Abstract:
:Hepatitis C virus (HCV) replication in infected patients produces large and diverse viral populations, which give rise to drug-resistant and immune escape variants. Here, we analyzed HCV populations during transmission and diversification in longitudinal and cross-sectional samples using 454/Roche pyrosequencing, in total analyzing 174,185 sequence reads. To sample diversity, four locations in the HCV genome were analyzed, ranging from high diversity (the envelope hypervariable region 1 [HVR1]) to almost no diversity (the 5' untranslated region [UTR]). For three longitudinal samples for which early time points were available, we found that only 1 to 4 viral variants were present, suggesting that productive infection was initiated by a very small number of HCV particles. Sequence diversity accumulated subsequently, with the 5' UTR showing almost no diversification while the envelope HVR1 showed >100 variants in some subjects. Calculation of the transmission probability for only a single variant, taking into account the measured population structure within patients, confirmed initial infection by one or a few viral particles. These findings provide the most detailed sequence-based analysis of HCV transmission bottlenecks to date. The analytical methods described here are broadly applicable to studies of viral diversity using deep sequencing.
journal_name
J Viroljournal_title
Journal of virologyauthors
Wang GP,Sherrill-Mix SA,Chang KM,Quince C,Bushman FDdoi
10.1128/JVI.02271-09subject
Has Abstractpub_date
2010-06-01 00:00:00pages
6218-28issue
12eissn
0022-538Xissn
1098-5514pii
JVI.02271-09journal_volume
84pub_type
杂志文章abstract:UNLABELLED:Intron-containing mRNAs are subject to restricted nuclear export in higher eukaryotes. Retroviral replication requires the nucleocytoplasmic transport of both spliced and unspliced RNA transcripts, and RNA export mechanisms of gammaretroviruses are poorly characterized. Here, we report the involvement of the...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.03584-13
更新日期:2014-04-01 00:00:00
abstract::Chemokine receptors CCR5 and CXCR4 are the primary fusion coreceptors utilized for CD4-mediated entry by macrophage (M)- and T-cell line (T)-tropic human immunodeficiency virus type 1 (HIV-1) strains, respectively. Here we demonstrate that HIV-1 Tat protein, a potent viral transactivator shown to be released as a solu...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.72.11.8952-8960.1998
更新日期:1998-11-01 00:00:00
abstract::The ribonucleic acid (RNA) from Western equine encephalomyelitis (WEE) virions sedimented through sucrose gradients with a sedimentation coefficient of 40S. Another viral RNA which was always associated with infected cells possessed a sedimentation coefficient of 26S. Both 40S and 26S RNA had identical base compositio...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.2.6.558-566.1968
更新日期:1968-06-01 00:00:00
abstract::Simian virus 40 tumor (T) antigen, an established viral oncoprotein, causes alterations in cell growth control through interacting with, and altering the function of, cellular proteins. To examine the effects of T antigen on cell growth control, and to identify the cellular proteins with which it may functionally inte...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.69.2.756-763.1995
更新日期:1995-02-01 00:00:00
abstract::The 86-kDa IE-2 protein of human cytomegalovirus is able to autoregulate its own expression via a short nucleotide sequence, termed the cis repression signal (CRS), that is located between the TATA box and the cap site of the IE-1/2 enhancer-promoter. Here we report that the 86-kDa IE-2 protein can interact directly w...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.67.1.323-331.1993
更新日期:1993-01-01 00:00:00
abstract::Type I interferons induce a complex transcriptional program that leads to a generalized antiviral response against a large panel of viruses, including human immunodeficiency virus type 1 (HIV-1). However, despite the fact that interferons negatively regulate HIV-1 ex vivo, a chronic interferon state is linked to the p...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.02553-12
更新日期:2013-03-01 00:00:00
abstract::White root rot, caused by the ascomycete Rosellinia necatrix, is a devastating disease worldwide, particularly in fruit trees in Japan. Here we report on the biological and molecular properties of a novel bipartite double-stranded RNA (dsRNA) virus encompassing dsRNA-1 (8,931 bp) and dsRNA-2 (7,180 bp), which was isol...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01830-09
更新日期:2009-12-01 00:00:00
abstract::The emerging porcine epidemic diarrhea virus (PEDV) requires trypsin supplementation to activate its S protein for membrane fusion and virus propagation in cell culture. By substitution of a single amino acid in the S protein, we created a recombinant PEDV with an artificial furin protease cleavage site N terminal of ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00356-15
更新日期:2015-08-01 00:00:00
abstract::Poliovirus-specific RNA-dependent RNA polymerase (3Dpol) was purified to apparent homogeneity. A single polypeptide of an apparent molecular weight of 63,000 catalyzes the synthesis of dimeric and monomeric RNA products in response to the poliovirion RNA template. Analysis of purified 3Dpol by two-dimensional electrop...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.63.11.4563-4568.1989
更新日期:1989-11-01 00:00:00
abstract::West Nile virus has spread rapidly across the United States, and there is currently no approved human vaccine or therapy to prevent or treat disease. Passive immunization with antibodies against the envelope protein represents a promising means to provide short-term prophylaxis and treatment for West Nile virus infect...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.79.23.14606-14613.2005
更新日期:2005-12-01 00:00:00
abstract::The cellular tropism of the feline immunodeficiency virus (FIV) is affected by changes in variable region 3 (V3) of the surface (SU) envelope glycoprotein (Verschoor, E. J., et al., J. Virol. 69:4752-4757, 1995). By using high-dose DNA transfection, an FIV molecular clone with a non-CRFK-tropic V3 acquired the ability...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.71.9.7132-7135.1997
更新日期:1997-09-01 00:00:00
abstract::Sequences which encode Epstein-Barr virus (EBV) RNA in nasopharyngeal carcinoma (NPC) tissue have been identified. We utilized human biopsy material directly as well as NPC grown in nude mice. Total RNA was extracted from the tumor material and separated into polyadenylated and nonpolyadenylated fractions by oligodeox...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.48.3.580-590.1983
更新日期:1983-12-01 00:00:00
abstract::Picornaviruses are a family of positive-strand RNA viruses that are responsible for a variety of devastating human and animal diseases. An attenuated strain of mengovirus (vMC24) is serologically indistinguishable from the lethal murine wild-type mengovirus and encephalomyocarditis virus (EMCV). Immunogen-specific sti...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.69.8.4914-4923.1995
更新日期:1995-08-01 00:00:00
abstract::Nonstructural protein 1 (NS1) of yellow fever virus (YF) is a glycoprotein localized to extracytoplasmic compartments within infected cells. We have previously shown that NS1 can be supplied in trans and is required for viral RNA replication, a process thought to occur in membrane-bound cytoplasmic complexes. Here we ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.73.6.4611-4621.1999
更新日期:1999-06-01 00:00:00
abstract::Disulfide bonds reportedly stabilize the capsids of several viruses, including papillomavirus, polyomavirus, and simian virus 40, and have been detected in herpes simplex virus (HSV) capsids. In this study, we show that in mature HSV-1 virions, capsid proteins VP5, VP23, VP19C, UL17, and UL25 participate in covalent c...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00214-11
更新日期:2011-09-01 00:00:00
abstract::Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus that produces an acute, lethal infection in rainbow trout (Oncorhynchus mykiss). Fish that survive infection cease to produce detectable infectious virus at approximately 46 days after infection, yet there is evidence that survivor fish continue to harbor...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.73.1.843-849.1999
更新日期:1999-01-01 00:00:00
abstract::We have generated four mouse monoclonal antibodies (MAbs) to bovine papillomavirus virions that bound type-specific, adjacent, and conformationally dependent epitopes on the L1 major capsid protein. All four MAbs were neutralizing at ratios of 1 MAb molecule per 5 to 25 L1 molecules, but only three effectively blocked...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.68.11.7570-7574.1994
更新日期:1994-11-01 00:00:00
abstract:UNLABELLED:Influenza B virus causes annual epidemics and, along with influenza A virus, accounts for substantial disease and economic burden throughout the world. Influenza B virus infects only humans and some marine mammals and is not responsible for pandemics, possibly due to a very low frequency of reassortment and ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01576-15
更新日期:2015-12-01 00:00:00
abstract::The glucocorticoid-regulatory sequences from the murine mammary tumor virus long terminal repeat (MMTV LTR) were introduced into the LTR of Moloney murine leukemia virus (M-MuLV) by recombinant DNA techniques. The site of insertion was in the M-MuLV LTR U3 region at -150 base pairs with respect to the RNA cap site. In...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.54.1.133-144.1985
更新日期:1985-04-01 00:00:00
abstract::During the 2009 H1N1 influenza virus pandemic (pdmH1N1) outbreak, it was found that most individuals lacked antibodies against the new pdmH1N1 virus, and only the elderly showed anti-hemagglutinin (anti-HA) antibodies that were cross-reactive with the new strains. Different studies have demonstrated that prior contact...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.05540-11
更新日期:2012-02-01 00:00:00
abstract::Recombination is one of the driving forces of viral evolution. RNA recombination events among similar RNA viruses are frequent, although RNA recombination could also take place among unrelated viruses. In this paper, we have established efficient interviral recombination systems based on yeast and plants. We show that...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01015-19
更新日期:2019-12-12 00:00:00
abstract::The C-terminal half of the replicase ORF1a polyprotein of the arterivirus equine arteritis virus is processed by a chymotrypsinlike serine protease (SP) (E. J. Snijder et al., J. Biol. Chem. 271:4864-4871, 1996) located in nonstructural protein 4 (nsp4). Three probable SP cleavage sites had previously been identified ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.71.12.9313-9322.1997
更新日期:1997-12-01 00:00:00
abstract::Human metapneumovirus (hMPV) is a respiratory paramyxovirus of global clinical relevance. Despite the substantial knowledge generated during the last 10 years about hMPV infection, information regarding the activation of the immune response against this virus remains largely unknown. In this study, we demonstrated tha...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01213-12
更新日期:2013-01-01 00:00:00
abstract::The human immunodeficiency virus (HIV) Tat protein has a critical role in viral transcription, but this study focuses on its additional role as an extracellular effector of lymphocyte cell death. It is well known that Tat induces tumor necrosis factor-related apoptosis-induced ligand (TRAIL) in peripheral blood mononu...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/jvi.77.12.6700-6708.2003
更新日期:2003-06-01 00:00:00
abstract::A number of cDNA clones complementary to measles virus mRNA and 50S genome RNA have been generated. These clones have been mapped by restriction enzyme analysis and were subsequently sequenced by the method of Maxam and Gilbert (A. M. Maxam and W. Gilbert, Methods Enzymol. 65:499-560, 1980). Computer analysis of these...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.54.1.186-193.1985
更新日期:1985-04-01 00:00:00
abstract:UNLABELLED:Bovine papillomavirus 1 E6 interacts with two similar proteins that regulate cell attachment and cell migration called paxillin (PXN) and HIC-5 (also known as HIC5, ARA55, HIC-5, TSC-5, and TGFB1I1). Despite the similarity between HIC-5 and paxillin, paxillin is required for E6 to transform mouse embryo fibr...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00552-14
更新日期:2014-09-01 00:00:00
abstract::Fluorosulfonylbenzoyl 5'-adenosine (FSBA) bound to one site in simian virus 40 large T antigen (T) and covalently modified greater than 95% of the molecules in a complete reaction. This analog for ATP specifically cross-links to the Mg-phosphate pocket in ATP-binding sites. Cyanogen bromide cleavage and tryptic digest...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.64.10.4939-4947.1990
更新日期:1990-10-01 00:00:00
abstract:UNLABELLED:Transmission of chronic wasting disease (CWD) between cervids is influenced by the primary structure of the host cellular prion protein (PrP(C)). In white-tailed deer, PRNP alleles encode the polymorphisms Q95 G96 (wild type [wt]), Q95 S96 (referred to as the S96 allele), and H95 G96 (referred to as the H95 ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.02010-15
更新日期:2015-12-01 00:00:00
abstract::The coronavirus nucleocapsid (N) protein is a structural protein that forms a ribonucleoprotein complex with genomic RNA. In addition to its structural role, it has been described as an RNA-binding protein that might be involved in coronavirus RNA synthesis. Here, we report a reverse genetic approach to elucidate the ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.79.11.6620-6630.2005
更新日期:2005-06-01 00:00:00
abstract::Normal replication of Moloney murine leukemia virus (MoMLV) requires the integration of a DNA copy of the viral RNA genome into a chromosome of the host. In this work, we characterize the DNA sequences at the ends of the linear proviral precursor that are required for integration in the presence of MoMLV integration p...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.64.11.5645-5648.1990
更新日期:1990-11-01 00:00:00