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Liu S, Hu M, Liu X, Liu X, Chen T, Zhu Y, Liang T, Xiao S, Li P, Ma X. Nanoparticles and Antiviral Vaccines. Vaccines (Basel) 2023; 12:30. [PMID: 38250843 PMCID: PMC10819235 DOI: 10.3390/vaccines12010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Viruses have threatened human lives for decades, causing both chronic and acute infections accompanied by mild to severe symptoms. During the long journey of confrontation, humans have developed intricate immune systems to combat viral infections. In parallel, vaccines are invented and administrated to induce strong protective immunity while generating few adverse effects. With advancements in biochemistry and biophysics, different kinds of vaccines in versatile forms have been utilized to prevent virus infections, although the safety and effectiveness of these vaccines are diverse from each other. In this review, we first listed and described major pathogenic viruses and their pandemics that emerged in the past two centuries. Furthermore, we summarized the distinctive characteristics of different antiviral vaccines and adjuvants. Subsequently, in the main body, we reviewed recent advances of nanoparticles in the development of next-generation vaccines against influenza viruses, coronaviruses, HIV, hepatitis viruses, and many others. Specifically, we described applications of self-assembling protein polymers, virus-like particles, nano-carriers, and nano-adjuvants in antiviral vaccines. We also discussed the therapeutic potential of nanoparticles in developing safe and effective mucosal vaccines. Nanoparticle techniques could be promising platforms for developing broad-spectrum, preventive, or therapeutic antiviral vaccines.
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Affiliation(s)
- Sen Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Meilin Hu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
| | - Xiaoqing Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xingyu Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
| | - Tao Chen
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
| | - Yiqiang Zhu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
| | - Taizhen Liang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
| | - Shiqi Xiao
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
| | - Peiwen Li
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
| | - Xiancai Ma
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou 510005, China; (S.L.); (M.H.); (X.L.); (X.L.); (T.C.); (Y.Z.); (T.L.); (S.X.); (P.L.)
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511400, China
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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Abstract
The reconstruction of genetic material of ancestral organisms constitutes a powerful application of evolutionary biology. A fundamental step in this inference is the ancestral sequence reconstruction (ASR), which can be performed with diverse methodologies implemented in computer frameworks. However, most of these methodologies ignore evolutionary properties frequently observed in microbes, such as genetic recombination and complex selection processes, that can bias the traditional ASR. From a practical perspective, here I review methodologies for the reconstruction of ancestral DNA and protein sequences, with particular focus on microbes, and including biases, recommendations, and software implementations. I conclude that microbial ASR is a complex analysis that should be carefully performed and that there is a need for methods to infer more realistic ancestral microbial sequences.
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Affiliation(s)
- Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
- Galicia Sur Health Research Institute (IIS Galicia Sur), Vigo, Spain.
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3
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Arenas M. ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation. Bioinformatics 2021; 38:58-64. [PMID: 34450622 PMCID: PMC8696103 DOI: 10.1093/bioinformatics/btab617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/24/2021] [Accepted: 08/24/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION The evolutionary processes of mutation and recombination, upon which selection operates, are fundamental to understand the observed molecular diversity. Unlike nucleotide sequences, the estimation of the recombination rate in protein sequences has been little explored, neither implemented in evolutionary frameworks, despite protein sequencing methods are largely used. RESULTS In order to accommodate this need, here I present a computational framework, called ProteinEvolverABC, to jointly estimate recombination and substitution rates from alignments of protein sequences. The framework implements the approximate Bayesian computation approach, with and without regression adjustments and includes a variety of substitution models of protein evolution, demographics and longitudinal sampling. It also implements several nuisance parameters such as heterogeneous amino acid frequencies and rate of change among sites and, proportion of invariable sites. The framework produces accurate coestimation of recombination and substitution rates under diverse evolutionary scenarios. As illustrative examples of usage, I applied it to several viral protein families, including coronaviruses, showing heterogeneous substitution and recombination rates. AVAILABILITY AND IMPLEMENTATION ProteinEvolverABC is freely available from https://github.com/miguelarenas/proteinevolverabc, includes a graphical user interface for helping the specification of the input settings, extensive documentation and ready-to-use examples. Conveniently, the simulations can run in parallel on multicore machines. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Del Amparo R, Branco C, Arenas J, Vicens A, Arenas M. Analysis of selection in protein-coding sequences accounting for common biases. Brief Bioinform 2021; 22:6105943. [PMID: 33479739 DOI: 10.1093/bib/bbaa431] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022] Open
Abstract
The evolution of protein-coding genes is usually driven by selective processes, which favor some evolutionary trajectories over others, optimizing the subsequent protein stability and activity. The analysis of selection in this type of genetic data is broadly performed with the metric nonsynonymous/synonymous substitution rate ratio (dN/dS). However, most of the well-established methodologies to estimate this metric make crucial assumptions, such as lack of recombination or invariable codon frequencies along genes, which can bias the estimation. Here, we review the most relevant biases in the dN/dS estimation and provide a detailed guide to estimate this metric using state-of-the-art procedures that account for such biases, along with illustrative practical examples and recommendations. We also discuss the traditional interpretation of the estimated dN/dS emphasizing the importance of considering complementary biological information such as the role of the observed substitutions on the stability and function of proteins. This review is oriented to help evolutionary biologists that aim to accurately estimate selection in protein-coding sequences.
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Affiliation(s)
- Roberto Del Amparo
- CINBIO (Biomedical Research Center), University of Vigo, 36310 Vigo, Spain.,Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Catarina Branco
- CINBIO (Biomedical Research Center), University of Vigo, 36310 Vigo, Spain.,Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Jesús Arenas
- Unit of Microbiology and Immunology, University of Zaragoza, 50013 Zaragoza, Spain
| | - Alberto Vicens
- CINBIO (Biomedical Research Center), University of Vigo, 36310 Vigo, Spain.,Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- CINBIO (Biomedical Research Center), University of Vigo, 36310 Vigo, Spain.,Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
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Gibson KM, Jair K, Castel AD, Bendall ML, Wilbourn B, Jordan JA, Crandall KA, Pérez-Losada M. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Sci Rep 2020; 10:1989. [PMID: 32029767 PMCID: PMC7004982 DOI: 10.1038/s41598-020-58410-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/31/2019] [Indexed: 11/08/2022] Open
Abstract
Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40-49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9-33.8% of the participants into clusters. HIV-TRACE grouped 2.9-12.8% of participants when using consensus sequences and 9.0-64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.
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Grants
- P30 AI117970 NIAID NIH HHS
- U01 AI069503 NIAID NIH HHS
- UM1 AI069503 NIAID NIH HHS
- This study was supported by the DC Cohort Study (U01 AI69503-03S2), a supplement from the Women’s Interagency Study for HIV-1 (410722_GR410708), a DC D-CFAR pilot award, and a 2015 HIV-1 Phylodynamics Supplement award from the District of Columbia for AIDS Research, an NIH funded program (AI117970), which is supported by the following NIH Co-Funding and Participating Institutes and Centers: NIAID, NCI, NICHD, NHLBI, NIDA, NIMH, NIA, FIC, NIGMS, NIDDK and OAR. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
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Affiliation(s)
- Keylie M Gibson
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA.
| | - Kamwing Jair
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Amanda D Castel
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Matthew L Bendall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Brittany Wilbourn
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Jeanne A Jordan
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Keith A Crandall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
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Del Amparo R, Vicens A, Arenas M. The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation. Bioinformatics 2020; 36:430-436. [PMID: 31304972 DOI: 10.1093/bioinformatics/btz558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The nonsynonymous/synonymous substitution rate ratio (dN/dS) is a commonly used parameter to quantify molecular adaptation in protein-coding data. It is known that the estimation of dN/dS can be biased if some evolutionary processes are ignored. In this concern, common ML methods to estimate dN/dS assume invariable codon frequencies among sites, despite this characteristic is rare in nature, and it could bias the estimation of this parameter. RESULTS Here we studied the influence of variable codon frequencies among genetic regions on the estimation of dN/dS. We explored scenarios varying the number of genetic regions that differ in codon frequencies, the amount of variability of codon frequencies among regions and the nucleotide frequencies at each codon position among regions. We found that ignoring heterogeneous codon frequencies among regions overall leads to underestimation of dN/dS and the bias increases with the level of heterogeneity of codon frequencies. Interestingly, we also found that varying nucleotide frequencies among regions at the first or second codon position leads to underestimation of dN/dS while variation at the third codon position leads to overestimation of dN/dS. Next, we present a methodology to reduce this bias based on the analysis of partitions presenting similar codon frequencies and we applied it to analyze four real datasets. We conclude that accounting for heterogeneous codon frequencies along sequences is required to obtain realistic estimates of molecular adaptation through this relevant evolutionary parameter. AVAILABILITY AND IMPLEMENTATION The applied frameworks for the computer simulations of protein-coding data and estimation of molecular adaptation are SGWE and PAML, respectively. Both are publicly available and referenced in the study. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Roberto Del Amparo
- Department of Biochemistry, Genetics and Immunology.,Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
| | - Alberto Vicens
- Department of Biochemistry, Genetics and Immunology.,Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology.,Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
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Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 63:346-359. [PMID: 28943406 PMCID: PMC5908768 DOI: 10.1016/j.meegid.2017.09.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/18/2022]
Abstract
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal; Children's National Medical Center, Washington, DC 20010, USA.
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago 8370146, Chile
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Chen M, Jia MH, Ma YL, Luo HB, Chen HC, Yang CJ, Dai J, Yang L, Dong LJ, Lu R, Song LJ, Han Y, Lu JY, Cheung AKL, Chen ZW, Lu L. The changing HIV-1 genetic characteristics and transmitted drug resistance among recently infected population in Yunnan, China. Epidemiol Infect 2018; 146:775-781. [PMID: 29534773 PMCID: PMC9134363 DOI: 10.1017/s0950268818000389] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/30/2017] [Accepted: 02/07/2018] [Indexed: 11/05/2022] Open
Abstract
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 (47.4%), unique recombinant forms (URFs) (18.2%), CRF01_AE (15.8%), CRF07_BC (14.4%), subtype C (2.7%), CRF55_01B (0.7%), subtype B (0.3%) and CRF64_BC (0.3%). CRF08_BC and CRF01_AE were the predominant genotypes among heterosexual and homosexual infections, respectively. CRF08_BC, URFs, CRF01_AE and CRF07_BC expanded with higher prevalence in central and eastern Yunnan. The recent common ancestor of CRF01_AE, CRF07_BC and CRF08_BC dated back to 1983.1, 1992.1 and 1989.5, respectively. The effective population sizes (EPS) for CRF01_AE and CRF07_BC increased exponentially during 1991-1999 and 1994-1999, respectively. The EPS for CRF08_BC underwent two exponential growth phases in 1994-1998 and 2001-2002. Lastly, TDR-associated mutations were identified in 1.8% of individuals. These findings not only enhance our understanding of HIV-1 evolution in Yunnan but also have implications for vaccine design and patient management strategies.
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Affiliation(s)
- M. Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - M. H. Jia
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Y. L. Ma
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - H. B. Luo
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - H. C. Chen
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - C. J. Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - J. Dai
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - L. Yang
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - L. J. Dong
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - R. Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - L. J. Song
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Y. Han
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - J. Y. Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - A. K. L. Cheung
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Z. W. Chen
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - L. Lu
- Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
- College of Public Health, Kunming Medical University, Kunming, Yunnan, China
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Gao Y, Wijewardhana C, Mann JFS. Virus-Like Particle, Liposome, and Polymeric Particle-Based Vaccines against HIV-1. Front Immunol 2018. [PMID: 29541072 PMCID: PMC5835502 DOI: 10.3389/fimmu.2018.00345] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
It is acknowledged that vaccines remain the best hope for eliminating the HIV-1 epidemic. However, the failure to produce effective vaccine immunogens and the inability of conventional delivery strategies to elicit the desired immune responses remains a central theme and has ultimately led to a significant roadblock in HIV vaccine development. Consequently, significant efforts have been applied to generate novel vaccine antigens and delivery agents, which mimic viral structures for optimal immune induction. Here, we review the latest developments that have occurred in the nanoparticle vaccine field, with special emphasis on strategies that are being utilized to attain highly immunogenic, systemic, and mucosal anti-HIV humoral and cellular immune responses. This includes the design of novel immunogens, the central role of antigen-presenting cells, delivery routes, and biodistribution of nanoparticles to lymph nodes. In particular, we will focus on virus-like-particle formulations and their preclinical uses within the HIV prophylactic vaccine setting.
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Affiliation(s)
- Yong Gao
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| | - Chanuka Wijewardhana
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
| | - Jamie F S Mann
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada
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10
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Pérez-Losada M, Castel AD, Lewis B, Kharfen M, Cartwright CP, Huang B, Maxwell T, Greenberg AE, Crandall KA. Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC. PLoS One 2017; 12:e0185644. [PMID: 28961263 PMCID: PMC5621693 DOI: 10.1371/journal.pone.0185644] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/16/2017] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Washington DC has a high burden of HIV with a 2.0% HIV prevalence. The city is a national and international hub potentially containing a broad diversity of HIV variants; yet few sequences from DC are available on GenBank to assess the evolutionary history of HIV in the US capital. Towards this general goal, here we analyze extensive sequence data and investigate HIV diversity, phylodynamics, and drug resistant mutations (DRM) in DC. METHODS Molecular HIV-1 sequences were collected from participants infected through 2015 as part of the DC Cohort, a longitudinal observational study of HIV+ patients receiving care at 13 DC clinics. Sequences were paired with Cohort demographic, risk, and clinical data and analyzed using maximum likelihood, Bayesian and coalescent approaches of phylogenetic, network and population genetic inference. We analyzed 601 sequences from 223 participants for int (~864 bp) and 2,810 sequences from 1,659 participants for PR/RT (~1497 bp). RESULTS Ninety-nine and 94% of the int and PR/RT sequences, respectively, were identified as subtype B, with 14 non-B subtypes also detected. Phylodynamic analyses of US born infected individuals showed that HIV population size varied little over time with no significant decline in diversity. Phylogenetic analyses grouped 13.5% of the int sequences into 14 clusters of 2 or 3 sequences, and 39.0% of the PR/RT sequences into 203 clusters of 2-32 sequences. Network analyses grouped 3.6% of the int sequences into 4 clusters of 2 sequences, and 10.6% of the PR/RT sequences into 76 clusters of 2-7 sequences. All network clusters were detected in our phylogenetic analyses. Higher proportions of clustered sequences were found in zip codes where HIV prevalence is highest (r = 0.607; P<0.00001). We detected a high prevalence of DRM for both int (17.1%) and PR/RT (39.1%), but only 8 int and 12 PR/RT amino acids were identified as under adaptive selection. We observed a significant (P<0.0001) association between main risk factors (men who have sex with men and heterosexuals) and genotypes in the five well-supported clusters with sufficient sample size for testing. DISCUSSION Pairing molecular data with clinical and demographic data provided novel insights into HIV population dynamics in Washington, DC. Identification of populations and geographic locations where clustering occurs can inform and complement active surveillance efforts to interrupt HIV transmission.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
- CIBIO-InBIO, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Amanda D. Castel
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Brittany Lewis
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Michael Kharfen
- District of Columbia Department of Health, Washington, DC, United States of America
| | | | - Bruce Huang
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Taylor Maxwell
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
| | - Alan E. Greenberg
- Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, The George Washington University, Washington, DC, United States of America
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Ashburn, VA, United States of America
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11
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Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. INFECTION GENETICS AND EVOLUTION 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
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12
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Chakravarthi PS, Ganta A, Kattimani VS, Tiwari RVC. Adult immunization-Need of the hour. J Int Soc Prev Community Dent 2016; 6:272-7. [PMID: 27583212 PMCID: PMC4981926 DOI: 10.4103/2231-0762.186797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Immunization is the process or the act of making individuals immune, which is usually done during childhood. Everyone is aware about immunization during childhood, however, very few know about adult immunization. This led us to review the adult immunization literature for the preventive strategies through various vaccination protocols. Adults do require vaccination protocols with booster doses for hepatitis B, Shingles, communicable diseases, traveler's diseases, etc. In this context, this article revises much of the available adult immunization literature and presents comprehensive guidelines. This article will increase the awareness regarding the importance of vaccination for adults to prevent a variety of conditions prevalent in our country as well as epidemics. The article comprehensively provides insights into the available vaccination and preventive strategy of human papilloma virus (HPV), hepatitis, and human immunodeficiency virus (HIV) infection in this part of the review. We strongly recommend all the health care professionals to educate their co-professionals and the public to use the benefits of adult immunization. It is the need of the hour and reduces the burden of treatment and increases productivity.
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Affiliation(s)
- P Srinivas Chakravarthi
- Department of Oral and Maxillofacial Surgery, Sibar Institute of Dental Sciences, Andhra Pradesh, India
| | - Avani Ganta
- Department of Internal Medicine, Division of Allergy Immunology and Gastroenterology, Tufts Medical Center, Boston, Masachuttes, United States of America
| | - Vivekanand S Kattimani
- Department of Oral and Maxillofacial Surgery, Sibar Institute of Dental Sciences, Andhra Pradesh, India
| | - Rahul V C Tiwari
- Department of Oral and Maxillofacial Surgery, Sibar Institute of Dental Sciences, Andhra Pradesh, India
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13
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Hait SH, Soares EA, Sprinz E, Arthos J, Machado ES, Soares MA. Worldwide Genetic Features of HIV-1 Env α4β7 Binding Motif: The Local Dissemination Impact of the LDI Tripeptide. J Acquir Immune Defic Syndr 2016; 70:463-71. [PMID: 26569174 DOI: 10.1097/qai.0000000000000802] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND HIV-1 gp120 binds to integrin α4β7, a homing receptor of lymphocytes to gut-associated lymphoid tissues. This interaction is mediated by the LDI/V tripeptide encoded in the V2-loop. This tripeptide mimics similar motifs in mucosal addressin cellular adhesion molecule (MAdCAM) and vascular CAM (VCAM), the natural ligands of α4β7. In this study, we explored the association of V2-loop LDI/V mimotopes with transmission routes and patterns of disease progression in HIV-infected adult and pediatric patients. HIV-1 env sequences available in the Los Alamos HIV Sequence database were included in the analyses. METHODS HIV-1 V2-loop sequences generated from infected adults and infants from South and Southeast Brazil, and also retrieved from the Los Alamos database, were assessed for α4β7 binding tripeptide composition. Chi-Square/Fisher Exact test and Mann Whitney U test were used for tripeptide comparisons. Shannon entropy was assessed for conservancy of the α4β7 tripeptide mimotope. RESULTS We observed no association between the tripeptide composition or conservation and virus transmission route or disease progression. However, LDI was linked to successful epidemic dissemination of HIV-1 subtype C in South America, and further to other expanding non-B subtypes in Europe and Asia. In Africa, subtypes showing increased LDV prevalence evidenced an ongoing process of selection toward LDI expansion, an observation also extended to subtype B in the Americas and Western Europe. CONCLUSIONS The V2-loop LDI mimotope was conserved in HIV-1C from South America and other expanding subtypes across the globe, which suggests that LDI may promote successful dissemination of HIV at local geographic levels by means of increased transmission fitness.
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Affiliation(s)
- Sabrina H Hait
- *Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; †Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; ‡Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Rio Grande do Sul, Brazil; §Laboratory of Immune Regulation, National Institutes of Health, Bethesda, MD; and ‖Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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14
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Arenas M. Trends in substitution models of molecular evolution. Front Genet 2015; 6:319. [PMID: 26579193 PMCID: PMC4620419 DOI: 10.3389/fgene.2015.00319] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/09/2015] [Indexed: 11/13/2022] Open
Abstract
Substitution models of evolution describe the process of genetic variation through fixed mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost 40 years after the development of first substitution models, highly sophisticated, and data-specific substitution models continue emerging with the aim of better mimicking real evolutionary processes. Here I describe current trends in substitution models of DNA, codon and amino acid sequence evolution, including advantages and pitfalls of the most popular models. The perspective concludes that despite the large number of currently available substitution models, further research is required for more realistic modeling, especially for DNA coding and amino acid data. Additionally, the development of more accurate complex models should be coupled with new implementations and improvements of methods and frameworks for substitution model selection and downstream evolutionary analysis.
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Affiliation(s)
- Miguel Arenas
- Institute of Molecular Pathology and Immunology of the University of Porto Porto, Portugal
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15
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Arenas M, Lorenzo-Redondo R, Lopez-Galindez C. Influence of mutation and recombination on HIV-1 in vitro fitness recovery. Mol Phylogenet Evol 2015; 94:264-70. [PMID: 26358613 DOI: 10.1016/j.ympev.2015.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 10/23/2022]
Abstract
The understanding of the evolutionary processes underlying HIV-1 fitness recovery is fundamental for HIV-1 pathogenesis, antiretroviral treatment and vaccine design. It is known that HIV-1 can present very high mutation and recombination rates, however the specific contribution of these evolutionary forces in the "in vitro" viral fitness recovery has not been simultaneously quantified. To this aim, we analyzed substitution, recombination and molecular adaptation rates in a variety of HIV-1 biological clones derived from a viral isolate after severe population bottlenecks and a number of large population cell culture passages. These clones presented an overall but uneven fitness gain, mean of 3-fold, respect to the initial passage values. We found a significant relationship between the fitness increase and the appearance and fixation of mutations. In addition, these fixed mutations presented molecular signatures of positive selection through the accumulation of non-synonymous substitutions. Interestingly, viral recombination correlated with fitness recovery in most of studied viral quasispecies. The genetic diversity generated by these evolutionary processes was positively correlated with the viral fitness. We conclude that HIV-1 fitness recovery can be derived from the genetic heterogeneity generated through both mutation and recombination, and under diversifying molecular adaptation. The findings also suggest nonrandom evolutionary pathways for in vitro fitness recovery.
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Affiliation(s)
- Miguel Arenas
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | - Ramon Lorenzo-Redondo
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Cecilio Lopez-Galindez
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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16
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Glycans flanking the hypervariable connecting peptide between the A and B strands of the V1/V2 domain of HIV-1 gp120 confer resistance to antibodies that neutralize CRF01_AE viruses. PLoS One 2015; 10:e0119608. [PMID: 25793890 PMCID: PMC4368187 DOI: 10.1371/journal.pone.0119608] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 02/01/2015] [Indexed: 11/30/2022] Open
Abstract
Understanding the molecular determinants of sensitivity and resistance to neutralizing antibodies is critical for the development of vaccines designed to prevent HIV infection. In this study, we used a genetic approach to characterize naturally occurring polymorphisms in the HIV envelope protein that conferred neutralization sensitivity or resistance. Libraries of closely related envelope genes, derived from virus quasi-species, were constructed from individuals infected with CRF01_AE viruses. The libraries were screened with plasma containing broadly neutralizing antibodies, and neutralization sensitive and resistant variants were selected for sequence analysis. In vitro mutagenesis allowed us to identify single amino acid changes in three individuals that conferred resistance to neutralization by these antibodies. All three mutations created N-linked glycosylation sites (two at N136 and one at N149) proximal to the hypervariable connecting peptide between the C-terminus of the A strand and the N-terminus of the B strand in the four-stranded V1/V2 domain β-sheet structure. Although N136 has previously been implicated in the binding of broadly neutralizing monoclonal antibodies, this glycosylation site appears to inhibit the binding of neutralizing antibodies in plasma from HIV-1 infected subjects. Previous studies have reported that the length of the V1/V2 domain in transmitted founder viruses is shorter and possesses fewer glycosylation sites compared to viruses isolated from chronic infections. Our results suggest that vaccine immunogens based on recombinant envelope proteins from clade CRF01_AE viruses might be improved by inclusion of envelope proteins that lack these glycosylation sites. This strategy might improve the efficacy of the vaccines used in the partially successful RV144 HIV vaccine trial, where the two CRF01_AE immunogens (derived from the A244 and TH023 isolates) both possessed glycosylation sites at N136 and N149.
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17
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Du S, Wang Y, Liu C, Wang M, Zhu Y, Tan P, Ren D, Li X, Tian M, Yin R, Li C, Jin N. Immunogenicity and virulence of attenuated vaccinia virus Tian Tan encoding HIV-1 muti-epitope genes, p24 and cholera toxin B subunit in mice. J Virol Methods 2015; 219:1-9. [PMID: 25796990 DOI: 10.1016/j.jviromet.2015.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/16/2015] [Accepted: 03/12/2015] [Indexed: 11/19/2022]
Abstract
No effective prophylactic or therapeutic vaccine against HIV-1 in humans is currently available. This study analyzes the immunogenicity and safety of a recombinant attenuated vaccinia virus. A chimeric gene of HIV-1 multi-epitope genes containing CpG ODN and cholera toxin B subunit (CTB) was inserted into Chinese vaccinia virus Tian Tan strain (VTT) mutant strain. The recombinant virus rddVTT(-CCMp24) was assessed for immunogenicity and safety in mice. Results showed that the protein CCMp24 was expressed stably in BHK-21 infected with rddVTT(-CCMp24). And the recombinant virus induced the production of HIV-1 p24 specific immunoglobulin G (IgG), IL-2 and IL-4. The recombinant vaccine induced γ-interferon secretion against HIV peptides, and elicited a certain levels of immunological memory. Results indicated that the recombinant virus had certain immunogenicity to HIV-1. Additionally, the virulence of the recombinant virus was been attenuated in vivo of mice compared with wild type VTT (wtVTT), and the introduction of CTB and HIV Mp24 did not alter the infectivity and virulence of defective vaccinia virus.
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Affiliation(s)
- Shouwen Du
- College of Veterinary Medicine, Jilin University, Changchun 130062, China; Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China
| | - Yuhang Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China; Changchun Bioxun Biotech Co., Ltd., Changchun 130122, China
| | - Cunxia Liu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China
| | - Maopeng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China
| | - Yilong Zhu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China
| | - Peng Tan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China
| | - Dayong Ren
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China
| | - Xiao Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China
| | - Mingyao Tian
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China
| | - Ronglan Yin
- Academy of Animal Science and Veterinary Medicine in Jilin Province, Changchun 130062, China
| | - Chang Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China.
| | - Ningyi Jin
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, AMMS, Changchun 130122, China.
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18
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Pérez-Losada M, Arenas M, Galán JC, Palero F, González-Candelas F. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:296-307. [PMID: 25541518 PMCID: PMC7106159 DOI: 10.1016/j.meegid.2014.12.022] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 02/08/2023]
Abstract
Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major areas in the evolutionary analysis of viral populations on which recombination has an impact. These include the evaluation of selective pressures acting on viral populations, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure.
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Affiliation(s)
- Marcos Pérez-Losada
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Portugal; Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA
| | - Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública, Spain
| | - Ferran Palero
- CIBER en Epidemiología y Salud Pública, Spain; Unidad Mixta Infección y Salud Pública, FISABIO-Universitat de València, Valencia, Spain
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Spain; Unidad Mixta Infección y Salud Pública, FISABIO-Universitat de València, Valencia, Spain.
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19
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Padhi A, Ma L. Genetic and epidemiological insights into the emergence of peste des petits ruminants virus (PPRV) across Asia and Africa. Sci Rep 2014; 4:7040. [PMID: 25391314 PMCID: PMC4229660 DOI: 10.1038/srep07040] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 10/27/2014] [Indexed: 11/09/2022] Open
Abstract
Small ruminants are important components in the livelihood of millions of households in many parts of the world. The spread of the highly contagious peste des petits ruminants (PPR) disease, which is caused by an RNA virus, PPRV, across Asia and Africa remains a major concern. The present study explored the evolutionary and epidemiological dynamics of PPRV through the analyses of partial N-gene and F-gene sequences of the virus. All the four previously described PPRV lineages (I-IV) diverged from their common ancestor during the late-19(th) to early-20(th) century. Among the four lineages, PPRV-IV showed pronounced genetic structuring across the region; however, haplotype sharing among the geographic regions, together with the presence of multiple genetic clusters within a country, indicates the possibility of frequent mobility of the diseased individuals across the region. The gradual decline in the effective number of infections suggests a limited genetic variation, which could be attributed to the effective vaccination that has been practiced since 1990s. However, the movement of infected animals across the region likely contributes to the spread of PPRV-IV. No evidence of positive selection was identified from this study.
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Affiliation(s)
- Abinash Padhi
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD-20742, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD-20742, USA
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20
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Benguigui M, Arenas M. Spatial and temporal simulation of human evolution. Methods, frameworks and applications. Curr Genomics 2014; 15:245-55. [PMID: 25132795 PMCID: PMC4133948 DOI: 10.2174/1389202915666140506223639] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/05/2014] [Accepted: 05/04/2014] [Indexed: 01/29/2023] Open
Abstract
Analyses of human evolution are fundamental to understand the current gradients of human diversity. In this concern, genetic samples collected from current populations together with archaeological data are the most important resources to study human evolution. However, they are often insufficient to properly evaluate a variety of evolutionary scenarios, leading to continuous debates and discussions. A commonly applied strategy consists of the use of computer simulations based on, as realistic as possible, evolutionary models, to evaluate alternative evolutionary scenarios through statistical correlations with the real data. Computer simulations can also be applied to estimate evolutionary parameters or to study the role of each parameter on the evolutionary process. Here we review the mainly used methods and evolutionary frameworks to perform realistic spatially explicit computer simulations of human evolution. Although we focus on human evolution, most of the methods and software we describe can also be used to study other species. We also describe the importance of considering spatially explicit models to better mimic human evolutionary scenarios based on a variety of phenomena such as range expansions, range shifts, range contractions, sex-biased dispersal, long-distance dispersal or admixtures of populations. We finally discuss future implementations to improve current spatially explicit simulations and their derived applications in human evolution.
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Affiliation(s)
- Macarena Benguigui
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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21
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Doyle VP, Andersen JJ, Nelson BJ, Metzker ML, Brown JM. Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster. Mol Phylogenet Evol 2014; 75:126-37. [PMID: 24589520 DOI: 10.1016/j.ympev.2014.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 11/28/2022]
Abstract
Stochastic models of sequence evolution have been developed to reflect many biologically important processes, allowing for accurate phylogenetic reconstruction when an appropriate model is selected. However, commonly used models do not incorporate several potentially important biological processes. Spurious phylogenetic inference may result if these processes play an important role in the evolution of a dataset yet are not incorporated into assumed models. Few studies have attempted to assess the relative importance of multiple processes in producing spurious inferences. The application of phylogenetic methods to infer the source of HIV-1 transmission clusters depends upon accurate phylogenetic results, yet there are several relevant unmodeled biological processes (e.g., recombination and convergence) that may cause complications. Here, through analyses of HIV-1 env sequences from a small, forensically important transmission cluster, we tease apart the impact of these processes and present evidence suggesting that convergent evolution and high rates of insertions and deletions (causing alignment uncertainty) led to spurious phylogenetic signal with forensic relevance. Previous analyses show paraphyly of HIV-1 lineages sampled from an individual who, based on non-phylogenetic evidence, had never acted as a source of infection for others in this transmission cluster. If true, this pattern calls into question assumptions underlying phylogenetic approaches to source and recipient identification. By systematically assessing the contribution of different unmodeled processes, we demonstrate that removal of sites likely influenced by strong positive selection both reduces the alignment-wide signal supporting paraphyly of viruses sampled from this individual and eliminates support for the effects of recombination. Additionally, the removal of ambiguously aligned sites alters strongly supported relationships among viruses sampled from different individuals. These observations highlight the need to jointly consider multiple unmodeled evolutionary processes and motivate a phylogenomic perspective when inferring viral transmission histories.
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Affiliation(s)
- Vinson P Doyle
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - John J Andersen
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Bradley J Nelson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Michael L Metzker
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, and Cell and Molecular Biology Program, Baylor College of Medicine, Houston, TX, USA
| | - Jeremy M Brown
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
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22
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Novitsky V, Bussmann H, Logan A, Moyo S, van Widenfelt E, Okui L, Mmalane M, Baca J, Buck L, Phillips E, Tim D, McLane MF, Lei Q, Wang R, Makhema J, Lockman S, DeGruttola V, Essex M. Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana. PLoS One 2013; 8:e80589. [PMID: 24349005 PMCID: PMC3859477 DOI: 10.1371/journal.pone.0080589] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/04/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Determining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities. METHODS To reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C env sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010-2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C env sequences and bootstrap support of splits. RESULTS The overall proportion of clustered HIV-1C env sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non-Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters. CONCLUSIONS The study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages.
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Affiliation(s)
- Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | | | - Andrew Logan
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Lillian Okui
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Mompati Mmalane
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Jeannie Baca
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Lauren Buck
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Eleanor Phillips
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - David Tim
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Mary Fran McLane
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Quanhong Lei
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Rui Wang
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph Makhema
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Shahin Lockman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Victor DeGruttola
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - M. Essex
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Arenas M. The importance and application of the ancestral recombination graph. Front Genet 2013; 4:206. [PMID: 24133504 PMCID: PMC3796270 DOI: 10.3389/fgene.2013.00206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 09/24/2013] [Indexed: 11/13/2022] Open
Affiliation(s)
- Miguel Arenas
- Centre for Molecular Biology “Severo Ochoa,” Consejo Superior de Investigaciones Científicas, Universidad Autónoma de MadridMadrid, Spain
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24
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Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions. AIDS 2013; 27:1045-57. [PMID: 23902920 DOI: 10.1097/qad.0b013e32835cffd9] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Arenas M. Computer programs and methodologies for the simulation of DNA sequence data with recombination. Front Genet 2013; 4:9. [PMID: 23378848 PMCID: PMC3561691 DOI: 10.3389/fgene.2013.00009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/17/2013] [Indexed: 11/13/2022] Open
Abstract
Computer simulations are useful in evolutionary biology for hypothesis testing, to verify analytical methods, to analyze interactions among evolutionary processes, and to estimate evolutionary parameters. In particular, the simulation of DNA sequences with recombination may help in understanding the role of recombination in diverse evolutionary questions, such as the genome structure. Consequently, plenty of computer simulators have been developed to simulate DNA sequence data with recombination. However, the choice of an appropriate tool, among all currently available simulators, is critical if recombination simulations are to be biologically meaningful. This review provides a practical survival guide to commonly used computer programs and methodologies for the simulation of coding and non-coding DNA sequences with recombination. It may help in the correct design of computer simulation experiments of recombination. In addition, the study includes a review of simulation studies investigating the impact of ignoring recombination when performing various evolutionary analyses, such as phylogenetic tree and ancestral sequence reconstructions. Alternative analytical methodologies accounting for recombination are also reviewed.
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Affiliation(s)
- Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa," Consejo Superior de Investigaciones Científicas Madrid, Spain
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26
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Population-Sequencing as a Biomarker for Sample Characterization. J Biomark 2013; 2013:861823. [PMID: 26317024 PMCID: PMC4437355 DOI: 10.1155/2013/861823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 10/10/2013] [Indexed: 11/27/2022] Open
Abstract
Sequencing is accepted as the “gold” standard for genetic analysis and continues to be used as a validation and reference tool. The idea of using sequence analysis directly for sample characterization has been met with skepticism. However, herein, utility of direct use of sequencing to identify multiple genomes present in samples is presented and reviewed. All samples and “pure” isolates are populations of genomes. Population-Sequencing is the use of probabilistic matching tools in combination with large volumes of sequence information to identify genomes present, based on DNA analysis across entire genomes to determine genome assignments, to calculate confidence scores of major and minor genome content. Accurate genome identification from mixtures without culture purification steps can achieve phylogenetic classification by direct analysis of millions of DNA fragments. Genome sequencing data of mixtures can function as biomarkers for use to interrogate genetic content of samples and to establish a sample profile, inclusive of major and minor genome components, drill down to identify rare SNP and mutation events, compare relatedness of genetic content between samples, profile-to-profile, and provide a probabilistic or statistical scoring confidence for sample characterization and attribution. The application of Population-Sequencing will facilitate sample characterization and genome identification strategies.
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27
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Castro-Nallar E, Pérez-Losada M, Burton GF, Crandall KA. The evolution of HIV: inferences using phylogenetics. Mol Phylogenet Evol 2012; 62:777-92. [PMID: 22138161 PMCID: PMC3258026 DOI: 10.1016/j.ympev.2011.11.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 12/02/2022]
Abstract
Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).
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Affiliation(s)
- Eduardo Castro-Nallar
- Department of Biology, 401 Widtsoe Building, Brigham Young University, Provo, UT 84602-5181, USA.
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28
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Eshleman SH, Hudelson SE, Redd AD, Wang L, Debes R, Chen YQ, Martens CA, Ricklefs SM, Selig EJ, Porcella SF, Munshaw S, Ray SC, Piwowar-Manning E, McCauley M, Hosseinipour MC, Kumwenda J, Hakim JG, Chariyalertsak S, de Bruyn G, Grinsztejn B, Kumarasamy N, Makhema J, Mayer KH, Pilotto J, Santos BR, Quinn TC, Cohen MS, Hughes JP. Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial. J Infect Dis 2011; 204:1918-26. [PMID: 21990420 DOI: 10.1093/infdis/jir651] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The HIV Prevention Trials Network (HPTN) 052 trial demonstrated that early initiation of antiretroviral therapy (ART) reduces human immunodeficiency virus (HIV) transmission from HIV-infected adults (index participants) to their HIV-uninfected sexual partners. We analyzed HIV from 38 index-partner pairs and 80 unrelated index participants (controls) to assess the linkage of seroconversion events. METHODS Linkage was assessed using phylogenetic analysis of HIV pol sequences and Bayesian analysis of genetic distances between pol sequences from index-partner pairs and controls. Selected samples were also analyzed using next-generation sequencing (env region). RESULTS In 29 of the 38 (76.3%) cases analyzed, the index was the likely source of the partner's HIV infection (linked). In 7 cases (18.4%), the partner was most likely infected from a source other than the index participant (unlinked). In 2 cases (5.3%), linkage status could not be definitively established. CONCLUSIONS Nearly one-fifth of the seroconversion events in HPTN 052 were unlinked. The association of early ART and reduced HIV transmission was stronger when the analysis included only linked events. This underscores the importance of assessing the genetic linkage of HIV seroconversion events in HIV prevention studies involving serodiscordant couples.
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Affiliation(s)
- Susan H Eshleman
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA.
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