Viral Nucleic Acid Research Articles

Evaluation of a concentration method for the recovery of human adenovirus from mineral water, tap water and well water.

Evaluation of a concentration method for the recovery of human adenovirus from mineral water, tap water and well water.

Detection and prevalence of avian influenza epidemic in the southwest of Poyang Lake and analysis of the influence of meteorological factors.

Detection and prevalence of avian influenza epidemic in the southwest of Poyang Lake and analysis of the influence of meteorological factors.

Proliferation of Trionyx sinensis hemorrhagic syndrome virus using primary alveolar macrophages invitro.

Proliferation of Trionyx sinensis hemorrhagic syndrome virus using primary alveolar macrophages invitro.

Indoor air sampling for detection of viral nucleic acids

Indoor air sampling for detection of viral nucleic acids

Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay

BackgroundCervical cancer screening programs are increasingly relying on sensitive molecular approaches as primary tests to detect high-risk human papillomaviruses (hrHPV), the causative agents of cervix cancer. Although hrHPV infection is a pre-requisite for the development of most precancerous lesions, the mere detection of viral nucleic acids, also present in transient infections, is not specific of the underlying cellular state, resulting in poor positive predictive values (PPV) regarding lesional states. There is a need to increase the specificity of molecular tests for better stratifying individuals at risk of cancer and to adapt follow-up strategies.MethodsHPV-RNA-SEQ, a targeted RNA next generation sequencing assay allowing the detection of up to 16 hrHPV splice events and key human transcripts, has previously shown encouraging PPV for the detection of precancerous lesions. Herein, on 302 patients with normal cytology (NILM, n = 118), low-grade (LSIL, n = 104) or high-grade squamous intraepithelial lesions (HSIL, n = 80), machine learning-based model improvement was applied to reach 2-classes (NILM vs HSIL) or 3-classes (NILM, LSIL, HSIL) predictive models.ResultsLinear (elastic net) and nonlinear (random forest) approaches resulted in five 2-class models that detect HSIL vs NILM in a validation set with specificity up to 0.87, well within the range of PPV of other competing RNA-based tests in a screening population.ConclusionsHPV-RNA-SEQ improves the detection of HSIL lesions and has the potential to complete and eventually replace current molecular approaches as a first-line test. Further performance evaluation remains to be done on larger and prospective cohorts.

Seroprevalence, and molecular detection of Peste des Petits Ruminants in selected districts of Tigray Region, Ethiopia

Peste des Petits Ruminants is a contagious trans-boundary viral disease affecting domestic and wild small ruminants, causing high mortality and morbidity. A cross-sectional study was conducted from January to December 2024 in the Enderta and Kilteawulaelo districts of the Tigray region, Ethiopia. The study aimed to assess the seroprevalence, associated risk factors, and investigate the recent circulation of the Peste des Petits Ruminants virus strains in small ruminants. A total of 384 serum samples were collected from 133 sheep and 251 goats in the study districts using multistage sampling methods. In addition, 43 swab samples were obtained from animals suspected of having Peste des Petits Ruminants to detect the viral antigen. Peste des Petits Ruminants specific antibodies and viral nucleic acid were identified using the virus neutralization test and real-time PCR, respectively. The relationship between Peste des Petits Ruminants seroprevalence and the possible risk factors was examined using Pearson's chi-square and logistic regression analysis using STATA version 14. Of the 384 serum samples tested, 41.9% (n = 161) were positive for Peste des Petits Ruminants Virus antibodies. The seroprevalence in the districts of Enderta and Kilteawulaelo was 47.6% (n = 98) and 35% (n = 63), respectively, while at the species level, it was 36.8% (n = 49) in sheep and 44.6% (n = 112) in goats. The logistic regression model revealed that districts and flock size were significant risk factors of Peste des Petits Ruminants seropositivity in sheep and goats with P = 0.016 and P = 0.025 respectively. Out of 43 swab samples about 23.26% (n = 10) of the clinical samples were positive for viral nucleic acid via real-time Peste des Petits Ruminants. The serological and molecular results both confirm the presence of the Peste des Petits Ruminants virus circulating among sheep and goat populations in the study areas. Key risk factors include flock size and districts. Ongoing infections, indicated by viral nucleic acid detection, highlight the potential for wider spread. The study recommends routine vaccination, movement restrictions, continuous surveillance, farmer education, and further genetic research.

In-depth analysis of the risk factors for persistent severe acute respiratory syndrome coronavirus 2 infection and construction of predictive models: an exploratory research study

BackgroundPersistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection differs from long coronavirus disease (COVID-19) (acute symptoms ≥ 12 weeks post-clearance). The Omicron BA.5 variant has a shorter median clearance time (10–14 days) than the Delta variant, suggesting that the traditional 20-day diagnostic threshold may delay interventions in high-risk populations. This study integrated multi-threshold analysis (14/20/30 days), whole-genome sequencing, and machine learning to investigate diagnostic thresholds for persistent SARS-CoV-2 infection and developed a generalizable risk prediction model.MethodsThis retrospective study analyzed data from 1,216 patients with COVID-19 hospitalized at Aerospace Center Hospital between January 2021 and October 2024. We used whole-genome sequencing to genotype all COVID-19 cases and to identify major variants (such as Omicron BA. 5, Delta). The outcome, “persistent SARS-CoV-2 infection,” was defined as viral nucleic acid positivity ≥ 14 days. Risk factors associated with persistent infection were identified through subgroup analysis with multiple logistic regression (adjusted for age, comorbidities, vaccination status, and virus strain) and machine learning models (70% training, 30% testing dataset).ResultsPersistent SARS-CoV-2 infection was identified in 15.5% (188/1,216) of hospitalized COVID-19 patients. Key predictors included comorbidities—hypertension, diabetes, and active malignancy—and immune dysfunction, marked by reduced B-cell and CD4 + T-cell counts. Unvaccinated patients exhibited an 82% higher risk of persistent infection. Elevated inflammatory markers (C-reactive protein and interleukin-6) and bilateral lung infiltrates on computed tomography further distinguished persistent cases. The predictive model demonstrated strong discrimination with an area under the curve (AUC) of 0.847 (95% confidence interval: 0.815–0.879) and an AUC of 0.81 externally in external validation, underscoring its clinical utility for risk stratification.ConclusionsHypertension, diabetes, malignancy, immunosuppression (low B/CD4 + cells), and non-vaccination are independent risk factors for persistent SARS-CoV-2 infection. Integrating these factors into clinical risk stratification may optimize management of high-risk populations.

Recent advances in treatment and detection of Rift Valley fever virus: a comprehensive overview.

Rift Valley fever virus (RVFV) is a newly discovered arboviral pathogen that infects humans and livestock. Numerous outbreaks have occurred in Africa and the Arab Peninsula. Epizootics of RVFV are sporadic and frequently associated with ongoing floods and excessive rainfall. This leads to the development of infected Aedes mosquitoes, which then amplify transmission by other mosquito species (like Anopheles and Culex genera). In animals, it typically results in high rates of death and abortion. In humans, Rift Valley fever (RVF) manifests as clinical symptoms that may vary in intensity from minor to severe. Common symptoms include retinitis, hepatitis, delayed onset encephalitis, and hemorrhagic illness. The possibilities for containing RVFV outbreaks are limited due to the lack of authorized human vaccinations and treatments. Although molecular detection techniques are available, they can only recognize viral nucleic acids during the short viremic phase. There are currently no specific treatments for RVFV infection. Ribavirin is one of the few therapies for viral hemorrhagic fevers, but severe adverse effects restrict its use. Significant studies have been done in recent years on using Nanotechnology to diagnose and treat viruses. This review summarizes the common and recent diagnostic and therapeutic approaches for RVFV, including nanoparticles, intravenous immunoglobulin (IVIG), stem cells, vaccines, and antibody-based therapies.

The Epithelial Immune Response to Human Papillomavirus Infection.

The skin is a complex organ, containing an intricate network of immune cells that are crucial for host barrier function and defence against pathogens. Human papillomavirus (HPV) exclusively infects the skin, and its lifecycle is intimately associated with epithelial cell division and differentiation. There are over 450 HPV types, 12 of which are classified as carcinogenic. The primary focus of this review is the epithelial immune response to HPV infection of the cervix during the initial stages of infection, productive infection, and disease progression. During the early stages of infection, cells are HPV-positive; however, there are no attributable histological changes to the epithelium. The HPV-infected cells have the capacity for innate sensing and signalling through toll-like receptors in response to viral nucleic acids. However, HPV has evolved multiple mechanisms to evade the innate response. During productive infection, all viral antigens are expressed and there are visible histological changes to the epithelium, including koilocytosis. Disease regression is associated with Tbet positive cells in the infected epithelium and the presence of CD4 and CD8 T cells in the lamina propria. Disease progression is associated with the overexpression of the E6 and E7 oncoproteins after integration of viral genomes into the host chromosomal DNA. Histologically, the epithelium is less differentiated, and changes to cells include a higher nuclear-to-cytoplasmic ratio and an increased mitotic index. Immune changes associated with disease progression include increased numbers of cells expressing suppressor molecules, such as FoxP3, Blimp-1, and HMGB1, and myeloid cell infiltrates with an M2-like phenotype. This review highlights the gaps in the understanding of the immune response in HPV-positive cervical neoplasia, and in regression and progression of disease. This knowledge is critical for the development of effective immunotherapies that reliably cause HPV-positive cervical neoplasia to regress.

Molecular detection of SARS-CoV-2 and medically important respiratory and gastrointestinal virus pathogens on Thai currency

Fomite-mediated viral transmission through using cash might be a potential risk to human health. Persistence of SARS-CoV-2, and other medically important viruses was investigated. A total of 300 samples (i.e., 150 banknotes and 150 coins) were randomly collected from nineteen fresh markets distributed across seventeen districts of Bangkok, Thailand. Every banknote or coin was entirely swabbed and generated a total of 100 pool samples. Total viral nucleic acid was extracted and subjected for multiplex real-time qRT-PCR using Allplex™ SARS-CoV-2/FluA/FluB/RSV assay and Allplex™ GI-virus assay. The results revealed detection rate of 4% (4/100), and they were only detected in banknote pooled samples. Two samples collected from fish shops tested positive for SARS-CoV-2 (2%, 2/100); meanwhile, two samples (2%, 2/100) from pork and chicken shops tested positive for rotavirus A. None of pool samples were detected for influenza A and B viruses, respiratory syncytial virus, norovirus genogroup I and II, adenovirus, astrovirus, and sapovirus. Phylogenetic analysis demonstrated that rotavirus A belonged to genotype G8; meanwhile, SARS-CoV-2 resembled omicron GRA JN.1 sub variant. Our finding is the first report for demonstrating the presence of SARS-CoV-2 and rotavirus A in Thai banknotes on real-world situation, implying the potential risk to human health and safety.

Application of quantitative real-time PCR for identifying respiratory tract pathogens in outpatients with RTIs.

Respiratory tract infections (RTIs) caused by various pathogens, including viruses, bacteria, and fungi, pose significant public health challenges worldwide. Understanding the etiology and epidemiology of RTIs is necessary for clinical management, rational drug use, formulation of preventive measures, and vaccine development. Quantitative real-time PCR was used to detect and analyze respiratory pathogens in outpatients at a hospital in Suzhou, including FluA, FluB, RSV, ADV, HRV, MP, and SARS-CoV-2. Among the 27,031 respiratory and throat swab samples, the positive rate of virus detection accounts for 25.6%. MP, SARS-CoV-2, and FluA, in particular, showed high positive rates among children, adolescents, and adults. The highest infection rates of RSV, HRV, and ADV were found in patients under 5 years old. High rates of FluA and FluB were observed in patients aged 5-17 and 18-44 years. However, the highest rate of SARS-CoV-2 infection was primarily observed in older adults. Seasonally, the infection rates of SARS-CoV-2 and FluA were highest in spring, FluB, RSV, and ADV in winter, HRV in autumn, and MP in summer and autumn. By analyzing the results of respiratory virus nucleic acid detection, we can gain a better understanding of the infection status of common respiratory viruses, providing a basis for clinical diagnosis and treatment.

Virucidal Efficacy of Laser-Generated Copper Nanoparticle Coatings against Model Coronavirus and Herpesvirus.

High-efficiency antiviral surfaces can be an effective means of fighting viral diseases, such as the recent COVID-19 pandemic. Copper and copper oxides, their nanoparticles (NPs) (CuNPs), and coatings are among the effective antiviral materials having internal and external biocidal effects on viruses. In this work, CuNP colloids were produced via femtosecond laser ablation of the metal target in water, a photophysical, cost-effective green synthesis alternative utilizing sodium citrate surfactant stabilizing the NPs. Raman spectroscopy and X-ray diffraction studies confirmed that the 32 nm mean size CuNPs are mixtures of mainly metallic copper and copper(I) oxide. Polyvinyl butyral was utilized as the binding agent for the CuNPs deposited via high-throughput spray-coating technology. The virucidal efficacy of such coatings containing Cu content ranging from 2.9 to 11.2 atom % was confirmed against animal-origin coronavirus containing ribonucleic acid, the agent of avian infectious bronchitis (IBV), and herpesvirus containing DNA, the agent of bovine herpesvirus (BoHV-1) infection. It was demonstrated that after a short time of exposure, the Cu NP-based coatings do not have a toxic effect on the cell cultures while demonstrating a negative effect on the biological activity of both model viruses that was confirmed by quantification of the viruses via the determination of tissue culture infectious dose (TCID50) virus titer and their viral nucleic acids via determination of threshold cycle (Ct) employing real-time polymerase chain reaction analysis. The assays showed that the decrease in TCID50 virus titer and increase in Ct values correlated with Cu content in Cu NP-based coatings for both investigated viruses. Contact with coatings decreased IBV and BoHV-1 numbers from 99.42% to 100.00% and from 98.65% to 99.96%, respectively. These findings suggest that CuNPs show inhibitory effects leading to the inactivation of viruses and their nuclei regardless of the presence of a viral envelope.

Nanostructures for Virus Detection and Tracking: An Overview

Treatment of viral diseases and subsequent patient recovery depends on the timely identification of analytes such as viral proteins, nucleic acids and antibodies that are produced as part of the body’s immune response to infection. Current diagnostic procedures require specialized and expensive personnel and are performed in special testing centers, leading to lengthy processes and delays in effective treatment. Due to the unique properties of Nanostructures that can be used to detect analytes in very small amounts, much research has been conducted on the use of nanostructures to detect and track viruses. In this article, we divide the nanostructures proposed in this field into 3 groups of carbon, inorganic and organic Nanostructures, and separately study their efficiency in the 2 fields of virus detection and tracking. HIGHLIGHTS Investigating Nanostructures based on carbon allotropes in the detection and tracking of viruses. Investigating Inorganic Nanostructures in the detection and tracking of viruses. Investigating Organic Nanostructures used for virus detection and tracking. GRAPHICAL ABSTRACT

Hepatitis E Virus in the Role of an Emerging Food-Borne Pathogen.

Viral hepatitis E represents an important global health problem caused by the hepatitis E virus (HEV). Cases of HEV infection are increasingly associated with food-borne transmissions after the consumption of raw or undercooked food products from infected animals in high-income regions. Although most cases of infection are asymptomatic, severe courses of infection have been reported in specific groups of people, predominantly among pregnant women and immunocompromised patients. The viral nucleic acid of HEV is increasingly being reported in food-producing animals and different products of an animal origin. Even though the incubation period for HEV infection is long, several direct epidemiological links between human cases and the consumption of HEV-contaminated meat and meat products have been described. In this article, we review the current knowledge on human HEV infections, HEV in different food-producing animals and products of an animal origin, as well as the accumulation and resistance to HEV in farm and slaughterhouse environments. We also provide preventive measures to help eliminate HEV from animals, the human population, and the environment.

The investigation and spatio-temporal analysis of first importation associated D8 genotype measles case in a child, Shandong Province, 2023

Objective: To analyze the epidemiological, etiological characteristics and transmission of an imported D8 genotype measles case in a child in Shandong Province, August 2023. Methods: A study was conducted on a measles case and 16 contacts in Shandong Province in August 2023. Field epidemiological surveys, including recent exposure and immunization history, were conducted. Serum and throat swab samples were collected from all 16 subjects. Measles IgM and IgG antibody levels and avidity were measured by ELISA, while virus detection and genotyping were performed using fluorescence quantitative PCR and RT-PCR. Genetic evolutionary analysis of the obtained sequences was conducted using MEGA and Beast software. Results: The case was an 11-year-old boy, a fifth-grade student, who developed symptoms on August 28, 2023. A total of five close contacts were investigated, including three family members (grandfather, father and sister) and two playmates. Additionally, 11 classmates who had close contact with the case's sister during the infectious period (within five days after the rash onset) were also investigated. Among the 16 serum samples tested, only one case was positive for IgM, while the other 15 samples were negative for IgM. The results of the serum antibody avidity test showed that among the 16 serum samples, 14 were positive for IgG. Of these, eight had a relative avidity index >55%, indicating high-avidity antibodies; one had a relative avidity index <45%, indicating low-avidity antibodies; and five had an avidity index between 45% and 55%. The IgG detection OD values for the case's sister and grandfather were higher than those of the other contacts. Based on the vaccination history of the subjects and the results of IgM and IgG tests, it was preliminarily determined that the case had a recent wild-type measles virus infection. The case's sister and grandfather had a history of measles wild-type virus infection, while the high-avidity antibodies in the other contacts were likely induced by the measles vaccine. The results of the pharyngeal swab tests showed that only the case was positive for measles virus nucleic acid, while the remaining 15 samples were negative for measles virus. The genetic evolutionary analysis revealed that the viral sequence of this case (Mvs/Shandong.CHN/38.23) had a 100% homology with the Hong Kong strain sequence from August 2023. It belonged to a different transmission chain from the D8 genotype strains that appeared in Shandong Province between 2018 and 2019, with sequence homology ranging from 98.0% to 98.8%. The sequence homology within the transmission chain of this case was between 99.1% and 100%. The evolutionary rate of this transmission chain was approximately 8.38×10-3 sub/site/year, and the most recent common ancestor was estimated to have emerged around the year 2011. Conclusion: This case is the first imported D8 genotype measles case in Shandong Province. There is no spatio-temporal correlation between this case and adult cases of D8 genotype imported from Shandong Province in 2018-2019, indicating a new D8 genotype imported epidemic.

Scientific Substantiation of Population Monitoring of Free-Living Protozoan Community in Natural Biotopes: Communication 2

Introduction: Studies of free-living protozoa cover a wide range of topics owing to their simplicity and variety of forms and functions in maintaining ecosystem balance in the microbiomes of reservoirs, soils, and human microbiota. Objective: To provide a scientific rationale for monitoring the circulation of free-living unicellular organisms of natural biocenoses in order to update and improve the Russian scientific and methodological research basis. Materials and methods: We conducted sanitary and hygienic, biological and parasitological studies of environmental samples, including 126 samples of wastewater and 360 samples of surface water, 30 samples of tap water, 210 samples of bottom sediments, 189 soil samples, and 300 samples of human feces taken in the Moscow Region in 2021–2023. Results: The protozoan index along the Moscow River ranged from null to 4.8 units/mL3 against the excessive total chloride level (Cl-); nucleic acids of viruses were determined in 11 types of ciliates; the contents of Cryptosporidium spp. and Lamblia spp. reached 4 lg and those of Blastocystis spp. and Entamoeba spp. were up to 6 lg. Contamination of tap water with cysts of Lamblia spp. was 3.2 %. The soil content of free-living protozoa in industrial areas was 2.1 times higher than in parks and 3.2 times higher than in residential areas (p = 0.0372). New data have been obtained on the effect of commensal amoebae Entamoeba spp. on changes in intestinal microbiota by the type of growth activation of five species of opportunistic bacteria. Conclusion: The paper outlines promising areas of sanitary (environmental) protistology within improvement of the scientific and methodological basis for the fundamental research into patterns of symbiotic relationships of free-living protozoa in the natural environment and in connection with medical aspects of applied research.

Natural pyrrolo[1,2-a]quinazolinone derivatives: Design, synthesis, characterization, and bio-evaluation as novel antiviral agents.

Natural pyrrolo[1,2-a]quinazolinone derivatives: Design, synthesis, characterization, and bio-evaluation as novel antiviral agents.

Origin and function of anti-interferon type I viral proteins.

Origin and function of anti-interferon type I viral proteins.

Gushan virus: a newly discovered virus found in mosquitoes of Shandong, China.

Arboviruses persist as a significant threat to global public and human health. The advent of macrogenomics technology has substantially expanded our understanding of mosquito-borne viruses by facilitating the direct identification and characterization of viruses from diverse environmental samples. In 2022, we conducted mosquito surveillance in the Shandong region of China and discovered a novel virus, tentatively named Gushan virus based on the site of discovery. In this study, a total of 3170 mosquitoes were collected and divided into 62 pools based on species and collection locations. Quantitative reverse transcription PCR (qRT-PCR) and nested PCR were employed to detect Gushan virus nucleic acids in all samples. The results revealed that 16 pools were positive, with a minimum infection rate (MIR) of 0.5% (16/3,170). Concurrently, we successfully obtained one complete genome sequence and six partial sequences. Nucleotide homology analysis demonstrated a high degree of sequence identity, indicating that Gushan virus may maintain a stable genetic profile in the region. Phylogenetic analyses revealed that Gushan virus is most closely related to Drosophila immigrans Nora virus of the family Noroviridae. Taxonomically, Gushan virus belongs to the order Picornavirales, family Noroviridae, and genus Orthonoravirus. This study contributes new insights into the diversity of mosquito-associated viruses.

Direct-Acting Antiviral Treatment Failure and Retreatment Strategies Following Hepatitis C-Positive Solid Organ Transplantation in Hepatitis C-Negative Recipients: A Multicenter Case Series.

Transplanting solid organs from hepatitis C virus (HCV) nucleic acid testing (NAT+) donors (D+) into HCV-negative recipients (R-) has become more common with the development of curative direct-acting antiviral (DAA) treatment. Limited information exists to guide retreatment strategies for patients not achieving sustained virologic response (SVR) with DAAs. This multisite case series examines retreatment strategies and subsequent SVR rates in HCV-negative solid-organ transplant (SOT) recipients who did not achieve SVR following reactive initial DAA therapy following NAT+ SOT. A retrospective multisite case series was conducted on patients not achieving SVR with initial DAA treatment post-NAT+ HCV SOT between September 2016 and September 2022 across four tertiary medical centers in the United States. Thirteen patients were identified, predominantly receiving HCV NAT+ kidneys (77%) and SOF/VEL for 12 weeks as initial DAA therapy (43%). Baseline resistance testing was not performed. Median time to treatment initiation post-SOT was 35 [IQR 22-41] days, and to retreatment postpositive viral load was 35 days [IQR 17-76]. Most patients (62%) were retreated with sofosbuvir/velpatasvir/voxilaprevir (SOF/VEL/VOX) for 12 weeks. Two patients required retreatment extension with SOF/VEL/VOX and SOF/VEL/VOX + ribavirin (RBV) from 12 to 24 weeks due to persistent viremia. Only one patient did not achieve SVR following retreatment with SOF/VEL/VOX for 12 weeks but did achieve SVR after a third course of treatment with SOF + GLE/PIB + RBV for 24 weeks. Despite initial DAA failures, all HCV-negative SOT recipients achieved SVR following one or more courses of retreatment with DAAs.