Acta virologica最新文献

{"title":"Comprehensive codon usage analysis of the African Swine Fever Virus","authors":"Makoye Mhozya Kanyema, Mingyang Cheng, Jiawei Luo, Mei Lu, Xinyuan Xing, Yu Sun, Junhong Wang, Yiyuan Lu, Chunwei Shi, Yan Zeng, Guilian Yang, Xin Cao, Chunfeng Wang","doi":"10.3389/av.2023.11562","DOIUrl":"https://doi.org/10.3389/av.2023.11562","url":null,"abstract":"The non-uniform usage of synonymous codons occurs in genomes of all organisms, including DNA and RNA viruses. The preferential selection of a codon at the expense of other synonymous codons within the same group is known as Codon Usage Bias. The understanding of this bias assists in unveiling the factors driving molecular evolution, as defined by the selection-mutation-drift theory. According to this model, molecular evolution is predominantly driven by mutation, natural selection, and genetic drift. Nevertheless, elements like nucleotide composition, gene length, and protein secondary structure also contribute to this process. Comprehensive genomic analyses that highlight the codon usage preference of the African Swine Fever Virus (ASFV) are infrequent. ASFV, a hemorrhagic and highly contagious viral disease, almost invariably results in 100% fatality among infected pigs and wild boars. This study, therefore, embarked on a thorough examination of codon usage patterns in ASFV’s complete genomic sequences, an endeavor of great relevance to molecular evolution studies, complex transmission models, and vaccine research. For an exhaustive evaluation of ASFV’s whole-genome codon usage, we used parameters like ENC, RSCU, and CAI. A Principal Component Analysis was carried out to reaffirm the interconnected RSCU lineages based on the continent, and their evolutionary relationships were later elucidated through phylogenetic tree construction. ASFV emerged as a low-biased codon user (ENC = 52.8) that is moderately adapted to its host. Its genome has a high AT composition (64.05%), suggesting the impact of mutational pressure on genomic evolution. However, neutrality plot analysis revealed natural selection’s slight supremacy over mutational pressure. The low codon bias (>45) implies ASFV’s diverse usage of synonymous codons within a given codon family, allowing for effective translation and subsequent successful viral replication cycles. Its moderate adaptation (CAI = 0.56) permits the virus to infect a range of hosts, including reservoirs such as warthogs and bush pigs. To the best of our knowledge, this is the pioneering report providing a comprehensive examination of ASFV’s complete genomic sequences. Consequently, research focusing on viral gene expression and regulation, gene function prediction, parasite-host interaction, immune dysfunction, and drug and vaccine design may find this report to be a valuable resource.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135153669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Berberine inhibitory action against zika and dengue viruses in cell cultures","authors":"Denise A. Giannone, Luana E. Piccini, J. E. Brunetti, V. M. Quintana, E. Damonte, V. Castilla","doi":"10.3389/av.2023.11931","DOIUrl":"https://doi.org/10.3389/av.2023.11931","url":null,"abstract":"Berberine (BBR) is a plant derived isoquinoline alkaloid that displays a great variety of biological activities. In this study we showed that BBR exhibits a strong antiviral activity with broad spectrum of inhibition against different strains of Zika virus (ZIKV) and the four serotypes of dengue virus (DENV) in Vero cells. The inhibitory effect of BBR on ZIKV and DENV-2 growth was also demonstrated in human cell lines. The analysis of BBR mode of action showed that the compound did not affect early events of viral multiplication cycle or viral protein expression. By contrast, BBR strongly impaired the formation of intracellular and extracellular infectious viral particles. Furthermore, BBR was able to inhibit ZIKV induced activation of ERK1/2 and p38 cell signaling pathways and also reduced p38 phosphorylation in uninfected cells. Like BBR, the p38 inhibitor SB202190 reduced p38 phosphorylation in both uninfected and ZIKV infected cultures and caused a significant diminishment of viral yields even when it was added late during the infection. These results suggest for the first time that the inhibitory effect of BBR on p38 signaling might contribute to the antiviral action of the compound against flaviviruses.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47774476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vitro induction of neutrophil extracellular traps by SARS-CoV-2 is biased by extracellular mitochondria","authors":"J. Janko, M. Sláviková, Boris Klempa, Peter Celec, Michal Pastorek","doi":"10.3389/av.2023.11801","DOIUrl":"https://doi.org/10.3389/av.2023.11801","url":null,"abstract":"The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has a highly variable course that is dependent on the host immune system reaction. Lung tissue damage, endothelial dysfunction, and microthrombosis in severe COVID-19 is linked to neutrophilia and the production of neutrophil extracellular traps (NETs). Previous studies have shown that NETs are involved in the pathology of COVID-19 and that the virus itself induces NET formation, although the underlying mechanisms are not clear. In this study, we aimed to investigate the induction of NETs by SARS-CoV-2 in vitro. We have found that both, infectious and heat-inactivated virus induce NETs formation. Surprisingly, cell culture media derived from uninfected Vero cells exhibit similar potency. This suggests that NET inducers other than the virus might be involved. Mitochondria released from dying cells during SARS-CoV-2 infection acting as damage-associated molecular patterns (DAMPs) were identified as potential contributors to neutrophil activation and NET formation. Our findings point to an important source of bias when analyzing NETs induction by SARS-CoV-2 in vitro, but also the immune reaction to viruses in general. Further implications for the understanding of COVID-19 pathogenesis remain to be elucidated.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47405949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immunity towards human respiratory syncytial virus","authors":"Dahiana Correa, Diana M Giraldo, Salomon Gallego, N. Taborda, Juan C. Hernández","doi":"10.3389/av.2023.11887","DOIUrl":"https://doi.org/10.3389/av.2023.11887","url":null,"abstract":"Respiratory infections remain a significant cause of morbidity and mortality, becoming a serious public health issue worldwide. The human respiratory syncytial virus (hRSV) is still one of the most relevant pathogenic agents involved in respiratory infections in children, the leading cause of bronchiolitis worldwide. In most cases, hRSV infection is not complicated; however, limited treatment and vaccine options increase the morbidity rates associated with bronchiolitis. The innate immune response governs the severity of the disease and controls the viral infection outcome. Current knowledge about the mechanisms involved in viral PAMPs (pathogen-associated molecular pattern molecules) recognition, genetic characteristics of the inflammatory response, and understanding of antiviral response is crucial for vaccine development and biomarker tools to predict complications and guide therapeutic management. Here, we review key concepts related to pathogenesis and immune response against hRSV, highlighting aspects that could be considered in vaccine development.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48258750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Initial high throughput proteomic analysis reveals alterations in CD19+ B lymphocyte profile in acute COVID-19 patients","authors":"Miroslav Marcin, Ondrej Zahornacký, Mária Kacírová, M. Sulíková, Miloslava Bajer-Ďuráčová, P. Rehulka, P. Bober, J. Fedacko, P. Jarčuška, J. Sabó","doi":"10.3389/av.2023.11702","DOIUrl":"https://doi.org/10.3389/av.2023.11702","url":null,"abstract":"The immune response to SARS-CoV-2, the virus responsible for COVID-19, involves intricate interactions between immune cells and viral antigens. CD19+ lymphocytes play a critical role in driving the humoral immune response. In this study, high-throughput proteomic analysis was performed using tandem mass spectrometry to investigate the changes in proteomic profiles of CD19+ whole cell lysates from 6 healthy individuals and 6 acute COVID-19 patients. The volcano plot and heat map showed significant differences in proteomic profiles between these two groups, indicating a distinct molecular signature associated with acute COVID-19. Enrichment analysis, especially over-representation analysis (ORA) using the Reactome database, revealed that proteins involved in neutrophil degranulation and interferon alpha/beta signaling pathways were among the most affected, indicating alterations in key defense processes. These findings, therefore, provide new insights into the molecular mechanisms underlying CD19+ cell responses in acute COVID-19.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45679641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vitro antiviral activity of abietane diterpenoids isolated from Torreya nucifera against rotavirus infection","authors":"J. S. Park, J. Bae, J. Jung, Joong-Sun Kim, Su-Jin Park","doi":"10.3389/av.2023.11630","DOIUrl":"https://doi.org/10.3389/av.2023.11630","url":null,"abstract":"Although vaccines have been developed for rotavirus infections, there is currently no effective therapeutic treatment. Therefore, this study aimed to evaluate the efficacy of 18-hydroxyferruginol (1) and 18-oxoferruginol (2) isolated from Torreya nucifera (T. nucifera) against bovine G8P[7] and porcine G5P[7] rotaviruses using two different assay strategies: 1) reduction of viral infectivity by neutralizing the virus (virucidal assay) and 2) inhibition of viral replication after infection (post-treatment assay). In the post-treatment assay, compounds 1 and 2 exhibited strong anti-rotavirus activity, with 50% effective concentration values of 24.7 μM (selectivity index; SI= 2.52) and 23.2 μM (SI= 1.75) against bovine G8P[7], 21.1 μM (SI= 2.95) and 22.6 μM (SI= 1.80) against porcine G5P[7], respectively. During viral replication, the two compounds demonstrated stronger inhibition of viral RNA synthesis in the late stages (18 h) than in the early stages (6 h). Compounds 1 and 2 also inhibited the synthesis of viral proteins such as VP6, as determined by immunofluorescence assay. Thus, it appears that compounds 1 and 2 isolated from T. nucifera possess strong antiviral activity against rotaviruses, inhibit viral replication, and may be developed into potential plant-derived therapeutic candidates against rotavirus infection.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":"1 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45220133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of multiple putative novel hepatitis B virus spliced DNA from a chronic hepatitis B patient","authors":"Yihan Xiao, Zhigang Cui, Xiaojun Zhou, Zong-Hua Li, Lihua Li, Lixian Wu, Long Sun, Xiuji Cui","doi":"10.3389/av.2023.11663","DOIUrl":"https://doi.org/10.3389/av.2023.11663","url":null,"abstract":"Spliced hepatitis B virus (HBV) RNA has been reported to affect the viral life cycle and progression of liver disease. As much as 30% of HBV RNA are spliced in infected cells, and some can be reverse transcribed to spliced DNA. To date, only a small number of spliced DNA have been identified and the majority require further investigation. This study aimed to identify the types of spliced DNA from the sera of a chronic hepatitis B patient. HBV DNA was isolated from the serum, and both full-length and spliced DNA were amplified by PCR. The amplified PCR products were then subcloned and sequenced using a Sanger sequence analysis. As a result, 19 types of spliced DNA were identified, 11 of which were assumed to be putative novel spliced DNA. These spliced DNA were doubly spliced with varied splice donor sites and splice acceptor sites. In addition to the frequently detected HBV SP1, SP2, and SP4, we also identified 11 putative novel spliced DNA in the serum. These findings indicate the complexity of HBV RNA splicing during viral life cycle.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47542519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of the SARS-CoV-2 Omicron (B.1.1.529) variant and booster vaccine doses on the seroprevalence of specific IgG antibodies in the staff of the Slovak Academy of Sciences","authors":"I. Kajanová, L. Jelenska, Ľ. Lukáčiková, Katarina Grossmannova, Martina Belisova, Nikola Istvanova, Natalia Gasparovicová, V. Zelník, S. Pastoreková, Z. Radiková, J. Kopáček","doi":"10.3389/av.2023.11637","DOIUrl":"https://doi.org/10.3389/av.2023.11637","url":null,"abstract":"The presented seroprevalence study focused on specific antibodies to the SARS-CoV-2 virus is the second survey conducted among SAS employees. Its realization enabled monitoring of the impact of booster vaccination doses and the spread of the Omicron variant in a defined group of people. The total seropositivity of the involved SAS employees in autumn 2022 was 96.04%. In the group of vaccinated participants (1,189) the seropositivity rate was 99.5%, while among unvaccinated participants (176) it was 72.73%. By October 2022, when the study was conducted, 65.05% (888) of the participants have had a positive PCR/Ag test for SARS-CoV-2 at least once. Based on the presence of antibodies against the nucleoprotein (NCP) of SARS-CoV-2 it was proven, that 27.39% of participants (25.12% of vaccinated; 51.22% of non-vaccinated) who have never had a positive PCR/Ag test for SARS-CoV-2, overcame the COVID-19. According to self-assessment of the disease course, it was shown that a severe course occurred in 6.31% of the participants who overcame the disease without prior vaccination and in 1.44% of the participants who overcame COVID-19 after completing the baseline vaccination scheme. The most significant finding of the study is the evidence of significantly lower levels of specific antibodies after overcoming the Omicron variant of SARS-CoV-2, and thus its reduced immunogenicity compared to ancestral virus and earlier variants of concern.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44382588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heat inactivation by high temperature as an approach to combat infections caused by airborne pathogens","authors":"M. Sláviková, J. Strukova, B. Klempa, F. Simančík, S. Pastoreková, V. Zelník, J. Kopáček","doi":"10.3389/av.2023.11640","DOIUrl":"https://doi.org/10.3389/av.2023.11640","url":null,"abstract":"The current pandemic of SARS-CoV-2 coronavirus infection has highlighted the importance of control measures to combat infections caused by airborne pathogens. Non-specific actions include various means of microorganism inactivation by chemical or physical methods targeting structural components of a given pathogen. Exposure of viruses and bacteria to elevated temperatures is one of the effective methods for discharging their harmful potential. Using a model of the Human Adenovirus 5 exposed to elevated temperatures with subsequent titration of the virus in vitro in A549 cells, we showed a dramatic decrease of the virus titer after heat treatment for 5 s at temperatures over 100°C. To verify the potential of the heat inactivation in a closed environment, the prototype of a high-capacity pathogen-cleaning device was constructed and tested. Application of the device for 2 h at an airflow rate of 900 m3/h in a room of 226 m3 reduced the total number of microorganisms in the air by more than 50% at all collection sites in the room.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42830268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The modulation of metabolomics and antioxidant stress is involved in the effect of nitazoxanide against influenza A virus in vitro","authors":"Zhen Huang, Haihong Zheng, Yanping Wang, Xiao-yang Wang, Chunmei Wang, Yingchun Liu, Wen Zhou, Zhaoxiong Wang, Ke‐Zhi Zhang","doi":"10.3389/av.2023.11612","DOIUrl":"https://doi.org/10.3389/av.2023.11612","url":null,"abstract":"The prevalence of highly infectious influenza A virus (IAV) is still a major threat to global human health. Nitazoxanide (NTZ) possesses potent antiviral properties against the influenza virus. However, the role of small molecular metabolites and antioxidant stress in the NTZ’s anti-influenza virus mechanism is not yet fully understood. This study compared the changes in cellular metabolism, ROS levels, antioxidant enzyme activities, and Keap-1/Nrf2 pathway in IAV-infected MDCK cells after NTZ treatment in vitro, using LC-MS-based metabolomics, flow cytometry, immunoblot. We observed that the NTZ treatment in the IAV-infected cells drastically altered the metabolism of small molecules, among which eleven metabolites were highly relevant to NTZ. The virus induced oxidative stress was also remarkably suppressed by NTZ. Meanwhile, the Nrf2 pathway and some proteins with modulating antiviral activity were activated after NTZ treatment, protecting cells from IAV injury. Therefore, regulation of the intracellular oxidative state is the primary outcome of NTZ treatment, which may underpin an antiviral mechanism attributed to the thiazolide.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42413702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}