Virus Types Research Articles

Burden of Common Respiratory Pathogens Among Cats in China.

Feline respiratory disease complex (FRDC) is a set of illnesses which are primarily associated with different types of viruses and bacteria. There is scarcity of data on pathogens associated with FRDC in China. The primary objective of this study was to investigate the prevalence and dynamics of FRDC pathogens in China. A total of 458 samples were retrieved from veterinary clinics during 2021-2024 from cats suffering from respiratory infections. Four viruses and three bacteria associated with FRDC were targeted for molecular detection with real time qPCR/RT-qPCR assays. At least 1 targeted respiratory pathogen was detected in 423 samples (92.3%), whereas no pathogens were detected in 7.7% of samples. Bacteria were detected in 32.1% of samples, and viruses were detected in 60.2% of samples. The prevalence of viruses detected were feline calicivirus (31.2%), feline herpesvirus-1 (24.6%), influenza A virus (2.8%) and severe acute respiratory syndrome coronavirus-2 (1.5%), whereas the detection rate for bacteria was Mycoplasma felis (15.5%), Chlamydia felis (10.2%) and Bordetella bronchiseptica (6.3%). Significantly higher cases were reported from kittens (57.4%). Pathogen detection was more common during the cold season. Mono-infections involving one bacteria or virus were detected in 44.7% of samples, whereas coinfections were detected in 47.5% of samples. No quadruple coinfections were recorded in this study. The frequency of detection of feline respiratory pathogens alone or in combinations among diseased cats was high, indicating a heavy burden of respiratory infections among cats in Kunshan, China. Continued surveillance is desired, and newly emerged respiratory pathogens should also be monitored in routine diagnostic testing.

Evaluation of Immunochromatographic Test for Rapid Detection of Norovirus, Rotavirus, and Adenovirus in Stool Samples.

Viral enteric infections are illnesses caused by several types of viruses that primarily affect the gastrointestinal system. Globally, three major viruses associated with gastroenteritis, including norovirus (NoV), rotavirus A (RVA), and human adenovirus (HAdV), have been widely recognized. Accordingly, a rapid and sensitive diagnostic tool, such as immunochromatographic (IC) test, for diarrheal virus detection is required and helpful for rapid diagnosis. The IP-Triple I IC test kit for simultaneous triple virus detections of NoV, RVA, and HAdV was evaluated for its efficacy by using stool specimens that were known positive for these viruses by real-time RT-PCR or PCR, which was used as the gold standard method. The results revealed that the IP-Triple I IC test kit exhibited a very high level of specificity (100%) for NoV, RVA, and HAdV detections, while the sensitivity was slightly different for these three viruses. The sensitivity of detection for RVA was 86.7%, whereas those for NoV and HAdV were 70.6% and 76.2%, respectively. This IP-Triple I IC kit could detect common antigens of a wide range of NoV, RVA, and HAdV genotypes (NoV GII.2, GII.4, GII.6, GII.7, GII.10, GII.17, RVA G1P[8], G2P[4], G3P[8], G8P[8], G9P[8], HAdV-C1, -C2, -C5, -A12, -F40, and -F41). Our results revealed that the IP-Triple I IC test kit is highly effective for simultaneous, direct detection of common antigens of several genotypes of NoV, RVA, and HAdV in stool specimens and useful for screening and rapid diagnosis of diarrheal viruses during the seasonal outbreak.

Research progress on environmental stability of SARS-CoV-2 and influenza viruses.

We reviewed research on SARS-CoV-2 and influenza virus detection on surfaces, their persistence under various conditions, and response to disinfectants. Viral contamination in community and healthcare settings was analyzed, emphasizing survival on surfaces influenced by temperature, pH, and material. Findings showed higher concentrations enhance survivability at room temperature, whereas stability increases at 4°C. Both viruses decline in low pH and high heat, with influenza affected by salinity. On various material surfaces, SARS-CoV-2 and influenza viruses demonstrate considerable variations in survival durations, and SARS-CoV-2 is more stable than influenza virus. On the skin, both virus types can persist for ≥2 h. Next, we delineated the virucidal efficacy of disinfectants against SARS-CoV-2 and influenza viruses. In daily life, exposure to ethanol (70%), isopropanol (70%), bleach (10%), or hydrogen peroxide (1-3%) for 15-30 min can effectively inactive various SARS-CoV-2 variants. Povidone-iodine (1 mg/mL, 1 min) or cetylpyridinium chloride (0.1 mg/mL, 2 min) may be used to inactive different SARS-CoV-2 variants in the mouth. Chlorine disinfectants (500 mg/L) or ultraviolet light (222 nm) can effectively inhibit different SARS-CoV-2 variants in public spaces. In conclusion, our study provides a scientific basis and practical guidance for reduction of viral persistence (retention of infectivity) on surfaces and environmental cleanliness.

Beneficial effect of sequential treatment with high-dose steroids and short-course oral glucocorticoids in patients with severe influenza virus-associated pneumonia

Accumulating evidence supports that glucocorticoid treatment for viral pneumonia (VPA) can shorten the disease course and improve survival. However, currently, the use of glucocorticoids in treating VPA remains controversial. Moreover, a unified standard for the dosage and duration of glucocorticoid therapy has not been presented in published articles. A retrospective analysis was conducted in patients who were hospitalized for severe influenza virus-associated pneumonia, and they received sequential treatment with high-dose glucocorticoids and short-course oral glucocorticoids. Patients were followed up for 3 months. A total of 11 patients were included in the study (average age 56 years). There was no gender difference, but age and underlying diseases could be risk factors for severe influenza virus-associated pneumonia. The types of viruses causing pneumonia included influenza A/B. The main clinical symptoms of patients were fever, cough, sputum production, and dyspnea. Chest computed tomography showed multiple ground-glass shadows in the lobes, and the presence of bacterial and fungal infections was accompanied by consolidation shadows. After glucocorticoid therapy, the symptoms improved. None of the patients underwent tracheal intubation, and all survived. After a 3-month follow-up, lung CT absorption in all patients had reached more than 80%, and lung imaging absorption in 20% patients was complete. No serious complications occurred in any of the patients. Sequential treatment with high-dose steroids and short-course oral glucocorticoids may be helpful for reducing the tracheal intubation rate and mortality rate in patients with severe influenza virus-associated pneumonia. Additionally, short-course oral glucocorticoids may reduce pulmonary fibrosis in patients with severe influenza virus-associated pneumonia without any serious complications.

Is There such a Thing as Post-Viral Depression?: Implications for Precision Medicine.

Viral infections are increasingly recognized as triggers for depressive disorders, particularly following the SARS-CoV-2 pandemic and the rise of long COVID. Viruses such as Herpes Simplex Virus (HSV), Epstein-Barr Virus (EBV), Cytomegalovirus (CMV), and Human Immunodeficiency Virus (HIV) are linked to depression through complex neurobiological mechanisms. These include immune system dysregulation, chronic inflammation, and neurotransmitter imbalances that affect brain function and mood regulation. Viral activation of the immune system leads to the release of pro-inflammatory cytokines, resulting in neuroinflammation and associated depressive symptoms. Furthermore, specific viruses can disrupt neurotransmitter systems, including serotonin, dopamine, and glutamate, all of which are essential for mood stabilization. The unique interactions of different viruses with these systems underscore the need for virus-specific therapeutic approaches. Current broad-spectrum treatments often overlook the precise neurobiological pathways involved in post-viral depression, reducing their efficacy. This review emphasizes the need to understand these virus-specific interactions to create tailored interventions that directly address the neurobiological effects induced by each type of virus. These interventions may include immunomodulatory treatments that target persistent inflammation, antiviral therapies to reduce the viral load, or neuroprotective strategies that restore neurotransmitter balance. Precision medicine offers promising avenues for the effective management of virus-induced depression, providing patient-specific approaches that address the specific biological mechanisms involved. By focusing on the development of these targeted treatments, this review aims to pave the way for a new era in psychiatric care that fully addresses the root causes of depression induced by viral infections.

Research Progress on Viruses of Passiflora edulis.

Passiflora edulis, also known as passion fruit, is celebrated for its rich nutritional content, distinctive flavour, and significant medicinal benefits. At present, viral diseases pose a major challenge to the passion fruit industry, affecting both the production and quality of the fruit. These diseases impede the sustainable and healthy growth of the passion fruit sector. In recent years, with the expansion of P. edulis cultivation areas, virus mutations, and advances in virus detection technology, an increasing number of virus species infecting P. edulis have been discovered. To date, more than 40 different virus species have been identified; however, there are different strains within the same virus. This poses a challenge for the control and prevention of P. edulis virus disease. Therefore, this review discusses the different types of viruses and their characteristics, modes of transmission, and effects on the growth of the passion fruit plant, as well as the mechanisms of virus generation and preventive measures, with the hope that these discussions will provide a comprehensive understanding of and countermeasures for viruses in passion fruit.

Application of Markov Chains and Artificial Neural Networks in the prediction of Hepatitis Cases in the southern states of Brazil

Viral hepatitis is a disease caused by five known types of virus and can be chronic or acute. This study collected historical data on hepatitis in the southern states of Brazil and applied Markov Chains as an input parameter for predicting cases, using Artificial Neural Networks (ANN). A comparison was then made between the method that includes the two methodologies and the prediction made by ANN using only the data from the historical series. The mean absolute error (MAE) and mean absolute percentage error (MAPE) were calculated to determine the best forecasting model for each state. It was not possible to determine a configuration that simultaneously presented the best MAE and MAPE values for each state, but it was found that the lowest errors were obtained by using Markov Chains as an information generator for the ANN models, with a MAPE of 4.45% using the Levenberg-Marquardt training algorithm, with a delay equal to 3 and a number of neurons equal to 60.

Molecular epidemiology and vaccine compatibility analysis of seasonal influenza A viruses in the context of COVID-19 epidemic in Wuhan, China.

The COVID-19 pandemic had a significant impact on the global influenza vaccination and the epidemics of seasonal influenza. To further explore the molecular epidemiology of influenza viruses and assess vaccine effectiveness, we collected influenza cases in Wuhan during the 2022-2023 influenza season. Among 1312 clinical samples, 312 samples tested positive for influenza viruses using reverse transcription polymerase chain reaction. These positive samples included 146A/H1N1 subtypes (46.8%), 164A/H3N2 subtypes (52.6%) and 2 influenza B virus types (0.6%). Based on the whole genome sequence information of hemagglutinin (HA) and neuraminidase (NA) from 27A/H1N1 influenza virus strains and 26A/H3N2 influenza virus strains obtained in this study, a phylogenetic analysis was conducted. The analysis revealed that all A/H1N1 strains belonged to the evolutionary branch 6B.1A.5a.2a, and they exhibited specific substitutions at positions K71Q, Q206E, E241A, and R276K. Similarly, all A/H3N2 strains were classified into the 3C.2a1b.2a.1a subclade and displayed amino acid substitutions at positions S172H, N175Y, I176T, K187N, and S214P. Notably, the A/H3N2 strains also acquired a new potential glycosylation site at position N174. Using an epitope model, the predicted vaccine effectiveness was assessed for the A/H1N1 and A/H3N2 strains. The predicted vaccine effectiveness against the Wuhan influenza epidemic strain was over 85% for the A/H1N1 vaccine strain. However, the effectiveness against the A/H3N2 vaccine strain was only 48.7%. To further verify the protection of influenza vaccine against circulating influenza viruses in the region, we conducted in vivo and in vitro animal studies. The results of in vitro neutralization experiment showed that rabbit serum antibodies inoculated with quadrivalent isolated influenza vaccine had neutralization ability against all 24 isolated influenza viruses. In vivo experiments showed that vaccinated mice had fewer lung lesions when infected with the influenza strain circulating in Wuhan, suggesting that vaccination can effectively reduce the occurrence of severe lung damage. These findings emphasize the importance of accurately predicting seasonal influenza strains for effective influenza prevention and control, especially during the co-circulation of SARS-CoV-2 and influenza viruses. This study provides valuable information on the seasonal influenza virus in Wuhan during the COVID-19 pandemic and serves as a basis for vaccine prediction and updates.

Antiviral Activity of Carbon Dots: Strategies and Mechanisms of Action

The COVID‐19 pandemic profoundly changes the perception of the impact of viral diseases on society and the consequent need to develop new and more effective technologies in vaccines and antivirals. Thus, research in the field of antivirals has received a new and strong impetus by considering new approaches and innovative methodologies. One example has been the numerous published studies on antiviral nanosystems developed from nanoparticles, among the most promising of which are carbon dots (C‐dots). C‐dots are effective antivirals due to multiple mechanisms of action. They are also, in general, water‐soluble and noncytotoxic. However, the data reported in the literature are still fragmented and cover different families of viruses and types of C‐dots. Therefore, a comparative study is needed to identify possible strategies for designing C‐dots with antiviral activity. This article aims to provide a comparative and critical analysis of the published data on C‐dots and their antiviral properties against various types of viruses. By exploring the relationship between the composition and properties of C‐dots, this article aims to shed light on the mechanism of their antiviral activity. The review has highlighted the potential of C‐dots as antiviral agents and would serve as a basis for further research in this field.

VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.

RNA viruses are ubiquitous across a broad spectrum of ecosystems. Therefore, beyond their significant implications for public health, RNA viruses are also key players in ecological processes. High-through sequencing has accelerated the discovery of RNA viruses. Nevertheless, many of these viruses lack taxonomic annotation, posing a challenge to functional inference and evolutionary study. In particular, virus classification at the genus level remains difficult due to the limited reference data and ambiguous boundaries between some closely related genera. We introduce VirTAXA, a robust classification tool that combines remote homology search and tree-based validation to enhance the genus-level taxonomic classification of RNA viruses. VirTAXA is able to predict the genus label of an assembled viral contig and provide evidence type for each prediction. It achieves comparable accuracy to state-of-the-art methods while assigning genus labels to a greater number of sequences. Specifically, on the Global Ocean RNA metatranscriptomic data, VirTAXA can assign genus labels for 18% more contigs than the second-best classification tool. Furthermore, we demonstrated that VirTAXA can be conveniently extended to other types of viruses. The source code and data of VirTAXA are available via https://github.com/JudithEllyn/VirTAXA.

The phenomenon of viral chromosomal integration

The literature review is devoted to the chromosomally integrating viruses, the integration property. These are revealed using modern diagnostic methods, including highthroughput sequencing. The review describes various types of viruses, such as retroviruses, adenoviruses, herpes viruses, papillomaviruses, hepatitis B, SARS-CoV-2 and others. These viruses have the ability to integrate their genomes into the host cell genomes and their prevalence. Modern information on the molecular mechanisms of viral integration and methods of differential diagnostics is presented. Each of these viruses has its own unique ways of interacting with the host cell genome to maintain a latent state, which determines the specifics of the infectious process and pathological consequences for the body due to the possibility of effective reactivation.

Penyuluhan Kesehatan tentang Kanker Serviks pada Wanita Usia Subur (WUS) di Desa Kertawinangun Kecamatan Kedawung Kabupaten Cirebon

Cervical cancer is a primary malignant tumor originating from squamous epithelial cells or cells originating from the vagina and urethra, usually occurring in the cervix or cervix which is located between the uterus and the sexual canal (vagina). According to WHO 2018, cervical cancer is the fourth leading cause of death in women throughout the world, estimated at 570,000, while new cases in 2018 or 6.6% of all cancers in women. Human papilloma virus or commonly called (HPV) is known to cause cervical cancer which can be transmitted through sexual intercourse, infection with several types of viruses, and personal hygiene. Symptoms of cervical cancer can be recognized by the presence of fluid from the birth canal, namely abnormal vaginal discharge, contact bleeding (bleeding during intercourse), and feeling pain during coitus / sexual intercourse as well as bleeding even after entering menopause. Early symptoms of pre-cancerous conditions are generally characterized by the discovery of abnormal cells. These abnormal cells develop into cervical cancer and then the following symptoms of cervical cancer appear; the appearance of pain and bleeding during sexual intercourse (contact bleeding), abnormal vaginal bleeding, such as bleeding outside the menstrual cycle, bleeding between regular menstrual periods, menstrual periods that are longer and more abundant than usual, bleeding after menopause, vaginal discharge excessive and abnormal, if the cancer has spread to the pelvis, the patient will suffer from complaints of pelvic pain, difficulty urinating, and enlarged kidneys. Cervical cancer can be prevented 100% by HPV vaccination, using condoms, avoiding tobacco consumption, and early detection and treatment of precancerous lesions.

Viral infections in etiology of mental disorders: a broad analysis of cytokine profile similarities - a narrative review.

The recent pandemic caused by the SARS-CoV-2 virus and the associated mental health complications have renewed scholarly interest in the relationship between viral infections and the development of mental illnesses, a topic that was extensively discussed in the previous century in the context of other viruses, such as influenza. The most probable and analyzable mechanism through which viruses influence the onset of mental illnesses is the inflammation they provoke. Both infections and mental illnesses share a common characteristic: an imbalance in inflammatory factors. In this study, we sought to analyze and compare cytokine profiles in individuals infected with viruses and those suffering from mental illnesses. The objective was to determine whether specific viral diseases can increase the risk of specific mental disorders and whether this risk can be predicted based on the cytokine profile of the viral disease. To this end, we reviewed existing literature, constructed cytokine profiles for various mental and viral diseases, and conducted comparative analyses. The collected data indicate that the risk of developing a specific mental illness cannot be determined solely based on cytokine profiles. However, it was observed that the combination of IL-8 and IL-10 is frequently associated with psychotic symptoms. Therefore, to assess the risk of mental disorders in infected patients, it is imperative to consider the type of virus, the mental complications commonly associated with it, the predominant cytokines to evaluate the risk of psychotic symptoms, and additional patient-specific risk factors.

Virus and viral components transmitted through surgical smoke; a silent danger in operating room: a systematic review

BackgroundDuring surgical procedures, heat-generating devices are widely used producing surgical smoke (SS). Since the SS can transmit infectious viruses, this systematic review was designed to investigate the potential viruses transmitted through SS.MethodsPubMed, Scopus, Web of Science, ProQuest, and Embase databases, along with Cochran Library, and Google Scholar search engine were searched systematically (by April 21, 2024). No language, place, and time restrictions were considered. All studies evaluating the SS and virus transmission, and whole investigations regarding the viral infections transmitted through SS were totally considered inclusion criteria. Besides, non-original, qualitative, case reports, case series, letters to the editor, editorial, and review studies were excluded from the analysis. This study was conducted in accordance with the PRISMA 2020 statement.ResultsTwenty-six eligible studies were selected and reviewed for data extraction. The results showed that the SS contains virus and associated components. Six types of viruses or viral components were identified in SS including papillomavirus (HPV, BPV), Human Immunodeficiency Virus (HIV), varicella zoster, Hepatitis B (HBV), SARS-CoV-2, and Oral poliovirus (OPV), which are spread to surgical team through smoke-producing devices.ConclusionsSince the studies confirm the presence of viruses, and viral components in SS, the potential risk to the healthcare workers, especially in operating room (OR), seems possible. Thus, the adoption of protective strategies against SS is critical. Despite the use of personal protective equipment (PPE), these viruses could affect OR personnel in surgical procedures.

The early communication stages between serine proteases and enterovirus capsids in the race for viral disintegration

Serine proteases are important environmental contributors of enterovirus biocontrol. However, the structural features of molecular interaction accounting for the susceptibility of enteroviruses to proteases remains unexplained. Here, we describe the molecular mechanisms involved in the recruitment of serine proteases to viral capsids. Among the virus types used, coxsackievirus A9 (CVA9), but not CVB5 and echovirus 11 (E11), was inactivated by Subtilisin A in a host-independent manner, while Bovine Pancreatic Trypsin (BPT) only reduced CVA9 infectivity in a host-dependent manner. Predictive interaction models of each protease with capsid protomers indicate the main targets as internal disordered protein (IDP) segments exposed either on the 5-fold vertex (DE loop VP1) or at the 5/2-fold intersection (C-terminal end VP1) of viral capsids. We further show that a functional binding protease/capsid depends on both the strength and the evolution over time of protease-VP1 complexes, and lastly on the local adaptation of proteases on surrounding viral regions. Finally, we predicted three residues on CVA9 capsid that trigger cleavage by Subtilisin A, one of which may act as a sensor residue contributing to enzyme recognition on the DE loop. Overall, this study describes an important biological mechanism involved in enteroviruses biocontrol.

Amino Acids at Positions 156 and 332 in the E Protein of the West Nile Virus Subtype Kunjin Virus Classical Strain OR393 Are Involved in Plaque Size, Growth, and Pathogenicity in Mice.

The West Nile virus (WNV) subtype Kunjin virus (WNVKUN) is endemic to Australia. Here, we characterized the classical WNVKUN strain, OR393. The original OR393 strain contained two types of viruses: small plaque-forming virus (SP) and large plaque-forming virus (LP). The amino acid residues at positions 156 and 332 in the E protein (E156 and E332) of SP were Ser and Lys (E156S/332K), respectively, whereas those in LP were Phe and Thr (E156F/332T). SP grew slightly faster than LP in vitro. The E protein of SP was N-glycosylated, whereas that of LP was not. Analysis using two recombinant single-mutant LP viruses, rKUNV-LP-EF156S and rKUNV-LP-ET332K, indicated that E156S enlarged plaques formed by LP, but E332K potently reduced them, regardless of the amino acid at E156. rKUNV-LP-EF156S showed significantly higher neuroinvasive ability than LP, SP, and rKUNV-LP-ET332K. Our results indicate that the low-pathogenic classical WNVKUN can easily change its pathogenicity through only a few amino acid substitutions in the E protein. It was also found that Phe at E156 of the rKUNV-LP-ET332K was easily changed to Ser during replication in vitro and in vivo, suggesting that E156S is advantageous for the propagation of WNVKUN in mammalian cells.

Sequence-specific nanoparticle barcode strategy for multiplex human enterovirus typing

Human enteroviruses (HEV) can cause a range of diseases from mild to potentially life-threatening. Identification and genotyping of HEV are crucial for disease management. Existing typing methods, however, have inherent limitations. Developing alternative methods to detect HEV with more virus types, high accuracy, and sensitivity in an accessible manner presents a technological and analytical challenge. Here, a sequence-specific nanoparticle barcode (SSNB) method is presented for simultaneous detection of 10 HEV types. This method significantly increases sensitivity, enhancing detection by 10-106 times over the traditional multiplex hybrid genotyping (MHG) method, by resolving cross-interference between the multiple primer sets. Furthermore, the SSNB method demonstrates a 100% specificity in accurately distinguishing between 10 different HEV types and other prevalent clinical viruses. In an analysis of 70 clinical throat swab samples, the SSNB method shows slightly higher detection rate for positive samples (50%) compared to the RT-PCR method (48.6%). Additionally, further assessment of the typing accuracy for samples identified as positive by SSNB using sequencing method reveals a concordance rate of 100%. The combined high sensitivity and specificity level of the methodology, together with the capability for multiple type analysis and compatibility with clinical workflow, make this approach a promising tool for clinical settings.

Implementasi Tangga Dramatik Dalam Dokumenter “Dua Sisi” Edisi “Kami Dan Rumah Singgah Kebaya”

HIV or Human Immunodeficiency Virus is a type of virus that infects white blood cells which causes a decrease in human immunity. It had established a Rumah Singgah Kebaya. It is a non-governmental organization (NGO) in Yogyakarta that cares to HIV/AIDS patient. The NGO presents as a transgender empowerment center that provides shelter and assistance for People with HIV/AIDS (ODHA). In order to make visual documentary of the NGO, it was decided to create a television documentary program entitled "Dua Sisi" Edition of "Kami dan Rumah Singgah Kebaya". The methods used in the creation of this television documentary work are research methods, field observations, interviews with source persons, as well as television documentaries. This documentary applies the four stages of Aristotle's dramatic structure and to attract the attention of the audience through the dramatics implemented in the script so it is not monotonous. The dramatic structure has four stages as follows: Protasis Stage, Epitasio Stage, Catastasis Stage, and Catastrophe Stage. The type of this documentary work is a portrait documentary and its duration is about 22 minutes 35 seconds. Based on the analysis, it can be concluded that the dramatic structure is successfully implemented in the creation of this television documentary “Dua Sisi” Edisi “Kami dan Rumah Singgah Kebaya”.

Genetic diversity and population structure of grapevine Roditis leaf discoloration‐associated virus in Turkey vineyards

AbstractGrapevine Roditis leaf discoloration‐associated virus (GRLDaV) is a type of virus that infects grapevines. This research aimed to determine the prevalence of GRLDaV in Turkey vineyards and investigate the genetic diversity and population structure of the selected viral isolates from Turkey compared to isolates from other countries. In this study, 800 shoot samples from Turkey vineyards were collected in late spring and autumn from different regions. The samples were analysed by RT‐PCR targeting the partial RNaseH‐like gene region of the virus genome. The overall prevalence of GRLDaV was 8.1% among the samples. Phylogenetic analysis of the GRLDaV genome showed that the GRLDaV isolates were clustered into two major lineages. The nucleotide diversity (π) value of Group I, including only Mediterranean isolates, was lower than Group II, suggesting little variation among isolates. Even though π values were low among the geographical regions in Turkey, the region with the highest nucleotide diversity was the Aegean population, followed by the Eastern and Mediterranean populations. Comparison between nonsynonymous and synonymous substitutions showed that negative selection acts on synonymous amino acids. Along with neutrality tests and gene flow analyses, it was emphasized that genetic drift played an important role in shaping the GRLDaV populations. This study provides important information on the prevalence and genetic diversity of GRLDaV in Turkey vineyards. The findings will help to develop better strategies to manage and control this virus, which can cause significant economic losses in grape industries.

A comparative analysis of RNA-Seq and NanoString technologies in deciphering viral infection response in upper airway lung organoids.

In this study, we delved into the comparative analysis of gene expression data across RNA-Seq and NanoString platforms. While RNA-Seq covered 19,671 genes and NanoString targeted 773 genes associated with immune responses to viruses, our primary focus was on the 754 genes found in both platforms. Our experiment involved 16 different infection conditions, with samples derived from 3D airway organ-tissue equivalents subjected to three virus types, influenza A virus (IAV), human metapneumovirus (MPV), and parainfluenza virus 3 (PIV3). Post-infection measurements, after UV (inactive virus) and Non-UV (active virus) treatments, were recorded at 24-h and 72-h intervals. Including untreated and Mock-infected OTEs as control groups enabled differentiating changes induced by the virus from those arising due to procedural elements. Through a series of methodological approaches (including Spearman correlation, Distance correlation, Bland-Altman analysis, Generalized Linear Models Huber regression, the Magnitude-Altitude Score (MAS) algorithm and Gene Ontology analysis) the study meticulously contrasted RNA-Seq and NanoString datasets. The Magnitude-Altitude Score algorithm, which integrates both the amplitude of gene expression changes (magnitude) and their statistical relevance (altitude), offers a comprehensive tool for prioritizing genes based on their differential expression profiles in specific viral infection conditions. We observed a strong congruence between the platforms, especially in identifying key antiviral defense genes. Both platforms consistently highlighted genes including ISG15, MX1, RSAD2, and members of the OAS family (OAS1, OAS2, OAS3). The IFIT proteins (IFIT1, IFIT2, IFIT3) were emphasized for their crucial role in counteracting viral replication by both platforms. Additionally, CXCL10 and CXCL11 were pinpointed, shedding light on the organ tissue equivalent's innate immune response to viral infections. While both platforms provided invaluable insights into the genetic landscape of organoids under viral infection, the NanoString platform often presented a more detailed picture in situations where RNA-Seq signals were more subtle. The combined data from both platforms emphasize their joint value in advancing our understanding of viral impacts on lung organoids.