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Brazilian Journal of Microbiology :... Sep 2023Porcine epidemic diarrhea virus (PEDV) is a virus that can cause diarrhea in pigs, resulting in significant economic losses to the pig industry. The mutation of the...
Phylogenetic analysis and molecular characterization of the co-infection of the new variant of the porcine epidemic diarrhea virus and the novel porcine kobuvirus isolated from piglets with diarrhea.
Porcine epidemic diarrhea virus (PEDV) is a virus that can cause diarrhea in pigs, resulting in significant economic losses to the pig industry. The mutation of the virus and its co-infection with other enteroviruses leads to poor control of PEDV infection. In this study, we found that the diarrhea outbreak in a pig farm in Shandong Province was mainly caused by PEDV infection. Through high-throughput sequencing, we also detected one other diarrhea-related virus (porcine kobuvirus). In the phylogenetic analysis and molecular characterization of the detected PEDV S gene and PKV, it was found that the S gene of the PEDV strain detected in this study (named SD22-2) had more mutations than the CV777 strain. The highest homology between PKV (named SD/2022/China) detected in this study and other strains was only 89.66%. Based on polyprotein, we divided SD/2022/China strains into a new grouping (designated group 4) and detected recombination signals. In summary, SD22-2 detected in this study is a new PEDV variant strain, and SD/2022/China strain might be a novel PKV strain. We also found the co-infection of the new PEDV variant and the novel PKV isolated from piglets with diarrhea. Our data suggested the importance of continuous surveillance of PEDV and PKV.
Topics: Animals; Swine; Phylogeny; Porcine epidemic diarrhea virus; Kobuvirus; Swine Diseases; Coinfection; Coronavirus Infections; Diarrhea; China
PubMed: 37344656
DOI: 10.1007/s42770-023-01025-y -
EBioMedicine Sep 2023Biomarkers predicting the outcome of HIV-1 virus control in natural infection and after therapeutic interventions in HIV-1 cure trials remain poorly defined. The BCN02...
BACKGROUND
Biomarkers predicting the outcome of HIV-1 virus control in natural infection and after therapeutic interventions in HIV-1 cure trials remain poorly defined. The BCN02 trial (NCT02616874), combined a T-cell vaccine with romidepsin (RMD), a cancer-drug that was used to promote HIV-1 latency reversal and which has also been shown to have beneficial effects on neurofunction. We conducted longitudinal plasma proteomics analyses in trial participants to define biomarkers associated with virus control during monitored antiretroviral pause (MAP) and to identify novel therapeutic targets that can improve future cure strategies.
METHODS
BCN02 was a phase I, open-label, single-arm clinical trial in early-treated, HIV infected individuals. Longitudinal plasma proteomes were analyzed in 11 BCN02 participants, including 8 participants that showed a rapid HIV-1 plasma rebound during a monitored antiretroviral pause (MAP-NC, 'non-controllers') and 3 that remained off ART with sustained plasma viremia <2000 copies/ml (MAP-C, 'controllers'). Inflammatory and neurological proteomes in plasma were evaluated and integration data analysis (viral and neurocognitive parameters) was performed. Validation studies were conducted in a cohort of untreated HIV-1+ individuals (n = 96) and in vitro viral replication assays using an anti-CD33 antibody were used for functional validation.
FINDINGS
Inflammatory plasma proteomes in BCN02 participants showed marked longitudinal alterations. Strong proteome differences were also observed between MAP-C and MAP-NC, including in baseline timepoints. CD33/Siglec-3 was the unique plasma marker with the ability to discriminate between MAPC-C and MAP-NC at all study timepoints and showed positive correlations with viral parameters. Analyses in an untreated cohort of PLWH confirmed the positive correlation between viral parameters and CD33 plasma levels, as well as PBMC gene expression. Finally, adding an anti-CD33 antibody to in vitro virus cultures significantly reduced HIV-1 replication and proviral levels in T cells and macrophages.
INTERPRETATION
This study indicates that CD33/Siglec-3 may serve as a predictor of HIV-1 control and as potential therapeutic tool to improve future cure strategies.
FUNDING
Spanish Science and Innovation Ministry (SAF2017-89726-R and PID2020-119710RB-I00), NIH (P01-AI131568), European Commission (GA101057548) and a Grifols research agreement.
Topics: Humans; CD4-Positive T-Lymphocytes; HIV Infections; HIV Seropositivity; HIV-1; Leukocytes, Mononuclear; Proteome; Proteomics; Sialic Acid Binding Ig-like Lectin 3; Vaccination; Viral Load; Anti-HIV Agents; Biomarkers
PubMed: 37506557
DOI: 10.1016/j.ebiom.2023.104732 -
Nature Aug 2023Most bacteria in the biosphere are predicted to be polylysogens harbouring multiple prophages. In studied systems, prophage induction from lysogeny to lysis is...
Most bacteria in the biosphere are predicted to be polylysogens harbouring multiple prophages. In studied systems, prophage induction from lysogeny to lysis is near-universally driven by DNA-damaging agents. Thus, how co-residing prophages compete for cell resources if they respond to an identical trigger is unknown. Here we discover regulatory modules that control prophage induction independently of the DNA-damage cue. The modules bear little resemblance at the sequence level but share a regulatory logic by having a transcription factor that activates the expression of a neighbouring gene that encodes a small protein. The small protein inactivates the master repressor of lysis, which leads to induction. Polylysogens that harbour two prophages exposed to DNA damage release mixed populations of phages. Single-cell analyses reveal that this blend is a consequence of discrete subsets of cells producing one, the other or both phages. By contrast, induction through the DNA-damage-independent module results in cells producing only the phage sensitive to that specific cue. Thus, in the polylysogens tested, the stimulus used to induce lysis determines phage productivity. Considering the lack of potent DNA-damaging agents in natural habitats, additional phage-encoded sensory pathways to lysis likely have fundamental roles in phage-host biology and inter-prophage competition.
Topics: Bacteriophages; Lysogeny; Prophages; Viral Proteins; Virus Activation; Bacteria; DNA Damage; DNA, Viral; Single-Cell Analysis; Transcription Factors; Host-Pathogen Interactions
PubMed: 37495698
DOI: 10.1038/s41586-023-06376-y -
Science Advances Jan 2024Miniaturized mobile electronic system is an effective candidate for in situ exploration of confined spaces. However, realizing such system still faces challenges in...
Miniaturized mobile electronic system is an effective candidate for in situ exploration of confined spaces. However, realizing such system still faces challenges in powering issue, untethered mobility, wireless data acquisition, sensing versatility, and integration in small scales. Here, we report a battery-free, wireless, and miniaturized soft electromagnetic swimmer (SES) electronic system that achieves multiple monitoring capability in confined water environments. Through radio frequency powering, the battery-free SES system demonstrates untethered motions in confined spaces with considerable moving speed under resonance. This system adopts soft electronic technologies to integrate thin multifunctional bio/chemical sensors and wireless data acquisition module, and performs real-time water quality and virus contamination detection with demonstrated promising limits of detection and high sensitivity. All sensing data are transmitted synchronously and displayed on a smartphone graphical user interface via near-field communication. Overall, this wireless smart system demonstrates broad potential for confined space exploration, ranging from pathogen detection to pollution investigation.
Topics: Water Quality; Electricity; Communication; Electric Power Supplies; Electronics
PubMed: 38198552
DOI: 10.1126/sciadv.adk6301 -
Cell Death & Disease Dec 2023The current study tested the expression and potential functions of Gαi1 in nasopharyngeal carcinoma (NPC). The Cancer Genome Atlas (TCGA) database results demonstrate...
The current study tested the expression and potential functions of Gαi1 in nasopharyngeal carcinoma (NPC). The Cancer Genome Atlas (TCGA) database results demonstrate that Gαi1 transcripts' number in NPC tissues is significantly higher than that in the normal nasal epithelial tissues. Its overexpression correlates with poor survival in certain NPC patients. Moreover, Gαi1 is significantly upregulated in NPC tissues of local primary patients and in different primary human NPC cells. Whereas its expression is relatively low in cancer-surrounding normal tissues and in primary nasal epithelial cells. Genetic silencing (via shRNA strategy) or knockout (via CRISPR-sgRNA method) of Gαi1 substantially suppressed viability, proliferation, cell cycle progression, and migration in primary NPC cells, causing significant caspase-apoptosis activation. Contrarily, ectopic Gαi1 expression exerted pro-tumorigenic activity and strengthened cell proliferation and migration in primary NPC cells. Gαi1 is important for Akt-mTOR activation in NPC cells. Akt-S6K phosphorylation was downregulated after Gαi1 shRNA or KO in primary NPC cells, but strengthened following Gαi1 overexpression. In Gαi1-silenced primary NPC cells, a S473D constitutively-active mutant Akt1 (caAkt1) restored Akt-S6K phosphorylation and ameliorated Gαi1 shRNA-induced proliferation inhibition, migration reduction and apoptosis. Bioinformatics analyses proposed zinc finger protein 384 (ZNF384) as a potential transcription factor of Gαi1. In primary NPC cells, ZNF384 shRNA or knockout (via CRISPR-sgRNA method) decreased Gαi1 mRNA and protein expression, whereas ZNF384 overexpression upregulated it. Importantly, there was an increased binding between ZNF384 protein and the Gαi1 promoter in human NPC tissues and different NPC cells. In vivo studies showed that intratumoral injection of Gαi1-shRNA-expressing adeno-associated virus (AAV) impeded subcutaneous NPC xenograft growth in nude mice. Gαi1 downregulation, Akt-mTOR inactivation, and apoptosis induction were detected in Gαi1-silenced NPC xenograft tissues. Gαi1 KO also effectively inhibited the growth of NPC xenografts in nude mice. Together, overexpressed Gαi1 exerts pro-tumorigenic activity in NPC possibly by promoting Akt-mTOR activation.
Topics: Animals; Humans; Mice; Cell Line, Tumor; Cell Proliferation; Mice, Nude; Nasopharyngeal Carcinoma; Nasopharyngeal Neoplasms; Proto-Oncogene Proteins c-akt; RNA, Guide, CRISPR-Cas Systems; RNA, Small Interfering; Signal Transduction; TOR Serine-Threonine Kinases; Transcription Factors; GTP-Binding Protein alpha Subunits, Gi-Go
PubMed: 38049415
DOI: 10.1038/s41419-023-06308-8 -
Family Medicine and Community Health Oct 2023The long-term time trend and seasonality variations of first-time medically attended respiratory syncytial virus (RSV) infections among young children are unknown. We...
OBJECTIVE
The long-term time trend and seasonality variations of first-time medically attended respiratory syncytial virus (RSV) infections among young children are unknown. We aim to examine the time trend of medically attended first-time RSV infections among young children in the USA from January 2010 through January 2023.
DESIGN
This is a population-based cohort study using electronic health records (EHRs). Monthly incidence rate of medically attended first-time RSV infection (cases per 10 000 000 person-days). A time-series regression model was used to model and predict time trends and seasonality.
SETTING
Multicenter and nationwide TriNetX Network in the USA.
PARTICIPANTS
The study population comprised children aged 0-5 years who had medical visits during the period of January 2010 to January 2023.
RESULTS
The data included 29 013 937 medical visits for children aged 05 years (46.5% girls and 53.5% boys) from January 2010 through January 2023. From 2010 through 2019, the monthly incidence rate of first-time medically attended RSV infection in children aged 05 years followed a consistent seasonal pattern. Seasonal patterns of medically attended RSV infections were significantly disrupted during the COVID-19 pandemic. In 2020, the seasonal variation disappeared with a peak incidence rate of 20 cases per 1 000 000 person-days, a decrease of 97.4% from the expected peak rate (rate ratio or RR: 0.026, 95% CI 0.017 to 0.040). In 2021, the seasonality returned but started 4 months earlier, lasted for 9 months, and peaked in August at a rate of 753 cases per 1 000 000 person-days, a decrease of 9.6% from the expected peak rate (RR: 0.90, 95% CI 0.82 to 0.99). In 2022, the seasonal pattern is similar to prepandemic years but reached a historically high rate of 2182 cases per 10 000 000 person-days in November, an increase of 143% from the expected peak rate (RR: 2.43, 95% CI 2.25 to 2.63). The time trend and seasonality of the EHR-based medically attended RSV infections are consistent with those of RSV-associated hospitalisations from the Centers for Disease Control and Prevention (CDC) survey-based surveillance system.
CONCLUSION
The findings show the disrupted seasonality during the COVID-19 pandemic and a historically high surge of paediatric RSV cases that required medical attention in 2022. Our study demonstrates the potential of EHRs as a cost-effective alternative for real-time pathogen and syndromic surveillance of unexpected disease patterns including RSV infection.
Topics: Male; Female; Humans; Child; Child, Preschool; Cohort Studies; Pandemics; COVID-19; Respiratory Syncytial Virus Infections; Respiratory Syncytial Virus, Human
PubMed: 37844966
DOI: 10.1136/fmch-2023-002453 -
Frontiers in Oncology 2023Hepatitis B virus (HBV) is identified as a major risk factor for hepatocellular carcinoma (HCC), resulting in so-called hepatitis B virus-related hepatocellular... (Review)
Review
Hepatitis B virus (HBV) is identified as a major risk factor for hepatocellular carcinoma (HCC), resulting in so-called hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC). Hepatectomy for HCC is acknowledged as an efficient treatment strategy, especially for early HCC. Furthermore, patients with advanced HCC can still obtain survival benefits through surgical treatment combined with neoadjuvant therapy, adjuvant therapy, transcatheter arterial chemoembolization, and radiofrequency ablation. Therefore, preoperative and postoperative predictors of HBV-related HCC have crucial indicative functions for the follow-up treatment of patients with feasible hepatectomy. This review covers a variety of research results on preoperative and postoperative predictors of hepatectomy for HBV-related HCC over the past decade and in previous landmark studies. The relevant contents of Hepatitis C virus-related HCC, non-HBV non-HCV HCC, and the artificial intelligence application in this field are briefly addressed in the extended content. Through the integration of this review, a large number of preoperative and postoperative factors can predict the prognosis of HBV-related HCC, while most of the predictors have no standardized thresholds. According to the characteristics, detection methods, and application of predictors, the predictors can be divided into the following categories: 1. serological and hematological predictors, 2. genetic, pathological predictors, 3. imaging predictors, 4. other predictors, 5. analysis models and indexes. Similar results appear in HCV-related HCC, non-HBV non-HCV HCC. Predictions based on AI and big biological data are actively being applied. A reasonable prediction model should be established based on the economic, health, and other levels in specific countries and regions.
PubMed: 37519791
DOI: 10.3389/fonc.2023.1230164 -
Frontiers in Microbiology 2023The integration of human papillomavirus (HPV) is closely related to the occurrence of cervical cancer. However, little is known about the complete state of HPV...
BACKGROUND
The integration of human papillomavirus (HPV) is closely related to the occurrence of cervical cancer. However, little is known about the complete state of HPV integration into the host genome.
METHODS
In this study, three HPV-positive cell lines, HeLa, SiHa, and CaSki, were subjected to NANOPORE long-read sequencing to detect HPV integration. Analysis of viral integration patterns using independently developed software (HPV-TSD) yielded multiple complete integration patterns for the three HPV cell lines.
RESULTS
We found distinct differences between the integration patterns of HPV18 and HPV16. Furthermore, the integration characteristics of the viruses were significantly different, even though they all belonged to HPV16 integration. The HPV integration in the CaSki cells was relatively complex. The HPV18 integration status in HeLa cells was the dominant, whereas the percentage of integrated HPV 16 in SiHa and CaSki cells was significantly lower. In addition, the virus sequences in the HeLa cells were incomplete and existed in an integrated state. We also identified a large number of tandem repeats in HPV16 and HPV18 integration. Our study not only clarified the feasibility of high-throughput long-read sequencing in the study of HPV integration, but also explored a variety of HPV integration models, and confirmed that viral integration is an important form of HPV in cell lines.
CONCLUSION
Elucidating HPV integration patterns will provide critical guidance for developing a detection algorithm for HPV integration, as well as the application of virus integration in clinical practice and drug research and development.
PubMed: 38169727
DOI: 10.3389/fmicb.2023.1294146 -
Journal of Infection and Public Health Aug 2023Treating marginalized populations with HCV infection for elimination is faced with the challenge for the integration of HCV screening service offered for patients often...
BACKGROUND
Treating marginalized populations with HCV infection for elimination is faced with the challenge for the integration of HCV screening service offered for patients often moving across multiple settings. We envisaged a novel collaborative care approach to identify to what extent HCV patients overlapped between and within these multiple institutions and reported the findings of treatment coverage of these marginalized populations after HCV care cascades.
METHODS
We enrolled 7765 patients residing in the Changhua County, Taiwan offered with HCV screening from correctional institutions, HIV clinics, methadone clinics, and the existing HIV surveillance program (four subgroups including police-arrested people, probationers, non-injection drug user, and high-risk behavior people) between 2019 and 2020. The collaborative care and information were integrated through a teamwork of gastroenterologists, psychologists, infectious disease specialists, and nursing coordinators under the auspices of local health authority.
RESULTS
The overall participation rate in HCV screening was 92.65% (7194/7765). The prevalence rate was the highest in methadone clinics (90.17%) followed by correctional institutions (37.67%), HIV clinics (34.60%), and the surveillance program (18.14%). We found 25.41% (77/303) of methadone clinic patients, 17.65% (129/731) of HIV clinic patients, and various proportions for 44.09% (41/93) of deferred prosecuted or probationers under surveillance program were also recruited into other settings. Individuals' patient flow within setting was more frequent than that between setting. After calibrating the overlap of patient flow, a total of 1700 anti-HCV positives out of 4074 after screening were traced with available follow-up information to complete 92.52% treatment coverage of 1177 RNA-positives (77.23%) diagnosed from 1524 undergoing RNA testing with similar findings across multiple settings.
CONCLUSION
A new collaborative integrated care was adopted for elucidating patient flow between and within multiple settings in order to calibrate the accurate demand for HCV care cascades and enhance HCV treatment coverage in marginalized populations.
Topics: Humans; HIV Infections; Substance Abuse, Intravenous; Hepatitis C; Hepacivirus; Methadone; Antiviral Agents
PubMed: 37271101
DOI: 10.1016/j.jiph.2023.05.019 -
PeerJ 2023Influenza viruses pose a significant and ongoing threat to human health. Many host factors have been identified to be associated with influenza virus infection. However,...
Influenza viruses pose a significant and ongoing threat to human health. Many host factors have been identified to be associated with influenza virus infection. However, there is currently a lack of an integrated resource for these host factors. This study integrated human genes and proteins associated with influenza virus infections for 14 subtypes of influenza A viruses, as well as influenza B and C viruses, and built a database named H2Flu to store and organize these genes or proteins. The database includes 28,639 differentially expressed genes (DEGs), 1,850 differentially expressed proteins, and 442 proteins with differential posttranslational modifications after influenza virus infection, as well as 3,040 human proteins that interact with influenza virus proteins and 57 human susceptibility genes. Further analysis showed that the dynamic response of human cells to virus infection, cell type and strain specificity contribute significantly to the diversity of DEGs. Additionally, large heterogeneity was also observed in protein-protein interactions between humans and different types or subtypes of influenza viruses. Overall, the study deepens our understanding of the diversity and complexity of interactions between influenza viruses and humans, and provides a valuable resource for further studies on such interactions.
Topics: Humans; Influenza, Human; Multiomics; Orthomyxoviridae Infections; Influenza A virus
PubMed: 37842064
DOI: 10.7717/peerj.16194