Next Issue
Previous Issue

E-Mail Alert

Add your e-mail address to receive forthcoming issues of this journal:

Journal Browser

Journal Browser

Table of Contents

Viruses, Volume 1, Issue 3 (December 2009), Pages 335-1363

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Readerexternal link to open them.
View options order results:
result details:
Displaying articles 1-49
Export citation of selected articles as:
Open AccessReview H5N1 Virus Evolution in Europe—An Updated Overview
Viruses 2009, 1(3), 1351-1363; https://doi.org/10.3390/v1031351
Received: 18 September 2009 / Revised: 28 November 2009 / Accepted: 18 December 2009 / Published: 23 December 2009
Cited by 16 | PDF Full-text (185 KB) | HTML Full-text | XML Full-text
Abstract
Since its emergence in South East Asia in 2003, Highly Pathogenic Avian Influenza (HPAI) A/H5N1 has reportedly caused outbreaks in poultry and/or wild birds in 62 countries, of which 24 were in Europe. Interestingly, out of the many genetic clades circulating in Asia,
[...] Read more.
Since its emergence in South East Asia in 2003, Highly Pathogenic Avian Influenza (HPAI) A/H5N1 has reportedly caused outbreaks in poultry and/or wild birds in 62 countries, of which 24 were in Europe. Interestingly, out of the many genetic clades circulating in Asia, the westward spread of HPAI A/H5N1 to Central Asia, the Middle East, Europe and Africa was dominated by one single clade, namely clade 2.2. In this paper, we review and update through phylogenetic and gene migrational analysis the information concerning the evolution and the molecular epidemiology of HPAI A/H5N1 on the European continent. Full article
(This article belongs to the Special Issue Influenza: Pandemics and Vaccinations)
Figures

Figure 1

Open AccessReview Satellite RNAs and Satellite Viruses of Plants
Viruses 2009, 1(3), 1325-1350; https://doi.org/10.3390/v1031325
Received: 28 October 2009 / Revised: 7 December 2009 / Accepted: 7 December 2009 / Published: 18 December 2009
Cited by 55 | PDF Full-text (214 KB) | HTML Full-text | XML Full-text
Abstract
The view that satellite RNAs (satRNAs) and satellite viruses are purely molecular parasites of their cognate helper viruses has changed. The molecular mechanisms underlying the synergistic and/or antagonistic interactions among satRNAs/satellite viruses, helper viruses, and host plants are beginning to be comprehended. This
[...] Read more.
The view that satellite RNAs (satRNAs) and satellite viruses are purely molecular parasites of their cognate helper viruses has changed. The molecular mechanisms underlying the synergistic and/or antagonistic interactions among satRNAs/satellite viruses, helper viruses, and host plants are beginning to be comprehended. This review aims to summarize the recent achievements in basic and practical research, with special emphasis on the involvement of RNA silencing mechanisms in the pathogenicity, population dynamics, and, possibly, the origin(s) of these subviral agents. With further research following current trends, the comprehensive understanding of satRNAs and satellite viruses could lead to new insights into the trilateral interactions among host plants, viruses, and satellites. Full article
(This article belongs to the Special Issue Subviral RNAs)
Figures

Figure 1

Open AccessReview Viral Hybrid Vectors for Somatic Integration - Are They the Better Solution?
Viruses 2009, 1(3), 1295-1324; https://doi.org/10.3390/v1031295
Received: 30 September 2009 / Revised: 4 December 2009 / Accepted: 10 December 2009 / Published: 15 December 2009
Cited by 10 | PDF Full-text (660 KB) | HTML Full-text | XML Full-text
Abstract
The turbulent history of clinical trials in viral gene therapy has taught us important lessons about vector design and safety issues. Much effort was spent on analyzing genotoxicity after somatic integration of therapeutic DNA into the host genome. Based on these findings major
[...] Read more.
The turbulent history of clinical trials in viral gene therapy has taught us important lessons about vector design and safety issues. Much effort was spent on analyzing genotoxicity after somatic integration of therapeutic DNA into the host genome. Based on these findings major improvements in vector design including the development of viral hybrid vectors for somatic integration have been achieved. This review provides a state-of-the-art overview of available hybrid vectors utilizing viruses for high transduction efficiencies in concert with various integration machineries for random and targeted integration patterns. It discusses advantages but also limitations of each vector system. Full article
(This article belongs to the Special Issue Novel Viral Vector Systems for Gene Therapy)
Figures

Figure 1

Open AccessReview Antibody-Mediated Fcγ Receptor-Based Mechanisms of HIV Inhibition: Recent Findings and New Vaccination Strategies
Viruses 2009, 1(3), 1265-1294; https://doi.org/10.3390/v1031265
Received: 30 September 2009 / Revised: 1 December 2009 / Accepted: 8 December 2009 / Published: 15 December 2009
Cited by 19 | PDF Full-text (295 KB) | HTML Full-text | XML Full-text
Abstract
The HIV/AIDS pandemic is one of the most devastating pandemics worldwide. Today, the major route of infection by HIV is sexual transmission. One of the most promising strategies for vaccination against HIV sexual infection is the development of a mucosal vaccine, which should
[...] Read more.
The HIV/AIDS pandemic is one of the most devastating pandemics worldwide. Today, the major route of infection by HIV is sexual transmission. One of the most promising strategies for vaccination against HIV sexual infection is the development of a mucosal vaccine, which should be able to induce strong local and systemic protective immunity. It is believed that both humoral and cellular immune responses are needed for inducing a sterilizing protection against HIV. Recently, passive administration of monoclonal neutralizing antibodies in macaques infected by vaginal challenge demonstrated a crucial role of FcγRs in the protection afforded by these antibodies. This questioned about the role of innate and adaptive immune functions, including ADCC, ADCVI, phagocytosis of opsonized HIV particles and the production of inflammatory cytokines and chemokines, in the mechanism of HIV inhibition in vivo. Other monoclonal antibodies - non-neutralizing inhibitory antibodies - which recognize immunogenic epitopes, have been shown to display potent FcγRs-dependent inhibition of HIV replication in vitro. The potential role of these antibodies in protection against sexual transmission of HIV and their biological relevance for the development of an HIV vaccine therefore need to be determined. This review highlights the potential role of FcγRsmediated innate and adaptive immune functions in the mechanism of HIV protection. Full article
(This article belongs to the Special Issue AIDS Vaccine)
Figures

Figure 1

Open AccessReview Interplay between Herpesvirus Infection and Host Defense by PML Nuclear Bodies
Viruses 2009, 1(3), 1240-1264; https://doi.org/10.3390/v1031240
Received: 18 November 2009 / Revised: 10 December 2009 / Accepted: 14 December 2009 / Published: 15 December 2009
Cited by 43 | PDF Full-text (197 KB) | HTML Full-text | XML Full-text
Abstract
In recent studies we and others have identified the cellular proteins PML, hDaxx, and Sp100, which form a subnuclear structure known as nuclear domain 10 (ND10) or PML nuclear bodies (PML-NBs), as host restriction factors that counteract herpesviral infections by inhibiting viral replication
[...] Read more.
In recent studies we and others have identified the cellular proteins PML, hDaxx, and Sp100, which form a subnuclear structure known as nuclear domain 10 (ND10) or PML nuclear bodies (PML-NBs), as host restriction factors that counteract herpesviral infections by inhibiting viral replication at different stages. The antiviral function of ND10, however, is antagonized by viral regulatory proteins (e.g., ICP0 of herpes simplex virus; IE1 of human cytomegalovirus) which induce either a modification or disruption of ND10. This review will summarize the current knowledge on how viral replication is inhibited by ND10 proteins. Furthermore, herpesviral strategies to defeat this host defense mechanism are discussed. Full article
(This article belongs to the Special Issue Antiviral Responses to Herpes Viruses)
Figures

Figure 1

Open AccessReview Current and Novel Inhibitors of HIV Protease
Viruses 2009, 1(3), 1209-1239; https://doi.org/10.3390/v1031209
Received: 8 October 2009 / Revised: 7 December 2009 / Accepted: 7 December 2009 / Published: 11 December 2009
Cited by 58 | PDF Full-text (1044 KB) | HTML Full-text | XML Full-text
Abstract
The design, development and clinical success of HIV protease inhibitors represent one of the most remarkable achievements of molecular medicine. This review describes all nine currently available FDA-approved protease inhibitors, discusses their pharmacokinetic properties, off-target activities, side-effects, and resistance profiles. The compounds in
[...] Read more.
The design, development and clinical success of HIV protease inhibitors represent one of the most remarkable achievements of molecular medicine. This review describes all nine currently available FDA-approved protease inhibitors, discusses their pharmacokinetic properties, off-target activities, side-effects, and resistance profiles. The compounds in the various stages of clinical development are also introduced, as well as alternative approaches, aiming at other functional domains of HIV PR. The potential of these novel compounds to open new way to the rational drug design of human viruses is critically assessed. Full article
(This article belongs to the Special Issue Retroviral Enzymes)
Figures

Graphical abstract

Open AccessArticle A Novel Duplex Real-Time Reverse-Transcription PCR Assay for the Detection of Influenza A and the Novel Influenza A(H1N1) Strain
Viruses 2009, 1(3), 1204-1208; https://doi.org/10.3390/v1031204
Received: 13 October 2009 / Revised: 28 November 2009 / Accepted: 4 December 2009 / Published: 9 December 2009
Cited by 3 | PDF Full-text (85 KB) | HTML Full-text | XML Full-text
Abstract
Timely implementation of antiviral treatment and other public health based responses are dependent on accurate and rapid diagnosis of the novel pandemic influenza A(H1N1) strain. In this study we developed a duplex real-time PCR (RT-PCR) (dFLU-TM) assay for the simultaneous detection of a
[...] Read more.
Timely implementation of antiviral treatment and other public health based responses are dependent on accurate and rapid diagnosis of the novel pandemic influenza A(H1N1) strain. In this study we developed a duplex real-time PCR (RT-PCR) (dFLU-TM) assay for the simultaneous detection of a broad range of influenza A subtypes and specific detection of the novel H1N1 2009 pandemic strain. The assay was compared to the combined results of two previously described monoplex RT-PCR assays using 183 clinical samples and 10 seasonal influenza A isolates. Overall, the results showed that the dFLU-TM RT-PCR method is suitable for detection of influenza A, including the novel H1N1 pandemic strain, in clinical samples. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
Open AccessReview Henipaviruses Employ a Multifaceted Approach to Evade the Antiviral Interferon Response
Viruses 2009, 1(3), 1190-1203; https://doi.org/10.3390/v1031190
Received: 2 October 2009 / Revised: 2 December 2009 / Accepted: 3 December 2009 / Published: 8 December 2009
Cited by 9 | PDF Full-text (397 KB) | HTML Full-text | XML Full-text
Abstract
Hendra and Nipah virus, which constitute the genus Henipavirus, are zoonotic paramyxoviruses that have been associated with sporadic outbreaks of severe disease and mortality in humans since their emergence in the late 1990s. Similar to other paramyxoviruses, their ability to evade the
[...] Read more.
Hendra and Nipah virus, which constitute the genus Henipavirus, are zoonotic paramyxoviruses that have been associated with sporadic outbreaks of severe disease and mortality in humans since their emergence in the late 1990s. Similar to other paramyxoviruses, their ability to evade the host interferon (IFN) response is conferred by the P gene. The henipavirus P gene encodes four proteins; the P, V, W and C proteins, which have all been described to inhibit the antiviral response. Further studies have revealed that these proteins have overlapping but unique properties which enable the virus to block multiple signaling pathways in the IFN response. The best characterized of these is the JAK-STAT signaling pathway which is targeted by the P, V and W proteins via an interaction with the transcription factor STAT1. In addition the V and W proteins can both limit virus-induced induction of IFN but they appear to do this via distinct mechanisms that rely on unique sequences in their C-terminal domains. The ability to generate recombinant Nipah viruses now gives us the opportunity to determine the precise role for each of these proteins and address their contribution to pathogenicity. Additionally, the question of whether these multiple anti-IFN strategies are all active in the different mammalian hosts for henipaviruses, particularly the fruit bat reservoir, warrants further exploration. Full article
(This article belongs to the Special Issue Interferon Antiviral Response and Viral Evasion)
Figures

Figure 1

Open AccessCommunication All Known Human Rhinovirus Species Are Present in Sputum Specimens of Military Recruits During Respiratory Infection
Viruses 2009, 1(3), 1178-1189; https://doi.org/10.3390/v1031178
Received: 1 September 2009 / Revised: 8 November 2009 / Accepted: 2 December 2009 / Published: 4 December 2009
Cited by 19 | PDF Full-text (153 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Human rhinoviruses (HRV) are known to cause common cold as well as more complicated respiratory infections. HRV species -A, -B and -C have all been associated with lower respiratory infections and exacerbations of asthma. However, the type distribution of strains connected to different
[...] Read more.
Human rhinoviruses (HRV) are known to cause common cold as well as more complicated respiratory infections. HRV species -A, -B and -C have all been associated with lower respiratory infections and exacerbations of asthma. However, the type distribution of strains connected to different kinds of lower respiratory conditions is not clearly known. We have analysed the presence of HRV in sputum specimens derived from military recruits with and without pre-diagnosed asthma at times of acute respiratory infection (CIAS Study, 2004-2005). The analysis was performed with HRV and HEV real-time RT-PCR assays. Subsequently we studied type distribution of HRV strains by genetic typing in the VP4/VP2 genomic region. In total 146 (38.8%) specimens were HRV-positive and 36 (9.3%) HEV-positive. No difference was found in HRV detection between the asthmatic vs. non-asthmatic patients. Most of the genetically typed strains, 18 (62.1%), belonged to HRV-A, while HRV-B strains constituted five (17.2%) of the HRV-positive strains. HRV-C strain was typed four times from the HRV-positive cases and a HEV-D strain twice. We further typed six HEV positive strains in the partial VP1 region. Three of these belonged to HRV-A and three to HEV-D. HRV-A strains were discovered throughout the study period, while HRV-C strains originated from winter and spring specimens. Interestingly, four out of five typed HRV-B strains originated from the summer season specimens. Full article
(This article belongs to the Special Issue Newly Identified Respiratory Viruses)
Figures

Figure 1

Open AccessArticle Complete Nucleotide Analysis of the Structural Genome of the Infectious Bronchitis Virus Strain Md27 Reveals its Mosaic Nature
Viruses 2009, 1(3), 1166-1177; https://doi.org/10.3390/v1031166
Received: 13 August 2009 / Revised: 19 November 2009 / Accepted: 1 December 2009 / Published: 4 December 2009
Cited by 7 | PDF Full-text (138 KB) | HTML Full-text | XML Full-text
Abstract
Infectious bronchitis virus (IBV) causes highly contagious respiratory or urogenital tract diseases in chickens. The Maryland 27(Md27) strain was first isolated in 1976 from diseased chicken flocks in the Delmarva Peninsula region. To understand the genetic diversity and phylogenetic relationship of existing strains
[...] Read more.
Infectious bronchitis virus (IBV) causes highly contagious respiratory or urogenital tract diseases in chickens. The Maryland 27(Md27) strain was first isolated in 1976 from diseased chicken flocks in the Delmarva Peninsula region. To understand the genetic diversity and phylogenetic relationship of existing strains with Md27, the complete nucleotide sequence of the 3’end coding region (~7.2 kb) of Md27 was determined and compared with other IBV strains and coronaviruses. It has the same S-3-M-5-N-3’ gene order, as is the case of other IBV strains. The spike gene of Md27 exhibits 97% identity with the SE17 strain. There are deletions at the spike gene, non-coding region between M and 5 genes, and at the 3’untranslated region (UTR), which is different from Ark-like strains. Phylogenetic analysis and sequence alignments demonstrate that Md27 is a chimera containing different gene segments that are most closely related to the SE17, Conn and JMK strains. This current study provides evidence for genomic mutations and intergenic recombination that have taken place in the evolution of IBV strain Md27. Full article
Figures

Figure 1

Open AccessReview Mutation Rates and Intrinsic Fidelity of Retroviral Reverse Transcriptases
Viruses 2009, 1(3), 1137-1165; https://doi.org/10.3390/v1031137
Received: 20 October 2009 / Revised: 3 December 2009 / Accepted: 3 December 2009 / Published: 4 December 2009
Cited by 48 | PDF Full-text (665 KB) | HTML Full-text | XML Full-text
Abstract
Retroviruses are RNA viruses that replicate through a DNA intermediate, in a process catalyzed by the viral reverse transcriptase (RT). Although cellular polymerases and host factors contribute to retroviral mutagenesis, the RT errors play a major role in retroviral mutation. RT mutations that
[...] Read more.
Retroviruses are RNA viruses that replicate through a DNA intermediate, in a process catalyzed by the viral reverse transcriptase (RT). Although cellular polymerases and host factors contribute to retroviral mutagenesis, the RT errors play a major role in retroviral mutation. RT mutations that affect the accuracy of the viral polymerase have been identified by in vitro analysis of the fidelity of DNA synthesis, by using enzymological (gel-based) and genetic assays (e.g., M13mp2 lacZ forward mutation assays). For several amino acid substitutions, these observations have been confirmed in cell culture using viral vectors. This review provides an update on studies leading to the identification of the major components of the fidelity center in retroviral RTs. Full article
(This article belongs to the Special Issue Retroviral Enzymes)
Figures

Graphical abstract

Open AccessReview HIV-1 Protease: Structural Perspectives on Drug Resistance
Viruses 2009, 1(3), 1110-1136; https://doi.org/10.3390/v1031110
Received: 1 October 2009 / Revised: 30 November 2009 / Accepted: 1 December 2009 / Published: 3 December 2009
Cited by 59 | PDF Full-text (1295 KB)
Abstract
Antiviral inhibitors of HIV-1 protease are a notable success of structure-based drug design and have dramatically improved AIDS therapy. Analysis of the structures and activities of drug resistant protease variants has revealed novel molecular mechanisms of drug resistance and guided the design of
[...] Read more.
Antiviral inhibitors of HIV-1 protease are a notable success of structure-based drug design and have dramatically improved AIDS therapy. Analysis of the structures and activities of drug resistant protease variants has revealed novel molecular mechanisms of drug resistance and guided the design of tight-binding inhibitors for resistant variants. The plethora of structures reveals distinct molecular mechanisms associated with resistance: mutations that alter the protease interactions with inhibitors or substrates; mutations that alter dimer stability; and distal mutations that transmit changes to the active site. These insights will inform the continuing design of novel antiviral inhibitors targeting resistant strains of HIV. Full article
(This article belongs to the Special Issue Retroviral Enzymes)
Open AccessReview Pandemic Influenza Vaccines – The Challenges
Viruses 2009, 1(3), 1089-1109; https://doi.org/10.3390/v1031089
Received: 14 August 2009 / Revised: 26 November 2009 / Accepted: 1 December 2009 / Published: 3 December 2009
Cited by 10 | PDF Full-text (161 KB) | HTML Full-text | XML Full-text
Abstract
Recent years’ enzootic spread of highly pathogenic H5N1 virus among poultry and the many lethal zoonoses in its wake has stimulated basic and applied pandemic vaccine research. The quest for an efficacious, affordable and timely accessible pandemic vaccine has been high on the
[...] Read more.
Recent years’ enzootic spread of highly pathogenic H5N1 virus among poultry and the many lethal zoonoses in its wake has stimulated basic and applied pandemic vaccine research. The quest for an efficacious, affordable and timely accessible pandemic vaccine has been high on the agenda. When a variant H1N1 strain of swine origin emerged as a pandemic virus, it surprised many, as this subtype is well-known to man as a seasonal virus. This review will cover some difficult vaccine questions, such as the immunological challenges, the new production platforms, and the limited supply and global equity issues. Full article
(This article belongs to the Special Issue Influenza: Pandemics and Vaccinations)
Open AccessReview HCV Innate Immune Responses
Viruses 2009, 1(3), 1073-1088; https://doi.org/10.3390/v1031073
Received: 27 August 2009 / Revised: 25 November 2009 / Accepted: 26 November 2009 / Published: 30 November 2009
Cited by 4 | PDF Full-text (396 KB) | HTML Full-text | XML Full-text
Abstract
Hepatitis C virus (HCV) establishes a persistent infection in more than 70% of infected individuals. This striking ability to evade the powerful innate immune system results from viral interference occurring at several levels of the interferon (IFN) system. There is strong evidence from
[...] Read more.
Hepatitis C virus (HCV) establishes a persistent infection in more than 70% of infected individuals. This striking ability to evade the powerful innate immune system results from viral interference occurring at several levels of the interferon (IFN) system. There is strong evidence from cell culture experiments that HCV can inhibit the induction of IFNβ by cleaving important proteins in the virus sensory pathways of cells such as MAVS and TRIF. There is also evidence that HCV interferes with IFNα signaling through the Jak-STAT pathway, and that HCV proteins target IFN effector systems such as protein kinase R (PKR). These in vitro findings will have to be confirmed in clinical trials investigating the molecular mechanisms of HCV interference with the innate immune system in liver samples. Full article
(This article belongs to the Special Issue Hepatitis Viruses)
Figures

Figure 1

Open AccessReview A Closer Look at the NS1 of Influenza Virus
Viruses 2009, 1(3), 1057-1072; https://doi.org/10.3390/v1031057
Received: 10 September 2009 / Revised: 13 November 2009 / Accepted: 25 November 2009 / Published: 26 November 2009
Cited by 30 | PDF Full-text (135 KB) | HTML Full-text | XML Full-text
Abstract
The Non-Structural 1 (NS1) protein is a multifactorial protein of type A influenza viruses that plays an important role in the virulence of the virus. A large amount of what we know about this protein has been obtained from studies using human influenza
[...] Read more.
The Non-Structural 1 (NS1) protein is a multifactorial protein of type A influenza viruses that plays an important role in the virulence of the virus. A large amount of what we know about this protein has been obtained from studies using human influenza isolates and, consequently, the human NS1 protein. The current global interest in avian influenza, however, has highlighted a number of sequence and functional differences between the human and avian NS1. This review discusses these differences in addition to describing potential uses of NS1 in the management and control of avian influenza outbreaks. Full article
(This article belongs to the Special Issue Influenza: Pandemics and Vaccinations)
Figures

Figure 1

Back to Top