Genomes and Genes
Summary: DNA sequences that form the coding region for the viral envelope (env) proteins in retroviruses. The env genes contain a cis-acting RNA target sequence for the rev protein (= GENE PRODUCTS, REV), termed the rev-responsive element (RRE).
- Coetzer M, Cilliers T, Papathanasopoulos M, Ramjee G, Karim S, Williamson C, et al. Longitudinal analysis of HIV type 1 subtype C envelope sequences from South Africa. AIDS Res Hum Retroviruses. 2007;23:316-21 pubmed..In both cases this coreceptor switch was associated with specific amino acid changes in the crown, an increased net amino acid charge in the V3 loop, and an increase in the length of the V1 region. ..
- Verhofstede C, Demecheleer E, De Cabooter N, Gaillard P, Mwanyumba F, Claeys P, et al. Diversity of the human immunodeficiency virus type 1 (HIV-1) env sequence after vertical transmission in mother-child pairs infected with HIV-1 subtype A. J Virol. 2003;77:3050-7 pubmed..Phylogenetic tree topologies argue against selection processes as the major mechanism driving mother-to-child transmission but support the hypothesis that virus variability is mainly driven by the inoculum level and/or exposure time. ..
- Churchill M, Sterjovski J, Gray L, Cowley D, Chatfield C, Learmont J, et al. Longitudinal analysis of nef/long terminal repeat-deleted HIV-1 in blood and cerebrospinal fluid of a long-term survivor who developed HIV-associated dementia. J Infect Dis. 2004;190:2181-6 pubmed..Thus, nef/LTR-deleted HIV-1 strains may undergo compartmentalized evolution in long-term survivors and cause neurologic disease. ..
- Travers S, Clewley J, Glynn J, Fine P, Crampin A, Sibande F, et al. Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1. J Virol. 2004;78:10501-6 pubmed..Here we suggest that the most recent common ancestor of subtype C appeared in the mid- to late 1960s. Sensitivity analyses, by which possible biases due to oversampling from one district were explored, gave very similar estimates. ..
- Daniels R, Wilson P, Patel D, Longhurst H, Patterson S. Analysis of full-length HIV type 1 env genes indicates differences between the virus infecting T cells and dendritic cells in peripheral blood of infected patients. AIDS Res Hum Retroviruses. 2004;20:409-13 pubmed..To test this hypothesis full length env genes have been amplified and sequenced from DC and T cells purified from the blood of five symptomatic HIV-1-infected ..
- Duarte A, Tavares L. Phylogenetic analysis of Portuguese Feline Immunodeficiency Virus sequences reveals high genetic diversity. Vet Microbiol. 2006;114:25-33 pubmed
- Baird H, Gao Y, Galetto R, Lalonde M, Anthony R, Giacomoni V, et al. Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination. Retrovirology. 2006;3:91 pubmed..Ability of one HIV-1 isolate to outgrow the other leads to reduced co-infections, heterozygous virus production, and recombination frequencies. ..
- Vidal N, Mulanga C, Bazepeo S, Mwamba J, Tshimpaka J, Kashi M, et al. Distribution of HIV-1 variants in the Democratic Republic of Congo suggests increase of subtype C in Kinshasa between 1997 and 2002. J Acquir Immune Defic Syndr. 2005;40:456-62 pubmed..These changes could have implications regarding the spread of HIV infection in the DRC as well on vaccine and/or treatment strategies. ..
- Aulicino P, Holmes E, Rocco C, Mangano A, Sen L. Extremely rapid spread of human immunodeficiency virus type 1 BF recombinants in Argentina. J Virol. 2007;81:427-9 pubmed..72 months. This rapid population growth is compatible with an elevated fitness for subtype BF compared to that for "pure" B and F viruses. ..
- de Parseval N, Lazar V, Casella J, Benit L, Heidmann T. Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. J Virol. 2003;77:10414-22 pubmed..The present study provides a comprehensive survey of candidate genes and tools for a precise evaluation of their involvement in these processes. ..
- Zhang H, Hoffmann F, He J, He X, Kankasa C, Ruprecht R, et al. Evolution of subtype C HIV-1 Env in a slowly progressing Zambian infant. Retrovirology. 2005;2:67 pubmed..Whether this pattern is typical of slow progressing subtype C HIV-1 infected infant needs to be further substantiated. ..
- Biek R, Drummond A, Poss M. A virus reveals population structure and recent demographic history of its carnivore host. Science. 2006;311:538-41 pubmed..We suggest that rapidly evolving pathogens may provide a complementary tool for studying population dynamics of their hosts in "shallow" time...
- Sandonis V, Casado C, Alvaro T, Pernas M, Olivares I, Garcia S, et al. A combination of defective DNA and protective host factors are found in a set of HIV-1 ancestral LTNPs. Virology. 2009;391:73-82 pubmed publisher..These HIV controllers presented a combination of deleted viral genomes and host protective factors. ..
- McCutchan F, Hoelscher M, Tovanabutra S, Piyasirisilp S, Sanders Buell E, Ramos G, et al. In-depth analysis of a heterosexually acquired human immunodeficiency virus type 1 superinfection: evolution, temporal fluctuation, and intercompartment dynamics from the seronegative window period through 30 months postinfection. J Virol. 2005;79:11693-704 pubmed
- Weaver E, Collisson E, Slater M, Zhu G. Phylogenetic analyses of Texas isolates indicate an evolving subtype of the clade B feline immunodeficiency viruses. J Virol. 2004;78:2158-63 pubmed..Statistical comparisons with other published sequences confirmed that the Texas group is a unique cluster, possibly a new subtype, arising from subtype B. ..
- Biek R, Rodrigo A, Holley D, Drummond A, Anderson C, Ross H, et al. Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars. J Virol. 2003;77:9578-89 pubmed..These results support the premise that FIVpco is well adapted to its cougar host and provide a basis for comparing lentivirus evolution in endemic and epidemic infections in natural hosts. ..
- Sanabani S, Neto W, de Sa Filho D, Diaz R, Munerato P, Janini L, et al. Full-length genome analysis of human immunodeficiency virus type 1 subtype C in Brazil. AIDS Res Hum Retroviruses. 2006;22:171-6 pubmed..The independent clustering of Brazilian subtype C on the phylogenetic tree suggests the profile of an ideal local candidate for the development of a single subtype vaccine. ..
- Travers S, Tully D, McCormack G, Fares M. A study of the coevolutionary patterns operating within the env gene of the HIV-1 group M subtypes. Mol Biol Evol. 2007;24:2787-801 pubmed
- Choisy M, Woelk C, Guégan J, Robertson D. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol. 2004;78:1962-70 pubmed..We found a significant tendency for positively selected sites to fall outside T-helper epitopes and for positively selected sites to be strongly associated with N glycosylation sites. ..
- Charpentier C, Nora T, Tenaillon O, Clavel F, Hance A. Extensive recombination among human immunodeficiency virus type 1 quasispecies makes an important contribution to viral diversity in individual patients. J Virol. 2006;80:2472-82 pubmed..Second, recombination between adjacent gene segments appeared to generate diversity in both pol and env genes. Thus, the shuffling of resistance mutations within the genes coding for the protease and reverse transcriptase, ..
- Ohagen A, Devitt A, Kunstman K, Gorry P, Rose P, Korber B, et al. Genetic and functional analysis of full-length human immunodeficiency virus type 1 env genes derived from brain and blood of patients with AIDS. J Virol. 2003;77:12336-45 pubmed..In this study, we analyzed 37 full-length env genes from uncultured brain biopsy and blood samples from four patients with AIDS...
- Tagliamonte M, Vidal N, Tornesello M, Peeters M, Buonaguro F, Buonaguro L. Genetic and phylogenetic characterization of structural genes from non-B HIV-1 subtypes in Italy. AIDS Res Hum Retroviruses. 2006;22:1045-51 pubmed..These results confirm the constant HIV-1 molecular evolution and indicate the relevance of a continuous molecular monitoring of HIV-1 isolates for the development of appropriate vaccine candidates. ..
- Hayward J, Taylor J, Rodrigo A. Phylogenetic analysis of feline immunodeficiency virus in feral and companion domestic cats of New Zealand. J Virol. 2007;81:2999-3004 pubmed..In addition, 17 sequences were identified that were distinct from all known FIV clades, and we tentatively suggest these belong to a novel subtype. ..
- Bello G, Casado C, Garcia S, Rodriguez C, del Romero J, Carvajal Rodriguez A, et al. Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients. Virology. 2007;362:294-303 pubmed..These results support the existence of distinct patterns of env evolution in untreated HIV-1-infected patients. ..
- Kann R, Seddon J, Kyaw Tanner M, Meers J. Co-infection with different subtypes of feline immunodeficiency virus can complicate subtype assignment by phylogenetic analysis. Arch Virol. 2007;152:1187-93 pubmed..Seven samples showed discrepancies in subtype assignment from analyses of their env gene sequences. Nucleotide differences of 19.6% and 20.9% in overlapping regions in two cats suggest co-infection with subtypes A and C...
- Niesalla H, de Andrés X, Barbezange C, Fraisier C, Reina R, Arnarson H, et al. Systemic DNA immunization against ovine lentivirus using particle-mediated epidermal delivery and modified vaccinia Ankara encoding the gag and/or env genes. Vaccine. 2009;27:260-9 pubmed publisher..vaccination protocol did not prevent infection, but immunization with the gag gene or a combination of gag and env genes resulted in significantly reduced provirus loads in blood and mediastinal lymph node, respectively...
- 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
- Iversen A, Learn G, Fugger L, Gerstoft J, Mullins J, Skinhoj P. Presence of multiple HIV subtypes and a high frequency of subtype chimeric viruses in heterosexually infected women. J Acquir Immune Defic Syndr. 1999;22:325-32 pubmed..Combined with the increased incidence of heterosexual transmission of HIV, the results imply that an increased subtype diversity can be anticipated in newly infected individuals. ..
- Oelrichs R, Shrestha I, Anderson D, Deacon N. The explosive human immunodeficiency virus type 1 epidemic among injecting drug users of Kathmandu, Nepal, is caused by a subtype C virus of restricted genetic diversity. J Virol. 2000;74:1149-57 pubmed
- Liitsola K, Holm K, Bobkov A, Pokrovsky V, Smolskaya T, Leinikki P, et al. An AB recombinant and its parental HIV type 1 strains in the area of the former Soviet Union: low requirements for sequence identity in recombination. UNAIDS Virus Isolation Network. AIDS Res Hum Retroviruses. 2000;16:1047-53 pubmed..This suggests that only short stretches of absolute sequence identity may be needed for efficient RNA recombination between HIV-1 subtypes. ..
- Vlahakis S, Algeciras Schimnich A, Bou G, Heppelmann C, Villasis Keever A, Collman R, et al. Chemokine-receptor activation by env determines the mechanism of death in HIV-infected and uninfected T lymphocytes. J Clin Invest. 2001;107:207-15 pubmed..These results suggest that activation of the chemokine receptor by HIVenv determines the mechanism of death for both infected and uninfected T lymphocytes. ..
- Dickover R, Garratty E, Plaeger S, Bryson Y. Perinatal transmission of major, minor, and multiple maternal human immunodeficiency virus type 1 variants in utero and intrapartum. J Virol. 2001;75:2194-203 pubmed..These data indicate that different selective pressures, depending on the timing of transmission, may be involved in determining the pattern of maternal HIV-1 variant transmission. ..
- Wei X, Decker J, Liu H, Zhang Z, Arani R, Kilby J, et al. Emergence of resistant human immunodeficiency virus type 1 in patients receiving fusion inhibitor (T-20) monotherapy. Antimicrob Agents Chemother. 2002;46:1896-905 pubmed..These findings provide the first evidence for the rapid emergence of clinical resistance to a novel class of HIV-1 entry inhibitors and may be relevant to future treatment strategies involving these agents. ..
- Buonaguro L, Tagliamonte M, Tornesello M, Ciuffreda D, Capiluppi B, Lopalco L, et al. Molecular and phylogenetic characterization of HIV variants in Italian primary HIV infections (PHI): identification of non-B subtype variants. J Biol Regul Homeost Agents. 2002;16:44-8 pubmed
- Avila M, Pando M, Carrion G, Peralta L, Salomon H, Carrillo M, et al. Two HIV-1 epidemics in Argentina: different genetic subtypes associated with different risk groups. J Acquir Immune Defic Syndr. 2002;29:422-6 pubmed..One, in heterosexual men and women, is dominated by env subtype F whereas the other, in homosexual men, is dominated by env subtype B, as determined by env HMA. ..
- Nappi F, Schneider R, Zolotukhin A, Smulevitch S, Michalowski D, Bear J, et al. Identification of a novel posttranscriptional regulatory element by using a rev- and RRE-mutated human immunodeficiency virus type 1 DNA proviral clone as a molecular trap. J Virol. 2001;75:4558-69 pubmed..Taken together, our results identify a novel posttranscriptional control element that uses a conserved cellular export mechanism. ..
- 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. ..
- Carpenter S, Dobbs D. Molecular and biological characterization of equine infectious anemia virus Rev. Curr HIV Res. 2010;8:87-93 pubmed..A comparative perspective of Rev activity may enhance understanding of an essential lentiviral protein and stimulate new strategies for treatment and prevention of lentivirus infections in vivo. ..
- Nameki D, Kodama E, Ikeuchi M, Mabuchi N, Otaka A, Tamamura H, et al. Mutations conferring resistance to human immunodeficiency virus type 1 fusion inhibitors are restricted by gp41 and Rev-responsive element functions. J Virol. 2005;79:764-70 pubmed..However, since this region also encoded the RRE, additional mutations were required to maintain viral replication. These results suggest that HIV fusion is one of the attractive targets for HIV chemotherapy. ..
- Luedtke N, Hwang J, Glazer E, Gut D, Kol M, Tor Y. Eilatin Ru(II) complexes display anti-HIV activity and enantiomeric diversity in the binding of RNA. Chembiochem. 2002;3:766-71 pubmed..Simple DNA duplexes show a consistent selectivity for Lambda-[Ru(bpy)(2)eilatin](2+) compared to Delta-[Ru(bpy)(2)eilatin](2+), while RNAs show more diverse enantiomeric selectivities. ..
- Harmon B, Campbell N, Ratner L. Role of Abl kinase and the Wave2 signaling complex in HIV-1 entry at a post-hemifusion step. PLoS Pathog. 2010;6:e1000956 pubmed publisher..These results suggest a potential utility of Abl kinase inhibitors to treat HIV-1 infected patients...
- Held D, Kissel J, Patterson J, Nickens D, Burke D. HIV-1 inactivation by nucleic acid aptamers. Front Biosci. 2006;11:89-112 pubmed..Additional nucleic acid-based strategies for inactivation of HIV-1 function (including RNAi, antisense, and ribozymes) have also demonstrated their utility. These approaches are reviewed in other chapters of this volume and elsewhere. ..
- Granados Gonzalez V, Piedrahita L, Martínez M, Genin C, Riffard S, Urcuqui Inchima S. [Role of the HIV-1 gp120 V1/V2 domains in the induction of neutralizing antibodies]. Enferm Infecc Microbiol Clin. 2009;27:523-30 pubmed publisher..Lastly, we will discuss the importance of NAb in the search for an effective vaccine against HIV-1. ..
- Bello G, Casado C, Sandonis V, Alvaro Cifuentes T, Dos Santos C, Garcia S, et al. Plasma viral load threshold for sustaining intrahost HIV type 1 evolution. AIDS Res Hum Retroviruses. 2007;23:1242-50 pubmed..These results suggest that the detection limit of ultrasensitive viremia assays could represent an important threshold below which intrahost HIV-1 evolution does not occur. ..
- Loemba H, Brenner B, Parniak M, Ma ayan S, Spira B, Moisi D, et al. Polymorphisms of cytotoxic T-lymphocyte (CTL) and T-helper epitopes within reverse transcriptase (RT) of HIV-1 subtype C from Ethiopia and Botswana following selection of antiretroviral drug resistance. Antiviral Res. 2002;56:129-42 pubmed..Further characterization of predicted CTL and T-helper anchor motifs and ARV-induced mutations in HIV-1 non-B subtype RTs is warranted. ..
- Allen T, Sherrill K, Crispell S, Perrott M, Carlson J, Demartini J. The jaagsiekte sheep retrovirus envelope gene induces transformation of the avian fibroblast cell line DF-1 but does not require a conserved SH2 binding domain. J Gen Virol. 2002;83:2733-42 pubmed..These findings suggest that more than one mechanism may be involved in JSRV env-mediated transformation...
- Weber J, Rangel H, Chakraborty B, Marotta M, Valdez H, Fransen K, et al. Role of Baseline pol Genotype in HIV-1 Fitness Evolution. J Acquir Immune Defic Syndr. 2003;33:448-60 pubmed..65, P < 0.0001). However, our results suggest that the preexistence of secondary mutations in protease genetic background may have implications in HIV-1 fitness evolution and virologic response to antiretroviral therapy. ..
- 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. ..
- Phuphuakrat A, Auewarakul P. Heterogeneity of HIV-1 Rev response element. AIDS Res Hum Retroviruses. 2003;19:569-74 pubmed..The uneven distribution of variation in both primary sequence and the stem structure put forward highly conserved sites that might be more crucial to the function of RRE than the less conserved parts. ..
- Tönjes R, Niebert M. Relative age of proviral porcine endogenous retrovirus sequences in Sus scrofa based on the molecular clock hypothesis. J Virol. 2003;77:12363-8 pubmed..The age determined for PERV correlates with the time of separation between pigs (Suidae, Sus scrofa) and their closest relatives, American-born peccaries (Tayassuidae, Pecari tajacu), 7.4 x 10(6) years ago. ..
- Phuphuakrat A, Paris R, Nittayaphan S, Louisirirotchanakul S, Auewarakul P. Functional variation of HIV-1 Rev Response Element in a longitudinally studied cohort. J Med Virol. 2005;75:367-73 pubmed..These data suggest that RRE heterogeneity may be important in viral pathogenesis and disease progression. ..
- 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. ..
- Sugaya M, Nishimura F, Katoh A, Harada K. Tailoring the peptide-binding specificity of an RNA by combinations of specificity-altering mutations. Nucleosides Nucleotides Nucleic Acids. 2008;27:534-45 pubmed publisher..It was shown that in most cases the results of the combination of individual mutations were of an additive nature, therefore providing a way to manipulate the peptide-binding specificity of an RNA in a predictable manner. ..