1 Post-pandemic Distribution Patterns of Respiratory Pathogens in Erzurum, Turkey: A Retrospective Analysis https://brieflands.com/journals/jjm/articles/169542 10.5812/jjm-169542 1 Background :This study aimed to investigate post-coronavirus disease 2019 (COVID-19) distribution patterns of respiratory pathogens using data from a tertiary care center in Erzurum, Turkey. Objectives :This study evaluated the post-pandemic distribution patterns of viral and bacterial respiratory pathogens detected by multiplex real-time polymerase chain reaction and described their associations with age, sex, and seasonal variation in patients with acute respiratory tract infections. Methods :This retrospective study analyzed respiratory samples submitted to Erzurum City Hospital between 2024 and 2025 for suspected acute respiratory tract infection. Pathogens were identified using a multiplex reverse transcription quantitative polymerase chain reaction panel targeting 15 viral and 5 bacterial agents and were analyzed according to age, sex, and season. A P-value < 0.05 was considered statistically significant. Results :A total of 3197 samples were analyzed. The median age was 6 years (interquartile range, 2 - 20 years), and 55.9% of the patients were male. Most samples were collected in winter. Respiratory syncytial virus (RSV) was the most commonly detected viral pathogen, followed by severe acute respiratory syndrome coronavirus 2 and influenza A virus. Streptococcus pneumoniae and Haemophilus influenzae were the predominant bacterial agents. Coinfections were observed mainly in children younger than 10 years, whereas adults more frequently had negative results and lower pathogen diversity. Respiratory syncytial virus, adenovirus, bocavirus, H. influenzae, Bordetella pertussis, and S. pneumoniae were associated with younger age (P < 0.05), whereas coronavirus NL63 was associated with older age (P < 0.001). Seasonal patterns showed that RSV and influenza A virus peaked in winter, influenza B virus peaked in spring, and severe acute respiratory syndrome coronavirus 2 was more prevalent in summer and autumn (P < 0.001). Conclusions :These findings demonstrate the re-emergence of RSV and influenza viruses, whereas severe acute respiratory syndrome coronavirus 2 circulation has shifted to lower levels. Bacterial detection by multiplex polymerase chain reaction requires cautious clinical interpretation. These data may inform diagnostic strategies and rational test use in acute respiratory tract infections. 1 9 Hacı Ahmet Aydemir Department of Family Medicine, Erzurum Faculty of Medicine, Health Sciences University, Erzurum, Turkey Turkey haciahmet.aydemir@sbu.edu.tr Aslan Mehtap Hülya Department of Microbiology, Erzurum Faculty of Medicine, Health Sciences University, Erzurum, Turkey Turkey hulya_mehtab@hotmail.com Abdulkadir Alğan Health and Ageing Centre, Balıkesir State Hospital, Balıkesir, Turkey Turkey dr.algan@hotmail.com No Keyword 1.pdf [0]José RJ.Respiratory infections: A global burden. Ann Res Hospitals. 2018;2:12. doi: 10.21037/arh.2018.09.01.##[1]Calderaro A, Buttrini M, Farina B, Montecchini S, De Conto F, Chezzi C.Respiratory Tract infections and laboratory diagnostic methods: A review with a focus on syndromic panel-based assays. Microorganisms. 2022;10(9). [PubMed ID: 36144458]. 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[PubMed Central ID: PMC11697200]. doi: 10.1038/s41598-024-84586-8.##[6]Dimaka K, Karampatakis T, Kachrimanidou M, Katsifa H, Exindari M.Epidemiology of bacterial respiratory tract infections during the pre-pandemic, COVID-19 pandemic and post-pandemic era: A retrospective study of hospitalized adults in northern Greece between 2018 and 2023. Diagn Microbiol Infect Dis. 2025;111(3):116710. [PubMed ID: 39892369]. doi: 10.1016/j.diagmicrobio.2025.116710.##[7]Jin Q, Yu S, Qu J.Epidemiological characteristics of respiratory tract infections during and after the pandemic of COVID-19 from 2021 - 2023 in Shenzhen, southern China. BMC Public Health. 2025;25(1):1724. [PubMed ID: 40346486]. [PubMed Central ID: PMC12063367]. doi: 10.1186/s12889-025-22884-0.##[8]Uğur M, Şahin AM.Distribution of Pathogens of Respiratory Tract Infections By Months and Age Groups. 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1 HTLV-1 Tax Transcriptionally Activates HMGB1 and Links Glycolytic Reprogramming to Immune-Evasion Phenotypes in Adult T-Cell Leukemia/Lymphoma https://brieflands.com/journals/jjm/articles/171048 10.5812/jjm-171048 1 Background :Adult T-cell leukemia/lymphoma (ATLL) is a human T-cell leukemia virus type 1 (HTLV-1)-associated T-cell malignancy marked by metabolic remodeling and immune escape. Whether the viral transactivator Tax directly engages host transcriptional regulators that connect these processes remains unclear. Objectives :This study tested whether Tax transcriptionally activates high mobility group box 1 (HMGB1) and whether the Tax-HMGB1 axis is associated with glycolytic and immune-evasion phenotypes in ATLL. Methods :Public Gene Expression Omnibus (GEO) cohorts were analyzed within cohort after dataset-specific preprocessing, probe-to-gene collapsing, and standardized signature scoring. Patient-cohort findings were interpreted as associations, whereas mechanistic ordering was examined in a Tax-inducible T-cell model by HMGB1 promoter luciferase assays, chromatin immunoprecipitation quantitative polymerase chain reaction (ChIP-qPCR), small interfering RNA (siRNA) knockdown/rescue, extracellular acidification rate (ECAR), lactate and glucose-uptake assays, flow cytometry, and donor-matched cytotoxic co-culture. Results :In ATLL samples, HMGB1 expression and predefined glycolysis and immune-inhibitory signature scores were higher than in normal CD4+ T-cell controls. Within ATLL, HMGB1 expression was positively associated with both scores and with programmed death-ligand 1 (PD-L1; CD274). Tax induction in a switch model increased HMGB1 expression together with glycolytic and checkpoint-related programs. In mechanistic assays, Tax increased HMGB1 promoter activity and enriched the HMGB1 promoter interval -1163 to -975 in ChIP-qPCR, whereas mutation of a C/EBP-like motif blunted reporter responsiveness. HMGB1 knockdown reduced lactate, ECAR, glucose uptake, PD-L1 and Galectin-9 surface expression, and resistance to cytotoxic killing; HMGB1 re-expression partially restored metabolic output. Lactate inhibition and PD-L1 blockade each partially rescued cytotoxic killing in donor-matched co-cultures. Conclusions :The experimental data support direct transcriptional activation of HMGB1 by Tax and place HMGB1 upstream of a lactate-associated immune-evasion phenotype in ATLL models. The public patient datasets provide complementary associative support but do not by themselves establish causality or resolve contributions from extracellular HMGB1 and tumor microenvironmental composition. 1 10 Ruoting Lin Department of Neurology, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, Fujian, China China rt-ling@163.com Shuang Zhou Department of Laboratory Medicine, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, Fujian, China China mxxhappygirl@163.com Hongzhi Gao Department of Neurosurgery, Clinic Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, Fujian, China China 13559040780@163.com Ruoteng Xie Department of Laboratory Medicine, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, Fujian, China China 13358597699@163.com No Keyword 2.pdf [0]El Hajj H, Bazarbachi A.Interplay between innate immunity and the viral oncoproteins Tax and HBZ in the pathogenesis and therapeutic response of HTLV-1 associated adult T cell leukemia. Frontiers in Immunology. 2022;13. 957535. [PubMed ID: 35935975]. [PubMed Central ID: PMC9352851]. doi: 10.3389/fimmu.2022.957535.##[1]Bellon M, Nicot C.HTLV-1 Tax Tug-of-War: Cellular Senescence and Death or Cellular Transformation. Pathogens. 2024;13(1):87. [PubMed ID: 38276160]. [PubMed Central ID: PMC10820833]. doi: 10.3390/pathogens13010087.##[2]Hleihel R, Skayneh H, de Thé H, Hermine O, Bazarbachi A.Primary cells from patients with adult T cell leukemia/lymphoma depend on HTLV-1 Tax expression for NF-κB activation and survival. Blood Cancer Journal. 2023;13(1):67. [PubMed ID: 37137914]. [PubMed Central ID: PMC10156663]. doi: 10.1038/s41408-023-00841-7.##[3]Shirasawa M, Nakajima R, Zhou Y, Fikriyanti M, Iwanaga R, Bradford A.Transcriptional Activation Mechanisms and Target Genes of the Oncogene Product Tax of Human T-Cell Leukemia Virus Type 1. Genes. 2025;16(10):1221. [PubMed ID: 41153438]. [PubMed Central ID: PMC12564054]. doi: 10.3390/genes16101221.##[4]Huang L, Chen X, Yan M, Xiang Z, Wu J.Lactate and lactylation in breast cancer: current understanding and therapeutic opportunities. Cancer Biol Med. 2025;22(7):789-805. [PubMed ID: 40671416]. [PubMed Central ID: PMC12302272]. doi: 10.20892/j.issn.2095-3941.2025.0173.##[5]Hubert P, Roncarati P, Demoulin S.Extracellular HMGB1 blockade inhibits tumor growth through profoundly remodeling immune microenvironment and enhances checkpoint inhibitor-based immunotherapy. Journal for Immunotherapy of Cancer. 2021;9(3). e001966. [PubMed ID: 33712445]. [PubMed Central ID: PMC7959241]. doi: 10.1136/jitc-2020-001966.##[6]Joo E, Bae J, Park J, Bang Y, Han J, Gulati N.Deconvolution of Adult T-Cell Leukemia/Lymphoma With Single-Cell RNA-Seq Using Frozen Archived Skin Tissue Reveals New Subset of Cancer-Associated Fibroblast. Frontiers in Immunology. 2022;13. 856363. [PubMed ID: 35464471]. [PubMed Central ID: PMC9021607]. doi: 10.3389/fimmu.2022.856363.##[7]Jalili-Nik M, Soltani A, Mashkani B, Rafatpanah H, Hashemy S.PD-1 and PD-L1 inhibitors foster the progression of adult T-cell Leukemia/Lymphoma. International Immunopharmacology. 2021;98. 107870. [PubMed ID: 34153661]. doi: 10.1016/j.intimp.2021.107870.##[8]Chiba M, Shimono J, Suto K.Whole-genome CRISPR screening identifies molecular mechanisms of PD-L1 expression in adult T-cell leukemia/lymphoma. Blood. 2024;143(14):1379-1390. [PubMed ID: 38142436]. [PubMed Central ID: PMC11033594]. doi: 10.1182/blood.2023021423.##[9]Chen Y, McCarthy D, Ritchie M.edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. Nucleic Acids Research. 2025;53(2). gkaf018. [PubMed ID: 39844453]. [PubMed Central ID: PMC11754124]. doi: 10.1093/nar/gkaf018.##

1 Development and Analytical Evaluation of a Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Seasonal Influenza A Virus Detection https://brieflands.com/journals/jjm/articles/169890 10.5812/jjm-169890 1 Background :Seasonal influenza A virus (IAV) continues to pose a substantial global health threat because of its high mutation rate, widespread prevalence, and the ongoing challenge of timely detection, particularly in resource-limited settings. Objectives :To address this gap, we developed and analytically evaluated a novel colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid, sensitive, and visually interpretable detection of seasonal IAV. Methods :Ten reported LAMP primer sets previously reported were initially screened for amplification efficiency using certified reference RNA materials from H1N1 and H3N2 as templates. Analytical sensitivity was assessed using serial dilutions of quantified RNA standards, and specificity was rigorously evaluated through both in silico analysis and experimental testing with a panel of common respiratory pathogens. Results :Sensitivity analyses based on triplicate serial dilution testing revealed preliminary limits of detection as low as 67 copies per reaction for H1N1 and 42 copies per reaction for H3N2, with performance matching or exceeding that reported in previous LAMP-based studies. No cross-reactivity with other respiratory pathogens was observed, confirming the high specificity of the assay. The assay targets the conserved matrix protein gene and detects IAV broadly; however, it does not differentiate between the H1N1 and H3N2 subtypes in a single reaction. Notably, incorporation of hydroxy naphthol blue (HNB) enabled direct visual detection via a distinct color change from violet to sky blue within 45 minutes under isothermal conditions, thereby eliminating the need for advanced instrumentation. Conclusions :The assay demonstrated high sensitivity and specificity, supporting future clinical validation studies to establish its utility for point-of-care testing (POCT) deployment. 1 9 Muhammed Jobarteh Anhui Province Clinical Research Center for Critical Respiratory Medicine, Wuhu, Anhui, China Department of Medical Microbiology and Immunology, Wannan Medical University, Wuhu, Anhui, China China China muhammedjobarteh24@gmail.com Qiancheng Xu Anhui Province Clinical Research Center for Critical Respiratory Medicine, Wuhu, Anhui, China Department of Critical Care Medicine, The First Affiliated Hospital of Wannan Medical University (Yijishan Hospital of Wannan Medical University), Wuhu, Anhui, China China China xu871011@126.com Wanyue Yu School of Clinical Medicine, Wannan Medical University, Wuhu, Anhui, China China 2261355263@qq.com Yujun Shuai Department of Parasitology, Wannan Medical University, Wuhu, Anhui, China China 1312713480@qq.com Zihe Shi Department of Medical Microbiology and Immunology, Wannan Medical University, Wuhu, Anhui, China China txsh330@163.com Leyi Wang School of Anesthesiology, Wannan Medical University, Wuhu, Anhui, China China 2929423765@qq.com Youkang Zhang School of Public Health, Wannan Medical University, Wuhu, Anhui, China China zyk4836503@163.com Xinkang Wang School of Clinical Medicine, Wannan Medical University, Wuhu, Anhui, China China 2593893649@qq.com Jinhong Zhao Department of Parasitology, Wannan Medical University, Wuhu, Anhui, China China zhaojh@wnmc.edu.cn Weihua Lu Anhui Province Clinical Research Center for Critical Respiratory Medicine, Wuhu, Anhui, China Department of Critical Care Medicine, The First Affiliated Hospital of Wannan Medical University (Yijishan Hospital of Wannan Medical University), Wuhu, Anhui, China China China lwh683@126.com Zhu Yang Department of Medical Microbiology and Immunology, Wannan Medical University, Wuhu, Anhui, China China zhuyang@wnmc.edu.cn No Keyword 3.pdf [0]Paules C, Subbarao K.Influenza. 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[PubMed Central ID: PMC9558625]. doi: 10.7717/peerj.14121.##[8]Goto M, Honda E, Ogura A, Nomoto A, Hanaki KI.Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue. Biotechniques. 2009;46(3):167-72. [PubMed ID: 19317660]. doi: 10.2144/000113072.##[9]Chen N, Si Y, Li G, Zong M, Zhang W, Ye Y, et al.Development of a loop-mediated isothermal amplification assay for the rapid detection of six common respiratory viruses. Eur J Clin Microbiol Infect Dis. 2021;40(12):2525-32. [PubMed ID: 34264402]. [PubMed Central ID: PMC8280575]. doi: 10.1007/s10096-021-04300-8.##[10]Song M, Hong S, Lee LP.Multiplexed ultrasensitive sample-to-answer RT-LAMP chip for the identification of SARS-CoV-2 and influenza viruses. Adv Mater. 2023;35(10). e2207138. 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1 Evaluation of Humoral Immunity Induced by Commonly Administered COVID-19 Vaccines in Middle-aged Iranians https://brieflands.com/journals/jjm/articles/166803 10.5812/jjm-166803 1 Background :Using a comparative analysis and assessment approach on a number of vaccine under investigation in a specific group is pertinent to local health policy and to our scientific understanding of vaccine responses. Objectives :In this double-blind, cross-sectional study, the efficacy of two platforms inactivated COVID-19 vaccines (CO-Iran Barekat and Sinopharm) and adenoviral-vector COVID-19 vaccines (AstraZeneca and Sputnik V) most commonly used in the Iranian population was evaluated. The target population was 40 - 60 years old. Humoral immune response evaluated by the production of virus-neutralizing antibodies and immunoglobulin G binding to the receptor-binding domain (RBD). Methods :Four hundred twenty volunteers aged 40 - 60 years were vaccinated with the COVID-19 vaccines including CO-Iran Barekat, Sinopharm, AstraZeneca and Sputnik. After receiving the second dose, the humoral immune response was assessed using a conventional neutralizing antibody assay and IgG ELISA. Results :Recipients of the Barekat and Sinopharm vaccines had negative IgG responses of ~15.3% and ~32.97% respectively, while a negative IgG response in the Sputnik V vaccine group showed 10.58%. No negative IgG response was noted with the AstraZeneca group. In the neutralizing antibody assay against SARS-CoV-2, AstraZeneca, Sputnik V, COV-Iran Barekat and Sinopharm showed effective protection in 87.73%, 59.61%, 54.23% and 35.16% respectively. The S1-IgG and SARS-CoV-2 neutralization responses found with Sinopharm and COV-Iran Barekat were similar to those seen vaccinated individuals. In contrast, the conventional live-virus neutralization titer (cVNT50) in SARS-CoV-2-AstraZeneca vaccines was much higher than any of the other three groups. Also data analysis of adverse vaccine event revealed that injection site pain is the most common adverse event in the four groups. Conclusions :The highest levels of neutralizing antibodies were found with AstraZeneca that further support its higher effective potential for protection to SARS-CoV-2. Antibody levels were measured with ELISA IgG Kits and a conventional neutralizing antibody assay technique. 1 10 Reza Jafari School of Allied Medical Sciences, Shahroud University of Medical Sciences, Shahroud, Iran Iran jafari.r@shmu.ac.ir Ashraf Mohammadi Department of Human Viral Vaccines, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran Iran amohammadi43@gmail.com Behnam Alirezaie Department of Human Viral Vaccines, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran Iran b.alirezaie@rvsri.ac.ir Raza Shahbazi Department of Human Viral Vaccines, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran Iran r.shahbazi@rvsri.ac.ir Mohammad Hassan Emamian Shahroud University of Medical Sciences, Shahroud, Iran Iran emamian@shmu.ac.ir No Keyword 4.pdf [0]Parums DV.Revised World Health Organization (WHO) terminology for variants of concern and variants of interest of SARS-CoV-2. 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