Objective:To investigate the dynamic changes of cellular miRNA expression profiles in EBV latently infected Raji cells upon reactivation with Phorbol ester (TPA).Methods:Total RNA was extracted using TRIzol reagent from Raji cells treated with TPA at different time points (0 h, 24 h, 48 h). Small RNA libraries were constructed and sequenced on an Illumina SE50 platform. Differentially expressed miRNAs were identified, and their target genes were predicted and functionally annotated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out through online tools. Additionally, miRanda and RNAhybrid software were used to predict cellular miRNAs targeting the EBV genome. Real-time RT-qPCR was employed to validate the expression levels of differentially expressed novel miRNAs.Results:High-throughput sequencing identified 1 301 celluar miRNAs, comprising 1 189 known and 112 novel miRNAs. A total of 264 known differentially expressed cellular miRNAs and 13 novel miRNAs were identified through high-throughput miRNA sequencing. Secondary structure prediction revealed that the novel miRNAs exhibited typical pre-miRNA hairpin structures. Stem-loop quantitative real-time PCR (RT-qPCR) validation of Novel_miR_183 and Novel_miR_242 did not exhibit a statistically significant difference ( F=1.407, P=0.370 7 for Novel_miR_183; F=1.277, P=0.397 0 for Novel_miR_242) between the TPA-stimulated and untreated groups. Target gene prediction analysis revealed that the differentially expressed cellular miRNAs were involved in various important biological processes and signaling pathways. Furthermore, 1 189 known cellular miRNAs and 108 novel miRNAs were predicted to target the EBV genome. Conclusions:Treatment of Raji cells with TPA stimulation successfully reactivated Raji cells and significantly altered their miRNA expression patterns. Differentially expressed miRNAs were identified, suggesting that these miRNAs probably play crucial roles in regulating EBV infection and replication by directly targeting the EBV genome.

Objective:To compare the enrichment effects of ultrafiltration, polyethylene glycol (PEG) precipitation, aluminum salt precipitation, and anionic membrane adsorption-elution on viruses in drinking water.Methods:Using phage MS2 as the target virus, three different concentrations of drinking water samples were prepared, and the samples were enriched by ultrafiltration 1, ultrafiltration 2, PEG precipitation, aluminum salt precipitation, and anionic membrane adsorption-elution method, respectively. Real-time fluorescence quantitative reverse transcription-polymerase chain reaction (RT-qPCR) was used to quantify MS2 nucleic acid in pre and post concentrated samples and the recovery rates of MS2 in samples with high, medium and low concentrations were compared among the five methods.Results:Comparing the MS2 enrichment recovery rates of individual enrichment method in water samples of different concentrations, ultrafiltration method 1, PEG precipitation method, aluminum salt precipitation method, and membrane adsorption-elution method were not affected by the sample concentration, and the differences of the recovery rates for the three concentration water samples among the four methods were not statistically significant ( P>0.05). The MS2 enrichment recovery rates of the five enrichment methods were significantly different in all concentration samples ( P<0.05). The recovery rates of ultrafiltration method 1 were higher in all three concentration samples, followed by aluminum salt precipitation and anionic membrane adsorption-elution, PEG precipitation were higher in high concentration samples, but lower in low and medium concentration samples, and the recovery rates of ultrafiltration method 2 were the lowest in all three concentration samples. Comparing the Ct values of MS2 in the enriched samples by five methods, the Ct values of ultrafiltration method 1 were the smallest in the three concentration water samples. There was no statistically significant difference in MS2 Ct values among the five enrichment methods in the medium and high concentration water samples ( P>0.05). In low concentration simulated water samples, only the difference of MS2 Ct value between ultrafiltration method 1 and ultrafiltration method 2 was statistically significant ( Z=16.000, P=0.016). Conclusions:Considering the operation simplicity, operation time and virus recovery rate after enrichment, ultrafiltration was the most effective method for virus enrichment in drinking water.

Objective:The SARS-CoV-2 has a high natural mutation rate, and dynamic monitoring of virus variants remains a key focus in current COVID-19 prevention and control efforts.Methods:In this study, a sensitive and rapid method for detecting SARS-CoV-2 omicron variant nucleic acid was established based on the BMD-PCR technology.Results:This method showed good specificity, and had no cross-reactivity with 11 common viruses transmitted via the respiratory and gastrointestinal tracts, and the limit of detection is 555 copies/ml. Compared with SARS-CoV-2 whole-genome sequencing result, among 50 samples with original Ct values ≤32 tested for the Omicron variant, 49 samples tested positive for the N679K mutation site using BMD-PCR Omicron variant detection, achieving a concordance rate of 98.00%. For 30 samples JN.1 lineage, 29 samples tested positive for the K356T mutation site using BMD-PCR JN.1 lineage detection, with a concordance rate of 96.67%. For 10 samples with original SARS-CoV-2 detection Ct values between 35 and 32, 7 samples tested positive for the N679K mutation site using BMD-PCR Omicron variant detection, Resultsing in a detection rate of 70.00%. For samples with SARS-CoV-2 nucleic acid detection Ct values>35, the detection rate for the N679K mutation site in the BMD-PCR Omicron variant was 20.00%.Conclusions:This method can serve as a high-throughput supplementary approach for the preliminary identification of SARS-CoV-2 variant genotypes.

Objective:In order to make up for the missed detection of the genus Rocahepevirus (HEV-C) infection in the current clinical test method and to quickly differentiate the infection from the hepatitis A virus (HAV) infection, a triple real-time fluorescence quantitative RT-PCR(qRT-PCR)detection method was established to simultaneously detect HAV, genus Paslahepevirus (HEV-A), and HEV-C. Methods:Three pairs of amplification primers and three TaqMan probes were selected to optimize the reaction system and amplification temperature to construct a triple qRT-PCR method ; standard curves were established by plasmid and the sensitivity of the method was evaluated; specificity was evaluated by other viruses; stability was evaluated by nucleic acid of HAV, HEV-A and HEV-C; samples from suspected hepatitis A or E cases were detected and compared with HAV (or HEV) IgM antibody and nested RT-PCR (nRT-PCR) detection result.Results:The correlation coefficient R2 of three standard curves of triple qRT-PCR were all greater than 0.99, and the slopes were close to -3.3. The minimum detection limits of HAV, HEV-A and HEV-C plasmids were 8 copies/μl, 5 copies/μl and 8 copies/μl, respectively. There was no cross reaction with hepatitis B virus and hepatitis C virus, etc. The coefficients of variation of intra-and inter-batch tests were less than 5%. The positive rates of HAV IgM antibody test, HAV nRT-PCR and triple qRT-PCR were 95.1% (58/61), 83.6% (51/61) and 83.6% (51/61) for serum from suspected hepatitis A cases, respectively. The coincidence rate of HAV IgM antibody test and HAV nRT-PCR (or triple qRT-PCR) was 85.2% (52/61), the difference was statistically significant ( χ2=4.00, P=0.039). The positive rates of HEV IgM antibody test, HEV nRT-PCR and triple qRT-PCR were 89.7%(61/68), 69.1%(47/68) and 72.1%(49/68) for serum from suspected hepatitis E cases, respectively. The coincidence rate of HEV IgM antibody test and triple qRT-PCR was 79.4% (54/68), difference was statistically significant ( χ2=8.64, P=0.002). The positive rates of HEV nRT-PCR and triple qRT-PCR for stool samples from suspected hepatitis E cases were 80.0% (20/25) and 76.0% (19/25), respectively; the coincidence rate was 96% (24/25), with no significant difference ( χ2=0, P>0.05). Conclusions:This study established a triple qRT-PCR detection method that can simultaneously and rapidly detect hepatitis A virus, genus Paslahepevirus or genus Rocahepevirus. It has high sensitivity, specificity and stability, and is suitable for rapid detection of specimens from patients recently infected with hepatitis A virus or hepatitis E virus.

Objective:This study aimed to analyze the genetic variation of the human papillomavirus (HPV) type 39 genomes and to predict and screen the dominant T-cell and B-cell epitopes of the viral early proteins (E1, E2, E6, E7) and late proteins (L1, L2).Methods:A total of 70 full-length sequences of HPV39 variants were retrieved from the clinical samples and the National Center for Biotechnology Information (NCBI) to construct a phylogenetic tree, analyze genetic polymorphisms, and predict the physicochemical properties of the viral proteins. Next, T-cell and B-cell epitopes were predicted using IEDB and ABCpred, and potential dominant epitopes were further selected based on parameters such as the secondary structure of the epitope region, peptide flexibility, hydrophilicity, surface accessibility and antigenicity. Finally, a homology analysis of the potential dominant epitopes was performed with 12 high-risk HPV types.Results:HPV39 variants from different sources can be clustered into two lineages (A and B), each exhibiting distinct mutation patterns. The mutation rate was the highest in E7 and the lowest in E1 among the different viral genes. However, these nucleotide/amino acid mutations did not significantly impact the physicochemical properties of the viral proteins. After prediction and screening, 5 and 6 potential dominant B-cell epitopes were identified in both L1 and L2, respectively. E1, E2, E6, and E7 yielded 18, 10, 4, and 1 potential dominant HLA-I restricted T-cell epitopes, respectively. Additionally, E1, E2, and E6 yielded 7, 3, and 2 potential dominant HLA-II restricted T-cell epitopes, respectively. Homology analysis indicated that T-cell dominant epitopes in E1, E2, and E6, as well as B-cell epitopes in L2, showed high homology (93%-100%) with HPV68, HPV33, HPV45, and HPV59.Conclusions:Bioinformatics analysis and prediction revealed that HPV39 variants can be clustered into two main evolutionary branches, A and B, each exhibiting a specific mutation pattern. The viral proteins contain potential dominant T-cell and B-cell epitopes that can be further investigated, providing valuable theoretical support for the development of HPV39-related peptide-based vaccines and therapeutics.

Objective:To investigate the role of ubiquitin-specific protease 21 (USP21) in enterovirus group A type 71 (EV-A71) infection.Methods:Peripheral blood mononuclear cells (PBMC) were obtained from a cohort of 24 children infected with EV-A71 and 24 healthy children. Expression of USP21 was determined by real-time fluorescence quantitative PCR (qPCR). Additionally, the impact of USP21 overexpression or knockout on EV-A71 replication was evaluated using a combination of qPCR and western blot (WB) analysis. Furthermore, WB was employed to measure the levels of EV-A71 structural protein VP1, phosphorylated interferon regulatory factor 3 (IRF3) and other key molecules in the RIG-I-like receptor (RLR) signaling pathway. Co-immunoprecipitation (Co-IP) was utilized to investigate the effects of USP21 on the ubiquitin levels of EV-A71 nonstructural protein 2A protease (2A pro). Results:In comparison to healthy children, the expression of USP21 mRNA in PBMC of children infected with EV-A71 was notably elevated. The overexpression of USP21 significantly enhanced the cytopathic effects induced by EV-A71, upregulated levels of VP1 mRNA and protein, and facilitated EV-A71 replication, leading to a decrease in cell activity with increasing levels of USP21 transfection. Following the knockout of the USP21 gene, the VP1 mRNA levels were significantly declined in comparison to the control group. Furthermore, the overexpression of USP21 was found to have no impact on the transcriptional activity of EV-A71 2A pro. However, it was observed to enhance the expression of 2A pro protein, reduce the ubiquitination of 2A pro, suppress the protein levels of mitochondrial antiviral signaling protein (MAVS) and melanoma differentiation-associated gene 5 (MDA5), as well as decrease the phosphorylation of IRF3. Additionally, the induction of IFN-β mRNA by EV-A71 infection was downregulated. Conclusions:USP21 has been shown to enhance the replication of EV-A71 through the downregulation of 2A pro ubiquitination, suppression of MAVS and MDA5 protein expression, and inhibition of the interferon signaling pathway.

Objective:To understand the molecular evolutionary characteristics of the recombinant strain GII.3[P12] of norovirus acute gastroenteritis outbreaks and aggregated outbreaks in China from 2022 to 2023.Methods:Epidemiological information, case information, clinical samples, as well as detection and genotyping information of norovirus outbreaks and aggregated outbreaks from 2022 to 2023 were collected; positive samples of the GII.3[P12] recombinant strain were subjected to nucleic acid extraction, whole-genome amplification, and sequence analysis; and homology simulation method were used to construct a three-dimensional structure and predict antigenic epitopes.Results:From January 2022 to December 2023, a total of 1 136 norovirus outbreaks and aggregated outbreaks were reported in China′s norovirus outbreak surveillance network, and genotyping result were successfully obtained for 942 outbreaks, with GII dominating, accounting for 76.0% (716/942), and the proportion of GI and mixed genotypes being 15.8% (149/942) and 8.2% (77/942). Norovirus outbreaks caused by GII were dominated by GII.3[P12] (22.5%, 161/716), while other major genotypes included GII.17[P17] (18.7%, 134/716), GII.4_Sydney 2012[P16] (11.6%, 83/716) and GII.6[P7] ( 11.3%, 81/716). 2022-2023 Outbreaks caused by GII.3[P12] were concentrated in February-March (54.0%, 87/161), with the main outbreaks occurring in nursery and primary schools (87.5%), the mode of transmission was mainly human-to-human (68.9%), and the main susceptible population was children aged 3-7 years (93.3%). In this study, the genome sequences of 25 GII.3[P12] recombinant strains were obtained, and according to the phylogenetic analysis, it was shown that the GII.3[P12] recombinant strains in China in 2022-2023 belonged to the Cluster IV cluster of sublineage b (7 strains) and sublineage c (18 strains). A total of 11 linear and 8 conformational epitopes were predicted by epitope prediction analysis, and the predicted linear and conformational epitopes had overlapping positions, and each conformational epitope was part of the predicted linear epitope with conserved potential antigen-binding and receptor-binding sites.Conclusions:The recombinant strain GII.3[P12] is one of the epidemic strains that will cause outbreaks and clusters of norovirus in China in 2022-2023, and its genome did not undergo significant mutation.

Severe fever with thrombocytopenia syndrome (SFTS), caused by caused by Bandavirus dabieense(formerly known as severe fever with thrombocytopenia syndrome Bunyavirus, SFTSV), is a tick-borne emerging infectious disease first identified in China in 2009. Since its discovery, the epidemic has expanded to 27 provinces nationwide. This article systematically reviews the epidemiological evolution, clinical treatment and prevention challenges of SFTS in China over the past 15 years. By integrating international case studies such as Nipah virus and monkeypox, we propose strategies including adopting orphan drug development incentive policies, standardizing clinical protocols, and implementing the " One Health" concept. These recommendations aim to provide actionable pathways for SFTS prevention, treatment, and reduction of disease burden.

Objective:To investigate the potential causes of the rising epidemic of severe fever with thrombocytopenia syndrome (SFTS) in Weifang, Shandong province.Methods:The temporal trend of SFTS epidemic was segmented using Joinpoint regression analysis. Changes in epidemiological characteristics across different periods were compared, and correlation analysis was conducted to identify meteorological factors influencing the epidemic trend.Results:Joinpoint regression revealed two distinct periods for SFTS epidemic in Weifang: 2015-2021 and 2022-2024. No significant trend was observed during 2015-2021 ( P=0.634), while a sharp annual increase of 46.69% occurred from 2022 to 2024 ( P=0.006). Spatial autocorrelation analysis demonstrated a global Moran’s I of 0.42 ( Z=8.55, P<0.001) for 2015-2021, with 15 high-high clustering areas identified. For 2022-2024, the global Moran’s I decreased to 0.37 ( Z=7.31, P<0.001), with 13 high-high clusters, including newly emerging hotspots in Anqiu and Zhucheng in the southeastern region. High-risk populations remained individuals aged ≥50 in mountainous and hilly areas, with a marked rise in incidence in these groups. The male-to-female ratio of cases was higher in plain areas than in mountainous/hilly regions. Autumn (September-November) temperatures from the preceding year showed a positive correlation with annual case numbers ( P=0.004, r=0.82). The linear regression expression is y=40.61x-580.78 (y is the annual incidence, and x is the average daily temperature of last autumn). Conclusions:The SFTS epidemic in Weifang is showing a rising trend. There is a linear correlation between the temperature of the previous autumn and the scale of SFTS epidemic in the following year. This correlation allows for predicting the subsequent year′s epidemic, thereby enabling early warning of SFTS.

Monkeypox virus (MPXV) is a double stranded DNA virus that can be transmitted through animal-human or human-human routes. The experimental method for detecting MPXV infection include virus isolation and culture, electron microscopic observation, antigen and/or antibody detection, and molecular biologic testing. Among them, polymerase chain reaction is the preferred detection method for screening MPXV in blood donors. Blood may not be the main route of interpersonal transmission of MPXV, but there is a potential risk of transfusion transmission of MPXV during the viremia stage, and multiple factors affect the possibility of transfusion transmission of MPXV. Pathogen reduction techniques are a proactive strategy to reduce the risk of transfusion transmission of MPXV in virus-endemic areas. The development of molecular method for rapid and accurate diagnosis of MPXV and the study of the infectious dose required for transfusion transmission of MPXV are essential for the development of effective strategies to maintain transfusion safety.