Viruses最新文献

{"title":"Complex Evolutionary Dynamics of H5N8 Influenza A Viruses Revealed by Comprehensive Reassortment Analysis","authors":"Egor Degtyarev, Sofia Feoktistova, Pavel Volchkov, Andrey Deviatkin","doi":"10.3390/v16091405","DOIUrl":"https://doi.org/10.3390/v16091405","url":null,"abstract":"Influenza A viruses (IAVs) circulate among different species and have the potential to cause significant pandemics in humans. This study focuses on reassortment events in the H5N8 subtype of IAV, which poses a serious threat to public health due to its high pathogenicity in birds and potential for cross-species transmission. We retrieved 2359 H5N8 IAV sequences from GISAID, and filtered and analyzed 442 complete genomic sequences for reassortment events using pairwise distance deviation matrices (PDDMs) and pairwise distance correspondence plots (PDCPs). This detailed case study of specific H5N8 viruses revealed previously undescribed reassortment events, highlighting the complex evolutionary history and potential pandemic threat of H5N8 IAVs.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation and Characterization of a Frog Virus 3 Strain from a Wood Frog (Rana sylvatica) in Wood Buffalo National Park","authors":"Samantha R. Logan, Sibelle Torres Vilaça, Joe-Felix Bienentreu, Danna M. Schock, David Lesbarrères, Craig R. Brunetti","doi":"10.3390/v16091411","DOIUrl":"https://doi.org/10.3390/v16091411","url":null,"abstract":"Members of the Iridoviridae family, genus Ranavirus, represent a group of globally emerging pathogens of ecological and economic importance. In 2017, an amphibian die-off of wood frogs (Rana sylvatica) and boreal chorus frogs (Pseudacris maculata) was reported in Wood Buffalo National Park, Canada. Isolation and complete genomic sequencing of the tissues of a wood frog revealed the presence of a frog virus 3 (FV3)-like isolate, Rana sylvatica ranavirus (RSR), with a genome size of 105,895 base pairs, 97 predicted open reading frames (ORFs) bearing sequence similarity to FV3 (99.98%) and a FV3-like isolate from a spotted salamander in Maine (SSME; 99.64%). Despite high sequence similarity, RSR had a unique genomic composition containing ORFs specific to either FV3 or SSME. In addition, RSR had a unique 13 amino acid insertion in ORF 49/50L. No differences were found in the in vitro growth kinetics of FV3, SSME, and RSR; however, genomic differences between these isolates were in non-core genes, implicated in nucleic acid metabolism and immune evasion. This study highlights the importance of viral isolation and complete genomic analysis as these not only provide information on ranavirus spatial distribution but may elucidate genomic factors contributing to host tropism and pathogenicity.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"mRNA Vaccination: An Outlook on Innate Sensing and Adaptive Immune Responses","authors":"Janan Shoja Doost, Fatemeh Fazel, Nitish Boodhoo, Shayan Sharif","doi":"10.3390/v16091404","DOIUrl":"https://doi.org/10.3390/v16091404","url":null,"abstract":"Vaccination has led to significant dismantling of infectious diseases worldwide. Since the dawn of the SARS-CoV-2 pandemic, there has been increased popularity in the usage and study of the mRNA vaccine platform. Here, we highlight fundamental knowledge on mRNA vaccine pharmacology, followed by the immunity conferred by innate sensing and adaptive responses resulting from exposure to the mRNA vaccine construct and encapsulation materials. A better understanding of these immune mechanisms will shed light on further improvements in mRNA vaccine design, aiming to improve efficiency and optimize immune responses upon inoculation.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards the Development of a Minigenome Assay for Species A Rotaviruses","authors":"Ola Diebold, Shu Zhou, Colin Peter Sharp, Blanka Tesla, Hou Wei Chook, Paul Digard, Eleanor R. Gaunt","doi":"10.3390/v16091396","DOIUrl":"https://doi.org/10.3390/v16091396","url":null,"abstract":"RNA virus polymerases carry out multiple functions necessary for successful genome replication and transcription. A key tool for molecular studies of viral RNA-dependent RNA polymerases (RdRps) is a ‘minigenome’ or ‘minireplicon’ assay, in which viral RdRps are reconstituted in cells in the absence of full virus infection. Typically, plasmids expressing the viral polymerase protein(s) and other co-factors are co-transfected, along with a plasmid expressing an RNA encoding a fluorescent or luminescent reporter gene flanked by viral untranslated regions containing cis-acting elements required for viral RdRp recognition. This reconstitutes the viral transcription/replication machinery and allows the viral RdRp activity to be measured as a correlate of the reporter protein signal. Here, we report on the development of a ‘first-generation’ plasmid-based minigenome assay for species A rotavirus using a firefly luciferase reporter gene.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High Levels of Incidental COVID-19 Infection in Emergency Urology Admissions: A Propensity Score-Matched Real World Data Analysis across Surgical Specialties","authors":"Alex Qinyang Liu, Eric Ka-Ho Choy, Peter Ka-Fung Chiu, Chi-Hang Yee, Chi-Fai Ng, Jeremy Yuen-Chun Teoh","doi":"10.3390/v16091402","DOIUrl":"https://doi.org/10.3390/v16091402","url":null,"abstract":"Background: An incidental COVID-19 infection is often found in patients admitted for non-COVID-19-related conditions. This study aims to investigate the incidence of COVID-19 infections across surgical specialties including urology, general surgery, and orthopaedic surgery. Methods: This is a retrospective cohort study based on a territory-wide electronic database in Hong Kong. All emergency in-hospital admissions under the urology, general surgery, and orthopaedic surgery divisions in the public healthcare system in Hong Kong from January to September 2022 were included. All patients were routinely screened for SARS-CoV-2, based on admission protocols during the investigation period. Baseline characteristics were retrieved, with 1:1:1 propensity score matching being performed. Incidental COVID-19 rates were then compared across specialties. Results: A total of 126,034 patients were included. After propensity score matching, the baseline characteristics were well balanced, and 8535 patients in each group were analysed. Urology admission was noted to have a statistically significant higher incidence of incidental COVID-19 at 9.3%, compared to general surgery (5.4%) or orthopaedic surgery (5.6%). Amongst urology patients with incidental COVID-19 infection, 35.8% were admitted for retention of urine, 27.9% for haematuria, and 8.6% for a urinary tract infection. Conclusions: This large-scale cohort study demonstrated that incidental COVID-19 rates differ between surgical specialties, with urology having the highest proportion of incidental COVID-19 infection.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wastewater Surveillance of SARS-CoV-2: A Comparison of Two Concentration Methods","authors":"Christina Diamanti, Lambros Nousis, Petros Bozidis, Michalis Koureas, Maria Kyritsi, George Markozannes, Nikolaos Simantiris, Eirini Panteli, Anastasia Koutsolioutsou, Konstantinos Tsilidis, Christos Hadjichristodoulou, Alexandra Koutsotoli, Eirini Christaki, Dimitrios Alivertis, Aristides Bartzokas, Konstantina Gartzonika, Chrysostomos Dovas, Evangelia Ntzani","doi":"10.3390/v16091398","DOIUrl":"https://doi.org/10.3390/v16091398","url":null,"abstract":"Wastewater surveillance is crucial for the epidemiological monitoring of SARS-CoV-2. Various concentration techniques, such as skimmed milk flocculation (SMF) and polyethylene glycol (PEG) precipitation, are employed to isolate the virus effectively. This study aims to compare these two methods and determine the one with the superior recovery rates. From February to December 2021, 24-h wastewater samples were collected from the Ioannina Wastewater Treatment Plant’s inlet and processed using both techniques. Subsequent viral genome isolation and a real-time RT-qPCR detection of SARS-CoV-2 were performed. The quantitative analysis demonstrated a higher detection sensitivity with a PEG-based concentration than SMF. Moreover, when the samples were positive by both methods, PEG consistently yielded higher viral loads. These findings underscore the need for further research into concentration methodologies and the development of precise protocols to enhance epidemiological surveillance through wastewater analysis.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Torque Teno Sus Virus 1: A Potential Surrogate Pathogen to Study Pig-Transmitted Transboundary Animal Diseases","authors":"Xiaolong Li, Brandon M. Parker, Raoul K. Boughton, James C. Beasley, Timothy J. Smyser, James D. Austin, Kim M. Pepin, Ryan S. Miller, Kurt C. Vercauteren, Samantha M. Wisely","doi":"10.3390/v16091397","DOIUrl":"https://doi.org/10.3390/v16091397","url":null,"abstract":"Understanding the epidemiology and transmission dynamics of transboundary animal diseases (TADs) among wild pigs (Sus scrofa) will aid in preventing the introduction or containment of TADs among wild populations. Given the challenges associated with studying TADs in free-ranging populations, a surrogate pathogen system may predict how pathogens may circulate and be maintained within wild free-ranging swine populations, how they may spill over into domestic populations, and how management actions may impact transmission. We assessed the suitability of Torque teno sus virus 1 (TTSuV1) to serve as a surrogate pathogen for molecular epidemiological studies in wild pigs by investigating the prevalence, persistence, correlation with host health status and genetic variability at two study areas: Archbold’s Buck Island Ranch in Florida and Savannah River Site in South Carolina. We then conducted a molecular epidemiological case study within Archbold’s Buck Island Ranch site to determine how analysis of this pathogen could inform transmission dynamics of a directly transmitted virus. Prevalence was high in both study areas (40%, n = 190), and phylogenetic analyses revealed high levels of genetic variability within and between study areas. Our case study showed that pairwise host relatedness and geographic distance were highly correlated to pairwise viral genetic similarity. Molecular epidemiological analyses revealed a distinct pattern of direct transmission from pig to pig occurring within and between family groups. Our results suggest that TTSuV1 is highly suitable for molecular epidemiological analyses and will be useful for future studies of transmission dynamics in wild free-ranging pigs.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Prevalence and Molecular Characterization of Bovine Leukemia Virus among Dairy Cattle in Henan Province, China","authors":"Yuxi Zhao, Xiaojie Zhu, Zhen Zhang, Jianguo Chen, Yingyu Chen, Changmin Hu, Xi Chen, Ian D. Robertson, Aizhen Guo","doi":"10.3390/v16091399","DOIUrl":"https://doi.org/10.3390/v16091399","url":null,"abstract":"Enzootic bovine leukosis, a neoplastic disease caused by the bovine leukemia virus (BLV), was the primary cancer affecting cattle in China before 1985. Although its prevalence decreased significantly between 1986 and 2000, enzootic bovine leukosis has been re-emerging since 2000. This re-emergence has been largely overlooked, possibly due to the latent nature of BLV infection or the perceived lack of sufficient evidence. This study investigated the molecular epidemiology of BLV infections in dairy cattle in Henan province, Central China. Blood samples from 668 dairy cattle across nine farms were tested using nested polymerase chain reaction assays targeting the partial envelope (env) gene (gp51 fragment). Twenty-three samples tested positive (animal-level prevalence of 3.4%; 95% confidence interval: 2.2, 5.1). The full-length env gene sequences from these positive samples were obtained and phylogenetically analyzed, along with previously reported sequences from the GenBank database. The sequences from positive samples were clustered into four genotypes (1, 4, 6, and 7). The geographical annotation of the maximum clade credibility trees suggested that the two genotype 1 strains in Henan might have originated from Japan, while the genotype 7 strain is likely to have originated from Moldova. Subsequent Bayesian stochastic search variable selection analysis further indicated a strong geographical association between the Henan strains and Japan, as well as Moldova. The estimated substitution rate for the env gene ranged from 4.39 × 10−4 to 2.38 × 10−3 substitutions per site per year. Additionally, codons 291, 326, 385, and 480 were identified as positively selected sites, potentially associated with membrane fusion, epitope peptide vaccine design, and transmembrane signal transduction. These findings contribute to the broader understanding of BLV epidemiology in Chinese dairy cattle and highlight the need for measures to mitigate further BLV transmission within and between cattle herds in China.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resistance of the CRISPR-Cas13a Gene-Editing System to Potato Spindle Tuber Viroid Infection in Tomato and Nicotiana benthamiana","authors":"Ying Wei Khoo, Qingsong Wang, Shangwu Liu, Binhui Zhan, Tengfei Xu, Wenxia Lv, Guangjing Liu, Shifang Li, Zhixiang Zhang","doi":"10.3390/v16091401","DOIUrl":"https://doi.org/10.3390/v16091401","url":null,"abstract":"Gene-editing technology, specifically the CRISPR-Cas13a system, has shown promise in breeding plants resistant to RNA viruses. This system targets RNA and, theoretically, can also combat RNA-based viroids. To test this, the CRISPR-Cas13a system was introduced into tomato plants via transient expression and into Nicotiana benthamiana through transgenic methods, using CRISPR RNAs (crRNAs) targeting the conserved regions of both sense and antisense genomes of potato spindle tuber viroid (PSTVd). In tomato plants, the expression of CRISPR-Cas13a and crRNAs substantially reduced PSTVd accumulation and alleviated disease symptoms. In transgenic N. benthamiana plants, the PSTVd levels were lower as compared to wild-type plants. Several effective crRNAs targeting the PSTVd genomic RNA were also identified. These results demonstrate that the CRISPR-Cas13a system can effectively target and combat viroid RNAs, despite their compact structures.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Israeli Acute Paralysis Virus Is an Emerging Pathogen Contributing to Brood Disease of Apis cerana","authors":"Yanling Xie, Shuai Wang, Yao Liu, Jie Deng, Xiaoling Su, Zhichu Huang, Huoqing Zheng","doi":"10.3390/v16091395","DOIUrl":"https://doi.org/10.3390/v16091395","url":null,"abstract":"Larval mortality is the primary symptom of diseased Apis cerana colonies, often attributed to sacbrood virus (SBV) and Melissococcus plutonius. However, the impact of other common honeybee viruses is frequently overlooked, and their pathogenicity to A. cerana remains poorly understood. To investigate the causes of the increasing disease incidence in A. cerana brood, we conducted an epidemiological survey, collecting 70 samples from 19 sites across nine provinces in China. Furthermore, we examined the pathogenicity of Israeli acute paralysis virus (IAPV) in A. cerana brood through artificial inoculation experiments. Our results demonstrate that, besides SBV and M. plutonius, the infection rate and viral load of IAPV in diseased brood are significantly high. Brood artificially inoculated with high concentrations of IAPV exhibited a significant increase in mortality and displayed clinical symptoms similar to those observed in naturally infected colonies. Moreover, a limited resistance to IAPV was observed in A. cerana brood, with some individuals able to restrict viral proliferation. Our study highlights the previously unrecognized pathogenicity of IAPV to A. cerana brood, demonstrating that IAPV poses a significant threat similar to SBV and M. plutonius. We emphasize that IAPV should be recognized as an emerging pathogen causing brood disease in A. cerana and managed accordingly in beekeeping practices.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}