Genomes and Genes
Summary: DNA sequences that form the coding region for proteins associated with the viral core in retroviruses. gag is short for group-specific antigen.
- Duarte A, Tavares L. Phylogenetic analysis of Portuguese Feline Immunodeficiency Virus sequences reveals high genetic diversity. Vet Microbiol. 2006;114:25-33 pubmed
- Brumme Z, Brumme C, Carlson J, Streeck H, John M, Eichbaum Q, et al. Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. J Virol. 2008;82:9216-27 pubmed publisher..Dramatic differences in escape and reversion rates across codons, genes, and HLA restrictions are observed, highlighting the complexity of viral adaptation to the host immune response. ..
- Duarte A, Marques M, Tavares L, Fevereiro M. Phylogenetic analysis of five Portuguese strains of FIV. Arch Virol. 2002;147:1061-70 pubmed..The study of these new FIV isolates showed the presence of Subtype B in Portugal and could provide a contribution for the understanding of FIV's genetic diversity. ..
- Smith J, Amara R, Campbell D, Xu Y, Patel M, Sharma S, et al. DNA/MVA vaccine for HIV type 1: effects of codon-optimization and the expression of aggregates or virus-like particles on the immunogenicity of the DNA prime. AIDS Res Hum Retroviruses. 2004;20:1335-47 pubmed..Based on the breadth of the T cell response and a trend toward higher titers of anti-Env Ab, we are moving forward with human trials of the noncodon-optimized VLP-expressing DNA. ..
- Santiago M, Range F, Keele B, Li Y, Bailes E, Bibollet Ruche F, et al. Simian immunodeficiency virus infection in free-ranging sooty mangabeys (Cercocebus atys atys) from the Taï Forest, Côte d'Ivoire: implications for the origin of epidemic human immunodeficiency virus type 2. J Virol. 2005;79:12515-27 pubmed
- Nason Burchenal K, Wolff L. Activation of c-myb is an early bone-marrow event in a murine model for acute promonocytic leukemia. Proc Natl Acad Sci U S A. 1993;90:1619-23 pubmed..This approach for detecting preleukemic cells will now allow the study of mechanisms by which these preleukemic cells progress to a more transformed state and, perhaps, to a more differentiated state. ..
- Peyerl F, Barouch D, Yeh W, Bazick H, Kunstman J, Kunstman K, et al. Simian-human immunodeficiency virus escape from cytotoxic T-lymphocyte recognition at a structurally constrained epitope. J Virol. 2003;77:12572-8 pubmed..Together, these data suggest that a compensatory mutation is selected for in SHIV strain 89.6P to facilitate the escape of that virus from CTL recognition of the dominant p11C, C-M epitope. ..
- Wang Y, Wills N, Du Z, Rangan A, Atkins J, Gesteland R, et al. Comparative studies of frameshifting and nonframeshifting RNA pseudoknots: a mutational and NMR investigation of pseudoknots derived from the bacteriophage T2 gene 32 mRNA and the retroviral gag-pro frameshift site. RNA. 2002;8:981-96 pubmed
- Marlowe N, Flys T, Hackett J, Schumaker M, Jackson J, Eshleman S. Analysis of insertions and deletions in the gag p6 region of diverse HIV type 1 strains. AIDS Res Hum Retroviruses. 2004;20:1119-25 pubmed..Further studies are needed to determine whether such genotypic differences influence viral replication capacity, antiretroviral drug susceptibility, or other phenotypic properties of these strains. ..
- Pal R, Wang S, Kalyanaraman V, Nair B, Whitney S, Keen T, et al. Polyvalent DNA prime and envelope protein boost HIV-1 vaccine elicits humoral and cellular responses and controls plasma viremia in rhesus macaques following rectal challenge with an R5 SHIV isolate. J Med Primatol. 2005;34:226-36 pubmed
- Kalish M, Korber B, Pillai S, Robbins K, Leo Y, Saekhou A, et al. The sequential introduction of HIV-1 subtype B and CRF01AE in Singapore by sexual transmission: accelerated V3 region evolution in a subpopulation of Asian CRF01 viruses. Virology. 2002;304:311-29 pubmed..The identification of a rapidly evolving population of CRF01AE variants should be considered when designing new candidate vaccines and when evaluating breakthrough strains from current vaccine trials. ..
- Qiao Y, Huang Y, Qiu C, Yue X, Deng L, Wan Y, et al. The use of PEGylated poly [2-(N,N-dimethylamino) ethyl methacrylate] as a mucosal DNA delivery vector and the activation of innate immunity and improvement of HIV-1-specific immune responses. Biomaterials. 2010;31:115-23 pubmed publisher..Overall, mPEG-b-PDMAEMA can be used as an efficient DNA vaccine vector which enhances adaptive immune responses by activating innate immunity. ..
- Telenti A, Martinez R, Munoz M, Bleiber G, Greub G, Sanglard D, et al. Analysis of natural variants of the human immunodeficiency virus type 1 gag-pol frameshift stem-loop structure. J Virol. 2002;76:7868-73 pubmed..In contrast, viruses with stem-loop structures associated with 16 to 42% reductions in frameshift efficiency displayed no significant viral replication deficit. ..
- Kubo Y, Nakagawa Y, Kakimi K, Matsui H, Higo K, Wang L, et al. Molecular cloning and characterization of a murine AIDS virus-related endogenous transcript expressed in C57BL/6 mice. J Gen Virol. 1994;75 ( Pt 4):881-8 pubmed..The recombinant virus was replication-competent, and the p12 region of the transcript retained the functional sequence present in the BM5eco virus. ..
- Takeda A, Igarashi H, Nakamura H, Kano M, Iida A, Hirata T, et al. Protective efficacy of an AIDS vaccine, a single DNA priming followed by a single booster with a recombinant replication-defective Sendai virus vector, in a macaque AIDS model. J Virol. 2003;77:9710-5 pubmed..6PD infections. ..
- Yu S, Feng X, Shu T, Matano T, Hasegawa M, Wang X, et al. Potent specific immune responses induced by prime-boost-boost strategies based on DNA, adenovirus, and Sendai virus vectors expressing gag gene of Chinese HIV-1 subtype B. Vaccine. 2008;26:6124-31 pubmed publisher..Its further studies as a promising scheme for therapeutic and/or prophylactic HIV-1 vaccines should be grounded. ..
- Lee S, Dykxhoorn D, Kumar P, Ranjbar S, Song E, Maliszewski L, et al. Lentiviral delivery of short hairpin RNAs protects CD4 T cells from multiple clades and primary isolates of HIV. Blood. 2005;106:818-26 pubmed..Thus, although 1 or 2 mutations at peripheral sites are tolerated, mutations in the central target cleavage region abolish RNAi activity. ..
- Iglesias Sanchez M, Lopez Galindez C. Each genomic RNA in HIV-1 heterozygous virus generate new virions. Virology. 2005;333:316-23 pubmed..These results demonstrate that the two genomic RNAs in HIV-1 heterozygous virions could be used in the generation of new viruses. This mechanism permits the recovery of deleterious mutants and enhances the evolutive potential of HIV-1. ..
- Cornelissen M, van den Burg R, Zorgdrager F, Goudsmit J. Spread of distinct human immunodeficiency virus type 1 AG recombinant lineages in Africa. J Gen Virol. 2000;81:515-23 pubmed..The recovery of AG recombinants from African countries a thousand miles apart indicates the active spread of new recombinants. ..
- Roy B, Russell R, Turner D, Liang C. The T12I mutation within the SP1 region of Gag restricts packaging of spliced viral RNA into human immunodeficiency virus type 1 with mutated RNA packaging signals and mutated nucleocapsid sequence. Virology. 2006;344:304-14 pubmed..Therefore, the MP2 mutation demonstrates a distinct role in HIV-1 RNA packaging that is neither pertained to the specific viral RNA packaging signal nor to the NC sequence. ..
- Sterner D, Murphy E. Regulation of the efficiency and thermodependence of murine sarcoma virus MuSVts110 RNA splicing by sequences in both exons. Virology. 1992;191:638-48 pubmed
- Momtaz H, Hemmatzadeh F, Keyvanfar H. Expression of bovine leukemia virus p24 protein in bacterial cell. Pak J Biol Sci. 2008;11:2433-7 pubmed
- Loh L, Kent S. Quantification of simian immunodeficiency virus cytotoxic T lymphocyte escape mutant viruses. AIDS Res Hum Retroviruses. 2008;24:1067-72 pubmed publisher..These data help refine our understanding of how CTL escape mutant viruses evolve...
- Dooher J, Schneider B, Reed J, Lingappa J. Host ABCE1 is at plasma membrane HIV assembly sites and its dissociation from Gag is linked to subsequent events of virus production. Traffic. 2007;8:195-211 pubmed..Moreover, the data suggest a linkage between Gag-ABCE1 dissociation and subsequent events of virion production...
- Heslop O, Smikle M, Deer D, Christian N, Vickers I, Harvey K, et al. Human immunodeficiency virus type-1 (HIV-1) subtypes in Jamaica. West Indian Med J. 2005;54:279-82 pubmed..This work supports the view of colleagues from the French and Spanish-speaking Caribbean that an epidemiological network supported by regional laboratories will help track this epidemic accurately with positive outcomes for the public. ..
- Takahashi H, Tatsumi M, Matsuda M, Nagashima K, Kurata T, Hall W. The role of topoisomerase I in HIV-1 replication. Leukemia. 1997;11 Suppl 3:26-8 pubmed..Moreover the findings suggest that other factors which remained to be identified, are involved in restricting HIV-1 replication in non-primate cells. ..
- Depil S, Roche C, Dussart P, Prin L. Expression of a human endogenous retrovirus, HERV-K, in the blood cells of leukemia patients. Leukemia. 2002;16:254-9 pubmed..This suggests that HERV-K relative overexpression in leukemia samples might be specifically associated with tumor development. The origin of these transcriptional variations is therefore worth being investigated further. ..
- Novitsky V, Rybak N, McLane M, Gilbert P, Chigwedere P, Klein I, et al. Identification of human immunodeficiency virus type 1 subtype C Gag-, Tat-, Rev-, and Nef-specific elispot-based cytotoxic T-lymphocyte responses for AIDS vaccine design. J Virol. 2001;75:9210-28 pubmed
- Takehisa J, Harada Y, Ndembi N, Mboudjeka I, Taniguchi Y, Ngansop C, et al. Natural infection of wild-born mandrills (Mandrillus sphinx) with two different types of simian immunodeficiency virus. AIDS Res Hum Retroviruses. 2001;17:1143-54 pubmed publisher..We therefore designated the Cameroonian SIVmnd as SIVmnd type 2 and redesignated SIVmndGB1 as SIVmnd type 1. To date, M. sphinx is the only primate species other than humans that is naturally infected with two different types of SIV...
- Ono R, Kobayashi S, Wagatsuma H, Aisaka K, Kohda T, Kaneko ishino T, et al. A retrotransposon-derived gene, PEG10, is a novel imprinted gene located on human chromosome 7q21. Genomics. 2001;73:232-7 pubmed..These data suggest that PEG10 is derived from a retrotransposon that was previously integrated into the mammalian genome. PEG10 is likely to be essential for understanding how exogenous genes become imprinted. ..
- O Sullivan C, Polony T, Paca R, Beemon K. Rous sarcoma virus negative regulator of splicing selectively suppresses SRC mRNA splicing and promotes polyadenylation. Virology. 2002;302:405-12 pubmed..In addition, increased transcriptional readthrough of the poly(A) site in the 3' LTR was observed with the NRS mutant viruses, suggesting that the wild-type NRS sequence promotes polyadenylation. ..
- Deng X, Liu H, Shao Y, Rayner S, Yang R. The epidemic origin and molecular properties of B': a founder strain of the HIV-1 transmission in Asia. AIDS. 2008;22:1851-8 pubmed publisher..Our results provide an important reference for HIV scientists, public health officials and HIV vaccine designers. ..
- Ayele W, Pollakis G, Abebe A, Fisseha B, Tegbaru B, Tesfaye G, et al. Development of a nucleic acid sequence-based amplification assay that uses gag-based molecular beacons to distinguish between human immunodeficiency virus type 1 subtype C and C' infections in Ethiopia. J Clin Microbiol. 2004;42:1534-41 pubmed
- Choge I, Cilliers T, Walker P, Taylor N, Phoswa M, Meyers T, et al. Genotypic and phenotypic characterization of viral isolates from HIV-1 subtype C-infected children with slow and rapid disease progression. AIDS Res Hum Retroviruses. 2006;22:458-65 pubmed..Similar to adults, CXCR4 usage was uncommon among HIV-1 subtype C isolates from pediatric infections. ..
- Kumar S, Seth P. Immunogenicity of recombinant Modified Vaccinia Ankara Viruses (rMVA) expressing HIV-1 Indian subtype C gag-protease and env-gp120 genes in mice. Viral Immunol. 2004;17:574-9 pubmed..These epitopes were distributed through out the length of gag and envelope gp120 proteins. ..
- Jones N, Wei X, Flower D, Wong M, Michor F, Saag M, et al. Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. J Exp Med. 2004;200:1243-56 pubmed
- Vershinin A, Ellis T. Heterogeneity of the internal structure of PDR1, a family of Ty1/copia-like retrotransposons in pea. Mol Gen Genet. 1999;262:703-13 pubmed..Combining both trees revealed clear and distinct subgroups among the Pisum ssp. ..
- Peterson Burch B, Voytas D. Genes of the Pseudoviridae (Ty1/copia retrotransposons). Mol Biol Evol. 2002;19:1832-45 pubmed..In several elements, this domain is flanked on both sides by RNA-binding domains. We propose that this monophyletic lineage defines a new Pseudoviridae genus, herein referred to as the AGROVIRUS: ..
- Liu W, Backes P, Lochelt M. Importance of the major splice donor and redefinition of cis-acting sequences of gutless feline foamy virus vectors. Virology. 2009;394:208-17 pubmed publisher..By minimizing the second cis-acting sequence in the pol gene, only 3.8 kb viral sequences are maintained in the novel gutless FFV RD vectors. ..
- Wertheim J, Worobey M. Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2. PLoS Comput Biol. 2009;5:e1000377 pubmed publisher..Our results suggest either that SIV is a surprisingly young lentiviral lineage or that SIV and, perhaps, HIV dating estimates are seriously compromised by unaccounted-for biases. ..
- Clemenceau B, Lalain S, Martignat L, Sai P. Porcine endogenous retroviral mRNAs in pancreas and a panel of tissues from specific pathogen-free pigs. Diabetes Metab. 1999;25:518-25 pubmed..Pig tissues may differ in their loads of PERV sequences, which could be a factor in the risk of PERV transmission during xenotransplantation...
- Garrido C, Li R, Samarut J, Gospodarowicz D, Saule S. v-erbA cooperates with bFGF in neuroretina cell transformation. Virology. 1993;192:578-86 pubmed..A likely explanation is that CNR cells carrying the cytoplasmic but not the nuclear oncogenes have already activated the bFGF signal transduction pathway. ..
- Lore K, Sonnerborg A, Olsson J, Patterson B, Fehniger T, Perbeck L, et al. HIV-1 exposed dendritic cells show increased pro-inflammatory cytokine production but reduced IL-1ra following lipopolysaccharide stimulation. AIDS. 1999;13:2013-21 pubmed
- Bourara K, Liegler T, Grant R. Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1. PLoS Pathog. 2007;3:1477-85 pubmed..Developing drugs that inhibit A3C may be a novel strategy for delaying viral escape from immune or antiretroviral inhibition. ..
- Rein A. Genetic footprinting of a retroviral Gag gene suggests an important role in virus replication. Proc Natl Acad Sci U S A. 2003;100:11929-30 pubmed
- Valiathan R, Resh M. Differential control of CXCR4 and CD4 downregulation by HIV-1 Gag. Virol J. 2008;5:23 pubmed publisher..HIV-1 Gag selectively modulates protein sorting at the MVB, interfering with ESCRT-I dependent but not ESCRT-I independent processes. ..
- Ouédraogo Traoré R, Montavon C, Sanou T, Vidal N, Sangare L, Sanou I, et al. CRF06-cpx is the predominant HIV-1 variant in AIDS patients from Ouagadougou, the capital city of Burkina Faso. AIDS. 2003;17:441-2 pubmed
- Mintsa Ndong A, Caron M, Plantier J, Makuwa M, Le Hello S, Courgnaud V, et al. High HIV Type 1 prevalence and wide genetic diversity with dominance of recombinant strains but low level of antiretroviral drug-resistance mutations in untreated patients in northeast Gabon, Central Africa. AIDS Res Hum Retroviruses. 2009;25:411-8 pubmed publisher..The wide diversity and the emergence of recombinant strains are in accordance with the rapid spread of new HIV strains in the population and, thus, the dynamic evolution of the epidemic. ..
- Jiang S, Rasmussen R, Nolan K, Frankel F, Lieberman J, McClure H, et al. Live attenuated Listeria monocytogenes expressing HIV Gag: immunogenicity in rhesus monkeys. Vaccine. 2007;25:7470-9 pubmed
- de Felipe P, Izquierdo M, Wandosell F, Lim F. Integrating retroviral cassette extends gene delivery of HSV-1 expression vectors to dividing cells. Biotechniques. 2001;31:394-402, 404-5 pubmed..These vectors have wide applications for the genetic modification of many cell types. ..