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Combining Short- and Long-Read Sequencing Technologies to Identify SARS-CoV-2 Variants in Wastewater. 结合短程和长程测序技术鉴定废水中的 SARS-CoV-2 变异株
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-21 DOI: 10.3390/v16091495
Gabrielle Jayme, Ju-Ling Liu, Jose Hector Galvez, Sarah Julia Reiling, Sukriye Celikkol, Arnaud N'Guessan, Sally Lee, Shu-Huang Chen, Alexandra Tsitouras, Fernando Sanchez-Quete, Thomas Maere, Eyerusalem Goitom, Mounia Hachad, Elisabeth Mercier, Stephanie Katharine Loeb, Peter A Vanrolleghem, Sarah Dorner, Robert Delatolla, B Jesse Shapiro, Dominic Frigon, Jiannis Ragoussis, Terrance P Snutch
{"title":"Combining Short- and Long-Read Sequencing Technologies to Identify SARS-CoV-2 Variants in Wastewater.","authors":"Gabrielle Jayme, Ju-Ling Liu, Jose Hector Galvez, Sarah Julia Reiling, Sukriye Celikkol, Arnaud N'Guessan, Sally Lee, Shu-Huang Chen, Alexandra Tsitouras, Fernando Sanchez-Quete, Thomas Maere, Eyerusalem Goitom, Mounia Hachad, Elisabeth Mercier, Stephanie Katharine Loeb, Peter A Vanrolleghem, Sarah Dorner, Robert Delatolla, B Jesse Shapiro, Dominic Frigon, Jiannis Ragoussis, Terrance P Snutch","doi":"10.3390/v16091495","DOIUrl":"https://doi.org/10.3390/v16091495","url":null,"abstract":"<p><p>During the COVID-19 pandemic, the monitoring of SARS-CoV-2 RNA in wastewater was used to track the evolution and emergence of variant lineages and gauge infection levels in the community, informing appropriate public health responses without relying solely on clinical testing. As more sublineages were discovered, it increased the difficulty in identifying distinct variants in a mixed population sample, particularly those without a known lineage. Here, we compare the sequencing technology from Illumina and from Oxford Nanopore Technologies, in order to determine their efficacy at detecting variants of differing abundance, using 248 wastewater samples from various Quebec and Ontario cities. Our study used two analytical approaches to identify the main variants in the samples: the presence of signature and marker mutations and the co-occurrence of signature mutations within the same amplicon. We observed that each sequencing method detected certain variants at different frequencies as each method preferentially detects mutations of distinct variants. Illumina sequencing detected more mutations with a predominant lineage that is in low abundance across the population or unknown for that time period, while Nanopore sequencing had a higher detection rate of mutations that are predominantly found in the high abundance B.1.1.7 (Alpha) lineage as well as a higher sequencing rate of co-occurring mutations in the same amplicon. We present a workflow that integrates short-read and long-read sequencing to improve the detection of SARS-CoV-2 variant lineages in mixed population samples, such as wastewater.</p>","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11437403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Validation of Saliva as the Clinical Specimen Type for a University-Wide COVID-19 Surveillance Program. 验证将唾液作为全校 COVID-19 监测计划的临床样本类型。
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-21 DOI: 10.3390/v16091494
Michael L Farrell, Anton V Bryksin, Emily Ryan, Jessica Lin, Naima Djeddar, German Khunteev, Benjamin Holton, Miles Paca, Nicholas Speller, James T Merrill, Ted M Ross, Robert J Hogan, Greg Gibson, Andrés J García, Michael P Shannon
{"title":"Validation of Saliva as the Clinical Specimen Type for a University-Wide COVID-19 Surveillance Program.","authors":"Michael L Farrell, Anton V Bryksin, Emily Ryan, Jessica Lin, Naima Djeddar, German Khunteev, Benjamin Holton, Miles Paca, Nicholas Speller, James T Merrill, Ted M Ross, Robert J Hogan, Greg Gibson, Andrés J García, Michael P Shannon","doi":"10.3390/v16091494","DOIUrl":"https://doi.org/10.3390/v16091494","url":null,"abstract":"<p><p>At the beginning of the COVID-19 pandemic, the Georgia Institute of Technology made the decision to keep the university doors open for on-campus attendance. To manage COVID-19 infection rates, internal resources were applied to develop and implement a mass asymptomatic surveillance program. The objective was to identify infections early for proper follow-on verification testing, contact tracing, and quarantine/isolation as needed. Program success depended on frequent and voluntary sample collection from over 40,000 students, faculty, and staff personnel. At that time, the nasopharyngeal (NP) swab, not saliva, was the main accepted sample type for COVID-19 testing. However, due to collection discomfort and the inability to be self-collected, the NP swab was not feasible for voluntary and frequent self-collection. Therefore, saliva was selected as the clinical sample type and validated. A saliva collection kit and a sample processing and analysis workflow were developed. The results of a clinical sample-type comparison study between co-collected and matched NP swabs and saliva samples showed 96.7% positive agreement and 100% negative agreement. During the Fall 2020 and Spring 2021 semesters, 319,988 samples were collected and tested. The program resulted in maintaining a low overall mean positivity rate of 0.78% and 0.54% for the Fall 2020 and Spring 2021 semesters, respectively. For this high-throughput asymptomatic COVID-19 screening application, saliva was an exceptionally good sample type.</p>","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11437455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Quadruple Gene-Deleted Live BoHV-1 Subunit RVFV Vaccine Vector Reactivates from Latency and Replicates in the TG Neurons of Calves but Is Not Transported to and Shed from Nasal Mucosa. 四倍基因缺失的 BoHV-1 亚基 RVFV 活疫苗载体可从潜伏期重新激活并在犊牛的 TG 神经元中复制,但不会被运输到鼻黏膜并从鼻黏膜中脱落。
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-21 DOI: 10.3390/v16091497
Selvaraj Pavulraj, Rhett W Stout, Daniel B Paulsen, Shafiqul I Chowdhury
{"title":"A Quadruple Gene-Deleted Live BoHV-1 Subunit RVFV Vaccine Vector Reactivates from Latency and Replicates in the TG Neurons of Calves but Is Not Transported to and Shed from Nasal Mucosa.","authors":"Selvaraj Pavulraj, Rhett W Stout, Daniel B Paulsen, Shafiqul I Chowdhury","doi":"10.3390/v16091497","DOIUrl":"https://doi.org/10.3390/v16091497","url":null,"abstract":"<p><p>Bovine herpesvirus type 1 (BoHV-1) establishes lifelong latency in trigeminal ganglionic (TG) neurons following intranasal and ocular infection in cattle. Periodically, the latent virus reactivates in the TG due to stress and is transported anterogradely to nerve endings in the nasal epithelium, where the virus replicates and sheds. Consequently, BoHV-1 is transmitted to susceptible animals and maintained in the cattle population. Modified live BoHV-1 vaccine strains (BoHV-1 MLV) also have a similar latency reactivation. Therefore, they circulate and are maintained in cattle herds. Additionally, they can regain virulence and cause vaccine outbreaks because they mutate and recombine with other circulating field wild-type (wt) strains. Recently, we constructed a BoHV-1 quadruple mutant virus (BoHV-1qmv) that lacks immune evasive properties due to UL49.5 and glycoprotein G (gG) deletions. In addition, it also lacks the gE cytoplasmic tail (gE CT) and Us9 gene sequences designed to make it safe, increase its vaccine efficacy against BoHV-1, and restrict its anterograde neuronal transport noted above. Further, we engineered the BoHV-1qmv-vector to serve as a subunit vaccine against the Rift Valley fever virus (BoHV-1qmv Sub-RVFV) (doi: 10.3390/v15112183). In this study, we determined the latency reactivation and nasal virus shedding properties of BoHV-1qmv (vector) and BoHV-1qmv-vectored subunit RVFV (BoHV-1qmv sub-RVFV) vaccine virus in calves in comparison to the BoHV-1 wild-type (wt) following intranasal inoculation. The real-time PCR results showed that BoHV-1 wt- but not the BoHV-1qmv vector- and BoHV-1qmv Sub-RVFV-inoculated calves shed virus in the nose following dexamethasone-induced latency reactivation; however, like the BoHV-1 wt, both the BoHV-1qmv vector and BoHV-1qmv Sub-RVFV viruses established latency, were reactivated, and replicated in the TG neurons. These results are consistent with the anterograde neurotransport function of the gE CT and Us9 sequences, which are deleted in the BoHV-1qmv and BoHV-1qmv Sub-RVFV.</p>","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11437494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimization of Cellular Transduction by the HIV-Based Pseudovirus Platform with Pan-Coronavirus Spike Proteins. 利用泛冠状病毒尖峰蛋白优化基于艾滋病毒的伪病毒平台的细胞转导。
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-20 DOI: 10.3390/v16091492
Syamala Rani Thimmiraju, Maria Jose Villar, Jason T Kimata, Ulrich Strych, Maria Elena Bottazzi, Peter J Hotez, Jeroen Pollet
{"title":"Optimization of Cellular Transduction by the HIV-Based Pseudovirus Platform with Pan-Coronavirus Spike Proteins.","authors":"Syamala Rani Thimmiraju, Maria Jose Villar, Jason T Kimata, Ulrich Strych, Maria Elena Bottazzi, Peter J Hotez, Jeroen Pollet","doi":"10.3390/v16091492","DOIUrl":"https://doi.org/10.3390/v16091492","url":null,"abstract":"<p><p>Over the past three years, new SARS-CoV-2 variants have continuously emerged, evolving to a point where an immune response against the original vaccine no longer provided optimal protection against these new strains. During this time, high-throughput neutralization assays based on pseudoviruses have become a valuable tool for assessing the efficacy of new vaccines, screening updated vaccine candidates against emerging variants, and testing the efficacy of new therapeutics such as monoclonal antibodies. Lentiviral vectors derived from HIV-1 are popular for developing pseudo and chimeric viruses due to their ease of use, stability, and long-term transgene expression. However, the HIV-based platform has lower transduction rates for pseudotyping coronavirus spike proteins than other pseudovirus platforms, necessitating more optimized methods. As the SARS-CoV-2 virus evolved, we produced over 18 variants of the spike protein for pseudotyping with an HIV-based vector, optimizing experimental parameters for their production and transduction. In this article, we present key parameters that were assessed to improve such technology, including (a) the timing and method of collection of pseudovirus supernatant; (b) the timing of host cell transduction; (c) cell culture media replenishment after pseudovirus adsorption; and (d) the centrifugation (spinoculation) parameters of the host cell+ pseudovirus mix, towards improved transduction. Additionally, we found that, for some pseudoviruses, the addition of a cationic polymer (polybrene) to the culture medium improved the transduction process. These findings were applicable across variant spike pseudoviruses that include not only SARS-CoV-2 variants, but also SARS, MERS, Alpha Coronavirus (NL-63), and bat-like coronaviruses. In summary, we present improvements in transduction efficiency, which can broaden the dynamic range of the pseudovirus titration and neutralization assays.</p>","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11437443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
RNAi-Induced Gene Silencing against Chikungunya and COVID-19: What Have We Learned So Far, and What Is the Way Forward? 针对基孔肯雅病毒和 COVID-19 的 RNAi- 诱导基因沉默:迄今为止我们学到了什么,未来的方向是什么?
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-20 DOI: 10.3390/v16091489
Kingshuk Panda, Kalichamy Alagarasu, Rajarshee Tagore, Mandar Paingankar, Satyendra Kumar, Manish Kumar Jeengar, Sarah Cherian, Deepti Parashar
{"title":"RNAi-Induced Gene Silencing against Chikungunya and COVID-19: What Have We Learned So Far, and What Is the Way Forward?","authors":"Kingshuk Panda, Kalichamy Alagarasu, Rajarshee Tagore, Mandar Paingankar, Satyendra Kumar, Manish Kumar Jeengar, Sarah Cherian, Deepti Parashar","doi":"10.3390/v16091489","DOIUrl":"https://doi.org/10.3390/v16091489","url":null,"abstract":"<p><p>RNA interference (RNAi) is a process in which small RNA molecules (such as small interfering RNAs or siRNAs) bind to specific messenger RNAs (mRNAs), leading to its degradation and inhibition of protein synthesis. Our studies have shown that RNAi can effectively silence genes involved in the replication of the Chikungunya virus (CHIKV) in cells. However, these investigations were performed only in laboratory settings and have yet to be tested in human clinical trials. Researchers need to conduct more research to determine the safety and efficacy of RNAi-based therapies as a therapeutic agent to treat viral infections. In this review, the history of evolution of siRNA as an inhibitor of protein synthesis, along with its current developments, is discussed based on our experience. Moreover, this review examines the hurdles and future implications associated with siRNA based therapeutic approaches.</p>","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11437507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Is Autophagy a Friend or Foe in SARS-CoV-2 Infection? 自噬在 SARS-CoV-2 感染中是敌是友?
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-20 DOI: 10.3390/v16091491
Asifa Khan, Jiaxin Ling, Jinlin Li
{"title":"Is Autophagy a Friend or Foe in SARS-CoV-2 Infection?","authors":"Asifa Khan, Jiaxin Ling, Jinlin Li","doi":"10.3390/v16091491","DOIUrl":"https://doi.org/10.3390/v16091491","url":null,"abstract":"<p><p>As obligate parasites, viruses need to hijack resources from infected cells to complete their lifecycle. The interaction between the virus and host determines the viral infection process, including viral propagation and the disease's outcome. Understanding the interaction between the virus and host factors is a basis for unraveling the intricate biological processes in the infected cells and thereby developing more efficient and targeted antivirals. Among the various fundamental virus-host interactions, autophagy plays vital and also complicated roles by directly engaging in the viral lifecycle and functioning as an anti- and/or pro-viral factor. Autophagy thus becomes a promising target against virus infection. Since the COVID-19 pandemic, there has been an accumulation of studies aiming to investigate the roles of autophagy in SARS-CoV-2 infection by using different models and from distinct angles, providing valuable information for systematically and comprehensively dissecting the interplay between autophagy and SARS-CoV-2. In this review, we summarize the advancements in the studies of the interaction between SARS-CoV-2 and autophagy, as well as detailed molecular mechanisms. We also update the current knowledge on the pharmacological strategies used to suppress SARS-CoV-2 replication through remodeling autophagy. These extensive studies on SARS-CoV-2 and autophagy can advance our understanding of virus-autophagy interaction and provide insights into developing efficient antiviral therapeutics by regulating autophagy.</p>","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11437447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
K103N, V106M and Y188L Significantly Reduce HIV-1 Subtype C Phenotypic Susceptibility to Doravirine. K103N、V106M 和 Y188L 能显著降低 HIV-1 C 亚型对多拉韦林的表型敏感性。
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-20 DOI: 10.3390/v16091493
Nikita Reddy, Maria Papathanasopoulos, Kim Steegen, Adriaan Erasmus Basson
{"title":"K103N, V106M and Y188L Significantly Reduce HIV-1 Subtype C Phenotypic Susceptibility to Doravirine.","authors":"Nikita Reddy, Maria Papathanasopoulos, Kim Steegen, Adriaan Erasmus Basson","doi":"10.3390/v16091493","DOIUrl":"https://doi.org/10.3390/v16091493","url":null,"abstract":"<p><p>Doravirine (DOR) is a non-nucleoside reverse transcriptase inhibitor (NNRTI) with efficacy against some NNRTI-resistant mutants. Although DOR resistance mutations are established for HIV-1 subtype B, it is less clear for non-B subtypes. This study investigated prevalent NNRTI resistance mutations on DOR susceptibility in HIV-1 subtype C. Prevalent drug resistance mutations were identified from a South African genotypic drug resistance testing database. Mutations, single or in combination, were introduced into replication-defective pseudoviruses and assessed for DOR susceptibility in vitro. The single V106M and Y188L mutations caused high-level resistance while others did not significantly impact DOR susceptibility. We observed an agreement between our in vitro and the Stanford HIVdb predicted susceptibilities. However, the F227L mutation was predicted to cause high-level DOR resistance but was susceptible in vitro. Combinations of mutations containing K103N, V106M or Y188L caused high-level resistance, in agreement with the predictions. These mutations are frequently observed in patients failing efavirenz- or nevirapine-based first-line regimens. However, they are also observed in those failing a protease inhibitor-based second-line regimen, as we have observed in our database. Genotypic drug resistance testing is therefore vital prior to the initiation of DOR-based treatment for those previously exposed to efavirenz or nevirapine.</p>","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11437401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
EZH2 Inhibition by DS3201 Triggers the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle and Potentiates the Effects Induced by SAHA in Primary Effusion Lymphoma Cells. DS3201 对 EZH2 的抑制会触发卡波西肉瘤相关疱疹病毒的溶解周期,并增强 SAHA 在原发性淋巴瘤细胞中诱导的效应。
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-20 DOI: 10.3390/v16091490
Roberta Gonnella, Flavia Collura, Vincenzo Corrado, Michele Di Crosta, Roberta Santarelli, Mara Cirone
{"title":"EZH2 Inhibition by DS3201 Triggers the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle and Potentiates the Effects Induced by SAHA in Primary Effusion Lymphoma Cells.","authors":"Roberta Gonnella, Flavia Collura, Vincenzo Corrado, Michele Di Crosta, Roberta Santarelli, Mara Cirone","doi":"10.3390/v16091490","DOIUrl":"https://doi.org/10.3390/v16091490","url":null,"abstract":"<p><p>Primary Effusion Lymphoma (PEL) cells carry Kaposi's sarcoma-associated herpesvirus (KSHV) in a latent state, except for a small number of cells in which the virus replicates to ensure its persistence into the infected host. However, the lytic cycle can be reactivated in vitro by exposing these lymphoma cells to various treatments, leading to cell lysis. To restrict viral antigen expression, KSHV induces repressive epigenetic changes, including DNA methylation and histone modifications. Among the latter, histone deacetylation and tri-methylation of Histone H3 lisyne-27 (H3K27me3) have been reported to play a role. Here, we found that the inhibition of H3K27 tri-methylation by valemetostat DS3201 (DS), a small molecule that inhibits Enhancer of Zeste Homolog 2 (EZH2) methyltransferase, induced the KSHV lytic cycle in PEL cells, and that this effect involved the activation of the wtp53-p21 axis and autophagic dysregulation. DS also potentiated the lytic cycle activation mediated by the Histone deacetylases (HDAC) inhibitor Suberoylanilide hydroxamic acid (SAHA) and reinforced its cytotoxic effect, suggesting that such a combination could be used to unbalance the latent/lytic cycle and further impair the survival of PEL cells.</p>","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11437442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Extensive Diversity of Viruses in Millipedes Collected in the Dong Nai Biosphere Reserve (Vietnam). 越南同奈生物圈保护区采集的千足虫体内病毒的广泛多样性。
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-19 DOI: 10.3390/v16091486
Alexander G Litov, Irina I Semenyuk, Oxana A Belova, Alexandra E Polienko, Nguyen Van Thinh, Galina G Karganova, Alexei V Tiunov
{"title":"Extensive Diversity of Viruses in Millipedes Collected in the Dong Nai Biosphere Reserve (Vietnam).","authors":"Alexander G Litov, Irina I Semenyuk, Oxana A Belova, Alexandra E Polienko, Nguyen Van Thinh, Galina G Karganova, Alexei V Tiunov","doi":"10.3390/v16091486","DOIUrl":"https://doi.org/10.3390/v16091486","url":null,"abstract":"<p><p>Advances in sequencing technologies and bioinformatics have led to breakthroughs in the study of virus biodiversity. Millipedes (Diplopoda, Myriapoda, Arthropoda) include more than 12,000 extant species, yet data on virus diversity in Diplopoda are scarce. This study aimed to explore the virome of the millipedes collected in the Dong Nai Biosphere Reserve in Vietnam. We studied 14 species of millipedes and managed to assemble and annotate the complete coding genomes of 16 novel viruses, the partial coding genomes of 10 more viruses, and several fragmented viral sequences, which may indicate the presence of about 54 more viruses in the studied samples. Among the complete and partial genomes, 27% were putative members of the order <i>Picornavirales</i>. Most of the discovered viruses were very distant from the viruses currently present in the relevant databases. At least eight viruses meet the criteria to be recognized as a new species by the International Committee on Taxonomy of Viruses, and, for two of them, a higher taxonomic status (genus and even family) can be suggested.</p>","PeriodicalId":49328,"journal":{"name":"Viruses-Basel","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11437466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Differing Transcriptomic Responses in High Titer versus Low Titer Aedes aegypti Mosquitoes after Oral Infection with Sindbis Virus. 埃及伊蚊口腔感染辛比斯病毒后的转录组反应有高有低
IF 3.8 3区 医学
Viruses-Basel Pub Date : 2024-09-19 DOI: 10.3390/v16091487
Peter Hodoameda, Robert E Ditter, Scott R Santos, Rollie J Clem
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