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hiv genotyping

Elodie Alessandri-Gradt, Fabienne De Oliveira, Marie Leoz, Véronique Lemee, David L Robertson, Felix Feyertag, Paul-Alain Ngoupo, Philippe Mauclere, François Simon, Jean-Christophe Plantier
OBJECTIVES: HIV/1 group P (HIV-1/P) is the last HIV/1 group discovered and to date, comprises only two strains. To obtain new insights into this divergent group, we screened for new infections by developing specific tools, and analysed phenotypic and genotypic properties of the prototypic strain RBF168. In addition, the follow-up of the unique patient monitored so far, has raised the knowledge of the natural history of this infection and its therapeutic management. DESIGN/METHODS: We developed an HIV-1/P specific sero-molecular strategy and screened over 29,498 specimen samples...
March 15, 2018: AIDS
J von Felden, J Vermehren, P Ingiliz, S Mauss, T Lutz, K G Simon, H W Busch, A Baumgarten, K Schewe, D Hueppe, C Boesecke, J K Rockstroh, M Daeumer, N Luebke, J Timm, J Schulze Zur Wiesch, C Sarrazin, S Christensen
BACKGROUND: Twelve weeks of the pangenotypic direct-acting antiviral (DAA) combination sofosbuvir/velpatasvir (SOF/VEL) was highly efficient in patients with hepatitis C virus (HCV) genotype 3 (GT3) infection in the ASTRAL-3 approval study. However, presence of resistance-associated substitutions (RASs) in the HCV nonstructural protein 5A (NS5A) was associated with lower treatment response. AIM: To assess the efficacy and safety of SOF/VEL ± ribavirin (RBV) and the impact of NS5A RASs and RBV use on treatment outcome in HCV GT3 infection in a real-world setting...
March 14, 2018: Alimentary Pharmacology & Therapeutics
Julia L Marcus, Leo B Hurley, Scott Chamberland, Jamila H Champsi, Laura C Gittleman, Daniel G Korn, Jennifer B Lai, Jennifer O Lam, Mary Patricia Pauly, Charles P Quesenberry, Joanna Ready, Varun Saxena, Suk Seo, David J Witt, Michael J Silverberg
BACKGROUND & AIMS: Treatment with the combination of ledipasvir and sofosbuvir for 12 weeks has been approved by the Food and Drug Administration for patients with genotype 1 hepatitis C virus (HCV) infection; some patients can be treated with an 8-week course. Guidelines recommend a 12-week treatment course for black patients, but studies have not compared the effectiveness of 8 vs 12 weeks in black patients who are otherwise eligible for an 8-week treatment regimen. METHODS: We conducted an observational study of Kaiser Permanente Northern California members with HCV genotype 1 infection who were eligible for 8 weeks of treatment with ledipasvir and sofosbuvir (treatment-naïve, no cirrhosis, no HIV infection, level of HCV RNA <6 million IU/mL) and were treated for 8 or 12 weeks from October 2014 through December 2016...
March 10, 2018: Clinical Gastroenterology and Hepatology
M Chen, M H Jia, Y L Ma, H B Luo, H C Chen, C J Yang, J Dai, L Yang, L J Dong, R Lu, L J Song, Y Han, J Y Lu, A K L Cheung, Z W Chen, L Lu
Multiple human immunodeficiency virus (HIV)-1 genotypes in China were first discovered in Yunnan Province before disseminating throughout the country. As the HIV-1 epidemic continues to expand in Yunnan, genetic characteristics and transmitted drug resistance (TDR) should be further investigated among the recently infected population. Among 2828 HIV-positive samples newly reported in the first quarter of 2014, 347 were identified as recent infections with BED-captured enzyme immunoassay (CEIA). Of them, 291 were successfully genotyped and identified as circulating recombinant form (CRF)08_BC (47...
March 14, 2018: Epidemiology and Infection
Francles Blanco-Guillot, M Lucía Castañeda-Cediel, Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Guadalupe Delgado-Sánchez, Elizabeth Ferreira-Guerrero, Rogelio Montero-Campos, Miriam Bobadilla-Del-Valle, Rosa Areli Martínez-Gamboa, Pedro Torres-González, Norma Téllez-Vazquez, Sergio Canizales-Quintero, Mercedes Yanes-Lane, Norma Mongua-Rodríguez, Alfredo Ponce-de-León, José Sifuentes-Osornio, Lourdes García-García
BACKGROUND: Genotyping and georeferencing in tuberculosis (TB) have been used to characterize the distribution of the disease and occurrence of transmission within specific groups and communities. OBJECTIVE: The objective of this study was to test the hypothesis that diabetes mellitus (DM) and pulmonary TB may occur in spatial and molecular aggregations. MATERIAL AND METHODS: Retrospective cohort study of patients with pulmonary TB. The study area included 12 municipalities in the Sanitary Jurisdiction of Orizaba, Veracruz, México...
2018: PloS One
Ross D Cranston, Michelle S Cespedes, Pawel Paczuski, Ming Yang, Robert W Coombs, Joan Dragavon, Alfred Saah, Catherine Godfrey, Jennifer Y Webster-Cyriaque, Elizabeth Y Chiao, Barbara Bastow, Timothy Wilkin
BACKGROUND: The quadrivalent human papillomavirus (HPV) vaccine (qHPV; types 6, 11, 16, 18) is indicated for men and women aged 9 to 26 years to prevent HPV associated anogenital high-grade squamous intraepithelial lesions (HSIL) and cancer. ACTG 5298 was a randomized placebo controlled Phase 3 study in human immunodeficiency virus (HIV)-infected men who have sex with men, and women of qHPV to prevent persistent anal HPV infection. Baseline data are presented here. METHODS: Human immunodeficiency virus-infected men who have sex with men, and women 27 years or older without previous anogenital or oral cancer were enrolled...
April 2018: Sexually Transmitted Diseases
James J Gilchrist, Anna Rautanen, Benjamin P Fairfax, Tara C Mills, Vivek Naranbhai, Holly Trochet, Matti Pirinen, Esther Muthumbi, Salim Mwarumba, Patricia Njuguna, Neema Mturi, Chisomo L Msefula, Esther N Gondwe, Jenny M MacLennan, Stephen J Chapman, Malcolm E Molyneux, Julian C Knight, Chris C A Spencer, Thomas N Williams, Calman A MacLennan, J Anthony G Scott, Adrian V S Hill
Nontyphoidal Salmonella (NTS) is a major cause of bacteraemia in Africa. The disease typically affects HIV-infected individuals and young children, causing substantial morbidity and mortality. Here we present a genome-wide association study (180 cases, 2677 controls) and replication analysis of NTS bacteraemia in Kenyan and Malawian children. We identify a locus in STAT4, rs13390936, associated with NTS bacteraemia. rs13390936 is a context-specific expression quantitative trait locus for STAT4 RNA expression, and individuals carrying the NTS-risk genotype demonstrate decreased interferon-γ (IFNγ) production in stimulated natural killer cells, and decreased circulating IFNγ concentrations during acute NTS bacteraemia...
March 9, 2018: Nature Communications
Oksana Pasechnik, Anna Vyazovaya, Stanislav Vitriv, Marina Tatarintseva, Aleksey Blokh, Vladimir Stasenko, Igor Mokrousov
This population-based study characterized Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative tuberculosis (TB) patients in the Omsk region in Western Siberia, Russia. We sought to gain insight into the major genotype families and epidemic and endemic clones of M. tuberculosis in the area with a high burden and adverse trend of TB/HIV coinfection. The study collection included M. tuberculosis isolates from 207 newly-diagnosed patients with pulmonary TB; 55 (26.5%) of patients were HIV-infected...
January 2018: Tuberculosis
Myint Aung, Tadashi Konoshita, Jagadissan Moodley, Prem Gathiram
INTRODUCTION: The exact cause of preeclampsia (PE) remains elusive. Recently, many researchers have focused on the role of genetic variations in pathogenesis of PE. The renin-angiotensin-aldosterone system is affected in the pathogenesis of PE. OBJECTIVES: To determine association of gene polymorphisms of aldosterone synthase (CYP11B2) and angiotensin converting enzyme (ACE) in PE and normotensive South African Black women. METHODS: A group of 603 South African Black pregnant women, 246 normotensive and 357 with PE, was recruited...
January 2018: Pregnancy Hypertension
Derek J Chan, Virginia Furner, Don E Smith, Mithilesh Dronavalli, Rohan I Bopage, Jeffrey J Post, Anjali K Bhardwaj
OBJECTIVE: To assess the prevalence of non-AIDS co-morbidities (NACs) and predictors of adverse health outcomes amongst people living with HIV in order to identify health needs and potential gaps in patient management. DESIGN: Retrospective, non-consecutive medical record audit of patients attending a publicly funded HIV clinic in metropolitan Sydney analysed for predictors of adverse health outcomes. We developed a scoring system based on the validated Charlson score method for NACs, mental health and social issues and confounders were selected using directed acyclic graph theory under the principles of causal inference...
March 8, 2018: AIDS Research and Therapy
I Ketut Agus Somia, Nipat Teeratakulpisarn, Wifanto S Jeo, Ilias A Yee, Tippawan Pankam, Siriporn Nonenoy, Deondara Trachuntong, Pravit Mingkwanrungrueng, Made Dewi D Sukmawati, Reshmie Ramautarsing, Hanny Nilasari, Nany Hairunisa, Iskandar Azwa, Evy Yunihastuti, Tuti P Merati, Praphan Phanuphak, Joel Palefsky, Nittaya Phanuphak
This study aimed to assess the prevalence of and associated risk factors for anal high-risk human papillomavirus (hr-HPV) infection among men who have sex with men (MSM) and transgender women (TGW) in Indonesia, Thailand, and Malaysia.This was baseline data from a prospective cohort study with clinic sites in Jakarta and Bali (Indonesia), Bangkok (Thailand), and Kuala Lumpur (Malaysia).MSM and TGW aged 18 years and older from Indonesia, Thailand, and Malaysia were enrolled. Demographic and behavioral characteristics were assessed, and anal samples were collected for HPV genotyping...
March 2018: Medicine (Baltimore)
Anne B Kristensen, Stephen J Kent, Matthew S Parsons
Antibody Fc-dependent functions are linked to prevention and control of HIV-1 infection. Basic NK cell biology is likely key to understanding the contributions anti-HIV-1 antibody-dependent NK cell activation and cytolysis make to HIV-1 susceptibility and disease progression. The importance of NK cell education through inhibitory receptors specific for self-HLA-I in determining the potency of anti-HIV-1 antibody mediated NK cell activation and cytolysis is controversial. To address this issue more definitively we utilized HLA-I genotyping, flow cytometry staining panels and cytolysis assays to assess the functionality of educated and non-educated peripheral blood NK cells...
March 7, 2018: Journal of Virology
Christoph Höner Zu Siederdissen, Peter Buggisch, Klaus Böker, Eckart Schott, Hartwig Klinker, Anita Pathil, Heike Pfeiffer-Vornkahl, Thomas Berg, Christoph Sarrazin, Dietrich Hüppe, Michael P Manns, Stefan Mauss
Background: In pivotal studies with direct-acting antivirals (DAAs), rates of sustained virological response in hepatitis C genotype 1 infection are >90%. Objective: The objective of this article is to assess real-world safety and effectiveness of DAA treatment in a prospective multicenter registry study. Methods: The German Hepatitis C-Registry includes 6606 patients with genotype 1 from 246 centers, treated between February 2014 and June 2016 at the discretion of the physician...
March 2018: United European Gastroenterology Journal
Phan Vuong Khac Thai, Dang Thi Minh Ha, Nguyen Thi Hanh, Jeremy Day, Sarah Dunstan, Nguyen Thi Quynh Nhu, Vo Sy Kiet, Nguyen Huu Lan, Nguyen Huy Dung, Nguyen Thi Ngoc Lan, Nguyen Thuong Thuong, Nguyen Ngoc Lan, Phạm Thị Thúy Liễu, Nguyễn Thị Hồng, Đào Công Điệp, Nguyễn Thị Kim Thanh, Nguyễn Văn Hội, Nguyễn Văn Nghĩa, Trương Ngọc Đại, Hoàng Quang Minh, Nguyễn Văn Thơm, Jeremy Farrar, Maxine Caws
BACKGROUND: Drug resistant tuberculosis (TB) is increasing in prevalence worldwide. Treatment failure and relapse is known to be high for patients with isoniazid resistant TB treated with standard first line regimens. However, risk factors for unfavourable outcomes and the optimal treatment regimen for isoniazid resistant TB are unknown. This cohort study was conducted when Vietnam used the eight month first line treatment regimen and examined risk factors for failure/relapse among patients with isoniazid resistant TB...
March 6, 2018: BMC Infectious Diseases
Luisa Zupin, Vania Polesello, Ludovica Segat, Anselmo Jiro Kamada, Louise Kuhn, Sergio Crovella
INTRODUCTION: Human Beta Defensin-1 (hBD-1) is a component of the innate immune system, the first line of defence against pathogens, already reported as involved in the susceptibility to HIV-1 infection and HIV-1 mother-to-child transmission (MTCT) in different populations. We investigated the role of DEFB1 gene (encoding for hBD-1) functional polymorphisms in the susceptibility to HIV-1 MTCT in a population from Zambia. METHODS: Four selected polymorphisms within DEFB1 gene, three at the 5' untranslated region (UTR), namely - 52G>A ( RS1799946 ), -44C>G ( RS1800972 ) and -20G>A ( RS11362 ) and one in the 3'UTR, c...
March 5, 2018: Journal of Maternal-fetal & Neonatal Medicine
Wassim Chehadeh, Osama Albaksami, Sonia Elezebeth John, Widad Al-Nakib
OBJECTIVES: To investigate the prevalence of non-polymorphic resistance-associated mutations (RAMs) in HIV-1 patients on first-line antiretroviral therapy in Kuwait. SUBJECTS AND METHODS: Total ribonucleic acid (RNA) was isolated from plasma samples of 42 patients who received first-line non-nucleoside reverse transcriptase inhibitor (NNRTI)-based regimen. HIV-1 protease and reverse transcriptase genetic regions were then amplified by nested reverse-transcription polymerase chain reaction (RT-PCR), and directly sequenced...
March 5, 2018: Medical Principles and Practice: International Journal of the Kuwait University, Health Science Centre
Leonardo Euripedes Andrade-Silva, Kennio Ferreira-Paim, Thatiana Bragine Ferreira, Anderson Vilas-Boas, Delio José Mora, Verônica Morais Manzato, Fernanda Machado Fonseca, Kelli Buosi, Juliana Andrade-Silva, Bruno da Silva Prudente, Natalia Evelyn Araujo, Helioswilton Sales-Campos, Marcus Vinicius da Silva, Virmondes Rodrigues Júnior, Wieland Meyer, Mario Léon Silva-Vergara
Cryptococcal infections are mainly caused by members of the Cryptococcus neoformans species complex (molecular types VNI, VNII, VNB, VNIV and the AD hybrid VNIII). PCR of the mating type loci and MLST typing using the ISHAM-MLST consensus scheme were used to evaluate the genetic relationship of 102 (63 clinical and 39 environmental) C. neoformans isolates from Uberaba, Brazil and to correlate the obtained genotypes with clinical, antifungal susceptibility and virulence factor data. All isolates were mating type alpha...
2018: PloS One
Monica B Arruda, Lídia T Boullosa, Cynthia C Cardoso, Carolina M da Costa, Carlos Rb Alves, Shirlene Ts de Lima, Helena T Kaminski, Agdemir W Aleixo, Ana Op Esposito, Ana Ms Cavalcanti, Maristela Riedel, José C Couto-Fernandez, Selma B Ferreira, Ivi Cm de Oliveira, Loreci E Portal, Hilda Hc Wolf, Sandra B Fernandes, Maria I de M C Pardini, Manoel Vc Feiteiro, Fernanda M Tolentino, Ricardo S Diaz, Giselle Isl Lopes, Roberta Bl Francisco, Nazle Mc Véras, Ana F Pires, Miriam Franchini, Fábio Mesquita, Amilcar Tanuri
INTRODUCTION: In Brazil, more than 487,450 individuals are currently undergoing antiretroviral treatment. In order to monitor the transmission of drug-resistant strains and HIV subtype distribution in the country, this work aimed to estimate its prevalence and to characterize the nationwide pretreatment drug resistance in individuals recently diagnosed with HIV between 2013 and 2015. METHODS: The HIV threshold survey methodology (HIV-THS, WHO) targeting antiretroviral-naive individuals with recent HIV diagnosis was utilized, and subjects were selected from 51 highly populated cities in all five Brazilian macroregions...
March 2018: Journal of the International AIDS Society
Brenda C M De Winter, Dennis A Hesselink, Nassim Kamar
Hepatitis E virus (HEV) is the most common cause of viral hepatitis worldwide. Genotypes 1 and 2 (GT1 and GT2) are mainly present in developing countries, while GT3 and GT4 are prevalent in developed and high-income countries. In the majority of cases, HEV causes a self-limiting hepatitis. GT3 and GT4 can be responsible for a chronic hepatitis that can lead to cirrhosis in immunocompromized patients, i.e. solid-organ- and stem-cell-transplant-patients, human immunodeficiency virus-infected patients, and patients receiving chemotherapy or immunotherapy...
February 27, 2018: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
Gurmit Kaur Jagjit Singh, Steve Kaye, James C Abbott, Christoph Boesecke, Juergen Rockstroh, Myra O McClure, Mark Nelson
Background The epidemic of acute HCV infection among HIV-infected men who have sex with men (MSM) is ongoing. Transmission of drug-resistant variants (DRVs) after HCV treatment failure could pose a major threat to the effectiveness of future therapies. We determined the baseline prevalence of pre-existing DRVs in the HCV NS3 protease gene and their effects on the addition of telaprevir (TVR) to standard pegylated interferon and ribavirin (PEG-IFN/RBV) for acute HCV infection in individuals enrolled in a multicentre randomized controlled trial (2013 and 2014)...
March 1, 2018: HIV Clinical Trials
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