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https://www.readbyqxmd.com/read/28712312/near-full-length-genome-sequence-of-a-novel-hiv-1-second-generation-recombinant-form-crf01_ae-crf07_bc-detected-among-blood-donors-in-north-china
#1
Wei He, Xiaoxu Han, Minghui An, Yanqiu Hai, Le Chang, Chao Liu, Lunan Wang, Hong Shang
In this study, a novel CRF01_AE/07_BC HIV-1 recombinant form, with five breakpoints in thepol, vpr, env and nef gene regions, was identified from a voluntary blood donor in North China. Our study showed that this HIV-1 recombinant form might be a second-generation recombinant form from two predominant strains inthe Men who have sex with men (MSM) population, with the CRF07_BC fragments belonging to a CRF07_BC lineage specific to Chinese MSM and the CRF01_AE fragments belonging to the CRF01_AE lineage 5 common among MSM in northern China...
July 16, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28705213/the-therapeutic-landscape-of-hiv-1-via-genome-editing
#2
REVIEW
Alexander Kwarteng, Samuel Terkper Ahuno, Godwin Kwakye-Nuako
Current treatment for HIV-1 largely relies on chemotherapy through the administration of antiretroviral drugs. While the search for anti-HIV-1 vaccine remain elusive, the use of highly active antiretroviral therapies (HAART) have been far-reaching and has changed HIV-1 into a manageable chronic infection. There is compelling evidence, including several side-effects of ARTs, suggesting that eradication of HIV-1 cannot depend solely on antiretrovirals. Gene therapy, an expanding treatment strategy, using RNA interference (RNAi) and programmable nucleases such as meganuclease, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR-Cas9) are transforming the therapeutic landscape of HIV-1...
July 14, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28702030/enrichment-of-hla-types-and-single-nucleotide-polymorphism-associated-with-non-progression-in-a-strictly-defined-cohort-of-hiv-1-controllers
#3
Samantha J Westrop, Alexander T H Cocker, Adriano Boasso, Ann K Sullivan, Mark R Nelson, Nesrina Imami
HIV-1 controllers (HIC) are extremely rare patients with the ability to control viral replication, maintain unchanging CD4 T-cell count, and evade disease progression for extensive periods of time, in the absence of antiretroviral therapy. In order to establish the representation of key genetic correlates of atypical disease progression within a cohort of HIV-1(+) individuals who control viral replication, we examine four-digit resolution HLA type and single-nucleotide polymorphisms (SNP) previously identified to be correlated to non-progressive infection, in strictly defined HIC...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28700743/polymorphisms-in-the-vitamin-d-receptor-gene-are-associated-with-reduced-rate-of-sputum-culture-conversion-in-multidrug-resistant-tuberculosis-patients-in-south-africa
#4
Matthew J Magee, Yan V Sun, James C M Brust, N Sarita Shah, Yuming Ning, Salim Allana, Angela Campbell, Qin Hui, Koleka Mlisana, Pravi Moodley, Neel R Gandhi
BACKGROUND: Vitamin D modulates the inflammatory and immune response to tuberculosis (TB) and also mediates the induction of the antimicrobial peptide cathelicidin. Deficiency of 25-hydroxyvitamin D and single nucleotide polymorphisms (SNPs) in the vitamin D receptor (VDR) gene may increase the risk of TB disease and decrease culture conversion rates in drug susceptible TB. Whether these VDR SNPs are found in African populations or impact multidrug-resistant (MDR) TB treatment has not been established...
2017: PloS One
https://www.readbyqxmd.com/read/28696820/viral-interactions-with-host-cell-rab-gtpases
#5
Paul Spearman
Viruses are obligate intracellular parasites that utilize cellular machinery for many aspects of their replication cycles. Enveloped viruses generally rely upon host vesicular trafficking machinery to direct their structural proteins and genomes to sites of virus replication, assembly, and budding. Rab GTPases have been implicated in the replication of many important viral pathogens infecting humans. This review provides a summary of virus-Rab protein interactions, with a particular focus on the role of Rab-related trafficking pathways on late events in the lifecycle of herpesviruses and of HIV-1...
July 11, 2017: Small GTPases
https://www.readbyqxmd.com/read/28695282/host-genetic-variation-and-hiv-disease-from-mapping-to-mechanism
#6
REVIEW
Vivek Naranbhai, Mary Carrington
This review aims to provide a summary of current knowledge of host genetic effects on human immunodeficiency virus (HIV) disease. Mapping of simple single nucleotide polymorphisms (SNP) has been largely successful in HIV, but more complex genetic associations involving haplotypic or epigenetic variation, for example, remain elusive. Mechanistic insights explaining SNP associations are incomplete, but continue to be forthcoming. The number of robust immunogenetic correlates of HIV is modest and their discovery mostly predates the genome-wide era...
July 10, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28692305/fight-fire-with-fire-gene-therapy-strategies-to-cure-hiv
#7
Jon Huyghe, Sips Magdalena, Linos Vandekerckhove
Human Immunodeficiency Virus (HIV) to date remains one of the most notorious viruses mankind has ever faced. Despite enormous investments in HIV research for more than 30 years an effective cure for HIV has been elusive. Areas covered: Combination antiretroviral therapy (cART) suppresses active viral replication, but is not able to eliminate the virus completely due to stable integration of HIV inside the host genome of infected cells and the establishment of a latent reservoir, that is insensitive to cART...
July 14, 2017: Expert Review of Anti-infective Therapy
https://www.readbyqxmd.com/read/28684413/a-crispr-cas9-approach-reveals-that-the-polymerase-activity-of-dna-polymerase-%C3%AE-is-dispensable-for-hiv-1-infection-in-dividing-and-nondividing-cells
#8
Russell W Goetze, Dong-Hyun Kim, Raymond F Schinazi, Baek Kim
Retrovirus integration into the host genome relies on several host enzymes, potentially including DNA polymerase β (Pol β). However, whether human Pol β; is essential for lentivirus replication in human cells is unclear. Here, we abolished Pol β expression by targeting its DNA polymerase domain with CRISPR/Cas9 in human monocytic THP-1 cells to investigate Pol β's role in HIV-1 transduction in both dividing and nondividing macrophage stages of THP-1 cells. Pol β-knockout was confirmed by enhanced sensitivity to methyl methanesulfonate - induced DNA damage...
July 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28679543/tracing-genetic-exchange-and-biogeography-of-cryptococcus-neoformans-var-grubii-at-the-global-population-level
#9
Johanna Rhodes, Christopher A Desjardins, Sean M Sykes, Mathew A Beale, Mathieu Vanhove, Sharadha Sakthikumar, Yuan Chen, Sharvari Gujja, Sakina Saif, Anuradha Chowdhary, Daniel John Lawson, Vinicius Ponzio, Arnaldo Lopes Colombo, Wieland Meyer, David M Engelthaler, Ferry Hagen, Maria Teresa Illnait-Zaragozi, Alexandre Alanio, Jo-Marie Vreulink, Joseph Heitman, John R Perfect, Anastasia Litvintseva, Tihana Bicanic, Thomas S Harrison, Matthew C Fisher, Christina A Cuomo
Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major subdivisions, their relative diversity and the level of genetic exchange between them...
July 5, 2017: Genetics
https://www.readbyqxmd.com/read/28674031/the-role-of-sapa-and-yfga-in-susceptibility-to-antibody-mediated-complement-dependent-killing-and-virulence-of-salmonella-enterica-typhimurium
#10
Edna M Ondari, Jennifer N Heath, Elizabeth J Klemm, Gemma Langridge, Lars Barquist, David A Goulding, Simon Clare, Gordon Dougan, Robert A Kingsley, Calman A MacLennan
The ST313 pathovar of S Typhimurium contributes to a high burden of invasive disease among African infants and HIV-infected adults. It is characterized by genome degradation (loss of coding capacity) and has increased resistance to antibody-dependent complement-mediated killing compared with enterocolitis-causing strains of S Typhimurium. Vaccination is an attractive disease-prevention strategy and leading candidates focus on the induction of bactericidal antibodies. Antibody-resistant strains arising through further gene deletion could compromise such a strategy...
July 3, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28673553/hiv-1-sequence-necessary-and-sufficient-to-package-non-viral-rnas-into-hiv-1-particles
#11
Yang Liu, Olga A Nikolaitchik, Sheikh Abdul Rahman, Jianbo Chen, Vinay K Pathak, Wei-Shau Hu
Genome packaging is an essential step to generate infectious HIV-1 virions and is mediated by interactions between the viral protein Gag and cis-acting elements in the full-length RNA. The sequence necessary and sufficient to allow RNA genome packaging into an HIV-1 particle has not been defined. Here, we used two distinct reporter systems to determine the HIV-1 sequence required for heterologous, non-viral RNAs to be packaged into viral particles. Although the 5' untranslated region (UTR) of the HIV-1 RNA is known to be important for RNA packaging, we found that its ability to mediate packaging relies heavily on the context of the downstream sequences...
June 30, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28672035/modern-day-siv-viral-diversity-generated-by-extensive-recombination-and-cross-species-transmission
#12
Sidney M Bell, Trevor Bedford
Cross-species transmission (CST) has led to many devastating epidemics, but is still a poorly understood phenomenon. HIV-1 and HIV-2 (human immunodeficiency virus 1 and 2), which have collectively caused over 35 million deaths, are the result of multiple CSTs from chimpanzees, gorillas, and sooty mangabeys. While the immediate history of HIV is known, there are over 45 lentiviruses that infect specific species of primates, and patterns of host switching are not well characterized. We thus took a phylogenetic approach to better understand the natural history of SIV recombination and CST...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28670581/mutant-cas9-transcriptional-activator-activates-hiv-1-in-u1-cells-in-the-presence-and-absence-of-ltr-specific-guide-rnas
#13
Veronica Kim, Brian M Mears, Bonita H Powell, Kenneth W Witwer
CRISPR/Cas9 systems have been advanced as promising tools in the HIV eradication armamentarium for sequence-specific disruption or latency reversal. Enthusiasm is balanced by concerns about off-target host genome modification and effects on HIV evolution. In the chronically HIV-1-infected U1 promonocytic latency model, we have confirmed stimulation of HIV-1 production by a mutant Cas9-transcriptional activator and guide RNAs with two guide RNAs apparently more potent than one. However, significant increases were also observed in the absence of guide RNAs...
2017: Matters (Zur)
https://www.readbyqxmd.com/read/28668335/unravelling-hiv-1-latency-one-cell-at-a-time
#14
REVIEW
Yik Lim Kok, Angela Ciuffi, Karin J Metzner
A single virus is capable of infecting and replicating in a single cell. Recent advances across single-cell omics technologies - genomics, epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics - will offer unprecedented opportunities to gain more insights into the various aspects of the life cycle of viruses and their impact on the host cell. Here, using the human immunodeficiency virus type 1 (HIV-1) as an example, we summarize the current knowledge and the future potential of single-cell omics in the investigation of an important aspect of the life cycle of HIV-1 that represents a major hurdle in achieving viral eradication, HIV-1 latency...
June 28, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28663444/atomic-structure-of-the-human-cytomegalovirus-capsid-with-its-securing-tegument-layer-of-pp150
#15
Xuekui Yu, Jonathan Jih, Jiansen Jiang, Z Hong Zhou
Herpesviruses possess a genome-pressurized capsid. The 235-kilobase genome of human cytomegalovirus (HCMV) is by far the largest of any herpesvirus, yet it has been unclear how its capsid, which is similar in size to those of other herpesviruses, is stabilized. Here we report a HCMV atomic structure consisting of the herpesvirus-conserved capsid proteins MCP, Tri1, Tri2, and SCP and the HCMV-specific tegument protein pp150-totaling ~4000 molecules and 62 different conformers. MCPs manifest as a complex of insertions around a bacteriophage HK97 gp5-like domain, which gives rise to three classes of capsid floor-defining interactions; triplexes, composed of two "embracing" Tri2 conformers and a "third-wheeling" Tri1, fasten the capsid floor...
June 30, 2017: Science
https://www.readbyqxmd.com/read/28663289/genome-sequence-of-a-novel-hiv-1-circulating-recombinant-form-crf77_cpx-identified-among-blood-donors-in-malaysia
#16
Kok Keng Tee, Abdul Hamid Bon, Wei Zhen Chow, Kim Tien Ng, Kok Gan Chan, Adeeba Kamarulzaman, Michael P Busch, Yutaka Takebe
We report here the first HIV-1 circulating recombinant form (CRF) complex identified among the blood donors in Malaysia. The CRF77_cpx mosaic genome consists of parental subtypes B', C, and CRF01_AE and is structurally related to CRF07_BC. The identification of CRF77_cpx underlines the genetic complexity and mobility of HIV-1 among the blood donors.
June 29, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28660234/isolation-of-exosomes-from-semen-for-in-vitro-uptake-and-hiv-1-infection-assays
#17
Marisa N Madison, Jennifer L Welch, Chioma M Okeoma
Exosomes are membranous extracellular nanovesicles of endocytic origin. Exosomes are known to carry host and pathogen-derived genomic, proteomic, lipidomic cargos and other extraneous molecules. Exosomes are secreted by diverse cell types into the extracellular milieu and are subsequently internalized by recipient neighboring or distal cells. Upon internalization, exosomes condition recipient cells by donating their cargos and/or activating various signal transduction pathways, consequently regulating physiological and pathophysiological processes...
April 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28647987/-distribution-of-hiv-1-subtypes-among-foreign-patients-in-guangzhou-between-2008-and-2010-and-in-2015
#18
Z G Han, H Wu, C Y Liang, K Gao, H X Mai, Y S Cai, H F Xu
Objective: To understand the characteristic of subtype distribution among foreigners who were living with HIV-1, in Guangzhou. Methods: HIV-1 RNAs were extracted from 114 serum specimens in foreigners diagnosed with HIV-1 infections between 2008 and 2010, and in 2015. Partial pol gene of HIV-1 genome from these RNA samples were amplified by nested reverse transcription polymerase chain reaction (nested-PCR) with nucleotide sequenced. Subsequently, phylogenetic tree was reconstructed using the pol sequences of samples and references...
June 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28646219/efficient-and-unbiased-metagenomic-recovery-of-rna-virus-genomes-from-human-plasma-samples
#19
Carmen F Manso, David F Bibby, Jean L Mbisa
RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses - HIV, HCV and HEV...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642469/tracing-the-epidemic-history-of-hiv-1-crf01_ae-clusters-using-near-complete-genome-sequences
#20
Xingguang Li, Haizhou Liu, Lu Liu, Yi Feng, Marcia L Kalish, Simon Y W Ho, Yiming Shao
Human immunodeficiency virus (HIV) has a number of circulating recombinant forms that are the product of recombination between different HIV subtypes. The first circulating recombinant form of HIV-1 to be identified was CRF01_AE, which originated in Central Africa and is now most prevalent in Southeast and East Asia. In this study, we investigated the timescale, evolutionary history, and population genetics of the HIV-1 CRF01_AE strains primarily responsible for the epidemic in Asia. A further aim of our study was to define and standardize the nomenclature and provide well-characterized reference sequences for the phylogenetic transmission clusters of CRF01_AE...
June 22, 2017: Scientific Reports
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