bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a Human Immunodeficiency Virus Type 1 V3 Deletion Mutation That Confers Resistance to CCR5 Inhibitors and the Ability To Use Aplaviroc-Bound Receptor
Authors: Nolan Katrina M. , Del Prete Gregory Q. , Jordan Andrea P. O. , Haggarty Beth , Romano Josephine , Leslie George J. , Hoxie James A. 
Published: February 2009

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) V3 loop is essential for coreceptor binding and principally determines tropism for the CCR5 and CXCR4 coreceptors. Using the dual-tropic virus HIV-1
R3A
, we previously made an extensive panel of V3 deletions and identified subdomains within V3 that could differentially mediate R5 and X4 tropism. A deletion of residues 9 to 12 on the N-terminal side of the V3 stem ablated X4 tropism while leaving R5 tropism intact. This mutation also resulted in complete resistance to several small-molecule CCR5 inhibitors. Here, we extend these studies to further characterize a variant of this mutant, Δ9-12a, adapted for growth in CCR5
+
SupT1 cells. Studies using coreceptor chimeras, monoclonal antibodies directed against the CCR5 amino terminus (NT) and extracellular loops, and CCR5 point mutants revealed that, relative to parental R3A, R5-tropic Δ9-12a was more dependent on the CCR5 NT, a region that contacts the gp120 bridging sheet and V3 base. Neutralization sensitivity assays showed that, compared to parental R3A, Δ9-12a was more sensitive to monoclonal antibodies b12, 4E10, and 2G12. Finally, cross-antagonism assays showed that Δ9-12a could use aplaviroc-bound CCR5 for entry. These studies indicate that increased dependence on the CCR5 NT represents a mechanism by which HIV envelopes acquire resistance to CCR5 antagonists and may have more general implications for mechanisms of drug resistance that arise in vivo. In addition, envelopes such as Δ9-12a may be useful for developing new entry inhibitors that target the interaction of gp120 and the CCR5 NT.
Lambda Interferon Inhibits Human Immunodeficiency Virus Type 1 Infection of Macrophages
Authors: Hou Wei , Wang Xu , Ye Li , Zhou Lin , Yang Zhan-Qiu , Riedel Eric , Ho Wen-Zhe 
Published: February 2009

ABSTRACTThe newly identified type III interferon (IFN-λ) has antiviral activity against a broad spectrum of viruses. We thus examined whether IFN-λ has the ability to inhibit human immunodeficiency virus type 1 (HIV-1) infection of blood monocyte-derived macrophages that expressed IFN-λ receptors. Both IFN-λ1 and IFN-λ2, when added to macrophage cultures, inhibited HIV-1 infection and replication. This IFN-λ-mediated anti-HIV-1 activity is broad, as IFN-λ could inhibit infection by both laboratory-adapted and clinical strains of HIV-1. Investigations of the mechanism(s) responsible for the IFN-λ action showed that although IFN-λ had little effect on HIV-1 entry coreceptor CCR5 expression, IFN-λ induced the expression of CC chemokines, the ligands for CCR5. In addition, IFN-λ upregulated intracellular expression of type I IFNs and APOBEC3G/3F, the newly identified anti-HIV-1 cellular factors. These data provide direct and compelling evidence that IFN-λ, through both extracellular and intracellular antiviral mechanisms, inhibits HIV-1 replication in macrophages. These findings indicate that IFN-λ may have therapeutic value in the treatment of HIV-1 infection.
The Human Immunodeficiency Virus Type 1 Nonnucleoside Reverse Transcriptase Inhibitor Resistance Mutation I132M Confers Hypersensitivity to Nucleoside Analogs
Authors: Ambrose Zandrea , Herman Brian D. , Sheen Chih-Wei , Zelina Shannon , Moore Katie L. , Tachedjian Gilda , Nissley Dwight V. , Sluis-Cremer Nicolas 
Published: February 2009

ABSTRACT
We previously identified a rare mutation in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), I132M, which confers high-level resistance to the nonnucleoside RT inhibitors (NNRTIs) nevirapine and delavirdine. In this study, we have further characterized the role of this mutation in viral replication capacity and in resistance to other RT inhibitors. Surprisingly, our data show that I132M confers marked hypersusceptibility to the nucleoside analogs lamivudine (3TC) and tenofovir at both the virus and enzyme levels. Subunit-selective mutagenesis studies revealed that the mutation in the p51 subunit of RT was responsible for the increased sensitivity to the drugs, and transient kinetic analyses showed that this hypersusceptibility was due to I132M decreasing the enzyme's affinity for the natural dCTP substrate but increasing its affinity for 3TC-triphosphate. Furthermore, the replication capacity of HIV-1 containing I132M is severely impaired. This decrease in viral replication capacity could be partially or completely compensated for by the A62V or L214I mutation, respectively. Taken together, these results help to explain the infrequent selection of I132M in patients for whom NNRTI regimens are failing and furthermore demonstrate that a single mutation outside of the polymerase active site and inside of the p51 subunit of RT can significantly influence nucleotide selectivity.
Cardioviruses Are Genetically Diverse and Cause Common Enteric Infections in South Asian Children
Authors: Blinkova Olga , Kapoor Amit , Victoria Joseph , Jones Morris , Wolfe Nathan , Naeem Asif , Shaukat Shahzad , Sharif Salmaan , Alam Muhammad Masroor , Angez Mehar , Zaidi Sohail , Delwart Eric L. 
Published: February 2009

ABSTRACT

Cardioviruses cause enteric infections in mice and rats which when disseminated have been associated with myocarditis, type 1 diabetes, encephalitis, and multiple sclerosis-like symptoms. Cardioviruses have also been detected at lower frequencies in other mammals. The
Cardiovirus
genus within the
Picornaviridae
family is currently made up of two viral species,
Theilovirus
and
Encephalomyocarditis virus
. Until recently, only a single strain of cardioviruses (Vilyuisk virus within the
Theilovirus
species) associated with a geographically restricted and prevalent encephalitis-like condition had been reported to occur in humans. A second theilovirus-related cardiovirus (
Saffold virus
[SAFV]) was reported in 2007 and subsequently found in respiratory secretions from children with respiratory problems and in stools of both healthy and diarrheic children. Using viral metagenomics, we identified RNA fragments related to SAFV in the stools of Pakistani and Afghani children with nonpolio acute flaccid paralysis (AFP). We sequenced three near-full-length genomes, showing the presence of divergent strains of SAFV and preliminary evidence of a distant recombination event between the ancestors of the Theiler-like viruses of rats and those of human SAFV. Further VP1 sequencing showed the presence of five new SAFV genotypes, doubling the reported genetic diversity of human and animal theiloviruses combined. Both AFP patients and healthy children in Pakistan were found to be excreting SAFV at high frequencies of 9 and 12%, respectively. Further studies are needed to examine the roles of these highly common and diverse SAFV genotypes in nonpolio AFP and other human diseases.
Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants
Authors: Abrahams M.-R. , Anderson J. A. , Giorgi E. E. , Seoighe C. , Mlisana K. , Ping L.-H. , Athreya G. S. , Treurnicht F. K. , Keele B. F. , Wood N. , Salazar-Gonzalez J. F. , Bhattacharya T. , Chu H. , Hoffman I. , Galvin S. , Mapanje C. , Kazembe P. , Thebus R. , Fiscus S. , Hide W. , Cohen M. S. , Karim S. Abdool , Haynes B. F. , Shaw G. M. , Hahn B. H. , Korber B. T. , Swanstrom R. , Williamson C. 
Published: February 2009

ABSTRACT
Identifying the specific genetic characteristics of successfully transmitted variants may prove central to the development of effective vaccine and microbicide interventions. Although human immunodeficiency virus transmission is associated with a population bottleneck, the extent to which different factors influence the diversity of transmitted viruses is unclear. We estimate here the number of transmitted variants in 69 heterosexual men and women with primary subtype C infections. From 1,505 env sequences obtained using a single genome amplification approach we show that 78% of infections involved single variant transmission and 22% involved multiple variant transmissions (median of 3). We found evidence for mutations selected for cytotoxic-T-lymphocyte or antibody escape and a high prevalence of recombination in individuals infected with multiple variants representing another potential escape pathway in these individuals. In a combined analysis of 171 subtype B and C transmission events, we found that infection with more than one variant does not follow a Poisson distribution, indicating that transmission of individual virions cannot be seen as independent events, each occurring with low probability. While most transmissions resulted from a single infectious unit, multiple variant transmissions represent a significant fraction of transmission events, suggesting that there may be important mechanistic differences between these groups that are not yet understood.
The Replication Cycle of Varicella-Zoster Virus: Analysis of the Kinetics of Viral Protein Expression, Genome Synthesis, and Virion Assembly at the Single-Cell Level
Authors: Reichelt Mike , Brady Jennifer , Arvin Ann M. 
Published: February 2009

ABSTRACT
Varicella-zoster virus (VZV) is a human alphaherpesvirus that is highly cell associated in cell culture. Because cell-free virus yields are too low to permit the synchronous infections needed for time-resolved analyses, information is lacking about the sequence of events during the VZV replication cycle. To address this challenge, we differentially labeled VZV-infected inoculum cells (input) and uninfected (output) cells with fluorescent cell dyes or endocytosed nanogold particles and evaluated newly infected cells by confocal immunofluorescence or electron microscopy (EM) at the single-cell level at defined intervals. We demonstrated the spatiotemporal expression of six major VZV proteins, ORF61, IE62, IE63, ORF29, ORF23, and gE, representing all putative kinetic classes, for the first time. Newly synthesized ORF61, as well as IE62, the major VZV transactivator, appeared within 1 h, and they were targeted to different subnuclear compartments. The formation of VZV DNA replication compartments started between 4 and 6 h, involved recruitment of ORF29 to putative IE62 prereplication sites, and resulted in large globular nuclear compartments where newly synthesized viral DNA accumulated. Although considered a late protein, gE accumulated in the Golgi compartment at as early as 4 h. ORF23 capsid protein was present at 9 h. The assembly of viral nucleocapsids and mature enveloped VZ virions was detected by 9 to 12 h by time-resolved EM. Although syncytium formation is a hallmark of VZV infection, infection of neighboring cells did not require cell-cell fusion; its occurrence from 9 h is likely to amplify VZV replication. Our results define the productive cycle of VZV infection in a single cell as occurring in 9 to 12 h.
Amino Acid Residues in the Fusion Peptide Pocket Regulate the pH of Activation of the H5N1 Influenza Virus Hemagglutinin Protein
Authors: Reed Mark L. , Yen Hui-Ling , DuBois Rebecca M. , Bridges Olga A. , Salomon Rachelle , Webster Robert G. , Russell Charles J. 
Published: February 2009

ABSTRACT
The receptor specificity and cleavability of the hemagglutinin (HA) protein have been shown to regulate influenza A virus transmissibility and pathogenicity, but little is known about how its pH of activation contributes to these important biological properties. To identify amino acid residues that regulate the acid stability of the HA protein of H5N1 influenza viruses, we performed a mutational analysis of the HA protein of the moderately pathogenic A/chicken/Vietnam/C58/04 (H5N1) virus. Nineteen HA proteins containing point mutations in the HA2 coiled-coil domain or in an HA1 histidine or basic patch were generated. Wild-type and mutant HA plasmids were transiently transfected in cell culture and analyzed for total protein expression, surface expression, cleavage efficiency, pH of fusion, and pH of conformational change. Four mutations to residues in the fusion peptide pocket, Y23H and H24Q in the HA1 subunit and E105K and N114K in the HA2 subunit, and a K58I mutation in the HA2 coiled-coil domain significantly altered the pH of activation of the H5 HA protein. In some cases, the magnitude and direction of changes of individual mutations in the H5 HA protein differed considerably from similar mutations in other influenza A virus HA subtypes. Introduction of Y23H, H24Q, K58I, and N114K mutations into recombinant viruses resulted in virus-expressed HA proteins with similar shifts in the pH of fusion. Overall, the data show that residues comprising the fusion peptide pocket are important in triggering pH-dependent activation of the H5 HA protein.
Detection and Characterization of Influenza A Virus PA-PB2 Interaction through a Bimolecular Fluorescence Complementation Assay
Authors: Hemerka Joseph N. , Wang Dan , Weng Yuejin , Lu Wuxun , Kaushik Radhey S. , Jin Jing , Harmon Aaron F. , Li Feng 
Published: February 2009

ABSTRACT
The influenza virus polymerase complex, consisting of the PA, PB1, and PB2 subunits, is required for the transcription and replication of the influenza A viral genome. Previous studies have shown that PB1 serves as a core subunit to incorporate PA and PB2 into the polymerase complex by directly interacting with PA and PB2. Despite numerous attempts, largely involving biochemical approaches, a specific interaction between PA and PB2 subunits has yet to be detected. In the current study, we developed and utilized bimolecular fluorescence complementation (BiFC) to study protein-protein interactions in the assembly of the influenza A virus polymerase complex. Proof-of-concept experiments demonstrated that BiFC can specifically detect PA-PB1 interactions in living cells. Strikingly, BiFC demonstrated an interaction between PA and PB2 that has not been reported previously. Deletion-based BiFC experiments indicated that the N-terminal 100 amino acid residues of PA are responsible for the PA-PB2 interaction observed in BiFC. Furthermore, a detailed analysis of subcellular localization patterns and temporal nuclear import of PA-PB2 binary complexes suggested that PA and PB2 subunits interacted in the cytoplasm initially and were subsequently transported as a dimer into the nucleus. Taken together, results of our studies reveal a previously unknown PA-PB2 interaction and provide a framework for further investigation of the biological relevance of the PA-PB2 interaction in the polymerase activity and viral replication of influenza A virus.
Kinetic Analysis of Human T-Cell Leukemia Virus Type 1 Gene Expression in Cell Culture and Infected Animals
Authors: Li Min , Kesic Matthew , Yin Han , Yu Lianbo , Green Patrick L. 
Published: February 2009

ABSTRACT

Human T-cell leukemia virus type 1 (HTLV-1) infection causes adult T-cell leukemia and is associated with a variety of lymphocyte-mediated disorders. It has been hypothesized that a highly regulated pattern of HTLV-1 gene expression is critical for virus survival and disease pathogenesis. In this study, real-time reverse transcriptase PCR was used to determine the kinetics of viral gene expression in cells transiently transfected with an HTLV-1 proviral plasmid, in newly infected human peripheral blood mononuclear cells (PBMCs), and in PBMCs from newly infected rabbits. The HTLV-1 gene expression profiles in transiently transfected and infected cells were similar; over time, all transcripts increased and then maintained stable levels.
gag/pol
,
tax/rex
, and
env
mRNA were detected first and at the highest levels, whereas the expression levels of the accessory genes, including the antisense
Hbz
, were significantly lower than the
tax/rex
levels (ranging from 1 to 4 logs depending on the specific mRNA). In infected rabbits,
tax/rex
and
gag/pol
mRNA levels peaked early after inoculation and progressively decreased, which correlated inversely with the proviral load and host antibody response against viral proteins. Interestingly,
Hbz
mRNA was detectable at 1 week postinfection and increased and stabilized. The expression levels of all other HTLV-1 genes in infected rabbit PBMCs were at or below our limit of detection. This analysis provides insight into viral gene expression under various in vitro and in vivo experimental conditions. Our in vivo data indicate that in infected rabbits,
Hbz
mRNA expression over time directly correlates with the proviral load, which provides the first evidence linking
Hbz
expression to proviral load and the survival of the virus-infected cell in the host.
Characterization of Genotype-Specific Carboxyl-Terminal Cleavage Sites of Hepatitis B Virus e Antigen Precursor and Identification of Furin as the Candidate Enzyme
Authors: Ito Kiyoaki , Kim Kyun-Hwan , Lok Anna Suk-Fong , Tong Shuping 
Published: February 2009

ABSTRACTHepatitis B e antigen (HBeAg) is a secreted version of hepatitis B virus (HBV) core protein that promotes immune tolerance and persistent infection. It is derived from a translation product of the precore/core gene by two proteolytic cleavage events: removal of the amino-terminal signal peptide and removal of the carboxyl-terminal arginine-rich sequence. Four RXXR motifs are present at the carboxyl terminus of the HBeAg precursor, with the first two fused as151RRGRSPR157. Genotype A possesses two extra amino acids at the first motif (151RRDRGRSPR159), which weakens the first motif and separates it from the second one. Western blot analysis of patient sera revealed a single HBeAg form for genotypes B to D but two additional forms of larger sizes for genotype A. Site-directed mutagenesis and transfection experiments with human hepatoma cell lines indicated that HBeAg of genotype B is derived from cleavage at the first (151RRGR154) motif. The major HBeAg form of genotype A corresponds to cleavage at the second (156RSPR159) motif, and the other two forms are cleavage products of the first (151RRDR154) and third (166RRRR169) motifs, respectively. Only the cleavage product of the third motif of genotype A was observed in furin-deficient LoVo cells, and an inhibitor of furin-like proprotein convertases blocked cleavage of the first and second motifs in human hepatoma cells. In conclusion, our study reveals genotypic differences in HBeAg processing and implicates furin as the major enzyme involved in the cleavage of the first and second RXXR motifs.
Electron Cryo-Microscopy and Single-Particle Averaging of Rift Valley Fever Virus: Evidence for G
N
-G
C
Glycoprotein Heterodimers
Authors: Huiskonen Juha T. , Överby Anna K. , Weber Friedemann , Grünewald Kay 
Published: February 2009

ABSTRACT

Rift Valley fever virus (RVFV) is a member of the genus
Phlebovirus
within the family
Bunyaviridae
. It is a mosquito-borne zoonotic agent that can cause hemorrhagic fever in humans. The enveloped RVFV virions are known to be covered by capsomers of the glycoproteins G
N
and G
C
, organized on a T=12 icosahedral lattice. However, the structural units forming the RVFV capsomers have not been determined. Conflicting biochemical results for another phlebovirus (Uukuniemi virus) have indicated the existence of either G
N
and G
C
homodimers or G
N
-G
C
heterodimers in virions. Here, we have studied the structure of RVFV using electron cryo-microscopy combined with three-dimensional reconstruction and single-particle averaging. The reconstruction at 2.2-nm resolution revealed the organization of the glycoprotein shell, the lipid bilayer, and a layer of ribonucleoprotein (RNP). Five- and six-coordinated capsomers are formed by the same basic structural unit. Molecular-mass measurements suggest a G
N
-G
C
heterodimer as the most likely candidate for this structural unit. Both leaflets of the lipid bilayer were discernible, and the glycoprotein transmembrane densities were seen to modulate the curvature of the lipid bilayer. RNP densities were situated directly underneath the transmembrane densities, suggesting an interaction between the glycoprotein cytoplasmic tails and the RNPs. The success of the single-particle averaging approach taken in this study suggests that it is applicable in the study of other phleboviruses, as well, enabling higher-resolution description of these medically important pathogens.
Engagement of the Lysine-Specific Demethylase/HDAC1/CoREST/REST Complex by Herpes Simplex Virus 1
Authors: Gu Haidong , Roizman Bernard 
Published: February 2009

ABSTRACT
Among the early events in herpes simplex virus 1 replication are localization of ICP0 in ND10 bodies and accumulation of viral DNA-protein complexes in structures abutting ND10. ICP0 degrades components of ND10 and blocks silencing of viral DNA, achieving the latter by dislodging HDAC1 or -2 from the lysine-specific demethylase 1 (LSD1)/CoREST/REST repressor complex. The role of this process is apparent from the observation that a dominant-negative CoREST protein compensates for the absence of ICP0 in a cell-dependent fashion. HDAC1 or -2 and the CoREST/REST complex are independently translocated to the nucleus once viral DNA synthesis begins. The focus of this report is twofold. First, we report that in infected cells, LSD1, a key component of the repressor complex, is partially degraded or remains stably associated with CoREST and is ultimately also translocated, in part, to the cytoplasm. Second, we examined the distribution of the components of the repressor complex and ICP8 early in infection in wild-type-virus- and ICP0 mutant virus-infected cells. The repressor component and ultimately ICP8 localize in structures that abut the ND10 nuclear bodies. There is no evidence that the two compartments fuse. We propose that ICP0 must dynamically interact with both compartments in order to accomplish its functions of degrading PML and SP100 and suppressing silencing of viral DNA through its interactions with CoREST. In turn, the remodeling of the viral DNA-protein complex enables recruitment of ICP8 and initiation of formation of replication compartments.