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Journal articles on the topic 'HIV-1 Sequence Analysis'

Author: Grafiati

Published: 4 June 2021

Last updated: 3 February 2022

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1

GUO, HONG-GUANG, JEAN-CLAUDE CHERMANN, DAVID WATERS, et al. "Sequence analysis of original HIV-1." Nature 349, no. 6312 (1991): 745–46. http://dx.doi.org/10.1038/349745a0.

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2

Goujon, C. P., V. M. Schneider, C. Jacomet, and J. C. Nicolas. "HIV-1 genotypic resistance: automated sequence analysis and interpretation." Bioinformatics 14, no. 10 (1998): 886–87. http://dx.doi.org/10.1093/bioinformatics/14.10.886.

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3

Sinha, Sahil, GaneshChandra Saho, SindhuPrabha Rana, et al. "NEXT GENERATION SEQUENCE ANALYSIS OF SEQUENCES FROM SRA FILE OF HIV-1 ENVELOPE PROTEIN." International Journal of Advanced Research 6, no. 9 (2018): 1118–30. http://dx.doi.org/10.21474/ijar01/7621.

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4

Raharjo, Irvan, and Afiono Agung Prasetyo. "A COMPLETE HIV-1 Env CODING SEQUENCES FROM HIV ISOLATED IN CENTRAL JAVA, INDONESIA." KnE Life Sciences 2, no. 1 (2015): 27. http://dx.doi.org/10.18502/kls.v2i1.112.

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Background:The HIV envelope glycoprotein (env) plays a central role in viral transmission to target cells.The genetic diversity of env gene contributes a great mechanism on how HIV-1 could survive.Aims:To determine the genotype and genetic relationship of our isolate compared to the other HIV-1 isolates, especially from Indonesia based on the env gene. Also, for further use, the molecular properties of our gene had been analyzed. Methods: A complete coding sequence of HIV-1 env gene was cloned from 09IDSKA-6 (HIV isolated in Central Java, Indonesia), inserted into an Escherichia coli expressio

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5

Wang, Yan, Reda Rawi, Daniel Hoffmann, Binlian Sun, and Rongge Yang. "Inference of global HIV-1 sequence patterns and preliminary feature analysis." Virologica Sinica 28, no. 4 (2013): 228–38. http://dx.doi.org/10.1007/s12250-013-3348-z.

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6

Aulicino, Paula C., Julieta Kopka, Carlos Rocco, Andrea Mangano, and Luisa Sen. "Sequence Analysis of a South American HIV Type 1 BC Recombinant." AIDS Research and Human Retroviruses 21, no. 10 (2005): 894–96. http://dx.doi.org/10.1089/aid.2005.21.894.

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7

WANG, Fu-xiang, Hui ZHOU, Hong LING, et al. "Subtype and sequence analysis of HIV-1 strains in Heilongjiang Province." Chinese Medical Journal 120, no. 22 (2007): 2006–10. http://dx.doi.org/10.1097/00029330-200711020-00013.

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8

Lee, Chun-Nan, Wei-Kung Wang, Wen-Sheng Fan, et al. "Determination of Human Immunodeficiency Virus Type 1 Subtypes in Taiwan by vpu Gene Analysis." Journal of Clinical Microbiology 38, no. 7 (2000): 2468–74. http://dx.doi.org/10.1128/jcm.38.7.2468-2474.2000.

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The genetic diversity of human immunodeficiency virus (HIV) type 1 (HIV-1) has been characterized mainly by analysis of theenv and gag genes. Information on thevpu genes in the HIV sequence database is very limited. In the present study, the nucleotide sequences of the vpugenes were analyzed, and the genetic subtypes determined by analysis of the vpu gene were compared with those previously determined by analysis of the gag and env genes. Thevpu genes were amplified by nested PCR of proviral DNA extracted from 363 HIV-1-infected individuals and were sequenced directly by use of the PCR product

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9

Ryland, Elizabeth G., Yanhua Tang, Celia D. Christie, and Margaret E. Feeney. "Sequence Evolution of HIV-1 following Mother-to-Child Transmission." Journal of Virology 84, no. 23 (2010): 12437–44. http://dx.doi.org/10.1128/jvi.01617-10.

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ABSTRACT The genetic heterogeneity of HIV-1 poses a major obstacle to vaccine development. Although most horizontally acquired HIV-1 infections are initiated by a single homogeneous virus, marked genetic diversification and evolution occur following transmission. The relative contribution of the antiviral immune response to intrahost viral evolution remains controversial, in part because the sequence of the transmitted virus and the array of T-cell epitopes targeted by both donor and recipient are seldom known. We directly compared predominant viral sequences derived from 52 mother-child trans

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10

Churchill, Melissa J., David I. Rhodes, Jennifer C. Learmont, et al. "Longitudinal Analysis of Human Immunodeficiency Virus Type 1 nef/Long Terminal Repeat Sequences in a Cohort of Long-Term Survivors Infected from a Single Source." Journal of Virology 80, no. 2 (2006): 1047–52. http://dx.doi.org/10.1128/jvi.80.2.1047-1052.2006.

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ABSTRACT We studied the evolution of human immunodeficiency virus type 1 (HIV-1) in a cohort of long-term survivors infected with an attenuated strain of HIV-1 acquired from a single source. Although the cohort members experienced differing clinical courses, we demonstrate similar evolution of HIV-1 nef/long-terminal repeat (LTR) sequences, characterized by progressive sequence deletions tending toward a minimal nef/LTR structure that retains only sequence elements required for viral replication. The in vivo pathogenicity of attenuated HIV-1 is therefore dictated by viral and/or host factors o

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11

Lole, Kavita S., Robert C. Bollinger, Ramesh S. Paranjape, et al. "Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination." Journal of Virology 73, no. 1 (1999): 152–60. http://dx.doi.org/10.1128/jvi.73.1.152-160.1999.

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ABSTRACT The development of an effective human immunodeficiency virus type 1 (HIV-1) vaccine is likely to depend on knowledge of circulating variants of genes other than the commonly sequenced gag andenv genes. In addition, full-genome data are particularly limited for HIV-1 subtype C, currently the most commonly transmitted subtype in India and worldwide. Likewise, little is known about sequence variation of HIV-1 in India, the country facing the largest burden of HIV worldwide. Therefore, the objective of this study was to clone and characterize the complete genome of HIV-1 from seroconverte

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12

Huang, Austin, Joseph W. Hogan, Sorin Istrail, Allison DeLong, David A. Katzenstein, and Rami Kantor. "Global analysis of sequence diversity within HIV-1 subtypes across geographic regions." Future Virology 7, no. 5 (2012): 505–17. http://dx.doi.org/10.2217/fvl.12.37.

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13

DeLong, Allison K., Mingham Wu, Diane Bennett, et al. "Sequence Quality Analysis Tool for HIV Type 1 Protease and Reverse Transcriptase." AIDS Research and Human Retroviruses 28, no. 8 (2012): 894–901. http://dx.doi.org/10.1089/aid.2011.0120.

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14

Lowe, Denise M., Vanita Parmar, Sharon D. Kemp, and Brendan A. Larder. "Mutational analysis of two conserved sequence motifs in HIV-1 reverse transcriptase." FEBS Letters 282, no. 2 (1991): 231–34. http://dx.doi.org/10.1016/0014-5793(91)80484-k.

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15

MEDINA, R. DANIELA FERNÁNDEZ, MARIANNE JANSSON, EVA HALAPI, JOSÉ CARLOS RUSSI, OSVALDO LIBONATTI, and HANS WIGZELL. "Sequence Note: Genetic Analysis of V3 Domain Sequences Obtained from Uruguayan HIV Type 1-Infected Individuals." AIDS Research and Human Retroviruses 12, no. 15 (1996): 1491–93. http://dx.doi.org/10.1089/aid.1996.12.1491.

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16

ARTENSTEIN, ANDREW W., PATRICIA A. HEGERICH, CHRIS BEYRER, KITTIPONG RUNGRUENGTHANAKIT, NELSON L. MICHAEL, and CHAWALIT NATPRATAN. "Sequence Note: Sequences and Phylogenetic Analysis of thenefGene from Thai Subjects Harboring Subtype E HIV-1." AIDS Research and Human Retroviruses 12, no. 6 (1996): 557–60. http://dx.doi.org/10.1089/aid.1996.12.557.

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17

Niubò, Jordi, Wuyi Li, Keith Henry, and Alejo Erice. "Recovery and Analysis of Human Immunodeficiency Virus Type 1 (HIV) RNA Sequences from Plasma Samples with Low HIV RNA Levels." Journal of Clinical Microbiology 38, no. 1 (2000): 309–12. http://dx.doi.org/10.1128/jcm.38.1.309-312.2000.

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ABSTRACT Amplification of human immunodeficiency virus type 1 (HIV) reverse transcriptase (RT) and protease (PT) sequences from plasma is difficult when HIV RNA levels are low, and it usually cannot be accomplished in samples with <1,000 HIV RNA copies/ml. Because the RNA extraction step is critical for the success of subsequent amplifications and sequence analyses, two RNA extraction methods were compared to study plasma samples with low HIV RNA levels. Forty-four plasma samples containing <500 HIV RNA copies/ml in a branched-DNA (bDNA) assay (Quantiplex HIV RNA assay version 2.0 [Chiro

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18

Paraskevis, D., M. Magiorkinis, A. M. Vandamme, L. G. Kostrikis, and A. Hatzakis. "Re-analysis of human immunodeficiency virus type 1 isolates from Cyprus and Greece, initially designated ‘subtype I’, reveals a unique complex A/G/H/K/? mosaic pattern." Journal of General Virology 82, no. 3 (2001): 575–80. http://dx.doi.org/10.1099/0022-1317-82-3-575.

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Human immunodeficiency virus type 1 (HIV-1) has been classified into three main groups and 11 distinct subtypes. Moreover, several circulating recombinant forms (CRFs) of HIV-1 have been recently documented to have spread widely causing extensive HIV-1 epidemics. A subtype, initially designated I (CRF04_cpx), was documented in Cyprus and Greece and was found to comprise regions of sequence derived from subtypes A and G as well as regions of unclassified sequence. Re-analysis of the three full-length CRF04_cpx sequences that were available revealed a mosaic genomic organization of unique comple

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19

Stoeckli, Thomas C., Samantha MaWhinney, Jonathan Uy, et al. "Phenotypic and Genotypic Analysis of Biologically Cloned Human Immunodeficiency Virus Type 1 Isolates from Patients Treated with Zidovudine and Lamivudine." Antimicrobial Agents and Chemotherapy 46, no. 12 (2002): 4000–4003. http://dx.doi.org/10.1128/aac.46.12.4000-4003.2002.

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ABSTRACT Mutations at reverse transcriptase codons 44, 118, 207, and 208 were significantly correlated with reduced zidovudine susceptibility in biologically cloned human immunodeficiency virus type 1 (HIV-1) isolates. Sequences from the Stanford HIV RT and Protease Sequence Database showed that these mutations were more common in HIV-1 isolates from patients treated with zidovudine and lamivudine than in patients not treated with these drugs.

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20

Land, Allison M., T. Blake Ball, Ma Luo, et al. "Human Immunodeficiency Virus (HIV) Type 1 Proviral Hypermutation Correlates with CD4 Count in HIV-Infected Women from Kenya." Journal of Virology 82, no. 16 (2008): 8172–82. http://dx.doi.org/10.1128/jvi.01115-08.

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ABSTRACT APOBEC3G is an important innate immune molecule that causes human immunodeficiency virus type 1 (HIV-1) hypermutation, which can result in detrimental viral genome mutations. The Vif protein of wild-type HIV-1 counteracts APOBEC3G activity by targeting it for degradation and inhibiting its incorporation into viral particles. Additional APOBEC cytidine deaminases have been identified, such as APOBEC3F, which has a similar mode of action but different sequence specificity. A relationship between APOBEC3F/G and HIV disease progression has been proposed. During HIV-1 sequence analysis of

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21

TSUCHIE, Hideaki, Takashi KURIMURA, Namiko YOSHIHARA, Takashi KITAMURA, Mitsunobu IMAI, and J. K. MANIAR. "SEQUENCE ANALYSIS OF V3 LOOP REGION OF HIV-1 STRAINS PREVALENT IN INDIA." Japanese Journal of Medical Science and Biology 46, no. 2 (1993): 95–100. http://dx.doi.org/10.7883/yoken1952.46.95.

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22

Vallejo, Alejandro, Lutz Gurtler, Leopold Zekeng, and Indira K. Hewlett. "Nucleotide sequence analysis of the accessory genes of HIV-1 group O isolates." Virus Research 91, no. 2 (2003): 189–93. http://dx.doi.org/10.1016/s0168-1702(02)00270-8.

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23

YOURNO, JOSEPH, STEVEN F. JOSEPHS, MARVIN REITZ, DANIEL ZAGURY, FLOSSIE WONG-STAAL, and ROBERT C. GALLO. "Nucleotide Sequence Analysis of theenvGene of a New Zairian Isolate of HIV-1." AIDS Research and Human Retroviruses 4, no. 3 (1988): 165–73. http://dx.doi.org/10.1089/aid.1988.4.165.

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24

Saladini, Francesco, Brian T. Foley, Andrea Rosi, et al. "Near Full-Length Sequence Analysis of HIV Type 1 BF Recombinants from Italy." AIDS Research and Human Retroviruses 28, no. 3 (2012): 299–303. http://dx.doi.org/10.1089/aid.2011.0002.

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25

Ping, Li-Hua, Julie A. E. Nelson, Irving F. Hoffman, et al. "Characterization of V3 Sequence Heterogeneity in Subtype C Human Immunodeficiency Virus Type 1 Isolates from Malawi: Underrepresentation of X4 Variants." Journal of Virology 73, no. 8 (1999): 6271–81. http://dx.doi.org/10.1128/jvi.73.8.6271-6281.1999.

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ABSTRACT We have examined the nature of V3 sequence variability among subtype C human immunodeficiency virus type 1 (HIV-1) sequences from plasma-derived viral RNA present in infected men from Malawi. Sequence variability was assessed by direct sequence analysis of the V3 reverse transcription-PCR products, examination of virus populations by a subtype C V3-specific heteroduplex tracking assay (V3-HTA), and selected sequence analysis of molecular clones derived from the PCR products. Sequence variability in V3 among the subtype C viruses was not associated with the presence of basic amino acid

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26

Bossi, Philippe, Mireille Mouroux, Anne Yvon, et al. "Polymorphism of the Human Immunodeficiency Virus Type 1 (HIV-1) Protease Gene and Response of HIV-1-Infected Patients to a Protease Inhibitor." Journal of Clinical Microbiology 37, no. 9 (1999): 2910–12. http://dx.doi.org/10.1128/jcm.37.9.2910-2912.1999.

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In order to analyze the impact of protease gene polymorphism on response to regimens containing a protease inhibitor, the entire protease coding domain from 58 human immunodeficiency virus type 1 (HIV-1)-infected patients who were protease inhibitor naive was sequenced before therapy was started. Plasma HIV-1 RNA levels were measured at baseline and at month 3 and month 6 after treatment. All patients were treated with a combination of two reverse transcriptase inhibitors and a protease inhibitor (saquinavir EOF [n = 28], ritonavir [n = 16], or indinavir [n = 14]). Before treatment, 30 differe

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27

Lorenzin, Giovanni, Franco Gargiulo, Arnaldo Caruso, et al. "Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis." Microorganisms 8, no. 1 (2019): 36. http://dx.doi.org/10.3390/microorganisms8010036.

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HIV-1 diversity is increasing in European countries due to immigration flows, as well as travels and human mobility, leading to the circulation of both new viral subtypes and new recombinant forms, with important implications for public health. We analyzed 710 HIV-1 sequences comprising protease and reverse-transcriptase (PR/RT) coding regions, sampled from 2011 to 2017, from naive patients in Spedali Civili Hospital, Brescia, Italy. Subtyping was performed by using a combination of different tools; the phylogenetic analysis with a structured coalescence model and Makarov Chain Monte Carlo was

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Apetrei, Cristian, Diane Descamps, Gilles Collin, et al. "Human Immunodeficiency Virus Type 1 Subtype F Reverse Transcriptase Sequence and Drug Susceptibility." Journal of Virology 72, no. 5 (1998): 3534–38. http://dx.doi.org/10.1128/jvi.72.5.3534-3538.1998.

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ABSTRACT We sequenced and phylogenetically analyzed the reverse transcriptase (RT) regions of the pol genes of 14 human immunodeficiency virus type 1 (HIV-1) isolates from Romanian patients, which were classified as subtype F on the basis ofenv gene structure. The RT sequences showed that the strains clustered phylogenetically and were equidistant from other HIV-1 subtypes as shown by the neighbor-joining and maximum-likelihood methods, allowing us to define HIV-1 subtype F according to thepol classification. The subtype F RT sequences differed from reported group M RT sequences by 10.94% (for

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Novitsky, Vlad, Melissa Zahralban-Steele, Mary Fran McLane, et al. "Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering." Journal of Clinical Microbiology 53, no. 8 (2015): 2581–92. http://dx.doi.org/10.1128/jcm.00756-15.

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The goal of the study was to improve the methodology of HIV genotyping for analysis of HIV drug resistance and HIV clustering. Using the protocol of Gall et al. (A. Gall, B. Ferns, C. Morris, S. Watson, M. Cotten, M. Robinson, N. Berry, D. Pillay, and P. Kellam, J Clin Microbiol 50:3838–3844, 2012, doi:10.1128/JCM.01516-12), we developed a robust methodology for amplification of two large fragments of viral genome covering about 80% of the unique HIV-1 genome sequence. Importantly, this method can be applied to both viral RNA and proviral DNA amplification templates, allowing genotyping in HIV

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Myers, Richard E., and Deenan Pillay. "Analysis of Natural Sequence Variation and Covariation in Human Immunodeficiency Virus Type 1 Integrase." Journal of Virology 82, no. 18 (2008): 9228–35. http://dx.doi.org/10.1128/jvi.01535-07.

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ABSTRACT Human immunodeficiency virus type 1 (HIV-1) integrase inhibitors are in clinical trials, and raltegravir and elvitegravir are likely to be the first licensed drugs of this novel class of HIV antivirals. Understanding resistance to these inhibitors is important to maximize their efficacy. It has been shown that natural variation and covariation provide valuable insights into the development of resistance for established HIV inhibitors. Therefore, we have undertaken a study to fully characterize natural polymorphisms and amino acid covariation within an inhibitor-naïve sequence set spa

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31

Piontkivska, Helen, and Austin L. Hughes. "Between-Host Evolution of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1: an Approach Based on Phylogenetically Independent Comparisons." Journal of Virology 78, no. 21 (2004): 11758–65. http://dx.doi.org/10.1128/jvi.78.21.11758-11765.2004.

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ABSTRACT In human immunodeficiency virus type 1 (HIV-1), mutations that escape from cytotoxic T-lymphocyte (CTL) recognition have been documented, and sequence analyses have provided indirect support for the hypothesis that natural selection has favored CTL escape mutants within an infected host. In spite of such evidence for within-host selection by CTL, it has been more difficult to determine how natural selection by host CTL has influenced long-term evolution of HIV-1. We used statistical analysis of published HIV-1 genomic sequences to examine the role of natural selection in between-host

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32

Kingwara, Leonard, Muthoni Karanja, Catherine Ngugi, et al. "From Sequence Data to Patient Result: A Solution for HIV Drug Resistance Genotyping With Exatype, End to End Software for Pol-HIV-1 Sanger Based Sequence Analysis and Patient HIV Drug Resistance Result Generation." Journal of the International Association of Providers of AIDS Care (JIAPAC) 19 (January 1, 2020): 232595822096268. http://dx.doi.org/10.1177/2325958220962687.

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Introduction: With the rapid scale-up of antiretroviral therapy (ART) to treat HIV infection, there are ongoing concerns regarding probable emergence and transmission of HIV drug resistance (HIVDR) mutations. This scale-up has to lead to an increased need for routine HIVDR testing to inform the clinical decision on a regimen switch. Although the majority of wet laboratory processes are standardized, slow, labor-intensive data transfer and subjective manual sequence interpretation steps are still required to finalize and release patient results. We thus set out to validate the applicability of

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33

Jagodzinski, L. L., J. D. Cooley, M. Weber, and N. L. Michael. "Performance Characteristics of Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping Systems in Sequence-Based Analysis of Subtypes Other than HIV-1 Subtype B." Journal of Clinical Microbiology 41, no. 3 (2003): 998–1003. http://dx.doi.org/10.1128/jcm.41.3.998-1003.2003.

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34

Kinloch, Natalie N., Daniel R. MacMillan, Anh Q. Le, et al. "Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic." Journal of Virology 90, no. 3 (2015): 1244–58. http://dx.doi.org/10.1128/jvi.02353-15.

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ABSTRACTHuman leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989;n= 338) and modern (2001 to 2011;n= 27

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35

Darcis, Gilles, Caroline Binda, Bep Klaver, Elena Herrera-Carrillo, Ben Berkhout, and Atze Das. "The Impact of HIV-1 Genetic Diversity on CRISPR-Cas9 Antiviral Activity and Viral Escape." Viruses 11, no. 3 (2019): 255. http://dx.doi.org/10.3390/v11030255.

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The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system is widely explored for sequence-specific attack on HIV-1 proviral DNA. We recently identified dual-guide RNA (dual-gRNA) combinations that can block HIV-1 replication permanently in infected cell cultures and prevent viral escape. Although the gRNAs were designed to target highly conserved viral sequences, their efficacy may be challenged by high genetic variation in the HIV-1 genome. We therefore evaluated the breadth of these dual-gRNA combinations against distinct HIV-1 isolates, including several subtypes. R

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Downing, Robert, Danuta Pieniazek, Dale J. Hu, et al. "Sequence Note: Genetic Characterization and Phylogenetic Analysis of HIV-1 Subtype C from Uganda." AIDS Research and Human Retroviruses 16, no. 8 (2000): 815–19. http://dx.doi.org/10.1089/088922200308819.

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37

BRANDFUL, J. A. M., W. K. AMPOFO, W. JANSSENS, et al. "Sequence Note: Genetic and Phylogenetic Analysis of HIV Type 1 Strains from Southern Ghana." AIDS Research and Human Retroviruses 14, no. 9 (1998): 815–19. http://dx.doi.org/10.1089/aid.1998.14.815.

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Jonassen, Tom ø., Kathrine Stene-Johansen, Einar S. Berg, et al. "Sequence Analysis of HIV-1 Group O from Norwegian Patients Infected in the 1960s1." Virology 231, no. 1 (1997): 43–47. http://dx.doi.org/10.1006/viro.1997.8510.

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Dayton, E., D. Powell, and A. Dayton. "Functional analysis of CAR, the target sequence for the Rev protein of HIV-1." Science 246, no. 4937 (1989): 1625–29. http://dx.doi.org/10.1126/science.2688093.

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40

Sivay, Mariya V., Mary Kathryn Grabowski, Yinfeng Zhang, et al. "Phylogenetic Analysis of Human Immunodeficiency Virus from People Who Inject Drugs in Indonesia, Ukraine, and Vietnam: HPTN 074." Clinical Infectious Diseases 71, no. 8 (2019): 1836–46. http://dx.doi.org/10.1093/cid/ciz1081.

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Abstract Background HIV Prevention Trials Network (HPTN) 074 evaluated human immunodeficiency virus (HIV) prevention interventions for people who inject drugs (PWID) in Indonesia, Ukraine, and Vietnam. Study interventions included support for HIV infection and substance use treatment. The study enrolled index participants living with HIV and injection partners who were not living with HIV. Seven partners acquired HIV infection during the study (seroconverters). We analyzed the phylogenetic relatedness between HIV strains in the cohort and the multiplicity of infection in seroconverters. Method

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Pace, Craig, Jean Keller, David Nolan, et al. "Population Level Analysis of Human Immunodeficiency Virus Type 1 Hypermutation and Its Relationship with APOBEC3G and vif Genetic Variation." Journal of Virology 80, no. 18 (2006): 9259–69. http://dx.doi.org/10.1128/jvi.00888-06.

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ABSTRACT APOBEC3G and APOBEC3F restrict human immunodeficiency virus type 1 (HIV-1) replication in vitro through the induction of G→A hypermutation; however, the relevance of this host antiviral strategy to clinical HIV-1 is currently not known. Here, we describe a population level analysis of HIV-1 hypermutation in near-full-length clade B proviral DNA sequences (n = 127). G→A hypermutation conforming to expected APOBEC3G polynucleotide sequence preferences was inferred in 9.4% (n = 12) of the HIV-1 sequences, with a further 2.4% (n = 3) conforming to APOBEC3F, and was independently associate

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42

SUSLOV, VALENTIN V., PETR M. PONOMARENKO, VADIM M. EFIMOV, LUDMILA K. SAVINKOVA, MIKHAIL P. PONOMARENKO, and NIKOLAY A. KOLCHANOV. "SNPS IN THE HIV-1 TATA BOX AND THE AIDS PANDEMIC." Journal of Bioinformatics and Computational Biology 08, no. 03 (2010): 607–25. http://dx.doi.org/10.1142/s0219720010004677.

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Evolutionary trends have been examined in 146 HIV-1 forms (2662 copies, 2311 isolates) polymorphic for the TATA box using the "DNA sequence→affinity for TBP" regression (TBP is the TATA binding protein). As a result, a statistically significant excess of low-affinity TATA box HIV-1 variants corresponding to a low level of both basal and TAT-dependent expression and, consequently, slow replication of HIV-1 have been detected. A detailed analysis revealed that the excess of slowly replicating HIV-1 is associated with the subtype E-associated TATA box core sequence "CATAAAA". Principal Component

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Kazennova, E. V., A. A. Antonova, E. N. Ozhmegova, et al. "GENETIC ANALYSIS OF HIV-1 IN THE ALTAI KRAY: THE FURTHER SPREAD OF THE CRF63_02A1 VARIANT IN WESTERN SIBERIA." HIV Infection and Immunosuppressive Disorders 12, no. 1 (2020): 47–57. http://dx.doi.org/10.22328/2077-9828-2020-12-1-47-57.

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IThe aim of this study was to characterize HIV-1 genetic strains currently circulating in Altay Kray (Western Siberia) and to analyze the HIV resistance on this territory.Materials and methods. Blood samples were collected, with informed consent, in 2017 from 82 HIV infected persons living in Altai Kray. Sequences of pol gene fragments coding protease and part of reverse transcriptase were obtained by in house system and Sanger sequencing. Genotyping, phylogenetic and recombinant analyses were carried out by HIVdbProgram: Sequence Analysis, COMET HIV-1, REGA HIV-1 Subtyping Tool (V 3.0), MEGA

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Cho, Young-Keol, Jung-Eun Kim, and Brian T. Foley. "Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years." Viruses 13, no. 5 (2021): 806. http://dx.doi.org/10.3390/v13050806.

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We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Overall, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Phylogenetic analysis indicated that within KSB, two FLs from plasma donors O and P comprised two clusters, together with 8 and

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Patro, Sean C., Leah D. Brandt, Michael J. Bale, et al. "Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors." Proceedings of the National Academy of Sciences 116, no. 51 (2019): 25891–99. http://dx.doi.org/10.1073/pnas.1910334116.

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Understanding HIV-1 persistence despite antiretroviral therapy (ART) is of paramount importance. Both single-genome sequencing (SGS) and integration site analysis (ISA) provide useful information regarding the structure of persistent HIV DNA populations; however, until recently, there was no way to link integration sites to their cognate proviral sequences. Here, we used multiple-displacement amplification (MDA) of cellular DNA diluted to a proviral endpoint to obtain full-length proviral sequences and their corresponding sites of integration. We applied this method to lymph node and periphera

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Quiñones-Mateu, Miguel E., Jamie L. Albright, Antonio Mas, Vicente Soriano, and Eric J. Arts. "Analysis of pol Gene Heterogeneity, Viral Quasispecies, and Drug Resistance in Individuals Infected with Group O Strains of Human Immunodeficiency Virus Type 1." Journal of Virology 72, no. 11 (1998): 9002–15. http://dx.doi.org/10.1128/jvi.72.11.9002-9015.1998.

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ABSTRACT Nucleotide sequences of the reverse transcriptase (RT) coding region have been compared in four new human immunodeficiency virus type 1 (HIV-1) group O isolates. Phylogenetic analysis of thispol region highlights a cluster of these four HIV-1 group O sequences with seven other group O isolates (5% intracluster nucleotide sequence diversity) similar to clusters classified as subtypes in HIV-1 group M (an average of 4.9% intrasubtype sequence diversity). Based on these analyses, this group O cluster has been designated subtype A-O. A longitudinal study of a heterosexual couple infected

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Girnary, Roseanne, Louise King, Laurence Robinson, Robert Elston, and Ian Brierley. "Structure–function analysis of the ribosomal frameshifting signal of two human immunodeficiency virus type 1 isolates with increased resistance to viral protease inhibitors." Journal of General Virology 88, no. 1 (2007): 226–35. http://dx.doi.org/10.1099/vir.0.82064-0.

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Expression of the pol-encoded proteins of human immunodeficiency virus type 1 (HIV-1) requires a programmed –1 ribosomal frameshift at the junction of the gag and pol coding sequences. Frameshifting takes place at a heptanucleotide slippery sequence, UUUUUUA, and is enhanced by a stimulatory RNA structure located immediately downstream. In patients undergoing viral protease (PR) inhibitor therapy, a p1/p6gag L449F cleavage site (CS) mutation is often observed in resistant isolates and frequently generates, at the nucleotide sequence level, a homopolymeric and potentially slippery sequence (UUU

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Badia, Roger, Eduardo Pauls, Eva Riveira-Munoz, Bonaventura Clotet, José A. Esté, and Ester Ballana. "Zinc Finger Endonuclease TargetingPSIP1Inhibits HIV-1 Integration." Antimicrobial Agents and Chemotherapy 58, no. 8 (2014): 4318–27. http://dx.doi.org/10.1128/aac.02690-14.

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ABSTRACTGenome editing using zinc finger nucleases (ZFNs) has been successfully applied to disrupt CCR5 or CXCR4 host factors and inhibit viral entry and infection. Gene therapy using ZFNs to modify thePSIP1gene, which encodes the lens epithelium-derived growth factor (LEDGF) protein, might restrain an early step of the viral replication cycle at the integration level. ZFNs targeting thePSIP1gene (ZFNLEDGF) were designed to specifically recognize the sequence after the integrase binding domain (IBD) of the LEDGF/p75 protein. ZFNLEDGFsuccessfully recognized the target region of thePSIP1gene in

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Gehringer, H., J. R. Bogner, F. D. Goebel, H. Nitschko, and K. von der Helm. "Sequence analysis of the HIV-1 protease coding region of 18 HIV-1-infected patients prior to HAART and possible implications on HAART." Journal of Clinical Virology 17, no. 2 (2000): 137–41. http://dx.doi.org/10.1016/s1386-6532(00)00086-x.

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Wagner, Thor A., Jen L. McKernan, Nicole H. Tobin, Ken A. Tapia, James I. Mullins, and Lisa M. Frenkel. "An Increasing Proportion of Monotypic HIV-1 DNA Sequences during Antiretroviral Treatment Suggests Proliferation of HIV-Infected Cells." Journal of Virology 87, no. 3 (2012): 1770–78. http://dx.doi.org/10.1128/jvi.01985-12.

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ABSTRACTUnderstanding how HIV-1 persists during effective antiretroviral therapy (ART) should inform strategies to cure HIV-1 infection. We hypothesize that proliferation of HIV-1-infected cells contributes to persistence of HIV-1 infection during suppressive ART. This predicts that identical or monotypic HIV-1 DNA sequences will increase over time during ART. We analyzed 1,656envandpolsequences generated following single-genome amplification from the blood and sputum of six individuals during long-term suppressive ART. The median proportion of monotypic sequences increased from 25.0% prior to

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