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Chen M, Chen H, Dai J, Dong L, Ma Y, Jia M. Identification of a Novel HIV-1 Circulating Recombinant Form (CRF150_Cpx) Among Men Who Have Sex with Men in China. AIDS Res Hum Retroviruses 2024. [PMID: 39113542 DOI: 10.1089/aid.2024.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024] Open
Abstract
Recent studies have reported increasing complexity in human immunodeficiency virus 1 (HIV-1) genotypes among men who have sex with men (MSM) in China. In an HIV-1 molecular epidemiological study conducted among MSM in Yunnan Province, China, we discovered that four samples could potentially represent a circulating recombinant form (CRF). In this study, we conducted further analysis on their nearly full-length genome (NFLG) sequences. The NFLG sequences formed a distinct monophyletic clade in the phylogenetic tree. Recombination analysis indicated that the four sequences were constructed upon the backbone of CRF149_01B, with the insertion of three CRF07_BC fragments. Consequently, they were designated as CRF150_cpx. Evolutionary analyses suggested that CRF150_cpx emerged between approximately 2014 and 2015. The identification of new CRFs not only deepens our understanding of HIV recombination but also aids in comprehending the prevalence and transmission history of HIV among specific populations.
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Affiliation(s)
- Min Chen
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Health Laboratory Center, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Huichao Chen
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Jie Dai
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Lijuan Dong
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Yanling Ma
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Manhong Jia
- Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China
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2
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Lebedev A, Kim K, Ozhmegova E, Antonova A, Kazennova E, Tumanov A, Kuznetsova A. Rev Protein Diversity in HIV-1 Group M Clades. Viruses 2024; 16:759. [PMID: 38793640 PMCID: PMC11125641 DOI: 10.3390/v16050759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The HIV-1 Rev protein expressed in the early stage of virus replication is involved in the nuclear export of some forms of virus RNA. Naturally occurring polymorphisms in the Rev protein could influence its activity. The association between the genetic features of different virus variants and HIV infection pathogenesis has been discussed for many years. In this study, Rev diversity among HIV-1 group M clades was analyzed to note the signatures that could influence Rev activity and, subsequently, clinical characteristics. From the Los Alamos HIV Sequence Database, 4962 Rev sequences were downloaded and 26 clades in HIV-1 group M were analyzed for amino acid changes, conservation in consensus sequences, and the presence of clade-specific amino acid substitutions (CSSs) and the Wu-Kabat protein variability coefficient (WK). Subtypes G, CRF 02_AG, B, and A1 showed the largest amino acid changes and diversity. The mean conservation of the Rev protein was 80.8%. In consensus sequences, signatures that could influence Rev activity were detected. In 15 out of 26 consensus sequences, an insertion associated with the reduced export activity of the Rev protein, 95QSQGTET96, was identified. A total of 32 CSSs were found in 16 clades, wherein A6 had the 41Q substitution in the functionally significant region of Rev. The high values of WK coefficient in sites 51 and 82, located on the Rev interaction surface, indicate the susceptibility of these positions to evolutionary replacements. Thus, the noted signatures require further investigation.
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Affiliation(s)
- Aleksey Lebedev
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
- Mechnikov Scientific Research Institute of Vaccines and Serums, 105064 Moscow, Russia
| | - Kristina Kim
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Ekaterina Ozhmegova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Anastasiia Antonova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Elena Kazennova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Aleksandr Tumanov
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Anna Kuznetsova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
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3
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Zani A, Messali S, Bugatti A, Uggeri M, Rondina A, Sclavi L, Caccuri F, Caruso A. Molecular mechanisms behind the generation of pro-oncogenic HIV-1 matrix protein p17 variants. J Gen Virol 2024; 105. [PMID: 38687324 DOI: 10.1099/jgv.0.001982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
HIV-1 matrix protein p17 variants (vp17s), characterized by amino acid insertions at the COOH-terminal region of the viral protein, have been recently identified and studied for their biological activity. Different from their wild-type counterpart (refp17), vp17s display a potent B cell growth and clonogenic activity. Recent data have highlighted the higher prevalence of vp17s in people living with HIV-1 (PLWH) with lymphoma compared with those without lymphoma, suggesting that vp17s may play a key role in lymphomagenesis. Molecular mechanisms involved in vp17 development are still unknown. Here we assessed the efficiency of HIV-1 Reverse Transcriptase (RT) in processing this genomic region and highlighted the existence of hot spots of mutation in Gag, at the end of the matrix protein and close to the matrix-capsid junction. This is possibly due to the presence of inverted repeats and palindromic sequences together with a high content of Adenine in the 322-342 nucleotide portion, which constrain HIV-1 RT to pause on the template. To define the recombinogenic properties of hot spots of mutation in the matrix gene, we developed plasmid vectors expressing Gag and a minimally modified Gag variant, and measured homologous recombination following cell co-nucleofection by next-generation sequencing. Data obtained allowed us to show that a wide range of recombination events occur in concomitance with the identified hot spots of mutation and that imperfect events may account for vp17s generation.
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Affiliation(s)
- Alberto Zani
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Serena Messali
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Antonella Bugatti
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Matteo Uggeri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandro Rondina
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Leonardo Sclavi
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Center for Advanced Medical and Pharmaceutical Research (CCAMF), George Emil Palade University of Medicine, Pharmacy, Science and Technology, Târgu Mures, Romania
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Center for Advanced Medical and Pharmaceutical Research (CCAMF), George Emil Palade University of Medicine, Pharmacy, Science and Technology, Târgu Mures, Romania
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4
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Switzer WM, Shankar A, Jia H, Knyazev S, Ambrosio F, Kelly R, Zheng H, Campbell EM, Cintron R, Pan Y, Saduvala N, Panneer N, Richman R, Singh MB, Thoroughman DA, Blau EF, Khalil GM, Lyss S, Heneine W. High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA. Virus Evol 2024; 10:veae015. [PMID: 38510920 PMCID: PMC10953796 DOI: 10.1093/ve/veae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/22/2024] Open
Abstract
We investigated transmission dynamics of a large human immunodeficiency virus (HIV) outbreak among persons who inject drugs (PWID) in KY and OH during 2017-20 by using detailed phylogenetic, network, recombination, and cluster dating analyses. Using polymerase (pol) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including Subtype B (44.6 per cent); numerous circulating recombinant forms (CRFs) including CRF02_AG (2.5 per cent) and CRF02_AG-like (21.8 per cent); and many unique recombinant forms composed of CRFs with major subtypes and sub-subtypes [CRF02_AG/B (24.3 per cent), B/CRF02_AG/B (0.5 per cent), and A6/D/B (6.4 per cent)]. Cluster analysis of sequences using a 1.5 per cent genetic distance identified thirteen clusters, including a seventy-five-member cluster composed of CRF02_AG-like and CRF02_AG/B, an eighteen-member CRF02_AG/B cluster, Subtype B clusters of sizes ranging from two to twenty-three, and a nine-member A6/D and A6/D/B cluster. Recombination and phylogenetic analyses identified CRF02_AG/B variants with ten unique breakpoints likely originating from Subtype B and CRF02_AG-like viruses in the largest clusters. The addition of contact tracing results from OH to the genetic networks identified linkage between persons with Subtype B, CRF02_AG, and CRF02_AG/B sequences in the clusters supporting de novo recombinant generation. Superinfection prevalence was 13.3 per cent (8/60) in persons with multiple specimens and included infection with B and CRF02_AG; B and CRF02_AG/B; or B and A6/D/B. In addition to the presence of multiple, distinct molecular clusters associated with this outbreak, cluster dating inferred transmission associated with the largest molecular cluster occurred as early as 2006, with high transmission rates during 2017-8 in certain other molecular clusters. This outbreak among PWID in KY and OH was likely driven by rapid transmission of multiple HIV-1 variants including de novo viral recombinants from circulating viruses within the community. Our findings documenting the high HIV-1 transmission rate and clustering through partner services and molecular clusters emphasize the importance of leveraging multiple different data sources and analyses, including those from disease intervention specialist investigations, to better understand outbreak dynamics and interrupt HIV spread.
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Affiliation(s)
- William M Switzer
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Anupama Shankar
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Hongwei Jia
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Sergey Knyazev
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- Oak Ridge Institute for Science and Education, 1299 Bethel Valley Rd, Oak Ridge, TN 37830, USA
| | - Frank Ambrosio
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Reagan Kelly
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- General Dynamics Information Technology, 3150 Fairview Park Dr, Falls Church, VA 22042, USA
| | - HaoQiang Zheng
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | | | - Roxana Cintron
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Yi Pan
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | | | - Nivedha Panneer
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Rhiannon Richman
- HIV Surveillance Program, Bureau of HIV/STI/Viral Hepatitis, Ohio Department of Health, 246 North High Street, Colombus, OH 43215, USA
| | - Manny B Singh
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
| | - Douglas A Thoroughman
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- ORR/Division of State and Local Readiness/Field Services Branch/CEFO Program, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Erin F Blau
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- Epidemic Intelligence Service, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - George M Khalil
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Sheryl Lyss
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- HIV Surveillance Program, Bureau of HIV/STI/Viral Hepatitis, Ohio Department of Health, 246 North High Street, Colombus, OH 43215, USA
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- Hamilton County Public Health, 250 William Howard Taft Rd, Cincinnati, OH 45219, USA
- Northern Kentucky Health Department, 8001 Veterans Memorial Drive, Florence, KY 41042, USA
| | - Walid Heneine
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
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5
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Rashid A, Kang L, Yi F, Mir F, Getaneh Y, Shao Y, Abidi SH. Characterization of HIV-1 CRF02_AG/A3/G unique recombinant forms identified among children in Larkana, Pakistan. Front Cell Infect Microbiol 2023; 13:1284815. [PMID: 37965253 PMCID: PMC10642767 DOI: 10.3389/fcimb.2023.1284815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Co-circulation of different human immunodeficiency virus type 1 HIV-1 subtypes among infected populations can lead to the generation of new recombinants. In Pakistan, subtype A1 and CRF02_AG are the dominant strains circulating among key populations. The high prevalence of new HIV infections among the key populations highlights the possibility of recombination between the dominant strains, which can lead to the generation of new recombinants. Here, we identified a recombinant cluster composed of CRF02_AG, sub-subtype A3, and subtype G among HIV-infected children in Larkana. For the study, 10 retrospectively collected samples, with recombination signals in the pol gene, were used to perform a near full-length genome NFLG sequencing. Of the 10 samples, NFLG was successfully sequenced from seven samples. Phylogenetic analysis of the seven NFLGs showed that all recombinants formed a distinct monophyletic cluster and were distinct from known HIV-1 circulating recombinant forms CRFs. Recombination analyses showed that all seven NFLGs shared a similar recombinant structure consisting of CRF02_AG, sub-subtype A3, and subtype G, with a sub-subtype A3 fragment inserted into pol and vif regions spanning from (HXB2: 4218-5518), and a subtype G fragment inserted into vpu, rev, tat and env regions spanning from (HXB2: 5957-8250) of the CRF02_AG backbone. The identification of unique recombinant forms may indicate the presence and transmission of several co-circulating lineages in Larkana, giving rise to newer CRFs. This study also highlights the importance of continuous molecular surveillance to fully understand HIV-1 genetic diversity in Pakistan, particularly in Larkana, which is the epicenter of HIV outbreaks.
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Affiliation(s)
- Abdur Rashid
- School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Kang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Feng Yi
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fatima Mir
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Yimam Getaneh
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Changping Laboratory, Beijing, China
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan
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6
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Zhang YN, Paynter J, Antanasijevic A, Allen JD, Eldad M, Lee YZ, Copps J, Newby ML, He L, Chavez D, Frost P, Goodroe A, Dutton J, Lanford R, Chen C, Wilson IA, Crispin M, Ward AB, Zhu J. Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimmers as HIV-1 vaccine candidates. Nat Commun 2023; 14:1985. [PMID: 37031217 PMCID: PMC10082823 DOI: 10.1038/s41467-023-37742-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/29/2023] [Indexed: 04/10/2023] Open
Abstract
Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. For 1c-SApNPs, glycan trimming improves recognition of the CD4 binding site without affecting broadly neutralizing antibodies (bNAbs) to major glycan epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increases the frequency of vaccine responders (FVR) and steers antibody responses away from immunodominant glycan holes and glycan patches. The mechanism of vaccine-induced immunity is examined in mice. Compared with the UFO trimer, the multilayered E2p and I3-01v9 1c-SApNPs show 420 times longer retention in lymph node follicles, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions. These findings can inform future HIV-1 vaccine development.
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Affiliation(s)
- Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jennifer Paynter
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Joel D Allen
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mor Eldad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yi-Zong Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Maddy L Newby
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deborah Chavez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Pat Frost
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Anna Goodroe
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - John Dutton
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Robert Lanford
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Christopher Chen
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Max Crispin
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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7
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Alessandri-Gradt E, Moisan A, Plantier JC. HIV-1 Non-Group M Strains and ART. Viruses 2023; 15:v15030780. [PMID: 36992488 PMCID: PMC10058373 DOI: 10.3390/v15030780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/31/2023] Open
Abstract
To eliminate HIV infection, there are several elements to take into account to limit transmission and break viral replication, such as epidemiological, preventive or therapeutic management. The UNAIDS goals of screening, treatment and efficacy should allow for this elimination if properly followed. For some infections, the difficulty is linked to the strong genetic divergence of the viruses, which can impact the virological and therapeutic management of patients. To completely eliminate HIV by 2030, we must therefore also be able to act on these atypical variants (HIV-1 non-group M) which are distinct from the group M pandemic viruses. While this diversity has had an impact on the efficacy of antiretroviral treatment in the past, recent data show that there is real hope of eliminating these forms, while maintaining vigilance and constant surveillance, so as not to allow more divergent and resistant forms to emerge. The aim of this work is therefore to share an update on the current knowledge on epidemiology, diagnosis and antiretroviral agent efficacy of HIV-1 non-M variants.
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Affiliation(s)
- Elodie Alessandri-Gradt
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, and CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France
| | - Alice Moisan
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, and CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France
| | - Jean-Christophe Plantier
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, and CHU Rouen, Department of Virology, National Reference Center of HIV, F-76000 Rouen, France
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8
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Gristick HB, Hartweger H, Loewe M, van Schooten J, Ramos V, Oliviera TY, Nishimura Y, Koranda NS, Wall A, Yao KH, Poston D, Gazumyan A, Wiatr M, Horning M, Keeffe JR, Hoffmann MA, Yang Z, Abernathy ME, Dam KMA, Gao H, Gnanapragasam PN, Kakutani LM, Pavlovitch-Bedzyk AJ, Seaman MS, Howarth M, McGuire AT, Stamatatos L, Martin MA, West AP, Nussenzweig MC, Bjorkman PJ. CD4 binding site immunogens elicit heterologous anti-HIV-1 neutralizing antibodies in transgenic and wild-type animals. Sci Immunol 2023; 8:eade6364. [PMID: 36763635 PMCID: PMC10202037 DOI: 10.1126/sciimmunol.ade6364] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023]
Abstract
Passive transfer of broadly neutralizing anti-HIV-1 antibodies (bNAbs) protects against infection, and therefore, eliciting bNAbs by vaccination is a major goal of HIV-1 vaccine efforts. bNAbs that target the CD4 binding site (CD4bs) on HIV-1 Env are among the most broadly active, but to date, responses elicited against this epitope in vaccinated animals have lacked potency and breadth. We hypothesized that CD4bs bNAbs resembling the antibody IOMA might be easier to elicit than other CD4bs antibodies that exhibit higher somatic mutation rates, a difficult-to-achieve mechanism to accommodate Env's N276gp120 N-glycan, and rare five-residue light chain complementarity-determining region 3. As an initial test of this idea, we developed IOMA germline-targeting Env immunogens and evaluated a sequential immunization regimen in transgenic mice expressing germline-reverted IOMA. These mice developed CD4bs epitope-specific responses with heterologous neutralization, and cloned antibodies overcame neutralization roadblocks, including accommodating the N276gp120 glycan, with some neutralizing selected HIV-1 strains more potently than IOMA. The immunization regimen also elicited CD4bs-specific responses in mice containing polyclonal antibody repertoires as well as rabbits and rhesus macaques. Thus, germline targeting of IOMA-class antibody precursors represents a potential vaccine strategy to induce CD4bs bNAbs.
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Affiliation(s)
- Harry B. Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harald Hartweger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Maximilian Loewe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jelle van Schooten
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y. Oliviera
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases,National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas S. Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Abigail Wall
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Poston
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marie Wiatr
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marcel Horning
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Magnus A.G. Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Morgan E. Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kim-Marie A. Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Leesa M. Kakutani
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Andrew T. McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
| | - Malcolm A. Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases,National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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9
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Sun N, Yau SST. In-depth investigation of the point mutation pattern of HIV-1. Front Cell Infect Microbiol 2022; 12:1033481. [PMID: 36457853 PMCID: PMC9705751 DOI: 10.3389/fcimb.2022.1033481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/25/2022] [Indexed: 04/29/2024] Open
Abstract
Mutations may produce highly transmissible and damaging HIV variants, which increase the genetic diversity, and pose a challenge to develop vaccines. Therefore, it is of great significance to understand how mutations drive the virulence of HIV. Based on the 11897 reliable genomes of HIV-1 retrieved from HIV sequence Database, we analyze the 12 types of point mutation (A>C, A>G, A>T, C>A, C>G, C>T, G>A, G>C, G>T, T>A, T>C, T>G) from multiple statistical perspectives for the first time. The global/geographical location/subtype/k-mer analysis results report that A>G, G>A, C>T and T>C account for nearly 64% among all SNPs, which suggest that APOBEC-editing and ADAR-editing may play an important role in HIV-1 infectivity. Time analysis shows that most genomes with abnormal mutation numbers comes from African countries. Finally, we use natural vector method to check the k-mer distribution changing patterns in the genome, and find that there is an important substitution pattern between nucleotides A and G, and 2-mer CG may have a significant impact on viral infectivity. This paper provides an insight into the single mutation of HIV-1 by using the latest data in the HIV sequence Database.
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Affiliation(s)
- Nan Sun
- Department of Mathematical Sciences, Tsinghua University, Beijing, China
| | - Stephen S.-T. Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing, China
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China
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10
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Dzhivhuho G, Holsey J, Honeycutt E, O'Farrell H, Rekosh D, Hammarskjold ML, Jackson PEH. HIV-1 Rev-RRE functional activity in primary isolates is highly dependent on minimal context-dependent changes in Rev. Sci Rep 2022; 12:18416. [PMID: 36319640 PMCID: PMC9626594 DOI: 10.1038/s41598-022-21714-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/30/2022] [Indexed: 01/01/2023] Open
Abstract
During HIV infection, intron-containing viral mRNAs are exported from the cell nucleus to the cytoplasm to complete the replication cycle. Cellular restrictions on the export of incompletely spliced transcripts are overcome by a viral protein, Rev, and an RNA structure found in all unspliced and incompletely spliced viral mRNAs, the Rev Response Element (RRE). Primary HIV isolates display substantial variation in the sequence and functional activity of Rev proteins. We analyzed Rev from two primary isolates with disparate activity that resulted in differences in in vitro fitness of replication-competent viral constructs. The results showed that amino acid differences within the oligomerization domain, but not the arginine-rich motif or the nuclear export signal, determined the level of Rev activity. Two specific amino acid substitutions were sufficient to alter the low-activity Rev to a high-activity phenotype. Other mutations in Rev sequences had unpredictable effects on activity that differed between the two Rev backbones. The sensitivity of Rev function level to small sequence changes likely permits modulation of Rev-RRE activity during HIV infection, which may play a role in pathogenesis. The functional consequences of Rev mutations differed between primary isolates, highlighting the challenge of generalizing studies of Rev conducted using laboratory HIV strains.
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Affiliation(s)
- Godfrey Dzhivhuho
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Jordan Holsey
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Ethan Honeycutt
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Heather O'Farrell
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - David Rekosh
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Patrick E H Jackson
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA.
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11
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Scheepers C, Richardson SI, Moyo-Gwete T, Moore PL. Antibody class-switching as a strategy to improve HIV-1 neutralization. Trends Mol Med 2022; 28:979-988. [PMID: 36117072 PMCID: PMC9617786 DOI: 10.1016/j.molmed.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 12/01/2022]
Abstract
Broadly neutralizing antibodies (bNAbs), when administered through passive immunization, are protective against HIV-1 infection. Current HIV-1 vaccine strategies are aimed at guiding the immune system to make bNAbs by mimicking their development during infection. Somatic hypermutation of the variable region is known to be crucial for the development of bNAbs. More recently, however, studies have shown how class-switch recombination (CSR) resulting in the generation of different antibody isotypes may serve as an additional mechanism through which antibodies can gain neutralization breadth and potency. In this review, we discuss the importance of different antibody isotypes for HIV-1 neutralization breadth and potency and how this information can be leveraged to improve passive and active immunization against HIV-1.
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Affiliation(s)
- Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Simone I Richardson
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L Moore
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal, South Africa, Discipline of Virology, University of KwaZulu-Natal, South Africa.
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12
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Optimal sequence-based design for multi-antigen HIV-1 vaccines using minimally distant antigens. PLoS Comput Biol 2022; 18:e1010624. [PMID: 36315492 PMCID: PMC9621458 DOI: 10.1371/journal.pcbi.1010624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
The immense global diversity of HIV-1 is a significant obstacle to developing a safe and effective vaccine. We recently showed that infections established with multiple founder variants are associated with the development of neutralization breadth years later. We propose a novel vaccine design strategy that integrates the variability observed in acute HIV-1 infections with multiple founder variants. We developed a probabilistic model to simulate this variability, yielding a set of sequences that present the minimal diversity seen in an infection with multiple founders. We applied this model to a subtype C consensus sequence for the Envelope (Env) (used as input) and showed that the simulated Env sequences mimic the mutational landscape of an infection with multiple founder variants, including diversity at antibody epitopes. The derived set of multi-founder-variant-like, minimally distant antigens is designed to be used as a vaccine cocktail specific to a HIV-1 subtype or circulating recombinant form and is expected to promote the development of broadly neutralizing antibodies. Diverse HIV-1 populations are generally thought to promote neutralizing responses. Current leading HIV-1 vaccine design strategies maximize the distance between antigens to attempt to cover global HIV-1 diversity or serialize immunizations to recapitulate the temporal evolution of HIV-1 during infection. To date, no vaccine has elicited broadly neutralizing antibodies. As we recently demonstrated that infection with multiple HIV-1 founder variants is predictive of neutralization breadth, we propose a novel strategy that endeavors to promote the development of broadly neutralizing antibodies by replicating the diversity of multi-founder variant acute infections. By training an HIV-1 Env consensus sequence on the diversity from acute infections with multiple founders, we derived in silico a set of minimally distant antigens that is representative of the diversity seen in a multi-founder acute infection. As the model is particular to the input sequence, it can produce antigens specific to any HIV-1 subtype or circulating recombinant form (CRF). We applied this to HIV-1 subtype C and obtained a set of minimally distant antigens that can be used as a vaccine cocktail.
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13
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A New HIV-1 K 28E 32-Reverse Transcriptase Variant Associated with the Rapid Expansion of CRF07_BC among Men Who Have Sex with Men. Microbiol Spectr 2022; 10:e0254522. [PMID: 36214682 PMCID: PMC9604004 DOI: 10.1128/spectrum.02545-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
HIV-1 CRF07_BC originated among injection drug users (IDUs) in China. After diffusing into men who have sex with men (MSM), CRF07_BC has shown a rapid expansion in this group; however, the mechanism remains unclear. Here, we identified a new K28E32 variant of CRF07_BC that was characterized by five specific mutations (E28K, K32E, E248V, K249Q, and T338S) in reverse transcriptase. This variant was mainly prevalent among MSM, and was overrepresented in transmission clusters, suggesting that it could have driven the rapid expansion of CRF07_BC in MSM, though founder effects cannot be ruled out. It was descended from an evolutionary intermediate accumulating four specific mutations and formed an independent phylogenetic node with an estimated origin time in 2003. The K28E32 variant was demonstrated to have significantly higher in vitro HIV-1 replication ability than the wild type. Mutations E28K and K32E play a critical role in the improvement of in vitro HIV-1 replication ability, reflected by improved reverse transcription activity. The results could allow public health officials to use this marker (especially E28K and K32E mutations in the reverse transcriptase (RT) coding region) to target prevention measures prioritizing MSM population and persons infected with this variant for test and treat initiatives. IMPORTANCE HIV-1 has very high mutation rate that is correlated with the survival and adaption of the virus. The variants with higher transmissibility may be more selective advantage than the strains with higher virulence. Several HIV-1 variants were previously demonstrated to be correlated with higher viral load and lower CD4 T cell count. Here, we first identified a new variant (the K28E32 variant) of HIV-1 CRF07_BC, described its origin and evolutionary dynamics, and demonstrated its higher in vitro HIV-1 replication ability than the wild type. We demonstrated that five RT mutations (especially E28K and K32E) significantly improve in vitro HIV-1 replication ability. The appearance of the new K28E32 variant was associated with the rapidly increasing prevalence of CRF07_BC among MSM.
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14
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Mótyán JA, Kassay N, Matúz K, Tőzsér J. Different Mutation Tolerance of Lentiviral (HIV-1) and Deltaretroviral (BLV and HTLV) Protease Precursors. Viruses 2022; 14:v14091888. [PMID: 36146695 PMCID: PMC9505669 DOI: 10.3390/v14091888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The bovine leukemia virus (BLV) and the human T-lymphothropic viruses (HTLVs) are members of the deltaretrovirus genus of Retroviridae family. An essential event of the retroviral life cycle is the processing of the polyproteins by the viral protease (PR); consequently, these enzymes became important therapeutic targets of the anti-retroviral drugs. As compared to human immunodeficiency viruses (HIVs), the deltaretroviruses have a different replication strategy, as they replicate predominantly in the DNA form, by forcing the infected cell to divide, unlike HIV-1, which replicates mainly by producing a vast number of progeny virions and by reinfection. Due to bypassing the error-prone reverse transcription step of replication, the PRs of deltaretroviruses did not undergo such extensive evolution as HIV PRs and remained more highly conserved. In this work, we studied the abilities of wild-type and modified BLV, HTLV (type 1, 2 and 3), and HIV-1 PRs (fused to an N-terminal MBP tag) for self-processing. We designed a cleavage site mutant MBP-fused BLV PR precursor as well, this recombinant enzyme was unable for self-proteolysis, the MBP fusion tag decreased its catalytic efficiency but showed an unusually low Ki for the IB-268 protease inhibitor. Our results show that the HTLV and BLV deltaretrovirus PRs exhibit lower mutation tolerance as compared to HIV-1 PR, and are less likely to retain their activity upon point mutations at various positions, indicating a higher flexibility of HIV-1 PR in tolerating mutations under selective pressure.
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Affiliation(s)
- János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
| | - Norbert Kassay
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Krisztina Matúz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
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15
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Functional and Highly Cross-Linkable HIV-1 Envelope Glycoproteins Enriched in a Pretriggered Conformation. J Virol 2022; 96:e0166821. [PMID: 35343783 DOI: 10.1128/jvi.01668-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Binding to the receptor, CD4, drives the pretriggered, "closed" (state-1) conformation of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) trimer into more "open" conformations (states 2 and 3). Broadly neutralizing antibodies, which are elicited inefficiently, mostly recognize the state-1 Env conformation, whereas the more commonly elicited poorly neutralizing antibodies recognize states 2/3. HIV-1 Env metastability has created challenges for defining the state-1 structure and developing immunogens mimicking this labile conformation. The availability of functional state-1 Envs that can be efficiently cross-linked at lysine and/or acidic amino acid residues might assist these endeavors. To that end, we modified HIV-1AD8 Env, which exhibits an intermediate level of triggerability by CD4. We introduced lysine/acidic residues at positions that exhibit such polymorphisms in natural HIV-1 strains. Env changes that were tolerated with respect to gp120-gp41 processing, subunit association, and virus entry were further combined. Two common polymorphisms, Q114E and Q567K, as well as a known variant, A582T, additively rendered pseudoviruses resistant to cold, soluble CD4, and a CD4-mimetic compound, phenotypes indicative of stabilization of the pretriggered state-1 Env conformation. Combining these changes resulted in two lysine-rich HIV-1AD8 Env variants (E.2 and AE.2) with neutralization- and cold-resistant phenotypes comparable to those of natural, less triggerable tier 2/3 HIV-1 isolates. Compared with these and the parental Envs, the E.2 and AE.2 Envs were cleaved more efficiently and exhibited stronger gp120-trimer association in detergent lysates. These highly cross-linkable Envs enriched in a pretriggered conformation should assist characterization of the structure and immunogenicity of this labile state. IMPORTANCE The development of an efficient vaccine is critical for combating HIV-1 infection worldwide. However, the instability of the pretriggered shape (state 1) of the viral envelope glycoprotein (Env) makes it difficult to raise neutralizing antibodies against HIV-1. Here, by introducing multiple changes in Env, we derived two HIV-1 Env variants that are enriched in state 1 and can be efficiently cross-linked to maintain this shape. These Env complexes are more stable in detergent, assisting their purification. Thus, our study provides a path to a better characterization of the native pretriggered Env, which should assist vaccine development.
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16
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Mótyán JA, Mahdi M, Hoffka G, Tőzsér J. Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease. Int J Mol Sci 2022; 23:3507. [PMID: 35408866 PMCID: PMC8998604 DOI: 10.3390/ijms23073507] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome 2 (SARS-CoV-2), has been one of the most devastating pandemics of recent times. The lack of potent novel antivirals had led to global health crises; however, emergence and approval of potent inhibitors of the viral main protease (Mpro), such as Pfizer's newly approved nirmatrelvir, offers hope not only in the therapeutic front but also in the context of prophylaxis against the infection. By their nature, RNA viruses including human immunodeficiency virus (HIV) have inherently high mutation rates, and lessons learnt from previous and currently ongoing pandemics have taught us that these viruses can easily escape selection pressure through mutation of vital target amino acid residues in monotherapeutic settings. In this paper, we review nirmatrelvir and its binding to SARS-CoV-2 Mpro and draw a comparison to inhibitors of HIV protease that were rendered obsolete by emergence of resistance mutations, emphasizing potential pitfalls in the design of inhibitors that may be of important relevance to the long-term use of novel inhibitors against SARS-CoV-2.
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Affiliation(s)
- János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
| | - Mohamed Mahdi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
| | - Gyula Hoffka
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
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17
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Ye L, Gribling-Burrer AS, Bohn P, Kibe A, Börtlein C, Ambi UB, Ahmad S, Olguin-Nava M, Smith M, Caliskan N, von Kleist M, Smyth RP. Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging. Nat Struct Mol Biol 2022; 29:306-319. [PMID: 35347312 PMCID: PMC9010304 DOI: 10.1038/s41594-022-00746-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
RNA dimerization is the noncovalent association of two human immunodeficiency virus-1 (HIV-1) genomes. It is a conserved step in the HIV-1 life cycle and assumed to be a prerequisite for binding to the viral structural protein Pr55Gag during genome packaging. Here, we developed functional analysis of RNA structure-sequencing (FARS-seq) to comprehensively identify sequences and structures within the HIV-1 5' untranslated region (UTR) that regulate this critical step. Using FARS-seq, we found nucleotides important for dimerization throughout the HIV-1 5' UTR and identified distinct structural conformations in monomeric and dimeric RNA. In the dimeric RNA, key functional domains, such as stem-loop 1 (SL1), polyadenylation signal (polyA) and primer binding site (PBS), folded into independent structural motifs. In the monomeric RNA, SL1 was reconfigured into long- and short-range base pairings with polyA and PBS, respectively. We show that these interactions disrupt genome packaging, and additionally show that the PBS-SL1 interaction unexpectedly couples the PBS with dimerization and Pr55Gag binding. Altogether, our data provide insights into late stages of HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging.
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Affiliation(s)
- Liqing Ye
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anne-Sophie Gribling-Burrer
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Patrick Bohn
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anuja Kibe
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Charlene Börtlein
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Uddhav B. Ambi
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Shazeb Ahmad
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Marco Olguin-Nava
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Maureen Smith
- grid.13652.330000 0001 0940 3744P5 Systems Medicine of Infectious Disease, Robert Koch-Institute, Berlin, Germany
| | - Neva Caliskan
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany ,grid.8379.50000 0001 1958 8658Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Max von Kleist
- grid.13652.330000 0001 0940 3744P5 Systems Medicine of Infectious Disease, Robert Koch-Institute, Berlin, Germany
| | - Redmond P. Smyth
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany ,grid.8379.50000 0001 1958 8658Faculty of Medicine, University of Würzburg, Würzburg, Germany
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18
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Olech M, Kuźmak J. Molecular Characterization of Small Ruminant Lentiviruses in Polish Mixed Flocks Supports Evidence of Cross Species Transmission, Dual Infection, a Recombination Event, and Reveals the Existence of New Subtypes within Group A. Viruses 2021; 13:2529. [PMID: 34960798 PMCID: PMC8708130 DOI: 10.3390/v13122529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 02/06/2023] Open
Abstract
Small ruminant lentiviruses (SRLVs) are a group of highly divergent viruses responsible for global infection in sheep and goats. In a previous study we showed that SRLV strains found in mixed flocks in Poland belonged to subtype A13 and A18, but this study was restricted only to the few flocks from Małopolska region. The present work aimed at extending earlier findings with the analysis of SRLVs in mixed flocks including larger numbers of animals and flocks from different part of Poland. On the basis of gag and env sequences, Polish SRLVs were assigned to the subtypes B2, A5, A12, and A17. Furthermore, the existence of a new subtypes, tentatively designed as A23 and A24, were described for the first time. Subtypes A5 and A17 were only found in goats, subtype A24 has been detected only in sheep while subtypes A12, A23, and B2 have been found in both sheep and goats. Co-infection with strains belonging to different subtypes was evidenced in three sheep and two goats originating from two flocks. Furthermore, three putative recombination events were identified within gag and env SRLVs sequences derived from three sheep. Amino acid (aa) sequences of immunodominant epitopes in CA protein were well conserved while Major Homology Region (MHR) had more alteration showing unique mutations in sequences of subtypes A5 and A17. In contrast, aa sequences of surface glycoprotein exhibited higher variability confirming type-specific variation in the SU5 epitope. The number of potential N-linked glycosylation sites (PNGS) ranged from 3 to 6 in respective sequences and were located in different positions. The analysis of LTR sequences revealed that sequences corresponding to the TATA box, AP-4, AML-vis, and polyadenylation signal (poly A) were quite conserved, while considerable alteration was observed in AP-1 sites. Interestingly, our results revealed that all sequences belonging to subtype A17 had unique substitution T to A in the fifth position of TATA box and did not have a 11 nt deletion in the R region which was noted in other sequences from Poland. These data revealed a complex picture of SRLVs population with ovine and caprine strains belonging to group A and B. We present strong and multiple evidence of dually infected sheep and goats in mixed flocks and present evidence that these viruses can recombine in vivo.
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Affiliation(s)
- Monika Olech
- Department of Swine Diseases, National Veterinary Research Institute, 24-100 Pulawy, Poland
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Pulawy, Poland;
| | - Jacek Kuźmak
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Pulawy, Poland;
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19
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RNA Structures and Their Role in Selective Genome Packaging. Viruses 2021; 13:v13091788. [PMID: 34578369 PMCID: PMC8472981 DOI: 10.3390/v13091788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.
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20
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Gallardo CM, Wang S, Montiel-Garcia DJ, Little SJ, Smith DM, Routh AL, Torbett BE. MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution. Nucleic Acids Res 2021; 49:e70. [PMID: 33849057 PMCID: PMC8266615 DOI: 10.1093/nar/gkab231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/31/2021] [Indexed: 12/31/2022] Open
Abstract
Technical challenges remain in the sequencing of RNA viruses due to their high intra-host diversity. This bottleneck is particularly pronounced when interrogating long-range co-evolved genetic interactions given the read-length limitations of next-generation sequencing platforms. This has hampered the direct observation of these genetic interactions that code for protein-protein interfaces with relevance in both drug and vaccine development. Here we overcome these technical limitations by developing a nanopore-based long-range viral sequencing pipeline that yields accurate single molecule sequences of circulating virions from clinical samples. We demonstrate its utility in observing the evolution of individual HIV Gag-Pol genomes in response to antiviral pressure. Our pipeline, called Multi-read Hairpin Mediated Error-correction Reaction (MrHAMER), yields >1000s of viral genomes per sample at 99.9% accuracy, maintains the original proportion of sequenced virions present in a complex mixture, and allows the detection of rare viral genomes with their associated mutations present at <1% frequency. This method facilitates scalable investigation of genetic correlates of resistance to both antiviral therapy and immune pressure and enables the identification of novel host-viral and viral-viral interfaces that can be modulated for therapeutic benefit.
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Affiliation(s)
- Christian M Gallardo
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Shiyi Wang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Daniel J Montiel-Garcia
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Susan J Little
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.,Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bruce E Torbett
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
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21
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Arze CA, Springer S, Dudas G, Patel S, Bhattacharyya A, Swaminathan H, Brugnara C, Delagrave S, Ong T, Kahvejian A, Echelard Y, Weinstein EG, Hajjar RJ, Andersen KG, Yozwiak NL. Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome. Cell Host Microbe 2021; 29:1305-1315.e6. [PMID: 34320399 DOI: 10.1016/j.chom.2021.07.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/23/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022]
Abstract
Anelloviruses are a ubiquitous component of healthy human viromes and remain highly prevalent after being acquired early in life. The full extent of "anellome" diversity and its evolutionary dynamics remain unexplored. We employed in-depth sequencing of blood-transfusion donor(s)-recipient pairs coupled with public genomic resources for a large-scale assembly of anellovirus genomes and used the data to characterize global and personal anellovirus diversity through time. The breadth of the anellome is much greater than previously appreciated, and individuals harbor unique anellomes and transmit lineages that can persist for several months within a diverse milieu of endemic host lineages. Anellovirus sequence diversity is shaped by extensive recombination at all levels of divergence, hindering traditional phylogenetic analyses. Our findings illuminate the transmission dynamics and vast diversity of anelloviruses and set the foundation for future studies to characterize their biology.
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Affiliation(s)
| | | | - Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg 413 19, Sweden
| | | | | | | | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Tuyen Ong
- Ring Therapeutics, Cambridge, MA 02139, USA
| | - Avak Kahvejian
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Yann Echelard
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Erica G Weinstein
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
| | - Roger J Hajjar
- Ring Therapeutics, Cambridge, MA 02139, USA; Flagship Pioneering, Cambridge, MA 02142, USA
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22
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Cai Q, Yuan R, He J, Li M, Guo Y. Predicting HIV drug resistance using weighted machine learning method at target protein sequence-level. Mol Divers 2021; 25:1541-1551. [PMID: 34241771 DOI: 10.1007/s11030-021-10262-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/19/2021] [Indexed: 11/29/2022]
Abstract
Acquired immune deficiency syndrome (AIDS) is a fatal disease caused by human immunodeficiency virus (HIV). Although 23 different drugs have been available, the treatment of AIDS remains challenging because the virus mutates very quickly which can lead to drug resistance. Therefore, predicting drug resistance before treatment is crucial for individual treatments. Here, based on HIV target protein sequence information, we analyzed 21-drug resistance caused by mutated residues using machine learning (ML) methods. To transform target sequences into numeric vectors, seven physicochemical properties were used, which can well represent the interacting characteristics of target proteins. Then, principal component analysis (PCA) method was adopted to reduce the feature dimensionality. Random forest (RF) and support vector machine (SVM) based on three different kernel functions, including linear, polynomial and radial basis function (RBF), were all employed. By comparisons, we found that RBF-based SVM method gives a comparative performance with RF model. Further, we added the weight information to RBF-based SVM method by four different weight evaluation methods of RF, eXtreme Gradient Boosting (XGB), CfsSubsetEval and ReliefFAttributeEval, respectively. Results show that the RF-weighted RBF-based SVM yield the superior performance and 13 out of 21 drug models provide the correlation coefficients (R2) over 0.8 and 3 of them are higher than 0.9. Finally, position-specific importance analysis indicates that most of the mutation residues with high RF weight scores are proved to be closely related with drug resistance, which has been revealed in previous reports. Overall, we can expect that this method can be a supplementary tool for predicting HIV drug resistance for newly discovered mutations. Here, based on HIV target protein sequence information, we analyzed 21-drug resistance caused by mutated residues using machine learning (ML) methods by fusing the weight information of different mutation positions.
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Affiliation(s)
- Qihang Cai
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Rongao Yuan
- College of Computer Science, Sichuan University, Chengdu, 610064, China
| | - Jian He
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
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23
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Weber IT, Wang YF, Harrison RW. HIV Protease: Historical Perspective and Current Research. Viruses 2021; 13:v13050839. [PMID: 34066370 PMCID: PMC8148205 DOI: 10.3390/v13050839] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/01/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
The retroviral protease of human immunodeficiency virus (HIV) is an excellent target for antiviral inhibitors for treating HIV/AIDS. Despite the efficacy of therapy, current efforts to control the disease are undermined by the growing threat posed by drug resistance. This review covers the historical background of studies on the structure and function of HIV protease, the subsequent development of antiviral inhibitors, and recent studies on drug-resistant protease variants. We highlight the important contributions of Dr. Stephen Oroszlan to fundamental knowledge about the function of the HIV protease and other retroviral proteases. These studies, along with those of his colleagues, laid the foundations for the design of clinical inhibitors of HIV protease. The drug-resistant protease variants also provide an excellent model for investigating the molecular mechanisms and evolution of resistance.
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Affiliation(s)
- Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
- Correspondence:
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
| | - Robert W. Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA;
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24
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Shah D, Freas C, Weber IT, Harrison RW. Evolution of drug resistance in HIV protease. BMC Bioinformatics 2020; 21:497. [PMID: 33375936 PMCID: PMC7772915 DOI: 10.1186/s12859-020-03825-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Drug resistance is a critical problem limiting effective antiviral therapy for HIV/AIDS. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice of therapy. These techniques can also be used to identify protease mutants for experimental studies of resistance and thereby assist in the development of next-generation therapies. Few studies, however, have assessed the evolution of resistance from genotype-phenotype data. RESULTS The machine learning produced highly accurate and robust classification of resistance to HIV protease inhibitors. Genotype data were mapped to the enzyme structure and encoded using Delaunay triangulation. Estimates of evolutionary relationships, based on this encoding, and using Minimum Spanning Trees, showed clusters of mutations that closely resemble the wild type. These clusters appear to evolve uniquely to more resistant phenotypes. CONCLUSIONS Using the triangulation metric and spanning trees results in paths that are consistent with evolutionary theory. The majority of the paths show bifurcation, namely they switch once from non-resistant to resistant or from resistant to non-resistant. Paths that lose resistance almost uniformly have far lower levels of resistance than those which either gain resistance or are stable. This strongly suggests that selection for stability in the face of a rapid rate of mutation is as important as selection for resistance in retroviral systems.
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Affiliation(s)
- Dhara Shah
- Department of Computer Science, 25 Park Place, Atlanta, GA 30303 USA
| | - Christopher Freas
- Department of Computer Science, 25 Park Place, Atlanta, GA 30303 USA
| | - Irene T. Weber
- Department of Biology, 100 Piedmont Ave., Atlanta, GA 30303 USA
| | - Robert W. Harrison
- Department of Computer Science, 25 Park Place, Atlanta, GA 30303 USA
- Department of Biology, 100 Piedmont Ave., Atlanta, GA 30303 USA
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25
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Abstract
The new severe acute respiratory syndrome coronavirus (SARS-CoV-2) has caused more than 40 million human infections since December 2019, when a cluster of unexplained pneumonia cases was first reported in Wuhan, China. Just a few days after the coronavirus was officially recognized, it was identified as the causative agent of this mysterious pneumonia. This paper discusses the pros and cons of antiviral drugs from the selective pressure and possible drug resistance point of view. We also address the key advantages of potential selective pressure-free treatment methods such as the use of sparsely and densely ionizing low-dose radiation (LDR). It is known that LDR has the capacity to modulate excessive inflammatory responses, regulate lymphocyte counts and control bacterial co-infections in patients with COVID-19 and different modalities. Substantial evidence shows that viruses are constantly mutating and evolving. When an antiviral immune response is unable to eliminate a virus, viral evolution is promoted. Therefore, it is of crucial importance to limit the use of antivirals/vaccines against SARS-CoV-2 when their effects on viral fitness are not fully understood. Furthermore, to limit the spread of the virus, it is essential to develop a vaccine that is available for as many people as possible. However, with the advent of vaccines or new therapies, the new situation may force the virus to evolve. Given this consideration, selective pressure-free treatments for COVID-19 are of great importance.
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26
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Wei H, Yu D, Geng X, He Y. Defective HIV-1 envelope gene promotes the evolution of the infectious strain through recombination in vitro. BMC Infect Dis 2020; 20:569. [PMID: 32753067 PMCID: PMC7401196 DOI: 10.1186/s12879-020-05288-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/26/2020] [Indexed: 11/10/2022] Open
Abstract
Background HIV-1 produces defective mutants in the process of reproduction. The significance of the mutants has not been well investigated. Methods The plasmids of wild type (HIV-1NL4–3) and Env-defective (HIV-1SG3ΔEnv) HIV-1 were co-transfected into HEK293T cells. The progeny virus was collected to infect MT4 cells. The env gene and near-full-length genome (NFLG) of HIV-1 were amplified and sequenced. The phylogenetic diversity, recombinant patterns and hotspots, and the functionality of HIV-1 Env were determined. Results A total of 42 env genes and 8 NFLGs were successfully amplified and sequenced. Five types of recombinant patterns of env were identified and the same recombinant sites were detected in different patterns. The recombination hotspots were found distributing mainly in conservative regions of env. The recombination between genes of HIV-1NL4–3 and HIV-1SG3Δenv increased the variety of viral quasispecies and resulted in progeny viruses with relative lower infectious ability than that of HIVNL4–3. The defective env genes as well as NFLG could be detected after 20 passages. Conclusion The existence of the defective HIV-1 promotes the phylogenetic evolution of the virus, thus increasing the diversity of virus population. The role of defective genes may be converted from junk genes to useful materials and cannot be neglected in the study of HIV-1 reservoir.
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Affiliation(s)
- Huamian Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Danwei Yu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiuzhu Geng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yuxian He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China. .,Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
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27
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Capoferri AA, Lamers SL, Grabowski MK, Rose R, Wawer MJ, Serwadda D, Gray RH, Quinn TC, Kigozi G, Kagaayi J, Laeyendecker O, Abeler-Dörner L, Ayles H, Bonsall D, Bowden R, Calvez V, Cohen M, Denis A, Frampton D, de Oliveira T, Essex M, Fidler S, Fraser C, Golubchik T, Hayes R, Herbeck JT, Hoppe A, Kaleebu P, Kellam P, Kityo C, Leigh-Brown A, Lingappa JR, Novitsky V, Paton N, Pillay D, Rambaut A, Ratmann O, Seeley J, Ssemwanga D, Tanser F. Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda. AIDS Res Hum Retroviruses 2020; 36:467-474. [PMID: 31914792 DOI: 10.1089/aid.2019.0150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from Sub-Saharan Africa. In this study, we examined a subset (n = 275) of sequences from Rakai, Uganda, collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and subtype D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1, which can further contribute to our understanding toward a universal HIV-1 vaccine.
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Affiliation(s)
- Adam A. Capoferri
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mary Kate Grabowski
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | | | - Maria J. Wawer
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Ronald H. Gray
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Thomas C. Quinn
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
| | | | | | - Oliver Laeyendecker
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
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28
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Leong FTL. Diversified Portfolio Model of Adaptability: A Natural History Perspective. COUNSELING PSYCHOLOGIST 2020. [DOI: 10.1177/0011000020904639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Using a natural history perspective, the diversified portfolio model (DPM) of adaptability developed by Chandra and Leong (2016) is described in this article as a representation of the latter author’s life work in researching diversity and adaptability. The primary thesis of the DPM is that a diversified portfolio of activities, roles, and experiences will lead to greater adaptability in life. The DPM was intended to address a gap in the literature by illuminating the antecedents of adaptive processes that have been studied in current models, including those for self-complexity, risk and resilience, and self-efficacy. This description is followed by an example of the application of the DPM in academic careers. The mechanisms underlying the DPM are then discussed in relation to mental models and mindfulness. Next, the negative effects of nondiversification are illustrated with examples of workaholism and loneliness. Finally, the DPM is linked to the author’s own diversified portfolio of roles and activities to illustrate its positive impact.
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29
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Raad NG, Ghattas IR, Amano R, Watanabe N, Sakamoto T, Smith CA. Altered‐specificity mutants of the HIV Rev arginine‐rich motif‐RRE IIB interaction. J Mol Recognit 2020; 33:e2833. [DOI: 10.1002/jmr.2833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/08/2019] [Accepted: 12/20/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Nicole G. Raad
- Department of BiologyAmerican University of Beirut Beirut Lebanon
| | | | - Ryo Amano
- Department of Life ScienceChiba Institute of Technology Chiba Japan
| | - Natsuki Watanabe
- Department of Life ScienceChiba Institute of Technology Chiba Japan
| | - Taiichi Sakamoto
- Department of Life ScienceChiba Institute of Technology Chiba Japan
| | - Colin A. Smith
- Department of BiologyAmerican University of Beirut Beirut Lebanon
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30
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Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol 2020; 6:veaa004. [PMID: 32395255 PMCID: PMC7204518 DOI: 10.1093/ve/veaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
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Affiliation(s)
- Heather E Grant
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Dan Frampton
- Division of Infection and Immunity, University College London, London, UK
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Paul Kellam
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Freddie Kibengo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Tsz Ho Kwan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rowland Kao
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Deenan Pillay
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
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31
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Brand L, Yang X, Liu K, Elbeleidy S, Wang H, Zhang H, Nie F. Learning Robust Multilabel Sample Specific Distances for Identifying HIV-1 Drug Resistance. J Comput Biol 2019; 27:655-672. [PMID: 31725323 DOI: 10.1089/cmb.2019.0329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIDS is a syndrome caused by the HIV. During the progression of AIDS, a patient's immune system is weakened, which increases the patient's susceptibility to infections and diseases. Although antiretroviral drugs can effectively suppress HIV, the virus mutates very quickly and can become resistant to treatment. In addition, the virus can also become resistant to other treatments not currently being used through mutations, which is known in the clinical research community as cross-resistance. Since a single HIV strain can be resistant to multiple drugs, this problem is naturally represented as a multilabel classification problem. Given this multilabel relationship, traditional single-label classification methods often fail to effectively identify the drug resistances that may develop after a particular virus mutation. In this work, we propose a novel multilabel Robust Sample Specific Distance (RSSD) method to identify multiclass HIV drug resistance. Our method is novel in that it can illustrate the relative strength of the drug resistance of a reverse transcriptase (RT) sequence against a given drug nucleoside analog and learn the distance metrics for all the drug resistances. To learn the proposed RSSDs, we formulate a learning objective that maximizes the ratio of the summations of a number of ℓ1-norm distances, which is difficult to solve in general. To solve this optimization problem, we derive an efficient, nongreedy iterative algorithm with rigorously proved convergence. Our new method has been verified on a public HIV type 1 drug resistance data set with over 600 RT sequences and five nucleoside analogs. We compared our method against several state-of-the-art multilabel classification methods, and the experimental results have demonstrated the effectiveness of our proposed method.
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Affiliation(s)
- Lodewijk Brand
- Department of Computer Science, Colorado School of Mines, Golden, Colorado
| | - Xue Yang
- Department of Computer Science, Colorado School of Mines, Golden, Colorado
| | - Kai Liu
- Department of Computer Science, Colorado School of Mines, Golden, Colorado
| | - Saad Elbeleidy
- Department of Computer Science, Colorado School of Mines, Golden, Colorado
| | - Hua Wang
- Department of Computer Science, Colorado School of Mines, Golden, Colorado
| | - Hao Zhang
- Department of Computer Science, Colorado School of Mines, Golden, Colorado
| | - Feiping Nie
- School of Computer Science and Center for OPTical IMagery Analysis and Learning (OPTIMAL), Northwestern Polytechnical University, Xi'an, P.R. China
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Gorai B, Das S, Maiti PK. Prediction and validation of HIV-1 gp41 ecto-transmembrane domain post-fusion trimeric structure using molecular modeling. J Biomol Struct Dyn 2019; 38:2592-2603. [DOI: 10.1080/07391102.2019.1635916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Biswajit Gorai
- Department of Physics, Indian Institute of Science, Bangalore, Karnataka, India
| | - Satyabrata Das
- Department of Physics, Indian Institute of Science, Bangalore, Karnataka, India
| | - Prabal K. Maiti
- Department of Physics, Indian Institute of Science, Bangalore, Karnataka, India
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HIV Silencing and Inducibility Are Heterogeneous and Are Affected by Factors Intrinsic to the Virus. mBio 2019; 10:mBio.00188-19. [PMID: 31239371 PMCID: PMC6593397 DOI: 10.1128/mbio.00188-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Transcriptionally silent HIV proviruses form the major obstacle to eradicating HIV. Many studies of HIV latency have focused on the cellular mechanisms that maintain silencing of proviral DNA. Here we show that viral sequence variation affecting replicative ability leads to variable rates of silencing and ability to reactivate. We studied naturally occurring and engineered polymorphisms in a recently identified exonic splice enhancer (ESEtat) that regulates tat mRNA splicing and constructed viruses with increased (strain M1), reduced (strain M2), or completely absent (strain ERK) binding of splicing factors essential for optimal production of tat mRNA resulting in a corresponding change in Tat activity. The mutations affected viral replication, with M1 having wild-type (WT) kinetics, M2 exhibiting reduced kinetics, and ERK showing completely abrogated replication. Using single-round infection with green fluorescent protein (GFP)-expressing viruses to study proviral gene expression, we observed progressively greater rates of silencing relating to the degree of ESEtat disruption, with the WT strain at 53%, strain M2 at 69%, and strain ERK at 94%. By stimulating infected cells with a latency reversal agent (phorbol myristate acetate [PMA], panobinostat, or JQ1), we observed that the dose required to achieve 50% of the maximum signal was lowest in the WT, intermediate in M2, and highest in ERK, indicating progressively higher thresholds for reactivation. These results suggest that the ability of silent proviruses to reactivate from latency is variable and that minor differences in the viral sequence can alter the proportion of silenced viruses as well as the threshold required to induce silenced viruses to reactivate and express.IMPORTANCE A reservoir of infected cells in which the HIV genome is transcriptionally silent is acknowledged to be the principal barrier to eradicating the virus from an infected person. A number of cellular processes are implicated in this silencing; however, the viral factors that may contribute remain underexplored. Here we examined mutations altering the correct splicing of HIV gene products as a model to study whether differences in viral sequence can affect either the proportion of viruses that are active or silent or their ability to reactivate. We found that some naturally occurring variations result in viruses that are silenced at a higher rate and require a proportionally increased stimulus for reactivation from latency. These data suggest that the silencing and reactivation behavior of HIV exists in a spectrum, influenced by factors intrinsic to the virus.
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D Urbano V, De Crignis E, Re MC. Host Restriction Factors and Human Immunodeficiency Virus (HIV-1): A Dynamic Interplay Involving All Phases of the Viral Life Cycle. Curr HIV Res 2019; 16:184-207. [PMID: 30117396 DOI: 10.2174/1570162x16666180817115830] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/31/2018] [Accepted: 08/09/2018] [Indexed: 02/08/2023]
Abstract
Mammalian cells have evolved several mechanisms to prevent or block lentiviral infection and spread. Among the innate immune mechanisms, the signaling cascade triggered by type I interferon (IFN) plays a pivotal role in limiting the burden of HIV-1. In the presence of IFN, human cells upregulate the expression of a number of genes, referred to as IFN-stimulated genes (ISGs), many of them acting as antiviral restriction factors (RFs). RFs are dominant proteins that target different essential steps of the viral cycle, thereby providing an early line of defense against the virus. The identification and characterization of RFs have provided unique insights into the molecular biology of HIV-1, further revealing the complex host-pathogen interplay that characterizes the infection. The presence of RFs drove viral evolution, forcing the virus to develop specific proteins to counteract their activity. The knowledge of the mechanisms that prevent viral infection and their viral counterparts may offer new insights to improve current antiviral strategies. This review provides an overview of the RFs targeting HIV-1 replication and the mechanisms that regulate their expression as well as their impact on viral replication and the clinical course of the disease.
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Affiliation(s)
- Vanessa D Urbano
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Elisa De Crignis
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maria Carla Re
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
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Abstract
Effective vaccination is based on three critical aspects of the B-cell response towards infectious agents: (i) that B-cells can generate specific antibodies towards a vast molecular diversity of antigens; proteins, sugars, DNA and lipids. There seems to be no limit to the ability to raise antibodies to everything. (ii) once stimulated, B-cells can perfect their antibodies through affinity maturation to complement every nook and cranny of the epitope and (iii) that the pathogen remains genetically stable and does not change to any great extent. Thus, antibodies produced against the vaccine and subsequent boosts recognize the viral virulent field isolates in future encounters and effectively knock them out. However, some vaccine targets, such as flu virus and HIV, are extremely genetically dynamic. The rapid genetic drift of these viruses renders them moving targets which assist in their ability to evade immune surveillance. Here we postulate that in the case of hyper-variable pathogens the B-cell response actually might be “too good”. We propose that restricting B-cell activities may prove effective in counteracting the genetic diversity of variant viruses such as flu and HIV. We suggest two levels of “B-cell restriction”: (i) to focus the B-cell response exclusively towards neutralizing epitopes by creating epitope-based immunogens; (ii) to restrict affinity maturation of B-cells to prevent the production of overly optimized exquisitely specific antibodies. Together, these “B-cell restrictions” provide a new modality for vaccine design.
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Affiliation(s)
- Jonathan M Gershoni
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University , Ramat Aviv , Tel Aviv , Israel
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Jackson PEH, Huang J, Sharma M, Rasmussen SK, Hammarskjold ML, Rekosh D. A novel retroviral vector system to analyze expression from mRNA with retained introns using fluorescent proteins and flow cytometry. Sci Rep 2019; 9:6467. [PMID: 31015546 PMCID: PMC6478720 DOI: 10.1038/s41598-019-42914-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/11/2019] [Indexed: 12/16/2022] Open
Abstract
The ability to overcome cellular restrictions that exist for the export and translation of mRNAs with retained introns is a requirement for the replication of retroviruses and also for the expression of many mRNA isoforms transcribed from cellular genes. In some cases, RNA structures have been identified in the mRNA that directly interact with cellular factors to promote the export and expression of isoforms with retained introns. In other cases, a viral protein is also required to act as an adapter. In this report we describe a novel vector system that allows measurement of the ability of cis- and trans-acting factors to promote the export and translation of mRNAs with retained introns. One reporter vector used in this system is derived from an HIV proviral clone engineered to express two different fluorescent proteins from spliced and unspliced transcripts. The ratio of fluorescent signals is a measurement of the efficiency of export and translation. A second vector utilizes a third fluorescent protein to measure the expression of viral export proteins that interact with some of the export elements. Both vectors can be packaged into viral particles and be used to transduce cells, allowing expression at physiological levels from the integrated vector.
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Affiliation(s)
- Patrick E H Jackson
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Jing Huang
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Monika Sharma
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Sara K Rasmussen
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - David Rekosh
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA.
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA.
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Compartmentalization of Subtype A17 of Small Ruminant Lentiviruses between Blood and Colostrum in Infected Goats Is Not Exclusively Associated to the env Gene. Viruses 2019; 11:v11030270. [PMID: 30889906 PMCID: PMC6466396 DOI: 10.3390/v11030270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/08/2019] [Accepted: 03/14/2019] [Indexed: 01/28/2023] Open
Abstract
The compartmentalization of small ruminant lentiviruses (SRLVs) subtype A17 was analyzed in colostrum and peripheral blood leukocyte cells of three naturally infected goats. This study aimed to analyze heterogeneity of the SRLV env (V4V5) gene, which encodes neutralizing epitopes of SU glycoprotein, the gag gene encoding capsid protein (CA), and LTR, a noncoding region, responsible for determination of cell tropism. Compartmentalization was assessed using six established tree or distance-based methods, including permutation test to determine statistical significance. We found statistical evidence of compartmentalization between blood and colostrum in all infected goats although phylogenetic evidence of such compartmentalization was not obvious. Our study demonstrated that compartmentalization is not exclusively specific to the env gene, as we revealed that gag and LTR sequences are also compartmentalized between blood and colostrum. The work also confirms the combined use of different methods as essential for reliable determination of intrahost viral compartmentalization. Identifying and characterizing distinct viral subpopulations and the genetic evolution of SRLV in specific anatomical sites enhances our overall understanding of SRLV pathogenesis, immune control, and particularly virus transmission.
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Abstract
BACKGROUND Drug resistance in HIV is the major problem limiting effective antiviral therapy. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice of therapy. These techniques can also be used to select protease mutants for experimental studies of resistance and thereby assist in the development of next-generation therapies. RESULTS The machine learning produced highly accurate and robust classification of HIV protease resistance. Genotype data were mapped to the enzyme structure and encoded using Delaunay triangulation. Generative machine learning models trained on one inhibitor could classify resistance from other inhibitors with varying levels of accuracy. Generally, the accuracy was best when the inhibitors were chemically similar. CONCLUSIONS Restricted Boltzmann Machines are an effective machine learning tool for classification of genomic and structural data. They can also be used to compare resistance profiles of different protease inhibitors.
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Affiliation(s)
- Shrikant D. Pawar
- Department of Computer Science, 25 Park Place, Atlanta, GA 30303 USA
- Department of Biology, 100 Piedmont Ave., Atlanta, GA 30303 USA
| | - Christopher Freas
- Department of Computer Science, 25 Park Place, Atlanta, GA 30303 USA
| | - Irene T. Weber
- Department of Biology, 100 Piedmont Ave., Atlanta, GA 30303 USA
| | - Robert W. Harrison
- Department of Computer Science, 25 Park Place, Atlanta, GA 30303 USA
- Department of Biology, 100 Piedmont Ave., Atlanta, GA 30303 USA
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Smyth RP, Negroni M, Lever AM, Mak J, Kenyon JC. RNA Structure-A Neglected Puppet Master for the Evolution of Virus and Host Immunity. Front Immunol 2018; 9:2097. [PMID: 30283444 PMCID: PMC6156135 DOI: 10.3389/fimmu.2018.02097] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 08/24/2018] [Indexed: 11/13/2022] Open
Abstract
The central dogma of molecular biology describes the flow of genetic information from DNA to protein via an RNA intermediate. For many years, RNA has been considered simply as a messenger relaying information between DNA and proteins. Recent advances in next generation sequencing technology, bioinformatics, and non-coding RNA biology have highlighted the many important roles of RNA in virtually every biological process. Our understanding of RNA biology has been further enriched by a number of significant advances in probing RNA structures. It is now appreciated that many cellular and viral biological processes are highly dependent on specific RNA structures and/or sequences, and such reliance will undoubtedly impact on the evolution of both hosts and viruses. As a contribution to this special issue on host immunity and virus evolution, it is timely to consider how RNA sequences and structures could directly influence the co-evolution between hosts and viruses. In this manuscript, we begin by stating some of the basic principles of RNA structures, followed by describing some of the critical RNA structures in both viruses and hosts. More importantly, we highlight a number of available new tools to predict and to evaluate novel RNA structures, pointing out some of the limitations readers should be aware of in their own analyses.
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Affiliation(s)
- Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Matteo Negroni
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Andrew M Lever
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Johnson Mak
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Julia C Kenyon
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Homerton College, Cambridge, United Kingdom
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Gesesew HA, Ward P, Woldemichael K, Mwanri L. Immunological failure in HIV-infected adults from 2003 to 2015 in Southwest Ethiopia: a retrospective cohort study. BMJ Open 2018; 8:e017413. [PMID: 30121586 PMCID: PMC6104792 DOI: 10.1136/bmjopen-2017-017413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE To assess the prevalence, trend and associated factors for immunological failure (IF), and the magnitude of antiretroviral therapy (ART) shift among adults infected with HIV in Southwest Ethiopia. SETTING A retrospective cohort study was undertaken using the data from ART clinic at Jimma University Teaching Hospital from 21 June 2003 to 15 March 2015. PARTICIPANTS Retrospective analysis of 4900 HIV-infected adult patient records dating from June 2003 to March 2015 was conducted. PRIMARY OUTCOME MEASURE The primary outcome was IF defined when cluster for differentiation 4 (CD4) count falls to the baseline (or below) or persistent CD4 levels below 100 cells/mm3 after 6 months of ART treatment. The analyses included descriptive and inferential statistics. RESULTS 546 (19.5%) adults had developed clinical failure (CF), 775 (19.7%) adults had developed IF and 1231 (25.1%) had developed either CF or IF or both. The prevalence of IF was consistently high throughout the decade. Age 25 to ≤50 years adjusted OR (AOR 1.5, 9% CI 1.2 to 2.4), being female (AOR 1.8, 95% CI 1.3 to 1.9), late presenter for HIV care (AOR 2.2, 95% CI 1.6 to 2.7) and having baseline CD4 count below 200 cells/mm3 (AOR 5.5, 95% CI 4.1 to 7.4), and having no history of HIV testing before diagnosis (AOR 0.7, 95% CI 0.5 to 0.9) were the predictors for IF. Only 29 (0.9%) adults infected with HIV were shifted to second-line ART regimen. CONCLUSIONS The magnitude of CF or IF or both was found significant and consistently high throughout the calendar year although ART shift was found minimal. HIV-infected adult patients with IF were early age adults, females, late presenters for HIV care, and those who had low baseline CD4 counts and history of HIV testing before diagnosis.
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Affiliation(s)
- Hailay Abrha Gesesew
- Public Health, Flinders University, Adelaide, South Australia, Australia
- Epidemiology, Jimma University, Jimma, Ethiopia
| | - Paul Ward
- Public Health, Flinders University, Adelaide, South Australia, Australia
| | | | - Lillian Mwanri
- Public Health, Flinders University, Adelaide, South Australia, Australia
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Lan Y, Zhu W, Hu F, Tang S, Li L, Cai X, Tang X, Cai W. Genetic characterization of a novel HIV-1 CRF01_AE/CRF07_BC recombinant form among men who have sex with men in Guangdong, China. Arch Virol 2018; 163:3093-3097. [PMID: 30030627 DOI: 10.1007/s00705-018-3928-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/03/2018] [Indexed: 11/29/2022]
Abstract
Genome recombination is a major strategy employed by HIV to generate new variants for the benefit of escaping immune surveillance. Near full-length genome phylogenic analysis was utilized to characterize HIV diversity in a male patient in Guangdong, China. The result showed a unique recombinant form (URF) composed of two circulating recombinant forms, CRF01_AE (92%) and CRF07_BC (8%), using six recombinant breakpoints, nt 2794, 3092, 4482, 5988, 7021, and 7722. The emergence of this URF indicates that HIV-1 co-infection or super-infections are common. The increasing genetic complexity of the HIV-1 epidemic in China warrants continued investigation.
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Affiliation(s)
- Yun Lan
- Infectious Disease Institute of Guangzhou Eighth People's Hospital, Guangzhou Medical University, No.627 Dong feng dong Road, Guangzhou, 510060, Guangdong, China
| | - Wenchang Zhu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Fengyu Hu
- Infectious Disease Institute of Guangzhou Eighth People's Hospital, Guangzhou Medical University, No.627 Dong feng dong Road, Guangzhou, 510060, Guangdong, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Linghua Li
- Infectious Disease Center of Guangzhou Eighth People's Hospital, Guangzhou Medical University, No.627 Dong feng dong Road, Guangzhou, 510060, Guangdong, China
| | - Xiaoli Cai
- Infectious Disease Institute of Guangzhou Eighth People's Hospital, Guangzhou Medical University, No.627 Dong feng dong Road, Guangzhou, 510060, Guangdong, China
| | - Xiaoping Tang
- Infectious Disease Institute of Guangzhou Eighth People's Hospital, Guangzhou Medical University, No.627 Dong feng dong Road, Guangzhou, 510060, Guangdong, China.
| | - Weiping Cai
- Infectious Disease Center of Guangzhou Eighth People's Hospital, Guangzhou Medical University, No.627 Dong feng dong Road, Guangzhou, 510060, Guangdong, China.
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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Abstract
BACKGROUND The broad genetic divergence of HIV-1/O relative to HIV-1/M has important implications for diagnosis, monitoring and treatment. Despite this divergence, some HIV-1/M+O dual infections and HIV-1/MO recombinant forms have been reported, mostly in Cameroon, where both groups are prevalent. Here, we describe the characteristics of such infections detected in France in 10 new patients, and discuss their implications for biological and clinical practice, owing to the presence of group O species. METHODS The French National Reference Centre for HIV received samples within the framework of mandatory notification of HIV infections, and for expert analysis. A strategy combining serotyping, viral quantification, group-specific molecular amplification and whole-genome sequencing was used for strain characterization and complementary investigations. RESULTS We identified one patient with M+O infection, three patients with M+O infection associated with an MO recombinant, and six patients with only an MO recombinant. These atypical infections were detected upon strain characterization (n = 4) or because of anomalies during patient monitoring (n = 6). We identified eight new URF_MO, all but one originating from Cameroon. Interestingly, two distinct recombinant strains were found in two unrelated patients, representing possible precursors of a CRF_MO. CONCLUSION Our work highlights the fact that the continuous evolution of HIV can hinder diagnosis and complicate clinical practice. We stress that unexpected results during diagnosis or monitoring necessitate further serological and molecular exploration, these atypical infections influence biological and therapeutic management and necessitate appropriate tools, and specific surveillance is necessary, especially as the frequency of such infections may be underestimated.
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Hebberecht L, Vancoillie L, Schauvliege M, Staelens D, Dauwe K, Mortier V, Verhofstede C. Frequency of occurrence of HIV-1 dual infection in a Belgian MSM population. PLoS One 2018; 13:e0195679. [PMID: 29624605 PMCID: PMC5889168 DOI: 10.1371/journal.pone.0195679] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/27/2018] [Indexed: 12/20/2022] Open
Abstract
Introduction HIV-1 dual infection is a condition that results from infection with at least two HIV-1 variants from different sources. The scarceness of information on this condition is partly due to the fact that its detection is technically challenging. Using next-generation sequencing we defined the extent of HIV-1 dual infection in a cohort of men who have sex with men (MSM). Material & methods Eighty-six MSM, diagnosed with HIV-1 subtype B infection between 2008 and 2013 were selected for next-generation sequencing of the HIV-1 envelope V3. Sequencing was performed on 2 plasma samples collected with an interval of > 6 months before the initiation of antiretroviral therapy. Maximum likelihood phylogenetic trees were inspected for dual infection, defined as the presence of two or more monophyletic clusters with ≥ 90% bootstrap support and a mean between-cluster genetic distance of ≥ 10%. To confirm dual infection, deep V3 sequencing of intermediate samples was performed as well as clonal sequencing of the HIV-1 protease-reverse transcriptase gene. Results Five of the 74 patients (6.8%) for whom deep sequencing was successful, showed clear evidence of dual infection. In 4 of them, the second strain was absent in the first sample but occurred in subsequent samples. This was highly suggestive for superinfection. In 3 patients both virus variants were of subtype B, in 2 patients at least one of the variants was a subtype B/non-B recombinant virus. Conclusions Dual infection was confirmed in 6.8% of MSM diagnosed with HIV-1 in Belgium. This prevalence is probably an underestimation, because stringent criteria were used to classify viral variants as originating from a new infection event.
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Affiliation(s)
- Laura Hebberecht
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Leen Vancoillie
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Kenny Dauwe
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
- * E-mail:
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45
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Carneiro J, Resende A, Pereira F. The HIV oligonucleotide database (HIVoligoDB). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074782. [PMID: 28365729 PMCID: PMC5502365 DOI: 10.1093/database/bax005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 01/16/2017] [Indexed: 02/04/2023]
Abstract
The human immunodeficiency virus (HIV) is associated with one of the most widespread infectious disease, the acquired immunodeficiency syndrome (AIDS). The development of antiretroviral drugs and methods for virus detection requires a comprehensive analysis of the HIV genomic diversity, particularly in the binding sites of oligonucleotides. Here, we describe a versatile online database (HIVoligoDB) with oligonucleotides selected for the diagnosis of HIV and treatment of AIDS. Currently, the database provides an interface for visualization, analysis and download of 380 HIV-1 and 65 HIV-2 oligonucleotides annotated according to curated reference genomes. The database also allows the selection of the most conserved HIV genomic regions for the development of molecular diagnostic assays and sequence-based candidate therapeutics. Database URL:http://portugene.com/HIVoligoDB
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Affiliation(s)
- João Carneiro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leix?Av. General Norton de Matos s/n 4450-208 Porto
| | - Adriana Resende
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leix?Av. General Norton de Matos s/n 4450-208 Porto
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Weber IT, Harrison RW. Decoding HIV resistance: from genotype to therapy. Future Med Chem 2017; 9:1529-1538. [PMID: 28791894 PMCID: PMC5694023 DOI: 10.4155/fmc-2017-0048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/03/2017] [Indexed: 01/14/2023] Open
Abstract
Genetic variation in HIV poses a major challenge for prevention and treatment of the AIDS pandemic. Resistance occurs by mutations in the target proteins that lower affinity for the drug or alter the protein dynamics, thereby enabling viral replication in the presence of the drug. Due to the prevalence of drug-resistant strains, monitoring the genotype of the infecting virus is recommended. Computational approaches for predicting resistance from genotype data and guiding therapy are discussed. Many prediction methods rely on rules derived from known resistance-associated mutations, however, statistical or machine learning can improve the classification accuracy and assess unknown mutations. Adding classifiers such as information on the atomic structure of the protein can further enhance the predictions.
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Affiliation(s)
- Irene T Weber
- Department of Biology, Georgia State University, PO Box 4010, Atlanta, GA 30302-4010, USA
| | - Robert W Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
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HIV drug resistance against strand transfer integrase inhibitors. Retrovirology 2017; 14:36. [PMID: 28583191 PMCID: PMC5460515 DOI: 10.1186/s12977-017-0360-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/30/2017] [Indexed: 12/03/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are the newest class of antiretroviral drugs to be approved for treatment and act by inhibiting the essential HIV protein integrase from inserting the viral DNA genome into the host cell’s chromatin. Three drugs of this class are currently approved for use in HIV-positive individuals: raltegravir (RAL), elvitegravir (EVG), and dolutegravir (DTG), while cabotegravir (CAB) and bictegravir (BIC) are currently in clinical trials. RAL and EVG have been successful in clinical settings but have relatively low genetic barriers to resistance. Furthermore, they share a high degree of cross-resistance, which necessitated the development of so-called second-generation drugs of this class (DTG, CAB, and BIC) that could retain activity against these resistant variants. In vitro selection experiments have been instrumental to the clinical development of INSTIs, however they cannot completely recapitulate the situation in an HIV-positive individual. This review summarizes and compares all the currently available information as it pertains to both in vitro and in vivo selections with all five INSTIs, and the measured fold-changes in resistance of resistant variants in in vitro assays. While the selection of resistance substitutions in response to RAL and EVG bears high similarity in patients as compared to laboratory studies, there is less concurrence regarding the “second-generation” drugs of this class. This highlights the unpredictability of HIV resistance to these inhibitors, which is of concern as CAB and BIC proceed in their clinical development.
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Abstract
Bioinformatic analysis can not only accelerate drug target identification and drug candidate screening and refinement, but also facilitate characterization of side effects and predict drug resistance. High-throughput data such as genomic, epigenetic, genome architecture, cistromic, transcriptomic, proteomic, and ribosome profiling data have all made significant contribution to mechanismbased drug discovery and drug repurposing. Accumulation of protein and RNA structures, as well as development of homology modeling and protein structure simulation, coupled with large structure databases of small molecules and metabolites, paved the way for more realistic protein-ligand docking experiments and more informative virtual screening. I present the conceptual framework that drives the collection of these high-throughput data, summarize the utility and potential of mining these data in drug discovery, outline a few inherent limitations in data and software mining these data, point out news ways to refine analysis of these diverse types of data, and highlight commonly used software and databases relevant to drug discovery.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa K1H 8M5, Canada
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Zanini F, Puller V, Brodin J, Albert J, Neher RA. In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus Evol 2017; 3:vex003. [PMID: 28458914 PMCID: PMC5399928 DOI: 10.1093/ve/vex003] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1 infection, we estimated mutation rates and fitness costs in HIV-1 from the dynamics of genetic variation. At approximately neutral sites, mutations accumulate with a rate of 1.2 × 10-5 per site per day, in agreement with the rate measured in cell cultures. We estimated the rate from G to A to be the largest, followed by the other transitions C to T, T to C, and A to G, while transversions are less frequent. At other sites, mutations tend to reduce virus replication. We estimated the fitness cost of mutations at every site in the HIV-1 genome using a model of mutation selection balance. About half of all non-synonymous mutations have large fitness costs (>10 percent), while most synonymous mutations have costs <1 percent. The cost of synonymous mutations is especially low in most of pol where we could not detect measurable costs for the majority of synonymous mutations. In contrast, we find high costs for synonymous mutations in important RNA structures and regulatory regions. The intra-patient fitness cost estimates are consistent across multiple patients, indicating that the deleterious part of the fitness landscape is universal and explains a large fraction of global HIV-1 group M diversity.
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Affiliation(s)
- Fabio Zanini
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Vadim Puller
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Johanna Brodin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, SE-171 76 Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska Institute, SE-171 76, Stockholm, Sweden
| | - Richard A. Neher
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
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