Abstract:
:Identifying and monitoring HIV clusters could be useful in tracking the leading edge of HIV transmission in epidemics. Currently, greater specificity in the definition of HIV clusters is needed to reduce confusion in the interpretation of HIV clustering results. We address sampling density as one of the key aspects of HIV cluster analysis. The proportion of viral sequences in clusters was estimated at sampling densities from 1.0% to 70%. A set of 1,248 HIV-1C env gp120 V1C5 sequences from a single community in Botswana was utilized in simulation studies. Matching numbers of HIV-1C V1C5 sequences from the LANL HIV Database were used as comparators. HIV clusters were identified by phylogenetic inference under bootstrapped maximum likelihood and pairwise distance cut-offs. Sampling density below 10% was associated with stochastic HIV clustering with broad confidence intervals. HIV clustering increased linearly at sampling density >10%, and was accompanied by narrowing confidence intervals. Patterns of HIV clustering were similar at bootstrap thresholds 0.7 to 1.0, but the extent of HIV clustering decreased with higher bootstrap thresholds. The origin of sampling (local concentrated vs. scattered global) had a substantial impact on HIV clustering at sampling densities ≥10%. Pairwise distances at 10% were estimated as a threshold for cluster analysis of HIV-1 V1C5 sequences. The node bootstrap support distribution provided additional evidence for 10% sampling density as the threshold for HIV cluster analysis. The detectability of HIV clusters is substantially affected by sampling density. A minimal genotyping density of 10% and sampling density of 50-70% are suggested for HIV-1 V1C5 cluster analysis.
journal_name
AIDS Res Hum Retrovirusesjournal_title
AIDS research and human retrovirusesauthors
Novitsky V,Moyo S,Lei Q,DeGruttola V,Essex Mdoi
10.1089/aid.2014.0173subject
Has Abstractpub_date
2014-12-01 00:00:00pages
1226-35issue
12eissn
0889-2229issn
1931-8405journal_volume
30pub_type
杂志文章abstract::The transmembrane envelope (TM) protein gp41 of HIV-1 is an attractive target when designing a vaccine to induce neutralizing antibodies. A few broadly neutralizing antibodies (2F5, 4E10, and 10E8) that target conserved epitopes in the membrane proximal external region (MPER) of gp41 have been isolated from infected i...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/AID.2013.0191
更新日期:2014-05-01 00:00:00
abstract::The first open reading frame of the HIV genome has been identified as the gag gene. The proteins encoded by this gene are p17 as the amino-terminal protein, p24 as the middle peptide, and p15 as the carboxyl-terminal end. A monoclonal antibody recognizing an antigenic determinant on a fragment of p15 has been develope...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.1987.3.253
更新日期:1987-10-01 00:00:00
abstract::Natural polymorphisms of HIV-1, often associated with drug resistance, are widely described in protease and reverse transcriptase regions but data on their presence in the integrase region, especially in non-B subtypes, are still very limited. We aimed to characterize naturally occurring polymorphisms in the integrase...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.2010.0097
更新日期:2010-10-01 00:00:00
abstract::Genetic polymorphisms within the MHC encoding region have the strongest impact on HIV disease progression of any in the human genome and provide important clues to the mechanisms of HIV immune control. Few analyses have been undertaken of HLA alleles associated with rapid disease progression. HLA-B*07:02 is an HLA cla...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/AID.2013.0197
更新日期:2014-05-01 00:00:00
abstract::The membrane glycolipids galactosylceramide (GalCer) and sulfatide (SGalCer) have been reported to act as receptors of human immunodeficiency virus (HIV) on CD4- cell lines. We show here that these glycolipids are present on CD4+ cells purified from human blood and on in vitro-differentiated monocyte-derived macrophag...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.1996.12.695
更新日期:1996-05-20 00:00:00
abstract::Even in the setting of maximally suppressive antiretroviral therapy (ART), HIV persists indefinitely. Several mechanisms might contribute to this persistence, including chronic inflammation and immune dysfunction. In this study, we have explored a preclinical model for the evaluation of potential interventions that mi...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/AID.2012.0162
更新日期:2013-02-01 00:00:00
abstract::We have previously used immunotoxins to select for HIV-1 variant cells that transcribe HIV at extremely low levels and fail to produce HIV proteins. Further observation of one of these variants (E9) demonstrated spontaneous in vitro activation of HIV production. The mechanism of activation is different from that of U1...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章,评审
doi:10.1089/088922299310052
更新日期:1999-10-10 00:00:00
abstract::HIV-1 disease is associated with many infectious and neoplastic complications. This is particularly true of the genitourinary tract, where high rates of renal disease, neoplasms, voiding and erectile dysfunction, hematuria, opportunistic genitourinary infections, and epididymo-orchitis are found in HIV-1-infected indi...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:
更新日期:1998-04-01 00:00:00
abstract::Depletion of mitochondrial DNA (mtDNA) and mtDNA-encoded respiratory chain proteins in subcutaneous (SC) fat from patients with HIV lipoatrophy have clearly demonstrated the role of mitochondrial dysfunction in this syndrome. Research in HIV lipoatrophy, however, has been severely hampered by the lack of a suitable su...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.2007.0262
更新日期:2008-10-01 00:00:00
abstract::To assess the impact of chronic viral liver disease (CVLD) on hospital admissions and death in HIV-infected patients since the introduction of highly active antiretroviral therapy, all hospital charts, from January 1996 to December 2000, in a large HIV/AIDS reference center in Madrid were reviewed. Discharge diagnosis...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/08892220152644160
更新日期:2001-11-01 00:00:00
abstract::Infection with drug-resistant human immunodeficiency virus type 1 (HIV-1) has been documented in all countries that have surveyed for it and may result in an unfavorable response to therapy. The prevalence and characteristics of individuals with transmitted resistance to antiretroviral drugs have been scarcely describ...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.2009.0012
更新日期:2009-09-01 00:00:00
abstract::Two cynomolgus macaques were infected with a genetically complex challenge stock of simian immunodeficiency virus (SIVmac251-32H). The polymerase chain reaction (PCR) was used to amplify the env gp41, rev, and nef overlapping coding sequences from provirus present in the blood of both animals at 1, 6, and 15 months po...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.1993.9.133
更新日期:1993-02-01 00:00:00
abstract::Thirty years after its beginning, the HIV/AIDS epidemic is still raging around the world. According to UNAIDS, in 2011 alone 1.7M deaths were attributable to AIDS, and 2.5M people were newly infected by the virus. Despite the success in treating HIV-infected people with potent antiretroviral drugs, preventing HIV infe...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章,评审
doi:10.1089/aid.2013.0122
更新日期:2013-11-01 00:00:00
abstract::C-C chemokine receptor (CCR) 5 (CCR5) is the main HIV-1 coreceptor involved in virus entry and cell-to-cell spread during acute and chronic infections: such CCR5 and T cell tropic viruses are adapted to and replicate in CD4+ memory T cells. Polymorphisms in CCR5 regulate CCR5 expression, which, in turn, influences HIV...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/AID.2020.0060
更新日期:2020-10-01 00:00:00
abstract::Human immunodeficiency virus type-1 (HIV-1) is a leading cause of mortality and morbidity in the world, with almost 46 million people infected globally. HIV-1 subtype C accounts for 55% of these infections. In Zambia, the majority of HIV-1 infections are subtype C. However, to its north most countries have non-subtype...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.2005.21.901
更新日期:2005-10-01 00:00:00
abstract::We aim to determine the prevalence of HIV nonsuppression and factors associated with it. This is a cross-sectional multicenter study carried out in January 2016 with data of the VACH Cohort, a registry participated by 23 hospitals from most regions of Spain. The prevalence of HIV nonsuppression, defined as HIV RNA ≥20...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/AID.2020.0016
更新日期:2020-11-01 00:00:00
abstract::The combination of didanosine (ddI) and lamivudine (3TC) is attractive considering its low cost, potency, tolerability, and convenience (once daily administration), but it is not recommended as first-line therapy for HIV infection. A prospective, multicenter, open, comparative trial was conducted in HIV-infected, anti...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章,多中心研究
doi:10.1089/aid.2006.0029
更新日期:2007-10-01 00:00:00
abstract::Most viral vaccines currently in use in humans are live attenuated strains of virus that lack pathogenic potential. In general, such live attenuated vaccines induce the strongest longest-lasting immunity. Live attenuated strains of human immunodeficiency virus type 1 (HIV-1) have not been previously considered as vacc...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章,评审
doi:10.1089/aid.1992.8.411
更新日期:1992-03-01 00:00:00
abstract::Although suppression of HIV-1 RNA below the limit of detection is associated with optimal outcomes, many patients can maintain or increase their CD4(+) count for prolonged time periods in the presence of persistent low-level viremia. We followed seven patients with prolonged (>5 years) discordant CD4(+)/viral load (VL...
journal_title:AIDS research and human retroviruses
pub_type: 临床试验,杂志文章
doi:10.1089/aid.2005.21.13
更新日期:2005-01-01 00:00:00
abstract::Retroviruses have been suggested as possible pathogenic factors in multiple sclerosis (MS), supported by the observation that endogenous retroviruses are activated in MS patients. Different members of the herpes family of which several are neurotropic have also been suggested as factors in MS pathogenesis. Further, in...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/088922204323048168
更新日期:2004-04-01 00:00:00
abstract::Bacterial vaginosis (BV) has been linked to an increased risk of human immunodeficiency virus (HIV) acquisition and transmission in observational studies, but the underlying biological mechanisms are unknown. We measured biomarkers of subclinical vaginal inflammation, endogenous antimicrobial activity, and vaginal flo...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.2015.0006
更新日期:2015-11-01 00:00:00
abstract::We have determined that polymeric IgA in saliva of HIV-1-uninfected individuals binds in varying degrees to components of culture supernatants containing HIV-1 recombinant proteins when ELISA is used for the determination. This finding did not extend to salivary IgG antibodies. Further, such problems were not encounte...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/088922200309016
更新日期:2000-04-10 00:00:00
abstract::Studies have shown a low frequency of HIV-1 protease drug resistance mutations in patients failing protease inhibitor (PI)-based therapy. Recent studies have identified mutations in Gag as an alternate pathway for PI drug resistance in subtype B viruses. We therefore genotyped the Gag and protease genes from 20 HIV-1 ...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/AID.2014.0349
更新日期:2015-08-01 00:00:00
abstract::HIV-1 subtype B isolates have previously been described in India only in the state of Andhra Pradesh, while subtype C isolates have been reported as widespread in the Bombay and Goa regions of India. Gag subtype was determined in HIV-1 isolates from six Indians and one Ethiopian. One Indian was a native of Goa resid...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.1996.12.641
更新日期:1996-05-01 00:00:00
abstract::Because mucosal inflammation contributes to colorectal carcinogenesis, we studied the impact of intestinal infections on risk of this malignancy among people with AIDS (PWA). Using the population-based HIV/AIDS Cancer Match, which includes approximately half of all PWA in the United States, the cancer registries ascer...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章,多中心研究
doi:10.1089/AID.2011.0185
更新日期:2012-09-01 00:00:00
abstract::The function of the p12(I) protein of human T cell lymphotropic virus type I (HTLV-I) has been under debate. p12K (lysine) and p12R (arginine) variants of this protein at amino acid 88 and a shorter life of p12K had been reported by another group. Because HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.2004.20.1092
更新日期:2004-10-01 00:00:00
abstract::In cell-mediated immunity T cells recognize peptide fragments of the antigenic protein in association with major histocompatibility complex (MHC) proteins. Synthetic 9- to 16-mer peptides have been widely used to identify the region(s) of a protein that act as T cell epitope. Here, we report antigenic peptides identif...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.1995.11.1335
更新日期:1995-11-01 00:00:00
abstract::Thymulin is a thymic peptide important for the maturation and differentiation of immature thymocytes, which have been found to be depressed in patients with low-level CD4(+) cell recovery despite viral control. Substance use is associated with faster progression of HIV disease, which has been ascribed to poor adherenc...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/AID.2010.0086
更新日期:2011-08-01 00:00:00
abstract::We set out to investigate whether there are clinically significant consequences when children with perinatal exposure to single-dose nevirapine are initiated on a nonnucleoside reverse transcriptase inhibitor (NNRTI) containing a highly active antiretroviral therapy (HAART) regimen. We carried out a chart and database...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.2009.0054
更新日期:2009-10-01 00:00:00
abstract::We describe four full-length genomic sequences of HIV-1 subtype B isolates from Russia. These full-length HIV-1 genomes were amplified by nested polymerase chain reaction and sequenced. The sequences obtained were subjected to neighbor-joining phylogenetic analysis using a Kimura two-parameter model and to detailed se...
journal_title:AIDS research and human retroviruses
pub_type: 杂志文章
doi:10.1089/aid.2006.22.1192
更新日期:2006-11-01 00:00:00