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Sun Z, Ouyang J, Zhao B, An M, Wang L, Ding H, Han X. Natural polymorphisms in HIV-1 CRF01_AE strain and profile of acquired drug resistance mutations in a long-term combination treatment cohort in northeastern China. BMC Infect Dis 2020; 20:178. [PMID: 32102660 PMCID: PMC7045473 DOI: 10.1186/s12879-020-4808-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The impacts of genetic polymorphisms on drug resistance mutations (DRMs) among various HIV-1 subtypes have long been debated. In this study, we aimed to analyze the natural polymorphisms and acquired DRM profile in HIV-1 CRF01_AE-infected patients in a large first-line antiretroviral therapy (ART) cohort in northeastern China. METHODS The natural polymorphisms of CRF01_AE were analyzed in 2034 patients from a long-term ART cohort in northeastern China. The polymorphisms in 105 treatment failure (TF) patients were compared with those in 1148 treatment success (TS) patients. The acquired DRM profile of 42 patients who experienced TF with tenofovir/lamivudine/efavirenz (TDF/3TC/EFV) treatment was analyzed by comparing the mutations at TF time point to those at baseline. The Stanford HIVdb algorithm was used to interpret the DRMs. Binomial distribution, McNemar test, Wilcoxon test and CorMut package were used to analyze the mutation rates and co-variation. Deep sequencing was used to analyze the evolutionary dynamics of co-variation. RESULTS Before ART, there were significantly more natural polymorphisms of 31 sites on reverse transcriptase (RT) in CRF01_AE than subtype B HIV-1 (|Z value| ≥ 3), including five known drug resistance-associated sites (238, 118, 179, 103, and 40). However, only the polymorphism at site 75 was associated with TF (|Z value| ≥ 3). The mutation rate at 14 sites increased significantly at TF time point compared to baseline, with the most common DRMs comprising G190S/C, K65R, K101E/N/Q, M184 V/I, and V179D/I/A/T/E, ranging from 66.7 to 45.2%. Moreover, two unknown mutations (V75 L and L228R) increased by 19.0 and 11.9% respectively, and they were under positive selection (Ka/Ks > 1, log odds ratio [LOD] > 2) and were associated with several other DRMs (cKa/Ks > 1, LOD > 2). Deep sequencing of longitudinal plasma samples showed that L228R occurred simultaneously or followed the appearance of Y181C. CONCLUSION The high levels of natural polymorphisms in CRF01_AE had little impact on treatment outcomes. The findings regarding potential new CRF01_AE-specific minor DRMs indicate the need for more studies on the drug resistance phenotype of CRF01_AE.
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Affiliation(s)
- Zesong Sun
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Jinming Ouyang
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China
| | - Bin Zhao
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Minghui An
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Lin Wang
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Haibo Ding
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China. .,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, China. .,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003, China.
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2
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Alwadani KG, Janes JK, Andrew RL. Chloroplast genome analysis of box-ironbark Eucalyptus. Mol Phylogenet Evol 2019; 136:76-86. [PMID: 30954587 DOI: 10.1016/j.ympev.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 11/17/2022]
Abstract
Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.
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Affiliation(s)
- Khawla G Alwadani
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science, Jazan University, Saudi Arabia
| | - Jasmine K Janes
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Biology Department, Faculty of Science and Technology, Vancouver Island University, British Columbia, Canada
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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3
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Iraola G, Forster SC, Kumar N, Lehours P, Bekal S, García-Peña FJ, Paolicchi F, Morsella C, Hotzel H, Hsueh PR, Vidal A, Lévesque S, Yamazaki W, Balzan C, Vargas A, Piccirillo A, Chaban B, Hill JE, Betancor L, Collado L, Truyers I, Midwinter AC, Dagi HT, Mégraud F, Calleros L, Pérez R, Naya H, Lawley TD. Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota. Nat Commun 2017; 8:1367. [PMID: 29118316 PMCID: PMC5678084 DOI: 10.1038/s41467-017-01449-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/15/2017] [Indexed: 12/31/2022] Open
Abstract
Campylobacter fetus is a venereal pathogen of cattle and sheep, and an opportunistic human pathogen. It is often assumed that C. fetus infection occurs in humans as a zoonosis through food chain transmission. Here we show that mammalian C. fetus consists of distinct evolutionary lineages, primarily associated with either human or bovine hosts. We use whole-genome phylogenetics on 182 strains from 17 countries to provide evidence that C. fetus may have originated in humans around 10,500 years ago and may have "jumped" into cattle during the livestock domestication period. We detect C. fetus genomes in 8% of healthy human fecal metagenomes, where the human-associated lineages are the dominant type (78%). Thus, our work suggests that C. fetus is an unappreciated human intestinal pathobiont likely spread by human to human transmission. This genome-based evolutionary framework will facilitate C. fetus epidemiology research and the development of improved molecular diagnostics and prevention schemes for this neglected pathogen.
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Affiliation(s)
- Gregorio Iraola
- Unidad de Bioinformática, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay. .,Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay. .,Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK
| | - Philippe Lehours
- Bordeaux Research in Translational Oncology, INSERM UMR1053, University of Bordeaux, 33076, Bordeaux, France.,French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, 33076, Bordeaux, France
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada, H9X 3Y3.,Départment de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, QC, Canada, H3T 1J4
| | - Francisco J García-Peña
- Departamento de Bacteriología, Laboratorio Central de Veterinaria de Algete (MAGRAMA), 28110, Algete, Spain
| | - Fernando Paolicchi
- Laboratorio de Bacteriología, EEA-INTA Balcarce, Balcarce, 7620, Argentina
| | - Claudia Morsella
- Laboratorio de Bacteriología, EEA-INTA Balcarce, Balcarce, 7620, Argentina
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743, Jena, Germany
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, Taipei, 10617, Taiwan
| | - Ana Vidal
- Animal and Plant Health Association (APHA), Addlestone, KT15 3NB, UK
| | - Simon Lévesque
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada, H9X 3Y3
| | - Wataru Yamazaki
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Claudia Balzan
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Agueda Vargas
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Alessandra Piccirillo
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, 35122, Italy
| | - Bonnie Chaban
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatchewan, SK, Canada, S7N 5A2
| | - Laura Betancor
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, 11600, Uruguay
| | - Luis Collado
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, 5090000, Valdivia, Chile
| | - Isabelle Truyers
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Anne C Midwinter
- EpiLab, Infectious Disease Research Centre, Massey University, Palmerston North, 4442, New Zealand
| | - Hatice T Dagi
- Department of Microbiology, Faculty of Medicine, Selçuk University, Selçuklu, 42250, Turkey
| | - Francis Mégraud
- Bordeaux Research in Translational Oncology, INSERM UMR1053, University of Bordeaux, 33076, Bordeaux, France.,French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, 33076, Bordeaux, France
| | - Lucía Calleros
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Hugo Naya
- Unidad de Bioinformática, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay.,Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, 12900, Montevideo, Uruguay
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.
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Ouyang Y, Yin Q, Li W, Li Z, Kong D, Wu Y, Hong K, Xing H, Shao Y, Jiang S, Ying T, Ma L. Escape from humoral immunity is associated with treatment failure in HIV-1-infected patients receiving long-term antiretroviral therapy. Sci Rep 2017; 7:6222. [PMID: 28740221 PMCID: PMC5524822 DOI: 10.1038/s41598-017-05594-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/31/2017] [Indexed: 01/22/2023] Open
Abstract
Interindividual heterogeneity in the disease progression of HIV-1-infected patients receiving long-term antiretroviral therapy suggests that some host-related factors may have limited treatment efficacy. To understand the nature of factors contributing to treatment failure, we performed a retrospective cohort study of 45 chronically HIV-1-infected individuals sharing a similar demographics and route of infection, compared the differences between virologically suppressed (VS) and treatment failure (TF) patients with respect to clinical, immunological and virological characteristics. We found that the baseline diversity of HIV-1 env quasispecies was the major difference between VS and TF group, and higher baseline diversity in TF patients. We further predicted TF-related env mutations using a selection pressure-based approach, followed by an analysis of these mutations based on the available three-dimensional structures of gp120/gp41 or their complexes with neutralizing antibodies. Notably, almost all of the identified residues could be mapped to the epitopes of known HIV-1 neutralizing antibodies, especially the epitopes of broadly neutralizing antibodies, and these mutations tended to compromise antibody-antigen interactions. These results indicate that the escape of HIV-1 from host humoral immunity may play a direct role in TF in long-term antiretroviral-experienced patients and that based on env gene sequence of the viruses in the patients.
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Affiliation(s)
- Yabo Ouyang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.,Beijing You'an Hospital, Capital Medical University, Beijing, China and Beijing Institute of Hepatology, Beijing, China
| | - Qianqian Yin
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Wei Li
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Protein Interactions Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Desheng Kong
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yanling Wu
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kunxue Hong
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hui Xing
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences, Fudan University, Shanghai, China. .,Lindsley F. Kimball Research Institute, New York Blood Center, New York, USA.
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Liying Ma
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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5
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Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev 2016; 116:6370-90. [PMID: 27074285 PMCID: PMC4901368 DOI: 10.1021/acs.chemrev.5b00631] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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Allosteric drug development holds
promise for delivering medicines
that are more selective and less toxic than those that target orthosteric
sites. To date, the discovery of allosteric binding sites and lead
compounds has been mostly serendipitous, achieved through high-throughput
screening. Over the past decade, structural data has become more readily
available for larger protein systems and more membrane protein classes
(e.g., GPCRs and ion channels), which are common allosteric drug targets.
In parallel, improved simulation methods now provide better atomistic
understanding of the protein dynamics and cooperative motions that
are critical to allosteric mechanisms. As a result of these advances,
the field of predictive allosteric drug development is now on the
cusp of a new era of rational structure-based computational methods.
Here, we review algorithms that predict allosteric sites based on
sequence data and molecular dynamics simulations, describe tools that
assess the druggability of these pockets, and discuss how Markov state
models and topology analyses provide insight into the relationship
between protein dynamics and allosteric drug binding. In each section,
we first provide an overview of the various method classes before
describing relevant algorithms and software packages.
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Affiliation(s)
- Jeffrey R Wagner
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Christopher T Lee
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Jacob D Durrant
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Robert D Malmstrom
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Victoria A Feher
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
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6
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Jiao Y, Li S, Li Z, Zhang Z, Zhao J, Li L, Wang L, Yin Q, Wang Y, Zeng Z, Shao Y, Ma L. HIV-1 transmitted drug resistance-associated mutations and mutation co-variation in HIV-1 treatment-naïve MSM from 2011 to 2013 in Beijing, China. BMC Infect Dis 2014; 14:689. [PMID: 25510523 PMCID: PMC4271504 DOI: 10.1186/s12879-014-0689-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 12/09/2014] [Indexed: 11/19/2022] Open
Abstract
Background Transmitted drug resistance (TDR) is an important public health issue, because TDR-associated mutation may affect the outcome of antiretroviral treatment potentially or directly. Men who have sex with men (MSM) constitute a major risk group for HIV transmission. However, current reports are scarce on HIV TDR-associated mutations and their co-variation among MSM. Methods Blood samples from 262 newly diagnosed HIV-positive, antiretroviral therapy (ART)-naïve MSM, were collected from January 2011 and December 2013 in Beijing. The polymerase viral genes were sequenced to explore TDR-associated mutations and mutation co-variation. Results A total of 223 samples were sequenced and analyzed. Among them, HIV-1 CRF01_AE are accounted for 60.5%, followed by CRF07_BC (27.8%), subtype B (9.9%), and others. Fifty-seven samples had at least one TDR-associated mutation, mainly including L10I/V (6.3%), A71L/T/V (6.3%), V179D/E (5.4%), and V106I (2.7%), with different distributions of TDR-associated mutations by different HIV-1 subtypes and by each year. Moreover, eight significant co-variation pairs were found between TDR-associated mutations (V179D/E) and seven overlapping polymorphisms in subtype CRF01_AE. Conclusions To date, this work consists the most comprehensive genetic characterization of HIV-1 TDR-associated mutations prevalent among MSM. It provides important information for understanding TDR and viral evolution among Chinese MSM, a population currently at particularly high risk of HIV transmission. Electronic supplementary material The online version of this article (doi:10.1186/s12879-014-0689-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Jiao
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China. .,Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing, 100021, China.
| | - Shuming Li
- Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing, 100021, China.
| | - Zhenpeng Li
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
| | - Zheng Zhang
- Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing, 100021, China.
| | - Jianhong Zhao
- Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing, 100021, China.
| | - Li Li
- Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing, 100021, China.
| | - Lijuan Wang
- Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing, 100021, China.
| | - Qianqian Yin
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
| | - Yan Wang
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
| | - Zhaoli Zeng
- Beijing Chaoyang District Centre for Disease Control and Prevention, Beijing, 100021, China.
| | - Yiming Shao
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
| | - Liying Ma
- State Key Laboratory for Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
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7
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Evering TH, Kamau E, St Bernard L, Farmer CB, Kong XP, Markowitz M. Single genome analysis reveals genetic characteristics of Neuroadaptation across HIV-1 envelope. Retrovirology 2014; 11:65. [PMID: 25125210 PMCID: PMC4145222 DOI: 10.1186/s12977-014-0065-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/24/2014] [Indexed: 01/25/2023] Open
Abstract
Background The widespread use of highly effective, combination antiretroviral therapy (cART) has led to a significant reduction in the incidence of HIV-associated dementia (HAD). Despite these advances, the prevalence of HIV-1 associated neurocognitive disorders (HANDs) has been estimated at approximately 40%-50%. In the cART era, the majority of this disease burden is represented by asymptomatic neurocognitive impairment and mild neurocognitive disorder (ANI and MND respectively). Although less severe than HAD, these diagnoses carry with them substantial morbidity. Results In this cross-sectional study, single genome amplification (SGA) was used to sequence 717 full-length HIV-1 envelope (env) clade B variants from the paired cerebrospinal fluid (CSF) and blood plasma samples of fifteen chronically infected HIV-positive individuals with normal neurocognitive performance (NCN), ANI and MND. Various degrees of compartmentalization were found across disease states and history of cART utilization. In individuals with compartmentalized virus, mean HIV-1 env population diversity was lower in the CSF than plasma-derived variants. Overall, mean V1V2 loop length was shorter in CSF-derived quasispecies when compared to contemporaneous plasma populations, and this was found to correlate with a lower mean number of N-linked glycosylation sites in this region. A number of discrete amino acid positions that correlate strongly with compartmentalization in the CSF were identified in both variable and constant regions of gp120 as well as in gp41. Correlated mutation analyses further identified that a subset of amino acid residues in these compartmentalization “hot spot” positions were strongly correlated with one another, suggesting they may play an important, definable role in the adaptation of viral variants to the CSF. Analysis of these hot spots in the context of a well-supported crystal structure of HIV-1 gp120 suggests mechanisms through which amino acid differences at the identified residues might contribute to viral compartmentalization in the CSF. Conclusions The detailed analyses of SGA-derived full length HIV-1 env from subjects with both normal neurocognitive performance and the most common HAND diagnoses in the cART era allow us to identify novel and confirm previously described HIV-1 env genetic determinants of neuroadaptation and relate potential motifs to HIV-1 env structure and function. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0065-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Teresa H Evering
- Aaron Diamond AIDS Research Center, an affiliate of the Rockefeller University, New York, USA.
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