Abstract:
:Viral codon usage bias may be the product of a number of synergistic or antagonistic factors, including genomic nucleotide composition, translational selection, genomic architecture, and mutational or repair biases. Most studies of viral codon bias evaluate only the relative importance of genomic base composition and translational selection, ignoring other possible factors. We analyzed the codon preferences of ssRNA (luteoviruses and potyviruses) and ssDNA (geminiviruses) plant viruses that infect translationally distinct monocot and dicot hosts. We found that neither genomic base composition nor translational selection satisfactorily explains their codon usage biases. Furthermore, we observed a strong relationship between the codon preferences of viruses in the same family or genus, regardless of host or genomic nucleotide content. Our results suggest that analyzing codon bias as either due to base composition or translational selection is a false dichotomy that obscures the role of other factors. Constraints such as genomic architecture and secondary structure can and do influence codon usage in plant viruses, and likely in viruses of other hosts.
journal_name
Virusesjournal_title
Virusesauthors
Cardinale DJ,DeRosa K,Duffy Sdoi
10.3390/v5010162subject
Has Abstractpub_date
2013-01-15 00:00:00pages
162-81issue
1issn
1999-4915pii
v5010162journal_volume
5pub_type
杂志文章相关文献
Viruses-Basel文献大全abstract::Influenza A viruses (IAV) carrying reporter genes provide a powerful tool to study viral infection and pathogenesis in vivo, however, incorporating a non-essential gene into the IAV genome often results in virus attenuation and genetic instability. Very few studies have systematically compared different reporter IAVs,...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v10120679
更新日期:2018-11-30 00:00:00
abstract::Food security is currently a global socio-political pressure point that is exacerbated by the everincreasing world population[...]. ...
journal_title:Viruses
pub_type: 社论
doi:10.3390/v12020210
更新日期:2020-02-13 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::Photodynamic inactivation (PDI) has been used to inactivate microorganisms through the use of photosensitizers. The inactivation of mammalian viruses and bacteriophages by photosensitization has been applied with success since the first decades of the last century. Due to the fact that mammalian viruses are known to p...
journal_title:Viruses
pub_type: 杂志文章,评审
doi:10.3390/v4071034
更新日期:2012-07-01 00:00:00
abstract::Rapid and sensitive detection of prions is important in managing prion diseases. The real-time quaking-induced conversion (RT-QuIC) assay for prion seeding activity has been applied to many prion diseases and provides for specific antemortem diagnostic testing. We evaluated RT-QuIC's long-term consistency and varied m...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v8050140
更新日期:2016-05-23 00:00:00
abstract::COVID-19 epidemic has been suppressed in Hungary due to timely non-pharmaceutical interventions, prompting a considerable reduction in the number of contacts and transmission of the virus. This strategy was effective in preventing epidemic growth and reducing the incidence of COVID-19 to low levels. In this report, we...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v12070708
更新日期:2020-06-30 00:00:00
abstract::Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v10060318
更新日期:2018-06-11 00:00:00
abstract::The chikungunya virus (CHIKV) is an emerging pathogen with widespread distribution in regions of Africa, India, and Asia that threatens to spread into temperate climates with the introduction of its major vector, Aedes albopictus. CHIKV causes a disease frequently misdiagnosed as dengue fever, with potentially life-th...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v8060163
更新日期:2016-06-10 00:00:00
abstract::Human metapneumovirus (hMPV), a leading cause of respiratory tract infections in infants, encodes a small hydrophobic (SH) protein of unknown function. Here we show that infection of plasmacytoid dendritic cells (pDCs) with a recombinant virus lacking SH expression (rhMPV-ΔSH) enhanced the secretion of type I interfer...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v10060278
更新日期:2018-05-23 00:00:00
abstract::West Nile virus (WNV) is prevalent in Africa, Europe, the Middle East, West Asia, and North America, and causes epidemic encephalitis. To date, no effective therapy for WNV infection has been developed; therefore, there is urgent need to find an efficient method to prevent WNV disease. In this study, we prepared and e...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v8120332
更新日期:2016-12-18 00:00:00
abstract:UNLABELLED:Cytomegalovirus (CMV) is a prevalent pathogen in the immunocompromised host and invasive pneumonia is a feared complication of the virus in this population. In this pediatric case series we characterized CMV lung infection in 15 non-HIV infected children (median age 3 years; IQR 0.2-4.9 years), using current...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v6052038
更新日期:2014-05-07 00:00:00
abstract::The honey bee queen is the central hub of a colony to produce eggs and release pheromones to maintain social cohesion. Among many environmental stresses, viruses are a major concern to compromise the queen's health and reproductive vigor. Viruses have evolved numerous strategies to infect queens either via vertical tr...
journal_title:Viruses
pub_type: 杂志文章,评审
doi:10.3390/v12030322
更新日期:2020-03-17 00:00:00
abstract::Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus that causes cancer (Adult T cell Leukemia, ATL) and a spectrum of inflammatory diseases (mainly HTLV-associated myelopathy-tropical spastic paraparesis, HAM/TSP). Since virions are particularly unstable, HTLV-1 transmission primarily occurs by transfer of a c...
journal_title:Viruses
pub_type: 杂志文章,评审
doi:10.3390/v7072793
更新日期:2015-07-07 00:00:00
abstract::Geminiviruses are important plant pathogens that affect crops around the world. In some geminivirus-host interactions, infected plants show recovery, a phenomenon characterized by symptom disappearance in newly emerging leaves. In pepper-Pepper golden mosaic virus (PepGMV) interaction, the host recovery process involv...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v12030286
更新日期:2020-03-05 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
abstract::West Nile virus (WNV) is an important emerging neurotropic virus, responsible for increasingly severe encephalitis outbreaks in humans and horses worldwide. However, the mechanism by which the virus gains entry to the brain (neuroinvasion) remains poorly understood. Hypotheses of hematogenous and transneural entry hav...
journal_title:Viruses
pub_type: 杂志文章,评审
doi:10.3390/v6072796
更新日期:2014-07-18 00:00:00
abstract::With ongoing colony losses driven in part by the Varroa mite and the associated exacerbation of the virus load, there is an urgent need to protect honey bees (Apis mellifera) from fatal levels of virus infection and from the non-target effects of insecticides used in agricultural settings. A continuously replicating c...
journal_title:Viruses
pub_type: 杂志文章,评审
doi:10.3390/v12020236
更新日期:2020-02-20 00:00:00
abstract::Despite significant improvements in therapy, the HIV/AIDS pandemic remains an important threat to public health. Current treatments fail to eradicate HIV as proviral DNA persists in long-living cellular reservoirs, leading to viral rebound whenever treatment is discontinued. Hence, a better understanding of viral rese...
journal_title:Viruses
pub_type: 杂志文章,评审
doi:10.3390/v11010012
更新日期:2018-12-26 00:00:00
abstract::Under physiological conditions, the function of astrocytes in providing brain metabolic support is compromised under pathophysiological conditions caused by human immunodeficiency virus (HIV) and opioids. Herein, we examined the role of autophagy, a lysosomal degradation pathway important for cellular homeostasis and ...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v9080201
更新日期:2017-07-28 00:00:00
abstract::Zika virus (ZIKV) is an emerging mosquito-borne pathogen associated with microcephaly and other congenital abnormalities in newborns as well as neurologic complications in adults. The explosive transmission of the virus in the last ten years put it in the limelight and improved our understanding of its biology and pat...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v12090926
更新日期:2020-08-23 00:00:00
abstract::Human T-cell leukemia virus type 1 (HTLV-1) is a complex retrovirus that infects CD4+ T cells and causes adult T-cell leukemia/lymphoma (ATLL) in 3%-5% of infected individuals after a long latent period. HTLV-1 Tax is a trans-activating protein that regulates viral gene expression and also modulates cellular signaling...
journal_title:Viruses
pub_type: 杂志文章,评审
doi:10.3390/v6103925
更新日期:2014-10-23 00:00:00
abstract::The hepatitis C virus (HCV), a hepatotropic plus-strand RNA virus of the family Flaviviridae, encodes a set of 10 viral proteins. These viral factors act in concert with host proteins to mediate virus entry, and to coordinate RNA replication and virus production. Recent evidence has highlighted the complexity of HCV a...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v2092078
更新日期:2010-09-01 00:00:00
abstract::One hundred Prunus trees, including almond (P. dulcis), apricot (P. armeniaca), nectarine (P. persica var. nucipersica), peach (P. persica), plum (P. domestica), purple leaf plum (P. cerasifera) and sweet cherry (P. avium), were selected from growing regions Australia-wide and tested for the presence of 34 viruses and...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v12020246
更新日期:2020-02-23 00:00:00
abstract::A lytic bacteriophage PHB01 specific for Pasteurella multocida type D was isolated from the sewage water collected from a pig farm. This phage had the typical morphology of the family Podoviridae, order Caudovirales, presenting an isometric polyhedral head and a short noncontractile tail. PHB01 was able to infect most...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v11010086
更新日期:2019-01-21 00:00:00
abstract::In Europe, cowpox virus (CPXV) infection in South American camelids occurs as a so-called spill-over infection. Although infected animals generally have a mild form of the disease and survive, cases of fatal generalised CPXV infection have also been described. Prevention by prophylactic vaccination is the only way to ...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v12020234
更新日期:2020-02-20 00:00:00
abstract::An effective vaccine is essential for controlling the spread of the SARS-CoV-2 virus. Here, we describe an influenza virus-based vaccine for SARS-CoV-2. We incorporated a membrane-anchored form of the SARS-CoV-2 spike receptor binding domain (RBD) in place of the neuraminidase (NA) coding sequence in an influenza viru...
journal_title:Viruses
pub_type: 评论,杂志文章
doi:10.3390/v12090987
更新日期:2020-09-05 00:00:00
abstract::Innate immune interferons (IFNs), including type I and III IFNs, constitute critical antiviral mechanisms. Recent studies reveal that IFN dysregulation is key to determine COVID-19 pathogenesis. Effective IFN stimulation or prophylactic administration of IFNs at the early stage prior to severe COVID-19 may elicit an a...
journal_title:Viruses
pub_type: 杂志文章,评审
doi:10.3390/v12121433
更新日期:2020-12-13 00:00:00
abstract::The success of oral infection by viruses depends on their capacity to overcome the gut epithelial barrier of their host to crossing over apical, mucous extracellular matrices. As orally transmitted viruses, densoviruses, are also challenged by the complexity of the insect gut barriers, more specifically by the chitino...
journal_title:Viruses
pub_type: 杂志文章
doi:10.3390/v11090870
更新日期:2019-09-17 00:00:00
abstract::Monoderm bacteria possess a cell envelope made of a cytoplasmic membrane and a cell wall, whereas diderm bacteria have and extra lipid layer, the outer membrane, covering the cell wall. Both cell types can also produce extracellular protective coats composed of polymeric substances like, for example, polysaccharidic c...
journal_title:Viruses
pub_type: 杂志文章,评审
doi:10.3390/v10080396
更新日期:2018-07-27 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