from our nationwide study of adult IPD surveillance and a multicenter study of pCAP were used. Results: The mean annual incidence of adult patients with IPD caused by all serotypes among adults aged [≥]65 years, which declined during the COVID-19 pandemic period, recovered to 89% of the pre-pandemic level in 2025. During 2023-2025, the proportion of PCV20-non-PCV21 serotypes was 8.5% for adults aged [≥]65 years. At the current vaccination coverage rate of 40%, the numbers of preventable IPD cases (per person per year) by PCV20 and PCV21 were 36 and 53, respectively. The preventable numbers of pCAP cases by PCV20 and PCV21 were 2,821 and 4,765, respectively. The estimated number of preventable pCAP cases was approximately 80-90 times higher than that of preventable IPD cases. Conclusion: Our data indicate that PCV21 could prevent 1.5-1.7 times as many pneumococcal disease cases as PCV20 among adults aged [≥] 65 years in Japan. However, PCV20 should be considered if the incidence of adult IPD cases caused by PCV20-non-PCV21 serotypes increases.
Zhong, K. X.; Chan, A. M.; Suttle, C. A.
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Oysters are vital to global aquaculture and marine ecosystems, yet, their associated RNA viruses remain largely unexplored. Here, we analysed ~1,000 publicly available metatranscriptomic datasets from 13 oyster species across 14 countries and 5 continents to characterize the oyster RNA virome (ORV). We identified 1,515 distinct RNA viruses putatively representing 17 viral orders and 766 species-level viral operational taxonomic units (vOTUs), with ~62% being previously undocumented putative species. These viruses not only populate extant branches of RNA virus evolution, but also represent previously unrecognized families and genera, and include viruses that putatively infect bacteria, fungi, protists, plants, invertebrates, and vertebrates. Based on sequence similarity, we found many calicivirus-like, orthoreovirus-like, astrovirus-like, and picornavirus-like viruses that do not infect invertebrates or microbes; thus, oysters accumulate diverse viruses from the surrounding water, and can potentially be interrogated as reporters of viruses circulating in the environment.
Kim, S.; Shakya, A. K.; Guo, H.
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Interferon gamma (IFN-{gamma}) is a potent cytokine secreted following primary varicella-zoster virus (VZV) infection. Our previous studies demonstrated that pretreatment with IFN-{gamma} completely inhibited VZV replication in lung fibroblast MRC-5 and retinal epithelial ARPE-19 but not in melanoma MeWo cells, suggesting that IFN-{gamma}-stimulated protein(s) inhibit viral replication. Our microarray analysis revealed that 34 interferon-stimulated genes (ISGs) were upregulated by greater than 2.5-fold at 8 h post-treatment in both ARPE-19 and MRC-5 cells compared to those of MeWo cells. The depletion of CTSS, GBP4, MX1, IFIT1, IFITM1 and IRF1 by siRNA in IFN-{gamma}-treated cells significantly increased VZV yields. Ectopic overexpression of interferon-induced myxovirus resistance 1 (MX1) or transmembrane protein 1 (IFITM1) significantly reduced VZV yield both in ARPE-19 and MeWo cells. IFITM1 abrogated viral major immediate-early IE62 protein-mediated trans-activation. IFITM1 reduced the level of VZV immediate-early IE62 protein, but not the IE62 mRNA, suggesting that IFITM1 expression reduces the expression level of IE62 by post-transcriptional regulation. Cell-free VZV failed to infect human primary epidermal keratinocytes, in which the basal level of endogenous MX1 gene expression is very high. Pharmacologic inhibition of JAK signaling reduced MX1 expression and enhanced VZV replication in calcium chloride-induced differentiated keratinocytes. Collectively, these findings identify MX1 and IFITM1 as key IFN-{gamma}-induced restriction factors that inhibit VZV replication and suggest that suppression of JAK-STAT signaling can promote VZV replication in differentiated keratinocytes.