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Domingo E, García-Crespo C, Soria ME, Perales C. Viral Fitness, Population Complexity, Host Interactions, and Resistance to Antiviral Agents. Curr Top Microbiol Immunol 2023; 439:197-235. [PMID: 36592247 DOI: 10.1007/978-3-031-15640-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fitness of viruses has become a standard parameter to quantify their adaptation to a biological environment. Fitness determinations for RNA viruses (and some highly variable DNA viruses) meet with several uncertainties. Of particular interest are those that arise from mutant spectrum complexity, absence of population equilibrium, and internal interactions among components of a mutant spectrum. Here, concepts, fitness measurements, limitations, and current views on experimental viral fitness landscapes are discussed. The effect of viral fitness on resistance to antiviral agents is covered in some detail since it constitutes a widespread problem in antiviral pharmacology, and a challenge for the design of effective antiviral treatments. Recent evidence with hepatitis C virus suggests the operation of mechanisms of antiviral resistance additional to the standard selection of drug-escape mutants. The possibility that high replicative fitness may be the driver of such alternative mechanisms is considered. New broad-spectrum antiviral designs that target viral fitness may curtail the impact of drug-escape mutants in treatment failures. We consider to what extent fitness-related concepts apply to coronaviruses and how they may affect strategies for COVID-19 prevention and treatment.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Carlos García-Crespo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - María Eugenia Soria
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040, Madrid, Spain.,Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain
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2
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Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc 2017; 12:1261-1276. [PMID: 28538739 PMCID: PMC5902022 DOI: 10.1038/nprot.2017.066] [Citation(s) in RCA: 689] [Impact Index Per Article: 98.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an Internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved in 1-2 d by starting with clinical samples and following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software. It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab.
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Affiliation(s)
- Joshua Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Steven T Pullan
- Public Health England, National Infection Service, Porton Down, Salisbury, UK
| | - Ingra M Claro
- Department of Infectious Disease and Institute of Tropical Medicine, University of Saõ Paulo, Saõ Paulo, Brazil
| | - Andrew D Smith
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Glenn Oliveira
- Scripps Translational Science Institute, La Jolla, California, USA
| | | | - Thomas F Rogers
- The Scripps Research Institute, La Jolla, California, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | | | | | - Marta Giovanetti
- Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
- University of Rome, Tor Vergata, Italy
| | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford, UK
| | - Allison Black
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Miles W Carroll
- Public Health England, National Infection Service, Porton Down, Salisbury, UK
- University of Southampton, South General Hospital, Southampton, UK
| | | | | | - Ester C Sabino
- Department of Infectious Disease and Institute of Tropical Medicine, University of Saõ Paulo, Saõ Paulo, Brazil
| | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Kristian G Andersen
- The Scripps Research Institute, La Jolla, California, USA
- Scripps Translational Science Institute, La Jolla, California, USA
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
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3
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Xia H, Beck AS, Gargili A, Forrester N, Barrett ADT, Bente DA. Transstadial Transmission and Long-term Association of Crimean-Congo Hemorrhagic Fever Virus in Ticks Shapes Genome Plasticity. Sci Rep 2016; 6:35819. [PMID: 27775001 PMCID: PMC5075774 DOI: 10.1038/srep35819] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 10/04/2016] [Indexed: 02/05/2023] Open
Abstract
The trade-off hypothesis, the current paradigm of arbovirus evolution, proposes that cycling between vertebrate and invertebrate hosts presents significant constraints on genetic change of arboviruses. Studying these constraints in mosquito-borne viruses has led to a new understanding of epizootics. The trade-off hypothesis is assumed to be applicable to tick-borne viruses too, although studies are lacking. Tick-borne Crimean-Congo hemorrhagic fever virus (CCHFV), a member of the family Bunyaviridae, is a major cause of severe human disease worldwide and shows an extraordinary amount of genetic diversity compared to other arboviruses, which has been linked to increased virulence and emergence in new environments. Using a transmission model for CCHFV, utilizing the main vector tick species and mice plus next generation sequencing, we detected a substantial number of consensus-level mutations in CCHFV recovered from ticks after only a single transstadial transmission, whereas none were detected in CCHFV obtained from the mammalian host. Furthermore, greater viral intra-host diversity was detected in the tick compared to the vertebrate host. Long-term association of CCHFV with its tick host for 1 year demonstrated mutations in the viral genome become fixed over time. These findings suggest that the trade-off hypothesis may not be accurate for all arboviruses.
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Affiliation(s)
- Han Xia
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Galveston National Laboratory, Galveston TX, USA.,Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Andrew S Beck
- Department of Pathology, and Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Naomi Forrester
- Department of Pathology, and Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, USA
| | - Alan D T Barrett
- Department of Pathology, and Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, USA
| | - Dennis A Bente
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Galveston National Laboratory, Galveston TX, USA
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Nascimento-Brito S, Paulo Zukurov J, Maricato JT, Volpini AC, Salim ACM, Araújo FMG, Coimbra RS, Oliveira GC, Antoneli F, Janini LMR. HIV-1 Tropism Determines Different Mutation Profiles in Proviral DNA. PLoS One 2015; 10:e0139037. [PMID: 26413773 PMCID: PMC4587555 DOI: 10.1371/journal.pone.0139037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/07/2015] [Indexed: 01/19/2023] Open
Abstract
In order to establish new infections HIV-1 particles need to attach to receptors expressed on the cellular surface. HIV-1 particles interact with a cell membrane receptor known as CD4 and subsequently with another cell membrane molecule known as a co-receptor. Two major different co-receptors have been identified: C-C chemokine Receptor type 5 (CCR5) and C-X-C chemokine Receptor type 4 (CXCR4) Previous reports have demonstrated cellular modifications upon HIV-1 binding to its co-receptors including gene expression modulations. Here we investigated the effect of viral binding to either CCR5 or CXCR4 co-receptors on viral diversity after a single round of reverse transcription. CCR5 and CXCR4 pseudotyped viruses were used to infect non-stimulated and stimulated PBMCs and purified CD4 positive cells. We adopted the SOLiD methodology to sequence virtually the entire proviral DNA from all experimental infections. Infections with CCR5 and CXCR4 pseudotyped virus resulted in different patterns of genetic diversification. CCR5 virus infections produced extensive proviral diversity while in CXCR4 infections a more localized substitution process was observed. In addition, we present pioneering results of a recently developed method for the analysis of SOLiD generated sequencing data applicable to the study of viral quasi-species. Our findings demonstrate the feasibility of viral quasi-species evaluation by NGS methodologies. We presented for the first time strong evidence for a host cell driving mechanism acting on the HIV-1 genetic variability under the control of co-receptor stimulation. Additional investigations are needed to further clarify this question, which is relevant to viral diversification process and consequent disease progression.
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Affiliation(s)
- Sieberth Nascimento-Brito
- Departamento de Microbiologia e Imunologia Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Rio de Janeiro, Brazil
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | | | - Juliana T. Maricato
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Angela C. Volpini
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Anna Christina M. Salim
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Flávio M. G. Araújo
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Roney S. Coimbra
- Biosystems Informatics Group, CPqRR, FIOCRUZ, Belo Horizonte, Brazil
| | - Guilherme C. Oliveira
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Fernando Antoneli
- Departamento de Informática em Saúde, EPM, UNIFESP, São Paulo, Brazil
- Laboratório de Biocomplexidade e Genômica Evolutiva, EPM, UNIFESP, São Paulo, Brazil
| | - Luiz Mário R. Janini
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Departamento de Medicina, EPM, UNIFESP, São Paulo, Brazil
- * E-mail:
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Arboviral bottlenecks and challenges to maintaining diversity and fitness during mosquito transmission. Viruses 2014; 6:3991-4004. [PMID: 25341663 PMCID: PMC4213574 DOI: 10.3390/v6103991] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/18/2014] [Accepted: 10/20/2014] [Indexed: 12/23/2022] Open
Abstract
The term arbovirus denotes viruses that are transmitted by arthropods, such as ticks, mosquitoes, and other biting arthropods. The infection of these vectors produces a certain set of evolutionary pressures on the virus; involving migration from the midgut, where the blood meal containing the virus is processed, to the salivary glands, in order to transmit the virus to the next host. During this process the virus is subject to numerous bottlenecks, stochastic events that significantly reduce the number of viral particles that are able to infect the next stage. This article reviews the latest research on the bottlenecks that occur in arboviruses and the way in which these affect the evolution and fitness of these viruses. In particular we focus on the latest research on three important arboviruses, West Nile virus, Venezuelan equine encephalitis virus and Chikungunya viruses and compare the differing effects of the mosquito bottlenecks on these viruses as well as other evolutionary pressures that affect their evolution and transmission.
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Carter RW, Sanford JC. A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918. Theor Biol Med Model 2012; 9:42. [PMID: 23062055 PMCID: PMC3507676 DOI: 10.1186/1742-4682-9-42] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/04/2012] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The H1N1 influenza A virus has been circulating in the human population for over 95 years, first manifesting itself in the pandemic of 1917-1918. Initial mortality was extremely high, but dropped exponentially over time. Influenza viruses have high mutation rates, and H1N1 has undergone significant genetic changes since 1918. The exact nature of H1N1 mutation accumulation over time has not been fully explored. METHODS We have made a comprehensive historical analysis of mutational changes within H1N1 by examining over 4100 fully-sequenced H1N1 genomes. This has allowed us to examine the genetic changes arising within H1N1 from 1918 to the present. RESULTS We document multiple extinction events, including the previously known extinction of the human H1N1 lineage in the 1950s, and an apparent second extinction of the human H1N1 lineage in 2009. These extinctions appear to be due to a continuous accumulation of mutations. At the time of its disappearance in 2009, the human H1N1 lineage had accumulated over 1400 point mutations (more than 10% of the genome), including approximately 330 non-synonymous changes (7.4% of all codons). The accumulation of both point mutations and non-synonymous amino acid changes occurred at constant rates (μ = 14.4 and 2.4 new mutations/year, respectively), and mutations accumulated uniformly across the entire influenza genome. We observed a continuous erosion over time of codon-specificity in H1N1, including a shift away from host (human, swine, and bird [duck]) codon preference patterns. CONCLUSIONS While there have been numerous adaptations within the H1N1 genome, most of the genetic changes we document here appear to be non-adaptive, and much of the change appears to be degenerative. We suggest H1N1 has been undergoing natural genetic attenuation, and that significant attenuation may even occur during a single pandemic. This process may play a role in natural pandemic cessation and has apparently contributed to the exponential decline in mortality rates over time, as seen in all major human influenza strains. These findings may be relevant to the development of strategies for managing influenza pandemics and strain evolution.
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Forrester NL, Guerbois M, Seymour RL, Spratt H, Weaver SC. Vector-borne transmission imposes a severe bottleneck on an RNA virus population. PLoS Pathog 2012; 8:e1002897. [PMID: 23028310 PMCID: PMC3441635 DOI: 10.1371/journal.ppat.1002897] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 07/25/2012] [Indexed: 11/28/2022] Open
Abstract
RNA viruses typically occur in genetically diverse populations due to their error-prone genome replication. Genetic diversity is thought to be important in allowing RNA viruses to explore sequence space, facilitating adaptation to changing environments and hosts. Some arboviruses that infect both a mosquito vector and a mammalian host are known to experience population bottlenecks in their vectors, which may constrain their genetic diversity and could potentially lead to extinction events via Muller's ratchet. To examine this potential challenge of bottlenecks for arbovirus perpetuation, we studied Venezuelan equine encephalitis virus (VEEV) enzootic subtype IE and its natural vector Culex (Melanoconion) taeniopus, as an example of a virus-vector interaction with a long evolutionary history. Using a mixture of marked VEEV clones to infect C. taeniopus and real-time RT-PCR to track these clones during mosquito infection and dissemination, we observed severe bottleneck events that resulted in a significant drop in the number of clones present. At higher initial doses, the midgut was readily infected and there was a severe bottleneck at the midgut escape. Following a lower initial dose, the major bottleneck occurred at initial midgut infection. A second, less severe bottleneck was identified at the salivary gland infection stage following intrathoracic inoculation. Our results suggest that VEEV consistently encounters bottlenecks during infection, dissemination and transmission by its natural enzootic vector. The potential impacts of these bottlenecks on viral fitness and transmission, and the viral mechanisms that prevent genetic drift leading to extinction, deserve further study. The ability of arboviruses to perpetuate in nature given that they must infect two disparate hosts (the mosquito vector and the vertebrate host) remains a mystery. We studied how viral genetic diversity is impacted by the dual host transmission cycle. Our studies of an enzootic cycle using Venezuelan equine encephalitis virus (VEEV) and its natural mosquito, Culex taeniopus, revealed the stages of infection that result in a viral population bottleneck. Using a set of marked VEEV clones and repeated sampling at various time points following C. taeniopus infection, we determined the number of clones in various mosquito tissues culminating in transmission. Bottlenecks were identified but the stage of occurrence was dependent on the dose that initiated infection. Understanding the points at which mosquito-borne viruses are constrained will shed light on the ways in which virus diversity varies, leading to selection of mutants that may result in host range changes or alterations in virulence.
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Affiliation(s)
- Naomi L. Forrester
- Institute for Human Infections and Immunity, Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Mathilde Guerbois
- Institute for Human Infections and Immunity, Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Robert L. Seymour
- Institute for Human Infections and Immunity, Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Heidi Spratt
- Sealy Center for Preventative Medicine and Preventative Medicine and Community Health, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Scott C. Weaver
- Institute for Human Infections and Immunity, Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
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Galkin AN, Bychenko AB, Kuznecovs G, Filinova EY. Isolation, characterization, and sequence analysis of a novel HIV type 1 subtype A1 strain from Russia. AIDS Res Hum Retroviruses 2012; 28:1139-46. [PMID: 22236080 DOI: 10.1089/aid.2011.0302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A new syncytia-inducing human immunodeficiency virus type 1 (HIV-1) strain designated PokA79 was first isolated from a peripheral blood mononuclear cells (PBMC) pool from 24 HIV-1-infected patients from Russia and adapted to growth in MT2, MT4, and U937 cell cultures. The full-length genome of this isolate was amplified by RT-two-round PCR and sequenced. The obtained sequence belongs to the A1 subtype and clustered with other A1 former Soviet Union (FSU) strains. Full-length genome analysis showed that some of the PokA79 genes contain insertions and frame shifts, and the gp120 V3 loop has the three amino acid insertion inside its apex, which is rare for subtype A1 sequences. Nonidentical insertions of the same size are also present in the V3 apex region of several HIV-1 sequences from Central Africa.
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Affiliation(s)
- Alexander N. Galkin
- Molecular Genetics Department, Advanced Biomedical Research Laboratory, Moscow, Russia
| | - Andrey B. Bychenko
- Cellular Biology Department, Advanced Biomedical Research Laboratory, Moscow, Russia
| | - Grigorije Kuznecovs
- Physics Analysis Methods Department, Advanced Biomedical Research Laboratory, Moscow, Russia
| | - Elena Y. Filinova
- Cellular Biology Department, Advanced Biomedical Research Laboratory, Moscow, Russia
- in vivo Assays Department, Advanced Biomedical Research Laboratory, Moscow, Russia
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Capel E, Martrus G, Parera M, Clotet B, Martínez MA. Evolution of the human immunodeficiency virus type 1 protease: effects on viral replication capacity and protease robustness. J Gen Virol 2012; 93:2625-2634. [PMID: 22933665 DOI: 10.1099/vir.0.045492-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rapid spread of human immunodeficiency virus type 1 (HIV-1) in humans has been accompanied by continuous extensive genetic diversification of the virus. The aim of this study was to investigate the impact of HIV-1 diversification on HIV-1 replication capacity (RC) and mutational robustness. Thirty-three HIV-1 protease sequences were amplified from three groups of viruses: two naïve sample groups isolated 15 years apart plus a third group of protease inhibitor-(PI) resistant samples. The amplified proteases were recombined with an HXB2 infectious clone and RC was determined in MT-4 cells. RC was also measured in these three groups after random mutagenesis in vitro using error-prone PCR. No significant RC differences were observed between recombinant viruses from either early or recent naïve isolates (P = 0.5729), even though the proteases from the recent isolates had significantly lower sequence conservation scores compared with a subtype B ancestral sequence (P<0.0001). Randomly mutated recombinant viruses from the three groups exhibited significantly lower RC values than the corresponding wild-type viruses (P<0.0001). There was no significant difference regarding viral infectivity reduction between viruses carrying randomly mutated naïve proteases from early or recent sample isolates (P = 0.8035). Interestingly, a significantly greater loss of RC was observed in the PI-resistant protease group (P = 0.0400). These results demonstrate that protease sequence diversification has not affected HIV-1 RC or protease robustness and indicate that proteases carrying PI resistance substitutions are less robust than naïve proteases.
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Affiliation(s)
- Elena Capel
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Barcelona, Spain
| | - Glòria Martrus
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Barcelona, Spain
| | - Mariona Parera
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Barcelona, Spain
| | - Bonaventura Clotet
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Barcelona, Spain
| | - Miguel Angel Martínez
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Barcelona, Spain
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Padhi A, Ross H, Terwee J, VandeWoude S, Poss M. Profound differences in virus population genetics correspond to protection from CD4 decline resulting from feline lentivirus coinfection. Viruses 2010; 2:2663-80. [PMID: 21994636 PMCID: PMC3185597 DOI: 10.3390/v2122663] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 11/25/2010] [Accepted: 11/29/2010] [Indexed: 11/25/2022] Open
Abstract
CD4 decline is a hallmark of disease onset in individuals infected with Feline Immunodeficiency Virus (FIV) or Human Immunodeficiency Virus type 1 (HIV-1). Cats that are infected with a poorly replicating, apathogenic FIV (PLV) prior to exposure to a virulent FIV strain (FIVC) maintain CD4 numbers by mechanisms that are not correlated with a measurable adaptive immune response or reduction in circulating viral load. We employed population genetic approaches based on the 3′ portion of the viral genome to estimate the population structure of FIVC from single and dual infected cats. In dual infected cats, FIVC effective population size was decreased during the initial viral expansion phase, and after three weeks of infection, the population declined sharply. The FIVC population recovered to pre-bottleneck levels approximately seven weeks post-FIVC infection. However, the population emerging from the bottleneck in dual infected cats was distinct based on estimates of temporal population structure and substitution profiles. The transition to transversion rate ratio (κ) increased from early to late phases in dual infected cats due primarily to a decrease in transversions whereas in single infected cats, κ declined over time. Although one clone with extensive G to A substitutions, indicative of host cytidine deaminase editing, was recovered from a dual infected cat during the bottleneck, the post bottleneck population had an overall reduction in G to A substitutions. These data are consistent with a model of PLV-induced host restriction, putatively involving host DNA editing, that alters the dynamics of FIVC throughout the course of infection leading to disease attenuation.
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Affiliation(s)
- Abinash Padhi
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA; E-Mail:
| | - Howard Ross
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand; E-Mail:
| | - Julie Terwee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Ft. Collins, CO 80523, USA; E-Mails: (J.T.); (S.V.)
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Ft. Collins, CO 80523, USA; E-Mails: (J.T.); (S.V.)
| | - Mary Poss
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA; E-Mail:
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
- 208 Mueller Lab, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-814-867 1213, Fax: +1-814-865 9131
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Abstract
The study on the evolutionary consequences of an RNA viral population's fluctuations can be approached by in vitro experiments. This work describes the fitness recovery of HIV-1 after 20 large-population passages in 10 debilitated clones. The serial passages promoted an increase in viral fitness. In addition, we detected a significant number of mutations fixed in the complete genome consensus sequence of the final viral populations. Among the mutations, events of convergent evolution with important phenotypic characteristics occurred in several independent clones. One common change, V35I, in the nuclear localization signal of the p17 protein appeared in four viruses of three different lineages. Other common alterations mapped in position E196K of the reverse transcriptase or in position S316K of the V3 loop of the gp120 residue that is associated with the X4/R5 phenotype. Together with this mutational analysis, we studied the quasispecies heterogeneity of the initial and final viruses, revealing that fitness increase correlated with an augmentation in the genetic heterogeneity of viral quasispecies. However, while heterogeneity was mostly composed of synonymous (dS) mutations in the first 10 passages performed, at passage 21 it switched to nonsynonymous (dN) substitutions, with significant differences in dN - dS values between passages 11 and 21. In summary, the HIV-1 in vitro fitness recovery depicts a multiphase process occurring first by generation of mutations followed by fixation of the beneficial ones, depicting a classical Darwinian process.
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Ali A, Roossinck MJ. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants. Virology 2010; 404:279-83. [PMID: 20542533 DOI: 10.1016/j.virol.2010.05.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 03/25/2010] [Accepted: 05/16/2010] [Indexed: 10/19/2022]
Abstract
Genetic bottlenecks are stochastic events that narrow variation in a population. We compared bottlenecks during the systemic infection of Cucumber mosaic virus (CMV) in four host plants. We mechanically inoculated an artificial population of twelve CMV mutants to young leaves of tomato, pepper, Nicotiana benthamiana, and squash. The inoculated leaves and primary and secondary systemically infected leaves were sampled at 2, 10, and 15 days post-inoculation. All twelve mutants were detected in all of the inoculated leaves. The number of mutants recovered from the systemically infected leaves of all host species was reduced significantly, indicating bottlenecks in systemic movement. The recovery frequencies of a few of the mutants were significantly different in each host probably due to host-specific selective forces. These results have implications for the differences in virus population variation that is seen in different host plants.
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Affiliation(s)
- Akhtar Ali
- Plant Biology Division, The Samuel Roberts Noble Foundation, P.O. Box 2180, Ardmore, OK 73401, USA
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13
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Bordería AV, Lorenzo-Redondo R, Pernas M, Casado C, Alvaro T, Domingo E, Lopez-Galindez C. Initial fitness recovery of HIV-1 is associated with quasispecies heterogeneity and can occur without modifications in the consensus sequence. PLoS One 2010; 5:e10319. [PMID: 20436678 PMCID: PMC2859943 DOI: 10.1371/journal.pone.0010319] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 03/29/2010] [Indexed: 12/14/2022] Open
Abstract
Background Fitness recovery of HIV-1 “in vitro” was studied using viral clones that had their fitness decreased as a result of plaque-to-plaque passages. Principal Findings After ten large population passages, the viral populations showed an average increase of fitness, although with wide variations among clones. While 5 clones showed significant fitness increases, 3 clones showed increases that were only marginally significant (p<0.1), and 4 clones did not show any change. Fitness recovery was not accompanied by an increase in p24 production, but was associated with an increase in viral titer. Few mutations (an average of 2 mutations per genome) were detected in the consensus nucleotide sequence of the entire genome in all viral populations. Five of the populations did not fix any mutation, and three of them displayed marginally significant fitness increases, illustrating that fitness recovery can occur without detectable alterations of the consensus genomic sequence. The investigation of other possible viral factors associated with the initial steps of fitness recovery, showed that viral quasispecies heterogeneity increased between the initial clones and the passaged populations. A direct statistical correlation between viral heterogeneity and viral fitness was obtained. Conclusions Thus, the initial fitness recovery of debilitated HIV-1 clones was mediated by an increase in quasispecies heterogeneity. This observation, together with the invariance of the consensus sequence despite fitness increases demonstrates the relevance of quasispecies heterogeneity in the evolution of HIV-1 in cell culture.
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Affiliation(s)
- Antonio V. Bordería
- Virologia Molecular, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ramon Lorenzo-Redondo
- Virologia Molecular, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Maria Pernas
- Virologia Molecular, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Concepción Casado
- Virologia Molecular, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Tamara Alvaro
- Virologia Molecular, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Cecilio Lopez-Galindez
- Virologia Molecular, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- * E-mail:
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14
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Amino acid covariation in a functionally important human immunodeficiency virus type 1 protein region is associated with population subdivision. Genetics 2009; 182:265-75. [PMID: 19279325 DOI: 10.1534/genetics.108.099853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The frequently reported amino acid covariation of the highly polymorphic human immunodeficiency virus type 1 (HIV-1) exterior envelope glycoprotein V3 region has been assumed to reflect fitness epistasis between residues. However, nonrandom association of amino acids, or linkage disequilibrium, has many possible causes, including population subdivision. If the amino acids at a set of sequence sites differ in frequencies between subpopulations, then analysis of the whole population may reveal linkage disequilibrium even if it does not exist in any subpopulation. HIV-1 has a complex population structure, and the effects of this structure on linkage disequilibrium were investigated by estimating within- and among-subpopulation components of variance in linkage disequilibrium. The amino acid covariation previously reported is explained by differences in amino acid frequencies among virus subpopulations in different patients and by nonsystematic disequilibrium among patients. Disequilibrium within patients appears to be entirely due to differences in amino acid frequencies among sampling time points and among chemokine coreceptor usage phenotypes of virus particles, but not source tissues. Positive selection explains differences in allele frequencies among time points and phenotypes, indicating that these differences are adaptive rather than due to genetic drift. However, the absence of a correlation between linkage disequilibrium and phenotype suggests that fitness epistasis is an unlikely cause of disequilibrium. Indeed, when population structure is removed by analyzing sequences from a single time point and phenotype, no disequilibrium is detectable within patients. These results caution against interpreting amino acid covariation and coevolution as evidence for fitness epistasis.
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15
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Repeated bottleneck transfers can lead to non-cytocidal forms of a cytopathic virus: implications for viral extinction. J Mol Biol 2007; 376:367-79. [PMID: 18158159 DOI: 10.1016/j.jmb.2007.11.042] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/12/2007] [Accepted: 11/13/2007] [Indexed: 11/23/2022]
Abstract
Several biological subclones of a biological clone of foot-and-mouth disease virus (FMDV) have been subjected to many plaque-to-plaque (serial bottleneck) transfers in cell culture. At transfer 190 to 409, clones underwent a transition towards a non-cytolytic (NC) phenotype in which the virus was unable to produce plaques, representing at least a 140-fold reduction in specific infectivity relative to the parental biological clone. NC clones, however, were competent in RNA replication and established a persistent infection in cell culture without an intervening cytolytic phase. In one clone, the transition to the NC phenotype was associated with the elongation of an internal oligodenylate tract that precedes the second functional AUG translation initiation codon. The pattern of mutations and their distribution along the FMDV genome of the clones subjected to serial bottleneck transfers were compared with the pattern of mutations in FMDV clones subjected to large population passages. Both the corrected ratios of non-synonymous to synonymous mutations and some specific mutations in coding and non-coding regions suggest participation of positive selection during large population passages and not during bottleneck transfers. Some mutations in the clones that attained the NC phenotype were located in genomic regions affecting the capacity of FMDV to kill BHK-21 cells. The resistance to extinction of clones subjected to plaque-to-plaque transfers marks a striking contrast with regard to the ease of extinction mediated by lethal mutagenesis. The results document a major phenotypic transition of a virus as a result of serial bottleneck events.
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16
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de la Iglesia F, Elena SF. Fitness declines in Tobacco etch virus upon serial bottleneck transfers. J Virol 2007; 81:4941-7. [PMID: 17344305 PMCID: PMC1900225 DOI: 10.1128/jvi.02528-06] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 02/23/2007] [Indexed: 01/10/2023] Open
Abstract
It has been well established that populations of RNA viruses transmitted throughout serial bottlenecks suffer from significant fitness declines as a consequence of the accumulation of deleterious mutations by the onset of Muller's ratchet. Bottlenecks are unavoidably linked to different steps of the infectious cycle of most plant RNA viruses, such as vector-mediated transmissions and systemic colonization of new leaves. Here we report evidence for fitness declines by the accumulation of deleterious mutations in the potyvirus Tobacco etch virus (TEV). TEV was inoculated into the nonsystemic host Chenopodium quinoa, and local lesions were isolated and used to initiate 20 independent mutation accumulation lineages. Weekly, a random lesion from each lineage was isolated and used to inoculate the next set of plants. At each transfer, the Malthusian growth rate was estimated. After 11 consecutive transfers, all lineages suffered significant fitness losses, and one even became extinct. The average rate of fitness decline was 5% per day. The average pattern of fitness decline was consistent with antagonistic epistasis between deleterious mutations, as postulated for antiredundant genomes. Temporal fitness fluctuations were not explained by random noise but reflected more complex underlying processes related to emergence and self-organization phenomena.
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Affiliation(s)
- Francisca de la Iglesia
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 València, Spain
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17
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Parris GE. Mechanism and history of evolution of symbiotic HIV strains into lethal pandemic strains: the key event may have been a 1927 trial of pamaquine in Leopoldville (Kinshasa), Congo. Med Hypotheses 2007; 69:838-48. [PMID: 17368749 DOI: 10.1016/j.mehy.2007.01.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 01/24/2007] [Indexed: 02/04/2023]
Abstract
In previous papers, I have rejected both the zoonosis and the serial transfer hypotheses of the origin and evolution of the current lethal pandemic strains of HIV. The hypothesis that fits the critical observations is that all the human and nonhuman primate species in central Africa (an area of hyper-endemic malaria) have shared (through inter-species transfers) a "primate T-cell retrovirus" (PTRV), which has adapted to each host species. This retrovirus is believed to assist primate T-cells attack the liver stage of the malaria infection. Each geographic region has a dominant primate host and a characteristic virus. Starting in 1955 and continuing into the late 1970s, chloroquine was provided by the WHO and used for prophylaxis against malaria. Chloroquine has a number of biochemical activities but two of the most important are blocking transcription of cellular genes and proviruses activated by NF-kappaB and blocking the glycosylation of surface proteins on viruses and cells. Concurrent with the development of resistance of the malaria parasite to chloroquine, HIV strains were quickly selected, which have enhanced transcription rates (by inclusion of multiple kappaB binding sites in their long terminal repeats by recombination) and enhanced infectivity (fusogenicity) (most likely by mutations in multiple viral genes that regulate glycosylation of Env). There also may have been mutations that enhanced activation of NF-kappaB in the host cell. These changes in the retrovirus genome were not manifest in effects of the HIV strains as long as the hosts were under the influence of chloroquine. But, when the virus infects people who are not protected by chloroquine, the virus multiplies more rapidly and is more communicable. Fortunately, most of these strains (i.e., HIV-2 groups, and HIV-1 O and HIV-1 N) self-regulate (i.e., infected cells kill infected cells) well enough that viral loads remain subdued and bystander cells of the immune system are not excessively attrited. In the case of HIV-1 group M, however, there is more going on. Following the work of Korber et al. on the phylogenetics of HIV-1 groups M, I reach the conclusion that the major subgroups giving rise to the worldwide pandemic, were founded in a 1927 clinical trial of pamaquine (plasmoquine) in Leopoldville (Kinshasa). This drug is much more toxic that chloroquine and appears to have strongly selected for resistance to apoptosis in infected cells, which allows these subgroups to attrite bystander cells leading to AIDS.
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18
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Carrasco P, Daròs JA, Agudelo-Romero P, Elena SF. A real-time RT-PCR assay for quantifying the fitness of tobacco etch virus in competition experiments. J Virol Methods 2007; 139:181-8. [PMID: 17092574 DOI: 10.1016/j.jviromet.2006.09.020] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 09/25/2006] [Accepted: 09/26/2006] [Indexed: 11/16/2022]
Abstract
Relative fitness determination has become a standard tool in experimental virus evolution studies. In this type of studies, the tested strain is mixed with a reference strain, which differs in an easy-to-score and genetically stable marker, and allowed to compete for a limited common pool of resources during a given number of generations. In this report, a TaqMan real-time PCR methodology is proposed for quantifying the relative fitness of tobacco etch potyvirus strains (TEV) in in planta mixed infections with a reference TEV strain. Two different forward primers along with a common reverse one are used into separated reactions mixes from the same RNA preparation. The reference strain, named TEV-PC1, was genetically engineered to carry a neutral marker in a highly conserved region of the RNA polymerase NIb gene. This marker allows tracking the frequency of both competitors during competition experiments by real-time quantitative PCR using specific primers. Both the reproducibility and sensitivity of the method have been explored. Reproducibility was assessed by running multiple competition experiments for the same genotype. Sensitivity was assessed by comparing the results of competition experiments against TEV-PC1 of 24 single-nucleotide substitutions mutants.
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Affiliation(s)
- P Carrasco
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Avenida de los naranjos s/n, 46022 València, Spain.
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19
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Bastolla U, Porto M, Roman HE, Vendruscolo M. Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity. STRUCTURAL APPROACHES TO SEQUENCE EVOLUTION 2007. [PMCID: PMC7123777 DOI: 10.1007/978-3-540-35306-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Ugo Bastolla
- Fac. de Ciencias, Universidad Autonoma Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Markus Porto
- Institut für Festkörperphysik, TU Darmstadt, Hochschulstr. 8, 64289 Darmstadt, Germany
| | - H. Eduardo Roman
- Dipartimento di Fisica, Universita di Milano-Bicocca, Piazza della Scienza 3, 29126 Milano, Italy
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
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20
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Galkin AN, Gagarina EY, Lukyanova NS, Danilova TV. Full-length genomic sequencing and analysis of four HIV type 1 subtype B isolates circulating in the territory of Russia. AIDS Res Hum Retroviruses 2006; 22:1192-7. [PMID: 17147510 DOI: 10.1089/aid.2006.22.1192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe four full-length genomic sequences of HIV-1 subtype B isolates from Russia. These full-length HIV-1 genomes were amplified by nested polymerase chain reaction and sequenced. The sequences obtained were subjected to neighbor-joining phylogenetic analysis using a Kimura two-parameter model and to detailed sequence analysis. Comparison of the sequences obtained with 68 near full-length HIV-1 subtype B sequences from different geographic regions of the world revealed that isolates from Russia did not cluster significantly with other subtype B genomes. Sequences AY819715 and AY751407 significantly formed one cluster, which indicates their close similarity. The HIV-1 genomes obtained from Russia did not form a distinct homogeneous group inside subtype B. Their genetic diversity probably reflects the result of multiple introduction events of different subtype B strains to Russia. Sequences AY819715 and AY751406 possess some features of viruses from long-term survivors, such as specific extensions of the Env V2 region.
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21
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da Silva J. Site-specific amino acid frequency, fitness and the mutational landscape model of adaptation in human immunodeficiency virus type 1. Genetics 2006; 174:1689-94. [PMID: 16849594 PMCID: PMC1667049 DOI: 10.1534/genetics.106.062885] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of the intensely studied HIV-1 gp120 V3 protein region reveals that the among-population mean site-specific frequency of an amino acid is a measure of its relative marginal fitness. This surprising result may arise if populations are displaced from mutation-selection equilibrium by fluctuating selection and if the probability of fixation of a beneficial amino acid is proportional to its selection coefficient.
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Affiliation(s)
- Jack da Silva
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia.
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22
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Domingo E, Gonzalez-Lopez C, Pariente N, Airaksinen A, Escarmís C. Population dynamics of RNA viruses: the essential contribution of mutant spectra. ARCHIVES OF VIROLOGY. SUPPLEMENTUM 2006:59-71. [PMID: 16355868 DOI: 10.1007/3-211-29981-5_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Cells and their viral and cellular parasites are genetically highly diverse, and their genomes contain signs of past and present variation and mobility. The great adaptive potential of viruses, conferred on them by high mutation rates and quasispecies dynamics, demands new strategies for viral disease prevention and control. This necessitates a more detailed knowledge of viral population structure and dynamics. Here we review studies with the important animal pathogen Foot-and-mouth disease virus (FMDV) that document modulating effects of the mutant spectra that compose viral populations. As a consequence of interactions within mutant spectra, enhanced mutagenesis may lead to viral extinction, and this is currently investigated as a new antiviral strategy, termed virus entry into error catastrophe.
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Affiliation(s)
- E Domingo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
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23
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Quiñones-Mateu ME, Arts EJ. Virus fitness: concept, quantification, and application to HIV population dynamics. Curr Top Microbiol Immunol 2006; 299:83-140. [PMID: 16568897 DOI: 10.1007/3-540-26397-7_4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Viral fitness has been broadly studied during the past three decades, mainly to test evolutionary models and population theories difficult to analyze and interpret with more complex organisms. More recent studies, however, are focused in the role of fitness on viral transmission, pathogenesis, and drug resistance. Here, we used human immunodeficiency virus (HIV) as one of the most relevant models to evaluate the importance of viral quasispecies and fitness in HIV evolution, population dynamics, disease progression, and potential clinical implications.
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Affiliation(s)
- M E Quiñones-Mateu
- Department of Molecular Genetics, Section Virology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue/NN10, Cleveland, OH 44195, USA.
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24
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Escarmís C, Lázaro E, Manrubia SC. Population bottlenecks in quasispecies dynamics. Curr Top Microbiol Immunol 2006; 299:141-70. [PMID: 16568898 DOI: 10.1007/3-540-26397-7_5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The characteristics of natural populations result from different stochastic and deterministic processes that include reproduction with error, selection, and genetic drift. In particular, population fluctuations constitute a stochastic process that may play a very relevant role in shaping the structure of populations. For example, it is expected that small asexual populations will accumulate mutations at a higher rate than larger ones. As a consequence, in any population the fixation of mutations is accelerated when environmental conditions cause population bottlenecks. Bottlenecks have been relatively frequent in the history of life and it is generally accepted that they are highly relevant for speciation. Although population bottlenecks can occur in any species, their effects are more noticeable in organisms that form large and heterogeneous populations, such as RNA viral quasispecies. Bottlenecks can also positively select and isolate particles that still keep the ability to infect cells from a disorganized population created by crossing the error threshold.
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Affiliation(s)
- C Escarmís
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
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25
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Elena SF, Carrasco P, Daròs JA, Sanjuán R. Mechanisms of genetic robustness in RNA viruses. EMBO Rep 2006; 7:168-73. [PMID: 16452927 PMCID: PMC1369264 DOI: 10.1038/sj.embor.7400636] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Accepted: 11/30/2005] [Indexed: 01/17/2023] Open
Abstract
Two key features of RNA viruses are their compacted genomes and their high mutation rate. Accordingly, deleterious mutations are common and have an enormous impact on viral fitness. In their multicellular hosts, robustness can be achieved by genomic redundancy, including gene duplication, diploidy, alternative metabolic pathways and biochemical buffering mechanisms. However, here we review evidence suggesting that during RNA virus evolution, alternative robustness mechanisms may have been selected. After briefly describing how genetic robustness can be quantified, we discuss mechanisms of intrinsic robustness arising as consequences of RNA-genome architecture, replication peculiarities and quasi-species population dynamics. These intrinsic robustness mechanisms operate efficiently at the population level, despite the mutational sensitivity shown by individual genomes. Finally, we discuss the possibility that viruses might exploit cellular buffering mechanisms for their own benefit, producing a sort of extrinsic robustness.
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Affiliation(s)
- Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n, 46022 València, Spain.
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26
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Ariën KK, Abraha A, Quiñones-Mateu ME, Kestens L, Vanham G, Arts EJ. The replicative fitness of primary human immunodeficiency virus type 1 (HIV-1) group M, HIV-1 group O, and HIV-2 isolates. J Virol 2005; 79:8979-90. [PMID: 15994792 PMCID: PMC1168791 DOI: 10.1128/jvi.79.14.8979-8990.2005] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The main (M) group of human immunodeficiency virus type 1 (HIV-1) is responsible for the global AIDS epidemic while HIV-1 group O (outlier) and HIV type 2 are endemic only in west and central Africa. The failure of HIV-2 and especially HIV-1 group O to spread following the initial zoonotic jumps is not well understood. This study was designed to examine the relative replicative capacities between these human lentiviruses. A pairwise competition experiment was performed with peripheral blood mononuclear cells with eight HIV-2 isolates, 6 group O viruses, and 15 group M viruses of subtype A (2 viruses), B (5 viruses), C (4 viruses), D (2 viruses) and CRF01_AE (2 viruses). HIV-1 group M isolates of any subtype were typically 100-fold-more fit than group O or HIV-2 strains when competed in peripheral blood mononuclear cells from various humans. This order in replicative fitness was also observed when virus pairs were added to human dendritic cells and then cocultured with primary, quiescent T cells, which is the model for HIV-1 transmission. These results suggest that reduced replicative and transmission fitness may be contributing to the low prevalence and limited geographical spread of HIV-2 and group O HIV-1 in the human population.
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Affiliation(s)
- Kevin K Ariën
- Centre for AIDS Research, Case Western Reserve University, Cleveland, OH, USA
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27
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Yuste E, Bordería AV, Domingo E, López-Galíndez C. Few mutations in the 5' leader region mediate fitness recovery of debilitated human immunodeficiency type 1 viruses. J Virol 2005; 79:5421-7. [PMID: 15827156 PMCID: PMC1082768 DOI: 10.1128/jvi.79.9.5421-5427.2005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Repeated bottleneck passages of RNA viruses result in fitness losses due to the accumulation of deleterious mutations. In contrast, repeated transfers of large virus populations result in exponential fitness increases. Human immunodeficiency virus type 1 (HIV-1) manifested a drastic fitness loss after a limited number of plaque-to-plaque transfers in MT-4 cells. An analysis of the mutations associated with fitness loss in four debilitated clones revealed mutation frequencies in gag that were threefold higher than those in env. We now show an increase in the fitness of the debilitated HIV-1 clones by repeated passages of large populations. An analysis of the entire genomic nucleotide sequences of these populations showed that few mutations, from two to seven per clone, mediated fitness recovery. Eight of the 20 mutations affected coding regions, mainly by the introduction of nonsynonymous mutations (75%). However, most of the mutations accumulated during fitness recovery (12 of 20) were located in the 5' untranslated leader region of the genome, and more specifically, in the primer binding site (PBS) loop. Two of the viruses incorporated the same mutation in the primer activation signal in the PBS loop, which is critical for the tRNA3Lys-mediated initiation of reverse transcription. Moreover, 25% of the mutations observed were reversions. This fact, together with the presence of a large proportion of nonsynonymous replacements, may disclose the operation, during large population passages, of strong positive selection for optimal HIV-1 replication, which seems to be primarily affected by binding of the tRNA to the PBS and the initiation of reverse transcription.
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Affiliation(s)
- Eloísa Yuste
- Centro de Biología Molecular "Severo Ochoa," CSIC-UAM, Universidad Autónoma, Cantoblanco, Madrid, Spain
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28
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Abstract
The extinction of foot-and-mouth disease virus (FMDV) is strongly influenced by mutation rates, types of mutations, relative viral fitness and virus population regimens during infection. Here we review experimental results and theoretical models that describe a contrast between the effective extinction of FMDV subjected to increased mutagenesis, and the remarkable resistance to extinction of the same and related FMDV clones subjected to serial bottleneck events. The results suggest procedures to master key parameters to develop effective antiviral strategies based on virus entry into error catastrophe.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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29
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Manrubia SC, Escarmís C, Domingo E, Lázaro E. High mutation rates, bottlenecks, and robustness of RNA viral quasispecies. Gene 2005; 347:273-82. [PMID: 15777632 DOI: 10.1016/j.gene.2004.12.033] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Revised: 12/13/2004] [Accepted: 12/21/2004] [Indexed: 10/25/2022]
Abstract
Population bottlenecks are stochastic events that strongly condition the structure and evolution of natural populations. Their effects are readily observable in highly heterogeneous populations, such as RNA viruses, since bottlenecks cause a fast accumulation of mutations. Considering that most mutations are deleterious, it was predicted that the frequent application of bottlenecks would yield a population unable to replicate. However, in vitro as well as in vivo systems evolving through bottlenecks present a remarkable resistance to extinction. This observation reveals the robustness of RNA viruses and points to the existence of internal mechanisms which must confer a high degree of adaptability to fast mutating populations. In this contribution, we review experimental observations regarding the survival of RNA viruses, both in laboratory experiments and in natural populations. By means of a simple theoretical model of evolution which incorporates strong reductions of the population size, we explore the relationship between the number of replication rounds that a single founder particle undergoes before the next bottleneck is applied, and the mutation rate in a particular environment. Our numerical results reveal that the mutation rate has evolved in a concerted way with the degree of optimization achieved by the population originated from the founder particle. We hypothesize that this mechanism generates a mutation-selection equilibrium in natural populations that maximizes adaptability while maintaining their structure.
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Affiliation(s)
- Susanna C Manrubia
- Centro de Astrobiología, INTA-CSIC, Instituto Nacional de Técnica Aeroespacial, Ctra de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain
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Li H, Roossinck MJ. Genetic bottlenecks reduce population variation in an experimental RNA virus population. J Virol 2004; 78:10582-7. [PMID: 15367625 PMCID: PMC516416 DOI: 10.1128/jvi.78.19.10582-10587.2004] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Accepted: 04/30/2004] [Indexed: 11/20/2022] Open
Abstract
Genetic bottlenecks are stochastic events that limit genetic variation in a population and result in founding populations that can lead to genetic drift. Evidence of past genetic bottlenecks in numerous biological systems, from mammals to viruses, has been described. In this study, we used an artificial population of Cucumber mosaic virus consisting of 12 restriction enzyme marker-bearing mutants. This population was inoculated onto young leaves of tobacco plants and monitored throughout the course of systemic infection. We show here that the genetic variation in a defined population of an RNA virus is significantly, stochastically, and reproducibly reduced during the systemic infection process, providing clear evidence of a genetic bottleneck.
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Affiliation(s)
- Hongye Li
- Plant Biology Division, The Samuel Roberts Noble Foundation, P.O. Box 2180, Ardmore, OK 73402, USA
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31
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Novella IS, Ebendick-Corpus BE. Molecular Basis of Fitness Loss and Fitness Recovery in Vesicular Stomatitis Virus. J Mol Biol 2004; 342:1423-30. [PMID: 15364571 DOI: 10.1016/j.jmb.2004.08.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Revised: 08/03/2004] [Accepted: 08/03/2004] [Indexed: 11/19/2022]
Abstract
Viral populations subjected to repeated genetic bottleneck accumulate deleterious mutations in a process known as Muller's ratchet. Asexual viruses, such as vesicular stomatitis virus (VSV) can recover from Muller's ratchet by replication with large effective population sizes. However, mutants with a history of bottleneck transmissions often show decreased adaptability when compared to non-bottlenecked populations. We have generated a collection of bottlenecked mutants and allowed them to recover by large population passages. We have characterized fitness changes and the complete genomes of these strains. Mutations accumulated during the operation of Muller's ratchet led to the identification of two potential mutational hot spots in the VSV genome. As in other viral systems, transitions were more common than transversions. Both back mutation and compensatory mutations contributed to recovery, although a significant level of fitness increase was observed in nine of the 13 bottlenecked strains with no obvious changes in the consensus sequence. Additional replication of three strains resulted in the fixation of single point mutations. Only two mutations previously found in non-bottlenecked, high-fitness populations that had been adapting to the same environment were identified in the recovered strains.
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Affiliation(s)
- I S Novella
- Department of Microbiology and Immunology, Medical College of Ohio, Toledo, OH 43614, USA.
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Lázaro E, Escarmís C, Pérez-Mercader J, Manrubia SC, Domingo E. Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss. Proc Natl Acad Sci U S A 2003; 100:10830-5. [PMID: 12960384 PMCID: PMC196888 DOI: 10.1073/pnas.1332668100] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA viruses display high mutation rates and their populations replicate as dynamic and complex mutant distributions, termed viral quasispecies. Repeated genetic bottlenecks, which experimentally are carried out through serial plaque-to-plaque transfers of the virus, lead to fitness decrease (measured here as diminished capacity to produce infectious progeny). Here we report an analysis of fitness evolution of several low fitness foot-and-mouth disease virus clones subjected to 50 plaque-to-plaque transfers. Unexpectedly, fitness decrease, rather than being continuous and monotonic, displayed a fluctuating pattern, which was influenced by both the virus and the state of the host cell as shown by effects of recent cell passage history. The amplitude of the fluctuations increased as fitness decreased, resulting in a remarkable resistance of virus to extinction. Whereas the frequency distribution of fitness in control (independent) experiments follows a log-normal distribution, the probability of fitness values in the evolving bottlenecked populations fitted a Weibull distribution. We suggest that multiple functions of viral genomic RNA and its encoded proteins, subjected to high mutational pressure, interact with cellular components to produce this nontrivial, fluctuating pattern.
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Affiliation(s)
- Ester Lázaro
- Centro de Astrobiología (Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial), Associated with the National Aeronautics and Space Administration Astrobiology Institute, Torrejón de Ardoz, Madrid, Spain
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Domingo E, Escarmís C, Baranowski E, Ruiz-Jarabo CM, Carrillo E, Núñez JI, Sobrino F. Evolution of foot-and-mouth disease virus. Virus Res 2003; 91:47-63. [PMID: 12527437 DOI: 10.1016/s0168-1702(02)00259-9] [Citation(s) in RCA: 221] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Foot-and-mouth disease virus evolution is strongly influenced by high mutation rates and a quasispecies dynamics. Mutant swarms are subjected to positive selection, negative selection and random drift of genomes. Adaptation is the result of selective amplification of subpopulations of genomes. The extent of adaptation to a given environment is quantified by a relative fitness value. Fitness values depend on the virus and its physical and biological environment. Generally, infections involving large population passages result in fitness gain and population bottlenecks lead to fitness loss. Very different types of mutations tend to accumulate in the foot-and-mouth disease virus (FMDV) genome depending on the virus population size during replication. Quasispecies dynamics predict higher probability of success of antiviral strategies based on multivalent vaccines and combination therapy, and this has been supported by clinical and veterinary practice. Quasispecies suggest also new antiviral strategies based on virus entry into error catastrophe, and such procedures are under investigation. Studies with FMDV have contributed to the understanding of quasispecies dynamics and some of its biological implications.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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Liang XZ, Lee BTK, Wong SM. Covariation in the capsid protein of hibiscus chlorotic ringspot virus induced by serial passaging in a host that restricts movement leads to avirulence in its systemic host. J Virol 2002; 76:12320-4. [PMID: 12414972 PMCID: PMC136860 DOI: 10.1128/jvi.76.23.12320-12324.2002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hibiscus chlorotic ringspot virus (HCRSV) from naturally infected Hibiscus rosa-sinensis L. loses virulence in its experimental systemic host Hibiscus cannabinus L. (kenaf) after serial passages in a local lesion host Chenopodium quinoa. Here we report the genetic changes responsible for the loss of virulence at the molecular level. A remarkable covariation of eight site-specific amino acids was found in the HCRSV capsid protein (CP) after serial passages in C. quinoa: Val(49)-->Ile, Ile(95)-->Val, Lys(270)-->Arg, Gly(272)-->Asp, Tyr(274)-->His, Ala(311)-->Asp, Asp(334)-->Ala, and Ala(335)-->Thr. Covariation of at least three of the eight amino acids, Val(49), Ile(95), and Lys(270), caused the virus to become avirulent in kenaf. Interestingly, the nature of the covariation was consistent and reproducible at each serial passage. These data indicate that the nonsynonymous substitutions of amino acids in the HCRSV CP after serial passages in C. quinoa are not likely to be random events but may be due to host-associated positive selection or accelerated genetic drift. The observed interdependence among the three amino acids leading to avirulence in kenaf may have implications for structural or functional relationships in this virus-host interaction.
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Affiliation(s)
- Xiao-Zhen Liang
- Department of Biological Sciences, The National University of Singapore, Singapore 117543, Republic of Singapore
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Lázaro E, Escarmís C, Domingo E, Manrubia SC. Modeling viral genome fitness evolution associated with serial bottleneck events: evidence of stationary states of fitness. J Virol 2002; 76:8675-81. [PMID: 12163587 PMCID: PMC136412 DOI: 10.1128/jvi.76.17.8675-8681.2002] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Evolution of fitness values upon replication of viral populations is strongly influenced by the size of the virus population that participates in the infections. While large population passages often result in fitness gains, repeated plaque-to-plaque transfers result in average fitness losses. Here we develop a numerical model that describes fitness evolution of viral clones subjected to serial bottleneck events. The model predicts a biphasic evolution of fitness values in that a period of exponential decrease is followed by a stationary state in which fitness values display large fluctuations around an average constant value. This biphasic evolution is in agreement with experimental results of serial plaque-to-plaque transfers carried out with foot-and-mouth disease virus (FMDV) in cell culture. The existence of a stationary phase of fitness values has been further documented by serial plaque-to-plaque transfers of FMDV clones that had reached very low relative fitness values. The statistical properties of the stationary state depend on several parameters of the model, such as the probability of advantageous versus deleterious mutations, initial fitness, and the number of replication rounds. In particular, the size of the bottleneck is critical for determining the trend of fitness evolution.
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Affiliation(s)
- Ester Lázaro
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain
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Domingo E, Ruiz-Jarabo CM, Sierra S, Arias A, Pariente N, Baranowski E, Escarmis C. Emergence and selection of RNA virus variants: memory and extinction. Virus Res 2002; 82:39-44. [PMID: 11885948 DOI: 10.1016/s0168-1702(01)00385-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two features of viral quasispecies are reviewed: the presence of memory genomes as minority components of their mutant spectra, and viral extinction due to enhanced mutagenesis. Memory has been documented with several genetic markers of the important animal picornavirus foot-and-mouth disease virus (FMDV). The presence of memory genomes in viral quasispecies may accelerate their adaptive response whenever a selective constraint has already been experienced by a viral population during previous stages of its evolution. Enhanced mutagenesis has been shown to lead to losses of infectivity of a number of RNA viruses: poliovirus, vesicular stomatitis virus, human immunodeficiency virus type 1 and FMDV. These observations, based on the theoretical prediction of the existence of a copying error-threshold for maintenance of genetic information, may contribute to the development of a new antiviral strategy.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular, Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Spain.
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Escarmís C, Gómez-Mariano G, Dávila M, Lázaro E, Domingo E. Resistance to extinction of low fitness virus subjected to plaque-to-plaque transfers: diversification by mutation clustering. J Mol Biol 2002; 315:647-61. [PMID: 11812137 DOI: 10.1006/jmbi.2001.5259] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plaque-to-plaque transfers of RNA viruses lead to accumulation of mutations and fitness decrease. To test whether continuing plaque-to-plaque transfers would lead to viral extinction, we have subjected several low fitness foot-and-mouth disease virus (FMDV) clones to up to 130 successive plaque transfers, and have analyzed the evolution of plaque titers and genomic nucleotide sequences. No case of viral extinction could be documented. Some low fitness clones that posses an internal poly(A) tract evaded extinction by modifying the length or base composition of the poly(A) tract. The comparison of entire genomic sequences of FMDV clones at increasing plaque transfer number revealed that mutations accumulated at a uniform rate, and that they were distributed unevenly along the genome. Clusters of mutations were identified at different genomic sites in two plaque transfer lineages. Mutation clustering appears to occur stochastically and could not be related to fixation of compensatory mutations. The results document resistance of viral clones to extinction, and suggest that mutation clustering may be a mechanism of genetic diversification of low fitness virus.
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Affiliation(s)
- Cristina Escarmís
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, Universidad Autónoma de Madrid, 28049, Spain
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Ruíz-Jarabo CM, Arias A, Molina-París C, Briones C, Baranowski E, Escarmís C, Domingo E. Duration and fitness dependence of quasispecies memory. J Mol Biol 2002; 315:285-96. [PMID: 11786012 DOI: 10.1006/jmbi.2001.5232] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The duration and fitness dependence of memory in viral quasispecies evolving in cell culture have been investigated using two genetic markers of foot-and-mouth disease virus (FMDV). In lineages of antigenic variant FMDV RED, which reverted to FMDV RGD, memory FMDV RED genomes were detected after 50 infectious cycles, and memory level was fitness dependent. In growth-competition experiments between a reference FMDV RGD and two different FMDV RED populations, a 7.6-fold higher fitness of the initial FMDV RED population resulted in 30 to 100-fold higher memory level. In lineages of low-fitness clones containing an elongated internal polyadenylate tract, revertants lacking excess adenylate residues became dominant by passage 20. However, genomes including a larger number of adenylate residues were detected as memory genomes after at least 150 infectious cycles. Thus, quasispecies memory can be durable and is fitness dependent, as predicted from the growth competition of two mutant forms of a genome. An understanding of factors influencing quasispecies memory levels and duration may have implications for the extended diagnosis of viruses based on the quantification of minority genomes.
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Affiliation(s)
- Carmen M Ruíz-Jarabo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco 28049, Spain
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Pariente N, Sierra S, Lowenstein PR, Domingo E. Efficient virus extinction by combinations of a mutagen and antiviral inhibitors. J Virol 2001; 75:9723-30. [PMID: 11559805 PMCID: PMC114544 DOI: 10.1128/jvi.75.20.9723-9730.2001] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of combinations of the mutagenic base analog 5-fluorouracil (FU) and the antiviral inhibitors guanidine hydrochloride (G) and heparin (H) on the infectivity of foot-and-mouth disease virus (FMDV) in cell culture has been investigated. Related FMDV clones differing up to 10(6)-fold in relative fitness in BHK-21 cells have been compared. Systematic extinction of intermediate fitness virus was attained with a combination of FU and G but not with the mutagen or the inhibitor alone. Systematic extinction of high-fitness FMDV required the combination of FU, G, and H. FMDV showing high relative fitness in BHK-21 cells but decreased replicative ability in CHO cells behaved as a low-fitness virus with regard to extinction mutagenesis in CHO cells. This confirms that relative fitness, rather than a specific genomic sequence, determines the FMDV response to enhanced mutagenesis. Mutant spectrum analysis of several genomic regions from a preextinction population showed a statistically significant increase in the number of mutations compared with virus passaged in parallel in the absence of FU and inhibitors. Also, in a preextinction population the types of mutations that can be attributed to the mutagenic action of FU were significantly more frequent than other mutation types. The results suggest that combinations of mutagenic agents and antiviral inhibitors can effectively drive high-fitness virus into extinction.
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Affiliation(s)
- N Pariente
- Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Janini M, Rogers M, Birx DR, McCutchan FE. Human immunodeficiency virus type 1 DNA sequences genetically damaged by hypermutation are often abundant in patient peripheral blood mononuclear cells and may be generated during near-simultaneous infection and activation of CD4(+) T cells. J Virol 2001; 75:7973-86. [PMID: 11483742 PMCID: PMC115041 DOI: 10.1128/jvi.75.17.7973-7986.2001] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
G-to-A hypermutation has been sporadically observed in human immunodeficiency virus type 1 (HIV-1) proviral sequences from patient peripheral blood mononuclear cells (PBMC) and virus cultures but has not been systematically evaluated. PCR primers matched to normal and hypermutated sequences were used in conjunction with an agarose gel electrophoresis system incorporating an AT-binding dye to visualize, separate, clone, and sequence hypermutated and normal sequences in the 297-bp HIV-1 protease gene amplified from patient PBMC. Among 53 patients, including individuals infected with subtypes A through D and at different clinical stages, at least 43% of patients harbored abundant hypermutated, along with normal, protease genes. In 70 hypermutated sequences, saturation of G residues in the GA or GG dinucleotide context ranged from 20 to 94%. Levels of other mutants were not elevated, and G-to-A replacement was entirely restricted to GA or GG, and not GC or GT, dinucleotides. Sixty-nine of 70 hypermutated and 3 of 149 normal sequences had in-frame stop codons. To investigate the conditions under which hypermutation occurs in cell cultures, purified CD4(+) T cells from normal donors were infected with cloned NL4-3 virus stocks at various times before and after phytohemagglutinin (PHA) activation. Hypermutation was pronounced when HIV-1 infection occurred simultaneously with, or a few hours after, PHA activation, but after 12 h or more after PHA activation, most HIV-1 sequences were normal. Hypermutated sequences generated in culture corresponded exactly in all parameters to those obtained from patient PBMC. Near-simultaneous activation and infection of CD4(+) T cells may represent a window of susceptibility where the informational content of HIV-1 sequences is lost due to hypermutation.
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Affiliation(s)
- M Janini
- Henry M. Jackson Foundation, Rockville, Maryland 20850, USA.
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Schneider WL, Roossinck MJ. Genetic diversity in RNA virus quasispecies is controlled by host-virus interactions. J Virol 2001; 75:6566-71. [PMID: 11413324 PMCID: PMC114380 DOI: 10.1128/jvi.75.14.6566-6571.2001] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many RNA viruses have genetically diverse populations known as quasispecies. Important biological characteristics may be related to the levels of diversity in the quasispecies (quasispecies cloud size), including adaptability and host range. Previous work using Tobacco mosaic virus and Cucumber mosaic virus indicated that evolutionarily related viruses have very different levels of diversity in a common host. The quasispecies cloud size for these viruses remained constant throughout serial passages. Inoculation of these viruses on a number of hosts demonstrated that quasispecies cloud size is not constant for these viruses but appears to be dependent on the host. The quasispecies cloud size remained constant as long as the viruses were maintained on a given host. Shifting the virus between hosts resulted in a change in cloud size to levels associated with the new host. Quasispecies cloud size for these viruses is related to host-virus interactions, and understanding these interactions may facilitate the prediction and prevention of emerging viral diseases.
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Affiliation(s)
- W L Schneider
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA
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