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hiv genotyping

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https://www.readbyqxmd.com/read/28650400/high-need-to-switch-cart-or-co-medication-with-the-initiation-of-daas-in-elderly-hiv-hcv-co-infected-patients
#1
Elise J Smolders, Colette Smit, Clara Tmm De Kanter, Anton Dofferhoff, Joop E Arends, Kees Brinkman, Bart Rijnders, Marc Van Der Valk, Peter Reiss, David M Burger
BACKGROUD: To describe the use of non-antiretroviral co-medication and combination antiretroviral therapy (cART) in HIV/hepatitis C virus (HCV) co-infected patients, and to predict the potential for drug-drug interactions (DDIs) with direct-acting antivirals (DAAs) against HCV. METHODS: This is a retrospective, cross-sectional study, using the Dutch nationwide ATHENA observational HIV cohort database. All patients with a known HIV/HCV co-infection on 1 January 2015 were included...
June 22, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/28650381/potential-for-immune-driven-viral-polymorphisms-to-compromise-antiretroviral-based-pre-exposure-prophylaxis-for-prevention-of-hiv-1-infection
#2
Hiroyuki Gatanaga, Zabrina L Brumme, Emily Adland, Gustavo Reyes-Terán, Santiago Avila-Rios, Carlos R Mejía-Villatoro, Tsunefusa Hayashida, Takayuki Chikata, Giang Van Tran, Kinh Van Nguyen, Rita I Meza, Elsa Y Palou, Humberto Valenzuela-Ponce, Juan M Pascale, Guillermo Porras-Cortés, Marvin Manzanero, Guinevere Q Lee, Jeffrey N Martin, Mary N Carrington, Mina John, Simon Mallal, Art F Y Poon, Philip Goulder, Masafumi Takiguchi, Shinichi Oka
OBJECTIVE: Long-acting rilpivirine is a candidate for pre-exposure prophylaxis (PrEP) for prevention of HIV-1 infection. However, rilpivirine resistance mutations at reverse transcriptase codon 138 (RT-E138X) occur naturally in a minority of HIV-1-infected persons; in particular those expressing Human Leukocyte Antigen (HLA)-B*18 where RT-E138X arises as an immune escape mutation. We investigate the global prevalence, B*18-linkage and replicative cost of RT-E138X and its regional implications for rilpivirine PrEP...
June 23, 2017: AIDS
https://www.readbyqxmd.com/read/28646219/efficient-and-unbiased-metagenomic-recovery-of-rna-virus-genomes-from-human-plasma-samples
#3
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/28644711/screening-for-squamous-cell-anal-cancer-in-hiv-positive-patients-a-five-year-experience
#4
Chiara Santorelli, Cosimo Alex Leo, Jonathan D Hodgkinson, Franco Baldelli, Francesco Cantarella, Emanuel Cavazzoni
AIM: Potential screening modalities for early diagnosis of squamous cell anal cancer (SCC) in HIV patients include digital anorectal examination (DARE), anal Papanicolaou testing (Pap test), human papilloma virus (HPV) co-testing, and high-resolution anoscopy. The aim of this study was to demonstrate the results of a five-year screening program for SCC in HIV patients. MATERIALS AND METHODS: We conducted a retrospective study on 204 HIV patients who underwent a screening program for SCC from October 2010 to January 2015...
June 23, 2017: Journal of Investigative Surgery: the Official Journal of the Academy of Surgical Research
https://www.readbyqxmd.com/read/28641707/analysis-of-transmitted-hiv-drug-resistance-from-2005-to-2015-in-victoria-australia-a-comparison-of-the-old-and-the-new
#5
Jodie D'Costa, Megan Gooey, Nicole Richards, Rizmina Sameer, Elaine Lee, Doris Chibo
Background: Baseline genotyping is part of standard-of-care treatment. It reveals that transmitted drug resistance (TDR) continues to be important for the management of HIV infection. Attention is typically focused on determining whether resistance to the protease inhibitors (PI) and reverse transcriptase inhibitors (RTI) occurs. However, the increasing use of integrase inhibitors (INIs) raises a concern that TDR to this class of antiretroviral drug may also occur. Methods: PI and RTI drug resistance genotyping was performed on blood samples collected between 2005 and 2015 from 772 treatment-naïve Victorian patients infected with HIV within the previous 12 months...
June 23, 2017: Sexual Health
https://www.readbyqxmd.com/read/28641212/association-of-gene-polymorphisms-of-four-components-of-renin-angiotensin-aldosterone-system-and-preeclampsia-in-south-african-black-women
#6
M Aung, T Konoshita, J Moodley, P Gathiram
OBJECTIVE: To investigate the association of the gene polymorphisms of: angiotensinogen (AGT), renin (REN), angiotensin II receptor 1 (AT1R) and angiotensin II receptor 2 (AT2R), in the pathogenesis of PE in South African Black women. METHODOLOGY (STUDY DESIGN): 603 pregnant women; 246 normotensive and 357 with PE (early-onset=187, late-onset=170), were recruited. Each study group was subdivided into HIV infected and uninfected groups. The distribution and frequencies of gene polymorphisms of AGT (M235T), REN (C-5312T), AT1R (A1166C) and AT2R (C3123A) were determined in purified DNA by Real Time Polymerase Chain Reaction...
May 18, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28637235/monotherapy-with-either-dolutegravir-or-raltegravir-fails-to-durably-suppress-hiv-viraemia-in-humanized-mice
#7
Alonso Heredia, Said Hassounah, Sandra Medina-Moreno, Juan C Zapata, Nhut M Le, Yingshan Han, James S Foulke, Charles Davis, Joseph Bryant, Robert R Redfield, Mark A Wainberg
Objectives: To compare the effectiveness of HIV integrase inhibitor monotherapy between raltegravir and dolutegravir as an approach to simplify therapy. Methods: We evaluated and compared the efficacy of 20 week monotherapy with dolutegravir or raltegravir in humanized mice (HSC-NSG) infected with HIV BaL . Plasma HIV RNA was measured by quantitative RT-PCR (limit of detection of 150 copies/45 μL of plasma) and drug levels by LC-MS/MS. Escape viruses were genotyped and analysed for replication capacity and drug susceptibility in tissue culture...
June 13, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28633097/results-of-the-first-international-hiv-1-coreceptor-proficiency-panel-test
#8
Eva Heger, Rolf Kaiser, Elena Knops, Maria Neumann-Fraune, Eugen Schuelter, Alejandro Pironti, Thomas Lengauer, Hauke Walter, Saleta Sierra
BACKGROUND: Quality Assurance (QA) programs are essential to evaluate performance in diagnostics laboratories. OBJECTIVES: We present the results from the first QA for HIV-1 genotypic tropism testing, organized and coordinated by the Institute of Virology at the University of Cologne. STUDY DESIGN: 12 cell culture-derived viral strains of different HIV-1 clades from the NIH AIDS Reagent Program were sent to the participants to be processed with their standard diagnostic methods Fasta files containing the V3 region sequence were centrally analyzed at the Institute of Virology, Cologne...
June 10, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28625824/polymorphism-study-of-cryptosporidium-hominis-gp60-subtypes-circulating-in-northern-tunisia
#9
Rym Essid, Hanen Chelbi, Siala Emna, Ines Bensghair, Jean Menotti, Aïda Bouratbine
Cryptosporidium spp. are a major cause of gastrointestinal diseases in humans worldwide. While a single subtype of Cryptosporidium hominis has been shown to be responsible for several large outbreaks related to water contamination in developed countries, little is known about the epidemiology of C. hominis in developing countries. This study reports the first genetic characterization of C. hominis at the subtype level in several human populations in an urban region of Tunisia using the gp60 gene. Among 511 stool samples that were collected from different human populations, Cryptosporidium 18S rRNA gene PCR was positive for 39 samples (7...
June 15, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28622345/the-infection-staging-and-profile-of-genotypic-distribution-and-drug-resistance-mutation-among-the-human-immunodeficiency-virus-1-infected-blood-donors-from-five-chinese-blood-centers-2012-2014
#10
Peibin Zeng, Yu Liu, Miao He, Jingxing Wang, Sheila Keating, Wei Mao, Mei Huang, Hongli Ma, Weilan He, Xinhong Bi, Dan Liao, Michael Busch, Paul Ness, Jing Liu, Hua Shan
The increasing complexity and diversity of the human immunodeficiency virus-1 (HIV-1) infections challenge the disease control and anti-retrovirus treatment in China. The infection stages and molecular characteristics of HIV-1 from infected Chinese blood donors were examined to shed light on the HIV genotype distribution and the status of drug resistance mutations (DRMs) in the changing HIV epidemic in China. Western blot (WB) confirmed HIV-1 positive plasma samples were collected from blood donors at five Chinese blood centers from April 16, 2012, through June 30, 2014...
2017: PloS One
https://www.readbyqxmd.com/read/28620613/evidence-of-divergent-amino-acid-usage-in-comparative-analyses-of-r5-and-x4-associated-hiv-1-vpr-sequences
#11
Gregory C Antell, Will Dampier, Benjamas Aiamkitsumrit, Michael R Nonnemacher, Vanessa Pirrone, Wen Zhong, Katherine Kercher, Shendra Passic, Jean Williams, Yucheng Liu, Tony James, Jeffrey M Jacobson, Zsofia Szep, Brian Wigdahl, Fred C Krebs
Vpr is an HIV-1 accessory protein that plays numerous roles during viral replication, and some of which are cell type dependent. To test the hypothesis that HIV-1 tropism extends beyond the envelope into the vpr gene, studies were performed to identify the associations between coreceptor usage and Vpr variation in HIV-1-infected patients. Colinear HIV-1 Env-V3 and Vpr amino acid sequences were obtained from the LANL HIV-1 sequence database and from well-suppressed patients in the Drexel/Temple Medicine CNS AIDS Research and Eradication Study (CARES) Cohort...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28618736/frequency-of-human-parvovirus-4-parv4-viremia-among-hbv-infected-patients-and-healthy-donors-in-shiraz-iran
#12
Fereshte Amirahmadi, Jamal Sarvari, Seyed Younes Hosseini, Neda Pirbonyeh, Ali Akbar Gorzin
BACKGROUND/AIM: PARV4, a small DNA virus belonging to the family Parvoviridae, was first isolated in an HBV injecting drug user. Several studies have investigated PARV4 co-infection with HBV and HCV and its effect on the progression of liver disease. The aim of this study was to determine the frequency of PARV4 among HBV-infected patients and healthy individuals. MATERIALS AND METHODS: A group of 90 HBV patients and a group of 90 healthy subjects were included in this study...
June 12, 2017: Turkish Journal of Medical Sciences
https://www.readbyqxmd.com/read/28618264/unconventional-interrogation-yields-hiv-s-escape-plan
#13
Thomas B Kepler
Chasing HIV-1 across the genotype landscape, unequipped to anticipate its maneuvers, the antibody variable-region genes pursue the virus in futility. In this issue of Cell Host & Microbe, Dingens et al. (2017) exhibit a powerful technology that reveals the escape pathways of HIV-1 and may enable its capture.
June 14, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28616444/incidence-of-hepatitis-c-virus-infection-in-the-human-immunodeficiency-virus-outpatient-study-cohort-2000-2013
#14
Taraz Samandari, Ellen Tedaldi, Carl Armon, Rachel Hart, Joan S Chmiel, John T Brooks, Kate Buchacz
BACKGROUND: There are few recent studies of incident hepatitis C virus (HCV) infection among human immunodeficiency virus (HIV)-infected patients in the United States. METHODS: We studied HIV Outpatient Study (HOPS) participants seen in 9 HIV-specialty clinics who had ≥1 clinical encounter during 2000-2013 and ≥2 HCV-related tests, the first of which was a negative HCV antibody test (Ab). Hepatitis C virus incident cases were identified by first positive HCV Ab, viral load, or genotype...
2017: Open Forum Infectious Diseases
https://www.readbyqxmd.com/read/28612194/clinical-and-pathological-risk-factors-associated-with-liver-fibrosis-and-steatosis-in-african-americans-with-chronic-hepatitis-c
#15
Ali Afsari, Edward Lee, Babak Shokrani, Tina Boortalary, Zaki A Sherif, Mehdi Nouraie, Adeyinka O Laiyemo, Kawtar Alkhalloufi, Hassan Brim, Hassan Ashktorab
BACKGROUND AND AIM: Several factors involved in the development of liver fibrosis in African-American patients with chronic hepatitis C have not been well studied. We aimed to evaluate some of these risk factors. METHODS: We reviewed pathology and medical records of 603 African-Americans with chronic hepatitis C virus (HCV) infection at Howard University Hospital from January 2004 to December 2013. Among the clinical and pathological data collected were HIV (human immunodeficiency virus), HCV genotype, hepatitis B virus (HBV), diabetes mellitus (DM), hypertension (HTN), body mass index (BMI), and hepatic steatosis...
June 13, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28608973/high-hepatitis-c-cure-rates-among-black-and-non-black-hiv-infected-adults-in-an-urban-center
#16
Oluwaseun Falade-Nwulia, Catherine Sutcliffe, Juhi Moon, Geetanjali Chander, Tanyaporn Wansom, Jeanne Keruly, Jennifer Katzianer, Amy Nathanson, Jillian Marks, Shruti Mehta, David Thomas, Richard Moore, Mark Sulkowski
Background Hepatitis C virus (HCV) cure rates have been similar in patients with and without HIV co-infection; however, in the ION-4 study, black patients treated with ledipasvir/sofosbuvir were significantly less likely to achieve cure (90%) compared to non-black patients (99%). There are limited real world data on the effectiveness of oral direct acting antivirals (DAAs) in predominantly minority HIV/HCV co-infected populations. Methods We analyzed HCV treatment outcomes among 255 HCV co-infected patients initiating DAAs between February 2014 and March 2016 in an urban clinic in Baltimore, Maryland...
June 13, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28605418/should-we-be-testing-for-baseline-integrase-resistance-in-patients-newly-diagnosed-with-hiv
#17
Yiannis Koullias, Paul E Sax, Naomi F Fields, Rochelle P Walensky, Emily P Hyle
Background: Current guidelines recommend genotype resistance testing at diagnosis to guide initial selection of antiretroviral therapy (ART). Many standard resistance genotypes exclude testing for resistance to integrase inhibitors ("IR-testing"), although this class of drugs is a component of most recommended first-line regimens. Methods: We compared the 96-week clinical outcomes and cost-effectiveness of two strategies: no IR-testing vs. IR-testing performed at HIV diagnosis...
June 9, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28602726/the-changing-molecular-epidemiology-of-hiv-in-the-philippines
#18
Edsel Maurice T Salvaña, Brian E Schwem, Patrick R Ching, Simon D W Frost, Sharie Keanne C Ganchua, Jill R Itable
BACKGROUND: The Philippines has one of the fastest-growing HIV epidemics in the world. Possible reasons for this include increased testing, increased local transmission, and possibly more aggressive strains of HIV. This study sought to determine whether local molecular subtypes of HIV have changed. METHODS: Viruses from 81 newly diagnosed, treatment-naive HIV patients were genotyped using protease and reverse transcriptase genes. Demographic characteristics and CD4 count data were collected...
June 21, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28599618/hiv-coinfected-patients-respond-worse-to-direct-acting-antiviral-based-therapy-against-chronic-hepatitis-c-in-real-life-than-hcv-monoinfected-individuals-a-prospective-cohort-study
#19
Karin Neukam, Luis E Morano-Amado, Antonio Rivero-Juárez, María Mancebo, Rafael Granados, Francisco Téllez, Antonio Collado, María J Ríos, Ignacio de Los Santos-Gil, Sergio Reus-Bañuls, Francisco Vera-Méndez, Paloma Geijo-Martínez, Marta Montero-Alonso, Marta Suárez-Santamaría, Juan A Pineda
OBJECTIVE: HIV/HCV-coinfected patients and hepatitis C virus (HCV) monoinfected subjects are thought to respond equally to direct-acting antiviral (DAA)-based therapy despite the lack of data derived from clinical trials. This study is aimed to evaluate the impact of HIV coinfection on the response to DAA-based treatment against HCV infection in the clinical practice. PATIENTS AND METHODS: In a prospective multicohort study, patients who initiated DAA-based therapy at the Infectious Disease Units of 33 hospitals throughout Spain were included...
May 2017: HIV Clinical Trials
https://www.readbyqxmd.com/read/28591401/an-overview-of-the-molecular-and-epidemiological-features-of-hiv-1-infection-in-two-major-cities-of-bahia-state-brazil
#20
Amanda Gm Amaral, Isabele B Oliveira, Diego C Carneiro, Luiz Cj Alcantara, Joana P Monteiro-Cunha
BACKGROUND: The high mutation rate of the human immunodeficiency virus (HIV) has created a public health challenge because the use of antiretroviral drugs can generate selective pressure that drives resistance in these viruses. OBJECTIVE: The aim of this work was to characterise the molecular and epidemiological profile of HIV in Bahia, Brazil. METHODS: DNA sequences from regions of HIV gag, pol, and env genes were obtained from previous studies performed in this area between 2002 and 2012...
June 2017: Memórias do Instituto Oswaldo Cruz
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