Abstract：
:The MinION sequencer is increasingly being used for the detection and outbreak surveillance of pathogens due to its rapid throughput. For RNA viruses, MinION's new direct RNA sequencing is the next significant development. Direct RNA sequencing studies are currently limited and comparisons of its diagnostic performance relative to different DNA sequencing approaches are lacking as a result. We sought to address this gap and sequenced six subtypes from the mycovirus CHV-1 using MinION's direct RNA sequencing and DNA sequencing based on a targeted viral amplicon. Reads from both techniques could correctly identify viral presence and species using BLAST, though direct RNA reads were more frequently misassigned to closely related CHV species. De novo consensus sequences were error prone but suitable for viral species identification. However, subtype identification was less accurate from both reads and consensus sequences. This is due to the high sequencing error rate and the limited sequence divergence between some CHV-1 subtypes. Importantly, neither RNA nor amplicon sequencing reads could be used to obtain reliable intra-host variants. Overall, both sequencing techniques were suitable for virus detection, though limitations are present due to the error rate of MinION reads.
journal_name
Virusesjournal_title
Virusesauthors
Leigh DM,Schefer C,Cornejo Cdoi
10.3390/v12080801subject
Has Abstractpub_date
2020-07-25 00:00:00issue
8issn
1999-4915pii
v12080801journal_volume
12pub_type
杂志文章相关文献
Viruses-Basel文献大全abstract：:A novel virus from moribund European chub (Squalius cephalus) was isolated on epithelioma papulosum cyprini (EPC) cells. Transmission electron microscopic examination revealed abundant non-enveloped, hexagonal virus particles in the cytoplasm of infected EPC cells consistent with an iridovirus. Illumina MiSeq sequence...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v11050440
更新日期：2019-05-15 00:00:00
abstract：:The ability of the host to trigger apoptosis in infected cells is perhaps the most powerful tool by which viruses can be cleared from the host organism. To avoid elimination by this mechanism, human papillomaviruses (HPV) have developed several mechanisms that enable the cells they infect to elude both extrinsic and i...
journal_title：Viruses
pub_type： 杂志文章,评审
doi：10.3390/v4123831
更新日期：2012-12-18 00:00:00
abstract：:Retroviruses are well known pathogens of mammals, birds and fish. Their potential to induce cancer in chickens was already described almost 100 years ago and murine retroviruses have been a subject of study for 50 years. The first human retroviruses, HTLV and HIV, were discovered more than 30 years ago, surprising res...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v3081312
更新日期：2011-08-01 00:00:00
abstract：:The two human oncogenic -herpesviruses, Epstein Barr virus (EBV) and Kaposi sarcoma-associated herpesvirus (KSHV), are prototypic pathogens that are controlled by T cell responses. Despite their ubiquitous distribution, persistent infections and transforming potential, most carriers' immune systems control them for li...
journal_title：Viruses
pub_type： 杂志文章,评审
doi：10.3390/v11121125
更新日期：2019-12-05 00:00:00
abstract：:Deoxynucleoside triphosphate (dNTP) molecules are essential for the replication and maintenance of genomic information in both cells and a variety of viral pathogens. While the process of dNTP biosynthesis by cellular enzymes, such as ribonucleotide reductase (RNR) and thymidine kinase (TK), has been extensively inves...
journal_title：Viruses
pub_type： 杂志文章,评审
doi：10.3390/v12040382
更新日期：2020-03-31 00:00:00
abstract：:The human OAS1 (hOAS1) gene produces multiple possible isoforms due to alternative splicing events and sequence variation among individuals, some of which affect splicing. The unique C-terminal sequences of the hOAS1 isoforms could differentially affect synthetase activity, protein stability, protein partner interacti...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v12020152
更新日期：2020-01-29 00:00:00
abstract：:Tetherin (BST2/CD317/HM1.24) has emerged as a key host-cell ·defence molecule that acts by inhibiting the release and spread of diverse enveloped virions from infected cells. We analysed the biological features of canine tetherin and found it to be an unstable hydrophilic type I transmembrane protein with one transmem...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v10100565
更新日期：2018-10-16 00:00:00
abstract：:The Megalocytivirus genus includes three genotypes, red sea bream iridovirus (RSIV), infectious spleen and kidney necrosis virus (ISKNV), and turbot reddish body iridovirus (TRBIV), and has caused mass mortalities in various marine and freshwater fish species in East and Southeast Asia. Of the three genotypes, TRBIV-l...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v12060681
更新日期：2020-06-24 00:00:00
abstract：:The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BA...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v11121085
更新日期：2019-11-21 00:00:00
abstract：:Viral CD8 T-cell epitopes, represented by viral peptides bound to major histocompatibility complex class-I (MHC-I) glycoproteins, are often identified by "reverse immunology", a strategy not requiring biochemical and structural knowledge of the actual viral protein from which they are derived by antigen processing. In...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v6020808
更新日期：2014-02-14 00:00:00
abstract：BACKGROUND:Zika virus is a mosquito-borne flavivirus responsible for recent outbreaks of epidemic proportions in Latin America. Sexual transmission of the virus has been reported in 13 countries and may be an important route of infection. Sexual transmission of ZIKV has mostly been male-to-female, and persistence of vi...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v11010042
更新日期：2019-01-09 00:00:00
abstract：:We describe herein, limitations on research at biosafety level 4 (BSL-4) containment laboratories, with regard to biosecurity regulations, safety considerations, research space limitations, and physical constraints in executing experimental procedures. These limitations can severely impact the number of collaborations...
journal_title：Viruses
pub_type： 杂志文章,评审
doi：10.3390/v4123932
更新日期：2012-12-01 00:00:00
abstract：:Dengue is a worldwide problem characterized by a multifactorial pathogenesis. Considering the viral components, it is known that high viremia or high levels of the secreted nonstructural protein 1 (NS1) may be associated with a more severe disease. We aimed to characterize the NS1 antigenemia and viremia in dengue fat...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v10060326
更新日期：2018-06-14 00:00:00
abstract：:MicroRNAs (miRNAs) are non-coding but functional RNA molecules of 21-25 nucleotides in length. MiRNAs play significant regulatory roles in diverse plant biological processes. In order to decipher the relationship between nbe-miR1919c-5p and the accumulations of tobacco curly shoot virus (TbCSV) and its betasatellite (...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v12040392
更新日期：2020-04-01 00:00:00
abstract：:Both temperature and humidity may independently or jointly contribute to the risk of human rhinovirus (HRV) infections, either through altered survival and spread of viruses in the environment or due to changes in host susceptibility. This study examined the relationship between short-term variations in temperature an...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v8090244
更新日期：2016-09-02 00:00:00
abstract：:Infectious bursal disease (IBD) is an immunosuppressive, highly contagious, and lethal disease of young chickens caused by IBD virus (IBDV). It results in huge economic loss to the poultry industry worldwide. Infection caused by very virulent IBDV (vvIBDV) strains results in high mortality in young chicken flocks. How...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v12020249
更新日期：2020-02-23 00:00:00
abstract：:Salmonid alphavirus (SAV) is the cause of pancreas disease and sleeping disease in farmed salmonid fish in Europe. The spread of these diseases has been difficult to control with biosecurity and current vaccination strategies, and increased understanding of the viral pathogenesis could be beneficial for the developmen...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v12101071
更新日期：2020-09-24 00:00:00
abstract：:Peste des Petits Ruminants (PPR) is a highly infectious disease caused by a virus of the Morbillivirus genus. The current PPR eradication effort relies mainly on the implementation of massive vaccination campaigns. One of the most widely used PPR vaccines is the Nigeria 75/1 strain obtained after attenuation by 75 ser...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v11080724
更新日期：2019-08-07 00:00:00
abstract：:The Pneumoviridae family includes human metapneumovirus (HMPV) and human orthopneumovirus, which is also known as a respiratory syncytial virus (HRSV). These are large enveloped, negative single-strand RNA viruses. HMPV and HRSV are the human members, which commonly infect children. HMPV, which was discovered in 2001,...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v12070781
更新日期：2020-07-20 00:00:00
abstract：:Background: Bats are known to host a number of nonpathogenic viruses, as well as highly pathogenic viruses causing fatal diseases like rabies. Serological surveys as part of active and passive bat rabies surveillance mainly use seroneutralization assays, demonstrating the presence of lyssavirus-specific antibodies in ...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v12030271
更新日期：2020-02-28 00:00:00
abstract：:The degree of antigenic drift in swine influenza A viruses (swIAV) has historically been regarded as minimal compared to that of human influenza A virus strains. However, as surveillance activities on swIAV have increased, more isolates have been characterized, revealing a high level of genetic and antigenic differenc...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v12020248
更新日期：2020-02-23 00:00:00
abstract：:On average, there are 3-5 million severe cases of influenza virus infections globally each year. Seasonal influenza vaccines provide limited protection against divergent influenza strains. Therefore, the development of a universal influenza vaccine is a top priority for the NIH. Here, we report a comprehensive summary...
journal_title：Viruses
pub_type： 杂志文章,评审
doi：10.3390/v12101186
更新日期：2020-10-20 00:00:00
abstract：:Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowle...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v11111042
更新日期：2019-11-08 00:00:00
abstract：:Positive-strand RNA (+RNA) viruses are an important group of human and animal pathogens that have significant global health and economic impacts. Notable members include West Nile virus, Dengue virus, Chikungunya, Severe acute respiratory syndrome (SARS) Coronavirus and enteroviruses of the Picornaviridae family.Unfor...
journal_title：Viruses
pub_type： 杂志文章,评审
doi：10.3390/v7082825
更新日期：2015-08-06 00:00:00
abstract：:Unlike other human herpesviruses, human herpesvirus 6A and 6B (HHV-6A/B) infection can lead to integration of the viral genome in human chromosomes. When integration occurs in germinal cells, the integrated HHV-6A/B genome can be transmitted to 50% of descendants. Such individuals, carrying one copy of the HHV-6A/B ge...
journal_title：Viruses
pub_type： 杂志文章,评审
doi：10.3390/v9070160
更新日期：2017-06-26 00:00:00
abstract：:Over the past 15 years we have been investigating an alternative approach to treating HIV-1/AIDS, based on the creation of a disease-resistant immune system through transplantation of autologous, gene-modified (HIV-1-resistant) hematopoietic stem and progenitor cells (GM-HSPC). We propose that the expression of select...
journal_title：Viruses
pub_type： 临床试验,杂志文章
doi：10.3390/v5112898
更新日期：2013-11-22 00:00:00
abstract：:Via virome sequencing, six viruses were detected from Magnaporthe oryzae strains YC81-2, including one virus in the family Tombusviridae, one virus in the family Narnaviridae and four viruses in the family Botourmiaviridae. Since the RNA-dependent RNA polymerase (RdRp) of one botourmiavirus show the highest identity (...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v12121383
更新日期：2020-12-03 00:00:00
abstract：:Like all other viruses, a successful egress of functional particles from infected cells is a prerequisite for foamy virus (FV) spread within the host. The budding process of FVs involves steps, which are shared by other retroviruses, such as interaction of the capsid protein with components of cellular vacuolar protei...
journal_title：Viruses
pub_type： 杂志文章,评审
doi：10.3390/v5041075
更新日期：2013-04-10 00:00:00
abstract：:West Nile virus (WNV) is a member of the genus Flavivirus in the family Flaviviridae. Flaviviruses replicate in the cytoplasm of infected cells and modify the host cell environment. Although much has been learned about virion structure and virion-endosomal membrane fusion, the cell receptor(s) used have not been defin...
journal_title：Viruses
pub_type： 杂志文章,评审
doi：10.3390/v6010013
更新日期：2013-12-27 00:00:00
abstract：:Laboratories throughout the world that perform work with Risk Group 4 Pathogens generally adopt one of two approaches within BSL-4 environments: either the use of positive pressure air-fed suits or using Class III microbiological safety cabinets and isolators for animal work. Within the UK at present, all laboratories...
journal_title：Viruses
pub_type： 杂志文章
doi：10.3390/v4081202
更新日期：2012-08-01 00:00:00
