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HIV molecular evolution

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https://www.readbyqxmd.com/read/29228218/nonhuman-primate-models-and-understanding-the-pathogenesis-of-hiv-infection-and-aids
#1
Ronald S Veazey, Andrew A Lackner
Research using nonhuman primates (NHPs) as models for human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) has resulted in tremendous achievements not only in the prevention and treatment of HIV, but also in biomedical research more broadly. Once considered a death sentence, HIV infection is now fairly well controlled with combination antiretroviral treatments, almost all of which were first tested for efficacy and safety in nonhuman primates or other laboratory animals...
December 8, 2017: ILAR Journal
https://www.readbyqxmd.com/read/29202081/phylodynamic-applications-in-21st-century-global-infectious-disease-research
#2
Brittany D Rife, Carla Mavian, Xinguang Chen, Massimo Ciccozzi, Marco Salemi, Jae Min, Mattia Cf Prosperi
Background: Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21st century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics...
2017: Global health research and policy
https://www.readbyqxmd.com/read/29163435/evolutionary-analysis-of-hiv-1-pol-proteins-reveals-representative-residues-for-viral-subtype-differentiation
#3
Shohei Nagata, Junnosuke Imai, Gakuto Makino, Masaru Tomita, Akio Kanai
RNA viruses have been used as model systems to understand the patterns and processes of molecular evolution because they have high mutation rates and are genetically diverse. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immune deficiency syndrome, is highly genetically diverse, and is classified into several groups and subtypes. However, it has been difficult to use its diverse sequences to establish the overall phylogenetic relationships of different strains or the trends in sequence conservation with the construction of phylogenetic trees...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29142136/size-composition-and-evolution-of-hiv-dna-populations-during-early-antiretroviral-therapy-and-intensification-with-maraviroc
#4
Antoine Chaillon, Sara Gianella, Steven M Lada, Josué Perez-Santiago, Parris Jordan, Caroline Ignacio, Maile Karris, Douglas Richman, Sanjay R Mehta, Susan J Little, Joel O Wertheim, Davey M Smith
Residual viremia is common during antiretroviral therapy (ART), and could be caused by ongoing low-level virus replication or by release of viral particles from infected cells. ART Intensification should impact ongoing viral propagation but not virion release. Eighteen acutely infected men were enrolled in a randomized controlled trial, and followed for a median of 107 weeks. Participants started ART with (n=9) or without (n=9) intensification with maraviroc (MVC) within 90 days of infection. Levels of HIV DNA and cell-free RNA were quantified by droplet digital PCR...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29137637/molecular-evolution-of-hiv-1-integrase-during-the-20%C3%A2-years-prior-to-the-first-approval-of-integrase-inhibitors
#5
Karolin Meixenberger, Kaveh Pouran Yousef, Maureen Rebecca Smith, Sybille Somogyi, Stefan Fiedler, Barbara Bartmeyer, Osamah Hamouda, Norbert Bannert, Max von Kleist, Claudia Kücherer
BACKGROUND: Detailed knowledge of the evolutionary potential of polymorphic sites in a viral protein is important for understanding the development of drug resistance in the presence of an inhibitor. We therefore set out to analyse the molecular evolution of the HIV-1 subtype B integrase at the inter-patient level in Germany during a 20-year period prior to the first introduction of integrase strand inhibitors (INSTIs). METHODS: We determined 337 HIV-1 integrase subtype B sequences (amino acids 1-278) from stored plasma samples of antiretroviral treatment-naïve individuals newly diagnosed with HIV-1 between 1986 and 2006...
November 14, 2017: Virology Journal
https://www.readbyqxmd.com/read/29054871/engineering-the-enantioselectivity-and-thermostability-of-a-%C3%AE-lactamase-from-microbacterium-hydrocarbonoxydans-for-the-kinetic-resolution-of-vince-lactam
#6
Shuaihua Gao, Shaozhou Zhu, Rong Huang, Hongxia Li, Hao Wang, Guojun Zheng
To produce promising biocatalysts, natural enzymes often need to be engineered to increase their catalytic performance. In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs such as carbovir and abacavir, which are used to fight against human HIV and hepatitis B viruses. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme...
October 20, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28971485/evolution-of-the-serologic-and-virologic-course-of-occult-hbv-infection-in-therapy-experienced-hiv-co-infected-patients
#7
Edina Amponsah-Dacosta, Selokela G Selabe, M Jeffrey Mphahlele
BACKGROUND: We investigated how the natural course of occult hepatitis B virus (HBV) infection (OBI) may evolve during HIV co-infection and long term HBV-active HAART. METHODS: From a cohort of 181 HIV infected patients who were consecutively recruited over a 5 year period, 28 HBV co-infected patients with sequential sera (n = 98) were identified. Iterative HBV serology and viral loads were determined before and during treatment. The viral HBsAg gene was then serially amplified, directly sequenced and molecularly characterized...
October 2, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28966263/creation-of-functional-molecules-based-on-biomolecular-interactions-development-toward-chemical-biology
#8
Wataru Nomura
Interactions between bio-macromolecules such as proteins, DNA, and polysaccharides play pivotal roles in maintaining homeostasis in living systems. For elucidating the function of biomolecules, peptides are powerful tools, compared to native proteins, because of their lower molecular weights, compatibility with chemical modification, and predictability of interaction with the target molecules. These advantages enabled us to develop peptide-based functional molecules. However, for the purposes of controlling or regulating biomolecule functions, designing artificial proteins is also an effective approach...
2017: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/28918303/decoding-noises-in-hiv-computational-genotyping
#9
MingRui Jia, Timothy Shaw, Xing Zhang, Dong Liu, Ye Shen, Amara E Ezeamama, Chunfu Yang, Ming Zhang
Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline...
November 2017: Virology
https://www.readbyqxmd.com/read/28912478/the-molecular-epidemiology-of-hiv-1-in-the-comunidad-valenciana-spain-analysis-of-transmission-clusters
#10
Juan Ángel Patiño-Galindo, Manoli Torres-Puente, María Alma Bracho, Ignacio Alastrué, Amparo Juan, David Navarro, María José Galindo, Dolores Ocete, Enrique Ortega, Concepción Gimeno, Josefina Belda, Victoria Domínguez, Rosario Moreno, Fernando González-Candelas
HIV infections are still a very serious concern for public heath worldwide. We have applied molecular evolution methods to study the HIV-1 epidemics in the Comunidad Valenciana (CV, Spain) from a public health surveillance perspective. For this, we analysed 1804 HIV-1 sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2004 and 2014. These sequences were subtyped and subjected to phylogenetic analyses in order to detect transmission clusters. In addition, univariate and multinomial comparisons were performed to detect epidemiological differences between HIV-1 subtypes, and risk groups...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28852479/collapsing-glomerulopathy-a-30-year-perspective-and-single-large-center-experience
#11
L Nicholas Cossey, Christopher P Larsen, Helen Liapis
Collapsing glomerulopathy (CGP) is a pattern of kidney injury seen on renal biopsy with multiple associations and etiologies. It is most commonly described in African-Americans and others with recent African ancestry. The disease is rapidly progressive and often presents with abrupt onset of renal failure and nephrotic-range proteinuria. Since its description 30 years ago, this entity has transformed from a morphologic diagnosis typically seen in the setting of HIV infection to a complicated diagnosis with numerous etiologies, many of which are associated with underlying apolipoprotein L1 (APOL1)-risk variants or other genetic disorders...
August 2017: Clinical Kidney Journal
https://www.readbyqxmd.com/read/28844146/a-novel-recombinant-form-of-hiv-1-crf01_ae-crf07_bc-identified-by-near-full-length-genome-in-shaanxi-china
#12
Mengyan Zhang, Ruolei Xin, Wenhui Chang
Recently multiple kinds of unique recombinant forms (URFs) of HIV-1 CRF01_AE/CRF07_BC were identified in China. In this study, we report another near full-length genome of a novel recombinant form (SN121) between CRF01_AE and CRF07_BC from an HIV-1 infected male through heterosexual behavior in Shaanxi province, China. The analysis of SN121 showed that the genome composed of 7 interlaced segments, including 3 CRF07_BC and 4 CRF01_AE segments with CRF01_AE as the backbone. Six breakpoints were observed in the pol and env gene regions, which are different from the previously identified CRF01_AE/07_BC recombinant forms in China...
August 26, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28843613/evolution-of-inhibitor-resistant-natural-mutant-forms-of-hiv-1-protease-probed-by-pre-steady-state-kinetic-analysis
#13
Maria Yu Zakharova, Alexandra A Kuznetsova, Elena N Kaliberda, Maria A Dronina, Alexander V Kolesnikov, Arina V Kozyr, Ivan V Smirnov, Lev D Rumsh, Olga S Fedorova, Dmitry G Knorre, Alexander G Gabibov, Nikita A Kuznetsov
Pre-steady state kinetic analysis of mechanistic features of substrate binding and processing is crucial for insight into the evolution of inhibitor-resistant forms of HIV-1 protease. These data may provide a correct vector for rational drug design assuming possible intrinsic dynamic effects. These data should also give some clues to the molecular mechanism of protease action and resistance to inhibitors. Here we report pre-steady state kinetics of the interaction of wild type or mutant forms of HIV-1 protease with a FRET-labeled peptide...
November 2017: Biochimie
https://www.readbyqxmd.com/read/28645318/detecting-consistent-patterns-of-directional-adaptation-using-differential-selection-codon-models
#14
Sahar Parto, Nicolas Lartillot
BACKGROUND: Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors...
June 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28586237/a-unique-second-generation-recombinant-form-of-hiv-1-identified-among-men-who-have-sex-with-men-population-in-beijing-china
#15
Xue Li, Mingqiang Hao, Yinxiao Hao, Jingrong Ye, Ruolei Xin, Hongyan Lu
In China, CRF01_AE and CRF07_BC are the most circulating strains of HIV-1, more and more second-generation recombinant forms have been isolated around the two strains. The same situation happened in Beijing in recent years. In our study, we have isolated a new second-generation recombinant form of HIV-1 from a male patient who was infected by homosexual behavior. Polygenetic analysis revealed that the sequence includes five CRF01_AE fragments and four CRF07_BC fragments. CRF01_AE is the skeleton of the recombinant which was inserted with four CRF07_BC fragments...
October 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28542584/the-emergence-and-evolution-of-the-research-fronts-in-hiv-aids-research
#16
David Fajardo-Ortiz, Malaquias Lopez-Cervantes, Luis Duran, Michel Dumontier, Miguel Lara, Hector Ochoa, Victor M Castano
In this paper, we have identified and analyzed the emergence, structure and dynamics of the paradigmatic research fronts that established the fundamentals of the biomedical knowledge on HIV/AIDS. A search of papers with the identifiers "HIV/AIDS", "Human Immunodeficiency Virus", "HIV-1" and "Acquired Immunodeficiency Syndrome" in the Web of Science (Thomson Reuters), was carried out. A citation network of those papers was constructed. Then, a sub-network of the papers with the highest number of inter-citations (with a minimal in-degree of 28) was selected to perform a combination of network clustering and text mining to identify the paradigmatic research fronts and analyze their dynamics...
2017: PloS One
https://www.readbyqxmd.com/read/28497113/toward-a-cure-does-host-immunity-play-a-role
#17
Jielin Zhang, Clyde S Crumpacker
Three decades of research on human immunodeficiency virus (HIV) and AIDS reveal that the human body has developed through evolution a genome immune system embodying epigenetic regulation against pathogenic nucleic acid invasion. In HIV infection, this epigenetic regulation plays a cardinal role in HIV RNA production that silences HIV transcription at a molecular (RNA) level, controls viral load at a cellular (biological) level, and governs the viremic stage of AIDS at the clinical (patient) level. Even though the human genome is largely similar among humans and HIV is a single viral species, human hosts show significant differences in viral RNA levels, ranging from cell to organ to individual and expressed as elite controllers, posttreatment controllers, and patients with AIDS...
March 2017: MSphere
https://www.readbyqxmd.com/read/28484443/impact-of-genetic-variations-in-hiv-1-tat-on-ltr-mediated-transcription-via-tar-rna-interaction
#18
Larance Ronsard, Nilanjana Ganguli, Vivek K Singh, Kumaravel Mohankumar, Tripti Rai, Subhashree Sridharan, Sankar Pajaniradje, Binod Kumar, Devesh Rai, Suhnrita Chaudhuri, Mohane S Coumar, Vishnampettai G Ramachandran, Akhil C Banerjea
HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans-activator of transcription (Tat), a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans-activation response (TAR) RNA. In this study, HIV-1 infected patients (n = 120) from North India revealed Ser46Phe (20%) and Ser61Arg (2%) mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28466391/mechanisms-of-hiv-1-control
#19
REVIEW
Mary Soliman, Geetha Srikrishna, Ashwin Balagopal
PURPOSE OF REVIEW: HIV-1 infection is of global importance, and still incurs substantial morbidity and mortality. Although major pharmacologic advances over the past two decades have resulted in remarkable HIV-1 control, a cure is still forthcoming. One approach to a cure is to exploit natural mechanisms by which the host restricts HIV-1. Herein, we review past and recent discoveries of HIV-1 restriction factors, a diverse set of host proteins that limit HIV-1 replication at multiple levels, including entry, reverse transcription, integration, translation of viral proteins, and packaging and release of virions...
June 2017: Current HIV/AIDS Reports
https://www.readbyqxmd.com/read/28454556/molecular-and-epidemiological-characterization-of-hiv-1-subtypes-among-libyan-patients
#20
Mohamed A Daw, Abdallah El-Bouzedi, Mohamed O Ahmed, Aghnyia A Dau
BACKGROUND: The epidemiological and clinical aspects of human immunodeficiency virus subtypes are of great interest worldwide. These subtypes are rarely studied in North African countries. Libya is a large country with the longest coast on the Mediterranean Sea, facing the Southern European countries. Studies on the characterization of HIV-1 subtypes are limited in Libya. This study aimed to determine the magnitude of the HIV problem among the Libyan population and to better understand the genetic diversity and the epidemiologic dynamics of HIV 1, as well as to correlate that with the risk factors involved...
April 28, 2017: BMC Research Notes
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