Genomes and Genes
Summary: DNA sequences that form the coding region for retroviral enzymes including reverse transcriptase, protease, and endonuclease/integrase. "pol" is short for polymerase, the enzyme class of reverse transcriptase.
- Stephensen C, Casebolt D, Gangopadhyay N. Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay. Virus Res. 1999;60:181-9 pubmed..This consensus PCR assay for the genus Coronavirus may be useful in identifying as yet unknown coronaviruses. ..
- Gao X, Havecker E, Baranov P, Atkins J, Voytas D. Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA. 2003;9:1422-30 pubmed..These retroelements have a conserved stem-loop at the end of gag, and likely express pol either by a novel means of internal ribosomal entry or by a bypass mechanism. ..
- Forbes E, Nieduszynska S, Brunton F, Gibson J, Glover L, Stansfield I. Control of gag-pol gene expression in the Candida albicans retrotransposon Tca2. BMC Mol Biol. 2007;8:94 pubmed..cerevisiae, indicating non-canonical mechanisms direct gag UGA bypass in Tca2. ..
- Saurya S, Lichtenstein Z, Karpas A. Characterization of pol, vif, vpr, and vpu genes of HIV type 1 in AIDS patients with high viral load and stable CD4+ T cell counts on combination therapy. AIDS Res Hum Retroviruses. 2002;18:1151-5 pubmed..In the same patient, the Vif protein was also truncated because of the deletion of 100 nucleotides at the 3' end of the vif gene. ..
- Yang Z, Nielsen R, Goldman N, Pedersen A. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 2000;155:431-49 pubmed..genes from hominoids, the hemagglutinin (HA) gene from human influenza virus A, and HIV-1 env, vif, and pol genes. Tests for the presence of positively selected sites and their subsequent identification appear quite robust to ..
- Beck I, Crowell C, Kittoe R, Bredell H, Machaba M, Willamson C, et al. Optimization of the oligonucleotide ligation assay, a rapid and inexpensive test for detection of HIV-1 drug resistance mutations, for non-North American variants. J Acquir Immune Defic Syndr. 2008;48:418-27 pubmed publisher..International laboratories experienced in molecular techniques were able to perform the OLA. ..
- Galli A, Lai A, Corvasce S, Saladini F, Riva C, Dehò L, et al. Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms. J Gen Virol. 2008;89:3119-25 pubmed publisher..These findings suggest that such hairpins may play a role in the higher recombination rates detected at these positions. ..
- Andreoletti L, Weiss L, Si Mohamed A, Piketty C, Prazuck T, Calamy G, et al. Multidrug-resistant HIV-1 RNA and proviral DNA variants harboring new dipeptide insertions in the reverse transcriptase pol gene. J Acquir Immune Defic Syndr. 2002;29:102-4 pubmed
- Sachdeva N, Sehgal S, Sud A, Datta U, Arora S. Incidence of lamivudine resistance associated mutations in pol-gene of HIV-1 in patients from north India: a preliminary report. Indian J Pathol Microbiol. 2005;48:337-40 pubmed
- Pandrea I, Robertson D, Onanga R, Gao F, Makuwa M, Ngari P, et al. Analysis of partial pol and env sequences indicates a high prevalence of HIV type 1 recombinant strains circulating in Gabon. AIDS Res Hum Retroviruses. 2002;18:1103-16 pubmed..Thirty-one strains were sequenced in the env and pol genes and phylogenetic analyses classified them as subtype A (n = 2), D (n = 4), G (n = 1), H (n = 1), CRF02 (n = 8), ..
- Auswinporn S, Jenwitheesuk E, Panburana P, Sirinavin S, Vibhagool A, Chantratita W. Prevalence of HIV-1 drug resistance in antiretroviral-naive pregnant Thai women. Southeast Asian J Trop Med Public Health. 2002;33:818-21 pubmed
- Hue S, Pillay D, Clewley J, Pybus O. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A. 2005;102:4425-9 pubmed..Our results provide insights into the complexity of HIV-1 epidemics that must be considered when developing HIV monitoring and prevention initiatives. ..
- Filice G, Soldini L, Orsolini P, Razzini E, Gulminetti R, Campisi D, et al. Sensitivity and specificity of anti-HIV ELISA employing recombinant (p24, p66, gp120) and synthetic (gp41) viral antigenic peptides. Microbiologica. 1991;14:185-94 pubmed..b. ..
- Böhmdorfer G, Luxa K, Frosch A, Garber K, Tramontano A, Jelenic S, et al. Virus-like particle formation and translational start site choice of the plant retrotransposon Tto1. Virology. 2008;373:437-46 pubmed publisher..Trans-complementation of the defective Tto element by gag starting at ATG1, but not by gag starting at ATG2, defines ATG1 as the functional translation initiation site. ..
- Op de Coul E, van den Burg R, Asjo B, Goudsmit J, Cupsa A, Pascu R, et al. Genetic evidence of multiple transmissions of HIV type 1 subtype F within Romania from adult blood donors to children. AIDS Res Hum Retroviruses. 2000;16:327-36 pubmed..The juvenile population was most likely infected with the HIV-1 subtype F virus on more than one occasion, presumably through HIV-contaminated blood (products) obtained from adults. ..
- Zazzi M, Romano L, Catucci M, Venturi G, De Milito A, Valensin P. Clinical evaluation of an in-house reverse transcription-competitive PCR for quantitation of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol. 1999;37:333-8 pubmed..Since the cost is 1/8 to 1/10 of those of reference commercial assays, this procedure could be conveniently used in medium-scale laboratories. ..
- Lu T, He J, Klotman P. Animal models of HIV-associated nephropathy. Curr Opin Nephrol Hypertens. 2006;15:233-7 pubmed..Transgenic animal models of HIV-1-associated nephropathy have contributed greatly to the progress made toward understanding the pathogenesis of this disease. ..
- Gladyshev E, Meselson M, Arkhipova I. A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers. Gene. 2007;390:136-45 pubmed..We describe the retrovirus-like structure of the new elements, containing gag, pol, and env-like open reading frames, and discuss their possible origins, transmission, and behavior in bdelloid genomes...
- McCrackin Stevenson M, McBroom D. In vitro characterization of FIV-pPPR, a pathogenic molecular clone of feline immunodeficiency virus, and two drug-resistant pol gene mutants. Am J Vet Res. 2001;62:588-94 pubmed..Thus, FIV-pPPR M183V may be a useful model for studying the in vivo effects of 3TC resistance on lentivirus pathogenesis. ..
- Henderson E, Tsygankov A, Merlo J, Romano G, Guan M. Altered replication of human immunodeficiency virus type 1 (HIV-1) in T cell lines retrovirally transduced to express Herpesvirus saimiri proteins StpC and/or Tip. Virology. 1999;264:125-33 pubmed..A better understanding of the effects of Tip and StpC proteins on the biology of human hemopoietic stem cells may lead to novel therapeutic interventions for the treatment of AIDS. ..
- Yi J, Takenaka O, Kim H. Expression and identification of HERV-W family in Japanese monkeys (Macaca fuscata). Zoolog Sci. 2004;21:649-59 pubmed..Identical sequences from different tissues of the monkey were found in env and pol clones of the HERV-W family. ..
- Zhong P, Pan Q, Ning Z, Xue Y, Gong J, Zhen X, et al. Genetic diversity and drug resistance of human immunodeficiency virus type 1 (HIV-1) strains circulating in Shanghai. AIDS Res Hum Retroviruses. 2007;23:847-56 pubmed..It is believed that this information may help to guide recommendations for diagnostic assays, vaccine design, and antiretroviral regimen strategies in China. ..
- Woo P, Lau S, Chu C, Chan K, Tsoi H, Huang Y, et al. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol. 2005;79:884-95 pubmed publisher..13 x 10(6) copies per ml, from a 35-year-old woman with pneumonia. Our data support the existence of a novel group 2 coronavirus associated with pneumonia in humans...
- Tong S, Chern S, Li Y, Pallansch M, Anderson L. Sensitive and broadly reactive reverse transcription-PCR assays to detect novel paramyxoviruses. J Clin Microbiol. 2008;46:2652-8 pubmed publisher..The assays were specific to the respective group of genera or subfamily viruses. This set of primers enhances our ability to look for novel viruses in outbreaks and diseases of unknown etiology. ..
- Shah C, Böni J, Huder J, Vogt H, Mühlherr J, Zanoni R, et al. Phylogenetic analysis and reclassification of caprine and ovine lentiviruses based on 104 new isolates: evidence for regular sheep-to-goat transmission and worldwide propagation through livestock trade. Virology. 2004;319:12-26 pubmed..Furthermore, infection of goats by subtypes A3 or A4 was significantly associated with documented contact with sheep, which also harbor these subtypes, thus indicating regularly occurring sheep-to-goat transmission...
- Kafri T. Gene delivery by lentivirus vectors an overview. Methods Mol Biol. 2004;246:367-90 pubmed..The ability to pseudotype retrovirus vectors with a variety of envelope proteins, including the vesicular stomatitis virus G glycoprotein (VSV-G), significantly broadens the tropism of replication-defective retrovirus vectors. ..
- Patzke S, Lindeskog M, Munthe E, Aasheim H. Characterization of a novel human endogenous retrovirus, HERV-H/F, expressed in human leukemia cell lines. Virology. 2002;303:164-73 pubmed
- Balduin M, Oette M, Däumer M, Hoffmann D, Pfister H, Kaiser R. Prevalence of minor variants of HIV strains at reverse transcriptase position 103 in therapy-naïve patients and their impact on the virological failure. J Clin Virol. 2009;45:34-8 pubmed publisher..There is some evidence for a higher risk of NNRTI-treatment failure in patients with K103N minorities; however, the majority of patients with minority underwent a successful first-line-treatment. ..
- Cornelissen M, van den Burg R, Zorgdrager F, Lukashov V, Goudsmit J. pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns, and common ancestry for subtypes B and D. J Virol. 1997;71:6348-58 pubmed..Our analysis suggests a common ancestry for subtypes B and D that is distinct from that of subtypes A and E. ..
- Gober M, Laing J, Burnett J, Aurelian L. The Herpes simplex virus gene Pol expressed in herpes-associated erythema multiforme lesions upregulates/activates SP1 and inflammatory cytokines. Dermatology. 2007;215:97-106 pubmed..The data indicate that Pol activates SP1, causing upregulation of SP1 target genes (notably TGF-beta) involved in localized inflammation. Upregulation is potentiated by IFN-gamma. ..
- Rhee S, Kantor R, Katzenstein D, Camacho R, Morris L, Sirivichayakul S, et al. HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. AIDS. 2006;20:643-51 pubmed
- Okamura T, Someya K, Matsuo K, Hasegawa A, Yamamoto N, Honda M. Recombinant vaccinia DIs expressing simian immunodeficiency virus gag and pol in mammalian cells induces efficient cellular immunity as a safe immunodeficiency virus vaccine candidate. Microbiol Immunol. 2006;50:989-1000 pubmed..to induce antigen-specific immunity, we generated a recombinant vaccinia DIs expressing fulllength gag and pol genes of simian immunodeficiency virus (SIV) (rDIsSIV gag/pol) and studied the biological and immunological ..
- Op de Coul E, van der Schoot A, Goudsmit J, van den Burg R, Janssens W, Heyndrickx L, et al. Independent introduction of transmissible F/D recombinant HIV-1 from Africa into Belgium and The Netherlands. Virology. 2000;270:267-77 pubmed..Two included large or smaller F1 fragments in gag and pol. The third strain was subtype D along the entire gag and pol fragment. A parental African subtype F that showed no evidence for recombination was not found. ..
- Thomson M, Delgado E, Manjon N, Ocampo A, Villahermosa M, Marino A, et al. HIV-1 genetic diversity in Galicia Spain: BG intersubtype recombinant viruses circulating among injecting drug users. AIDS. 2001;15:509-16 pubmed..The majority of individuals with non-B infections were IDU, most of them without known contacts with non-European sources, and among whom BG recombinant viruses are circulating. ..
- Reid W, Sadowska M, Denaro F, Rao S, Foulke J, Hayes N, et al. An HIV-1 transgenic rat that develops HIV-related pathology and immunologic dysfunction. Proc Natl Acad Sci U S A. 2001;98:9271-6 pubmed
- Jayaraman G, Archibald C, Kim J, Rekart M, Singh A, Harmen S, et al. A population-based approach to determine the prevalence of transmitted drug-resistant HIV among recent versus established HIV infections: results from the Canadian HIV strain and drug resistance surveillance program. J Acquir Immune Defic Syndr. 2006;42:86-90 pubmed..Given the public health implications of transmitting drug-resistant HIV, it is important to continue population-based drug resistance surveillance to guide optimum prevention and treatment of HIV infection. ..
- Grankvist O, Gustafsson A, Bredberg Raden U, Pallangyo K, Mhalu F, Biberfeld P, et al. Selection of primers of optimal sensitivity for the detection of HIV-1 from Africa and Europe by polymerase chain reaction. AIDS. 1991;5:575-8 pubmed..The new selection of primer parts can be used as an alternative to enhance the detection of HIV-1 of different origins. ..
- Eriksson L, Leitner T, Wahren B, Bostrom A, Falk K. A multiplex real-time PCR for quantification of HIV-1 DNA and the human albumin gene in CD4+ cells. APMIS. 2003;111:625-33 pubmed..17 and 51x10-3 copies per CD4+ cell and could be monitored longitudinally, including long-term PI-ART and STI. The measured HIV-1 DNA load may be used to select the best time for the institution or re-institution of therapy. ..
- Yamaguchi Y, Manita D, Takeuchi T, Kuramochi K, Kuriyama I, Sugawara F, et al. Novel terpenoids, trichoderonic acids A and B isolated from Trichoderma virens, are selective inhibitors of family X DNA polymerases. Biosci Biotechnol Biochem. 2010;74:793-801 pubmed..Compound 2 suppressed the growth of two human cancer cell lines, cervix carcinoma cells (HeLa) and breast carcinoma cells (MCF-7). The results suggest that these compounds identified inhibition among the families of mammalian pols. ..
- Nettles R, Kieffer T, Kwon P, Monie D, Han Y, Parsons T, et al. Intermittent HIV-1 viremia (Blips) and drug resistance in patients receiving HAART. JAMA. 2005;293:817-29 pubmed..Most blips in this population appear to represent random biological and statistical variation around mean HIV-1 levels below 50 copies/mL rather than clinically significant elevations in viremia. ..
- Didierlaurent A, Ramirez J, Gherardi M, Zimmerli S, Graf M, Orbea H, et al. Attenuated poxviruses expressing a synthetic HIV protein stimulate HLA-A2-restricted cytotoxic T-cell responses. Vaccine. 2004;22:3395-403 pubmed..In conclusion, the synthetic HIV polyantigen Gpn delivered by MVA is immunogenic, efficiently processed and presented by human MHC class I molecules. ..
- Dube D, Dube S, Erensoy S, Jones B, Bryz Gornia V, Spicer T, et al. Serological and nucleic acid analyses for HIV and HTLV infection on archival human plasma samples from Zaire. Virology. 1994;202:379-89 pubmed..The Zairean HTLV-II isolate is closely grouped with the HTLV-II substrain of isolates found in Paleo-Amerindians of the New World, making it unlikely that it represents an endemic African strain. ..
- Caumont A, Lan N, Uyen N, Hung P, Schvoerer E, Urriza M, et al. Sequence analysis of env C2/V3, gag p17/p24, and pol protease regions of 25 HIV type 1 isolates from Ho Chi Minh City, Vietnam. AIDS Res Hum Retroviruses. 2001;17:1285-91 pubmed..The polymorphism of pol protease was considered only for CRF01_AE isolates and is clearly different from that recorded for B viruses with substitutions at positions 13, 35, 36, 41, 69, and 89. ..
- Zhong P, Burda S, Konings F, Urbanski M, Ma L, Zekeng L, et al. Genetic and biological properties of HIV type 1 isolates prevalent in villagers of the Cameroon equatorial rain forests and grass fields: further evidence of broad HIV type 1 genetic diversity. AIDS Res Hum Retroviruses. 2003;19:1167-78 pubmed..This study further reveals the complexity of HIV-1 infection in rural Cameron and points to the future of the global epidemic, which may be characterized by more genetically diverse viruses. ..
- Burkala E, He J, West J, Wood C, Petito C. Compartmentalization of HIV-1 in the central nervous system: role of the choroid plexus. AIDS. 2005;19:675-84 pubmed..These studies suggest that the CPx may provide an environment that promotes the evolution of drug-resistant strains with central nervous system tropism, although it is unlikely to be a reservoir for archival HIV-1 variants. ..
- Qi P, Han J, Lu Y, Wang C, Zhu B. A transient three-plasmid expression system for the production of hepatocytes targeting retroviral vectors. Acta Biochim Biophys Sin (Shanghai). 2007;39:567-74 pubmed..This approach can be used to target hepatocytes selectively. ..
- Blum S, Forsdyke R, Forsdyke D. Three human homologs of a murine gene encoding an inhibitor of stem cell proliferation. DNA Cell Biol. 1990;9:589-602 pubmed..As such, it is a potential antioncogene. ..
- Katzenstein T, Petersen A, Storgaard M, Obel N, Jensen Fangel S, Nielsen C, et al. Phylogeny and resistance profiles of HIV-1 POL sequences from rectal biopsies and blood. J Med Virol. 2010;82:1103-9 pubmed publisher..These findings suggest that additional information regarding the antiviral resistance profile of the patient might be obtained by testing different anatomical sites...
- Montavon C, Toure Kane C, Nkengasong J, Vergne L, Hertogs K, Mboup S, et al. CRF06-cpx: a new circulating recombinant form of HIV-1 in West Africa involving subtypes A, G, K, and J. J Acquir Immune Defic Syndr. 2002;29:522-30 pubmed..Importantly, this new variant has also been documented on other continents (Europe [France] and Australia), showing that these viruses are spreading not only locally but globally. ..
- Park J, Nadeau P, Mergia A. A minimal genome simian foamy virus type 1 vector system with efficient gene transfer. Virology. 2002;302:236-44 pubmed..Transduction efficiencies were significantly reduced with the deletion mutations implicating that for optimum SFV-1 vector productions a packaging construct that includes the 5' R-U5 is required. ..
- Desport M, Stewart M, Mikosza A, Sheridan C, Peterson S, Chavand O, et al. Sequence analysis of Jembrana disease virus strains reveals a genetically stable lentivirus. Virus Res. 2007;126:233-44 pubmed..JDV appears to be remarkably stable genetically and has undergone minor genetic changes over a period of nearly 20 years in Bali despite becoming endemic in the cattle population of the island...
- Tramuto F, Vitale F, Bonura F, Romano N. Detection of HIV type 1 non-B subtypes in Sicily, Italy. AIDS Res Hum Retroviruses. 2004;20:251-4 pubmed
- Bovia F, Salmon P, Matthes T, Kvell K, Nguyen T, Werner Favre C, et al. Efficient transduction of primary human B lymphocytes and nondividing myeloma B cells with HIV-1-derived lentiviral vectors. Blood. 2003;101:1727-33 pubmed..In conclusion, HIV vectors are promising tools for studies of gene functions in primary human B cells and myeloma cells for the purposes of research and the development of gene therapies. ..