1
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Wu J, Bisaro DM. Cell-cell communication and initial population composition shape the structure of potato spindle tuber viroid quasispecies. THE PLANT CELL 2024; 36:1036-1055. [PMID: 38252648 PMCID: PMC10980348 DOI: 10.1093/plcell/koae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
RNA viruses and viroids replicate with high mutation rates, forming quasispecies, population of variants centered around dominant sequences. The mechanisms governing quasispecies remain unclear. Plasmodesmata regulate viroid movement and were hypothesized to impact viroid quasispecies. Here, we sequenced the progeny of potato spindle tuber viroid intermediate (PSTVd-I) strain from mature guard cells lacking plasmodesmal connections and from in vitro-cultivated mesophyll cell protoplasts from systemic leaves of early-infected tomato (Solanum lycopersicum) plants. Remarkably, more variants accumulated in guard cells compared to whole leaves. Similarly, after extended cell culture, we observed more variants in cultivated mesophyll protoplasts. Coinfection and single-cell sequencing experiments demonstrated that the same plant cell can be infected multiple times by the same or different PSTVd sequences. To study the impact of initial population composition on PSTVd-I quasispecies, we conducted coinfections with PSTVd-I and variants. Two inoculum ratios (10:1 or 1:10) established quasispecies with or without PSTVd-I as the master sequence. In the absence of the master sequence, the percentage of novel variants initially increased. Moreover, a 1:1 PSTVd-I/variant RNA ratio resulted in PSTVd-I dominating (>50%), while the variants reached 20%. After PSTVd-I-only infection, the variants reached around 10%, while after variant-only infection, the variants were significantly more than 10%. These results emphasize the role of cell-to-cell communication and initial population composition in shaping PSTVd quasispecies.
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Affiliation(s)
- Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
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2
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Jeronimo PMC, Aksenen CF, Duarte IO, Lins RD, Miyajima F. Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation. J Virol 2024; 98:e0140423. [PMID: 38088350 PMCID: PMC10804945 DOI: 10.1128/jvi.01404-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Coronaviruses are large RNA viruses that can infect and spread among humans and animals. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019, has evolved since its first detection in December 2019. Deletions are a common occurrence in SARS-CoV-2 evolution, particularly in specific genomic sites, and may be associated with the emergence of highly competent lineages. While deletions typically have a negative impact on viral fitness, some persist and become fixed in viral populations, indicating that they may confer advantageous benefits for the virus's adaptive evolution. This work presents a literature review and data analysis on structural losses in the SARS-CoV-2 genome and the potential relevance of specific signatures for enhanced viral fitness and spread.
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Affiliation(s)
| | - Cleber Furtado Aksenen
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Igor Oliveira Duarte
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Roberto D. Lins
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Pernambuco, Recife, Brazil
| | - Fabio Miyajima
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
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3
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Illingworth CJR, Guerra-Assuncao JA, Gregg S, Charles O, Pang J, Roy S, Abdelnabi R, Neyts J, Breuer J. Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus Evol 2024; 10:veae001. [PMID: 38486802 PMCID: PMC10939363 DOI: 10.1093/ve/veae001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 11/23/2023] [Accepted: 01/03/2024] [Indexed: 03/17/2024] Open
Abstract
Mutagenic antiviral drugs have shown promise against multiple viruses, but concerns have been raised about whether their use might promote the emergence of new and harmful viral variants. Recently, genetic signatures associated with molnupiravir use have been identified in the global SARS-COV-2 population. Here, we examine the consequences of using favipiravir and molnupiravir to treat SARS-CoV-2 infection in a hamster model, comparing viral genome sequence data collected from (1) untreated hamsters, and (2) from hamsters receiving effective and suboptimal doses of treatment. We identify a broadly linear relationship between drug dose and the extent of variation in treated viral populations, with a high proportion of this variation being composed of variants at frequencies of less than 1 per cent, below typical thresholds for variant calling. Treatment with an effective dose of antiviral drug was associated with a gain of between 7 and 10 variants per viral genome relative to drug-free controls: even after a short period of treatment a population founded by a transmitted virus could contain multiple sequence differences to that of the original host. Treatment with a suboptimal dose of drug showed intermediate gains of variants. No dose-dependent signal was identified in the numbers of single-nucleotide variants reaching frequencies in excess of 5 per cent. We did not find evidence to support the emergence of drug resistance or of novel immune phenotypes. Our study suggests that where onward transmission occurs, a short period of treatment with mutagenic drugs may be sufficient to generate a significant increase in the number of viral variants transmitted.
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Affiliation(s)
| | - Jose A Guerra-Assuncao
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH, UK
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Samuel Gregg
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Oscar Charles
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH, UK
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Juanita Pang
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Sunando Roy
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Leuven B-3000, Belgium
- The VirusBank Platform, Gaston Geenslaan, Leuven B-3000, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Leuven B-3000, Belgium
- The VirusBank Platform, Gaston Geenslaan, Leuven B-3000, Belgium
| | - Judith Breuer
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH, UK
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
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4
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Olofsson P, Chipkin L, Daileda RC, Azevedo RBR. Mutational meltdown in asexual populations doomed to extinction. J Math Biol 2023; 87:88. [PMID: 37994999 DOI: 10.1007/s00285-023-02019-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/03/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Asexual populations are expected to accumulate deleterious mutations through a process known as Muller's ratchet. Lynch and colleagues proposed that the ratchet eventually results in a vicious cycle of mutation accumulation and population decline that drives populations to extinction. They called this phenomenon mutational meltdown. Here, we analyze mutational meltdown using a multi-type branching process model where, in the presence of mutation, populations are doomed to extinction. We analyse the change in size and composition of the population and the time of extinction under this model.
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Affiliation(s)
- Peter Olofsson
- Department of Mathematics, Trinity University, San Antonio, TX, 78212, USA
- Department of Mathematics, Physics and Chemical Engineering, Jönköping University, 551 11, Jönköping, Sweden
| | - Logan Chipkin
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Ryan C Daileda
- Department of Mathematics, Trinity University, San Antonio, TX, 78212, USA
| | - Ricardo B R Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA.
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5
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Sanderson T, Hisner R, Donovan-Banfield I, Hartman H, Løchen A, Peacock TP, Ruis C. A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes. Nature 2023; 623:594-600. [PMID: 37748513 PMCID: PMC10651478 DOI: 10.1038/s41586-023-06649-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
Molnupiravir, an antiviral medication widely used against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), acts by inducing mutations in the virus genome during replication. Most random mutations are likely to be deleterious to the virus and many will be lethal; thus, molnupiravir-induced elevated mutation rates reduce viral load1,2. However, if some patients treated with molnupiravir do not fully clear the SARS-CoV-2 infections, there could be the potential for onward transmission of molnupiravir-mutated viruses. Here we show that SARS-CoV-2 sequencing databases contain extensive evidence of molnupiravir mutagenesis. Using a systematic approach, we find that a specific class of long phylogenetic branches, distinguished by a high proportion of G-to-A and C-to-T mutations, are found almost exclusively in sequences from 2022, after the introduction of molnupiravir treatment, and in countries and age groups with widespread use of the drug. We identify a mutational spectrum, with preferred nucleotide contexts, from viruses in patients known to have been treated with molnupiravir and show that its signature matches that seen in these long branches, in some cases with onward transmission of molnupiravir-derived lineages. Finally, we analyse treatment records to confirm a direct association between these high G-to-A branches and the use of molnupiravir.
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Affiliation(s)
| | - Ryan Hisner
- Department of Bioinformatics, University of Cape Town, Cape Town, South Africa
| | - I'ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health and Care Research, Liverpool, UK
| | | | | | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- The Pirbright Institute, Pirbright, UK
| | - Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council-Laboratory of Molecular Biology, Cambridge, UK.
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK.
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6
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Chardès V, Mazzolini A, Mora T, Walczak AM. Evolutionary stability of antigenically escaping viruses. Proc Natl Acad Sci U S A 2023; 120:e2307712120. [PMID: 37871216 PMCID: PMC10622963 DOI: 10.1073/pnas.2307712120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/24/2023] [Indexed: 10/25/2023] Open
Abstract
Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how this cost-benefit trade-off selects the mutation rate of viruses. Using a traveling wave model for the coevolution of viruses and host immune systems in a finite population, we investigate how immunity affects the evolution of the mutation rate and other nonantigenic traits, such as virulence. We first show that the nature of the wave depends on how cross-reactive immune systems are, reconciling previous approaches. The immune-virus system behaves like a Fisher wave at low cross-reactivities, and like a fitness wave at high cross-reactivities. These regimes predict different outcomes for the evolution of nonantigenic traits. At low cross-reactivities, the evolutionarily stable strategy is to maximize the speed of the wave, implying a higher mutation rate and increased virulence. At large cross-reactivities, where our estimates place H3N2 influenza, the stable strategy is to increase the basic reproductive number, keeping the mutation rate to a minimum and virulence low.
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Affiliation(s)
- Victor Chardès
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
- Center for Computational Biology, Flatiron Institute, New York, NY10010
| | - Andrea Mazzolini
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
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7
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Ojha D, Hill CS, Zhou S, Evans AB, Leung JM, Lewis CS, Amblard F, Schinazi RF, Baric RS, Peterson KE, Swanstrom R. N4 -Hydroxycytidine/Molnupiravir Inhibits RNA-Virus Induced Encephalitis by Producing Mutated Viruses with Reduced Fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554316. [PMID: 37662274 PMCID: PMC10473592 DOI: 10.1101/2023.08.22.554316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
A diverse group of RNA viruses including Rabies, Polio, La Crosse, West Nile, Zika, Nipah, Eastern and Western equine encephalitis, Venezuelan equine encephalitis, Japanese encephalitis, and tick-borne encephalitis viruses have the ability to gain access to and replicate in the central nervous system (CNS), causing severe neurological disease. Current treatment for these patients is generally limited to supportive care. To address the need for a generalizable antiviral, we utilized a strategy of mutagenesis to limit virus replication. We evaluated ribavirin (RBV), favipiravir (FAV) and N 4 -hydroxycytidine (NHC) against La Crosse virus (LACV) which is the primary cause of pediatric arboviral encephalitis cases in North America. NHC was more potent than RBV or FAV in neuronal cells. Oral administration of molnupiravir (MOV), the 5'-isobutyryl prodrug of NHC, decreased neurological disease development by 32% following intraperitoneal (IP) infection of LACV. MOV also reduced disease by 23% when virus was administered intranasally (IN). NHC and MOV produced less fit viruses by incorporating predominantly G-to-A or C-to-U mutations. Furthermore, NHC also inhibited two other orthobunyaviruses, Jamestown Canyon virus and Cache Valley virus. Collectively, these studies indicate that NHC/MOV has therapeutic potential to inhibit virus replication and subsequent neurological disease caused by this neurotropic RNA virus.
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8
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Lobinska G, Pilpel Y, Nowak MA. Evolutionary safety of lethal mutagenesis driven by antiviral treatment. PLoS Biol 2023; 21:e3002214. [PMID: 37552682 PMCID: PMC10409280 DOI: 10.1371/journal.pbio.3002214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
Nucleoside analogs are a major class of antiviral drugs. Some act by increasing the viral mutation rate causing lethal mutagenesis of the virus. Their mutagenic capacity, however, may lead to an evolutionary safety concern. We define evolutionary safety as a probabilistic assurance that the treatment will not generate an increased number of mutants. We develop a mathematical framework to estimate the total mutant load produced with and without mutagenic treatment. We predict rates of appearance of such virus mutants as a function of the timing of treatment and the immune competence of patients, employing realistic assumptions about the vulnerability of the viral genome and its potential to generate viable mutants. We focus on the case study of Molnupiravir, which is an FDA-approved treatment against Coronavirus Disease-2019 (COVID-19). We estimate that Molnupiravir is narrowly evolutionarily safe, subject to the current estimate of parameters. Evolutionary safety can be improved by restricting treatment with this drug to individuals with a low immunological clearance rate and, in future, by designing treatments that lead to a greater increase in mutation rate. We report a simple mathematical rule to determine the fold increase in mutation rate required to obtain evolutionary safety that is also applicable to other pathogen-treatment combinations.
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Affiliation(s)
- Gabriela Lobinska
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Martin A. Nowak
- Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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9
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Ren R, Zheng L, Han J, Perdoncini Carvalho C, Miyashita S, Zhang D, Qu F. Intracellular bottlenecking permits no more than three tomato yellow leaf curl virus genomes to initiate replication in a single cell. PLoS Pathog 2023; 19:e1011365. [PMID: 37126519 PMCID: PMC10174518 DOI: 10.1371/journal.ppat.1011365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/11/2023] [Accepted: 04/17/2023] [Indexed: 05/02/2023] Open
Abstract
Viruses are constantly subject to natural selection to enrich beneficial mutations and weed out deleterious ones. However, it remains unresolved as to how the phenotypic gains or losses brought about by these mutations cause the viral genomes carrying the very mutations to become more or less numerous. Previous investigations by us and others suggest that viruses with plus strand (+) RNA genomes may compel such selection by bottlenecking the replicating genome copies in each cell to low single digits. Nevertheless, it is unclear if similarly stringent reproductive bottlenecks also occur in cells invaded by DNA viruses. Here we investigated whether tomato yellow leaf curl virus (TYLCV), a small virus with a single-stranded DNA genome, underwent population bottlenecking in cells of its host plants. We engineered a TYLCV genome to produce two replicons that express green fluorescent protein and mCherry, respectively, in a replication-dependent manner. We found that among the cells entered by both replicons, less than 65% replicated both, whereas at least 35% replicated either of them alone. Further probability computation concluded that replication in an average cell was unlikely to have been initiated with more than three replicon genome copies. Furthermore, sequential inoculations unveiled strong mutual exclusions of these two replicons at the intracellular level. In conclusion, the intracellular population of the small DNA virus TYLCV is actively bottlenecked, and such bottlenecking may be a virus-encoded, evolutionarily conserved trait that assures timely selection of new mutations emerging through error-prone replication.
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Affiliation(s)
- Ruifan Ren
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
- Hunan Plant Protection Institute, Changsha, China
| | - Limin Zheng
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
| | - Junping Han
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
| | | | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Deyong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Hunan Plant Protection Institute, Changsha, China
| | - Feng Qu
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
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10
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Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.535005. [PMID: 37034621 PMCID: PMC10081308 DOI: 10.1101/2023.03.30.535005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and likely originated during persistent infection of immunocompromised hosts. To test the hypothesis that S:D614G facilitated emergence of such variants, S:D614G was reverted to the ancestral sequence in the context of sequential Spike sequences from an immunocompromised individual, and within each of the major SARS-CoV-2 variants of concern. In all cases, infectivity of the S:D614G revertants was severely compromised. The infectivity of atypical SARS-CoV-2 lineages that propagated in the absence of S:D614G was found to be dependent upon either S:Q613H or S:H655Y. Notably, Gamma and Omicron variants possess both S:D614G and S:H655Y, each of which contributed to infectivity of these variants. Among sarbecoviruses, S:Q613H, S:D614G, and S:H655Y are only detected in SARS-CoV-2, which is also distinguished by a polybasic S1/S2 cleavage site. Genetic and biochemical experiments here showed that S:Q613H, S:D614G, and S:H655Y each stabilize Spike on virions, and that they are dispensable in the absence of S1/S2 cleavage, consistent with selection of these mutations by the S1/S2 cleavage site. CryoEM revealed that either S:D614G or S:H655Y shift the Spike receptor binding domain (RBD) towards the open conformation required for ACE2-binding and therefore on pathway for infection. Consistent with this, an smFRET reporter for RBD conformation showed that both S:D614G and S:H655Y spontaneously adopt the conformation that ACE2 induces in the parental Spike. Data from these orthogonal experiments demonstrate that S:D614G and S:H655Y are convergent adaptations to the polybasic S1/S2 cleavage site which stabilize S1 on the virion in the open RBD conformation and act epistatically to promote the fitness of variants bearing complex combinations of clinically significant mutations.
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Affiliation(s)
- Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Shawn Egri
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- These authors contributed equally
| | - Marco A. Diaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Javier A. Jaimes
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Manish C. Choudhary
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jonathan Z. Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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11
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Suicidal Phenotype of Proofreading-Deficient Herpes Simplex Virus 1 Polymerase Mutants. J Virol 2023; 97:e0135922. [PMID: 36598203 PMCID: PMC9888220 DOI: 10.1128/jvi.01359-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) encodes a family B DNA polymerase (Pol) capable of exonucleolytic proofreading whose functions have been extensively studied in the past. Early studies on the in vitro activity of purified Pol protein found that the enzymatic functions of the holoenzyme are largely separate. Consequently, exonuclease activity can be reduced or abolished by certain point mutations within catalytically important regions, with no or only minor effects on polymerase activity. Despite unimpaired polymerase activity, the recovery of HSV-1 mutants with a catalytically inactive exonuclease has been so far unsuccessful. Hence, mutations such as D368A, which abolish exonuclease activity, are believed to be lethal. Here, we show that HSV-1 can be recovered in the absence of Pol intrinsic exonuclease activity and demonstrate that a lack of proofreading causes the rapid accumulation of likely detrimental mutations. Although mutations that abolish exonuclease activity do not appear to be lethal, the lack of proofreading yields viruses with a suicidal phenotype that cease to replicate within few passages following reconstitution. Hence, we conclude that high replication fidelity conferred by proofreading is essential to maintain HSV-1 genome integrity and that a lack of exonuclease activity produces an initially viable but rapidly suicidal phenotype. However, stably replicating viruses with reduced exonuclease activity and therefore elevated mutation rates can be generated by mutating a catalytically less important site located within a conserved exonuclease domain. IMPORTANCE Recovery of fully exonuclease-deficient herpes simplex virus 1 (HSV-1) DNA polymerase mutants has been so far unsuccessful. However, exonuclease activity is not known to be directly essential for virus replication, and the lethal phenotype of certain HSV-1 polymerase mutants is thus attributed to factors other than exonuclease activity. Here, we showed that the recovery of a variety of exonuclease-deficient HSV-1 polymerase mutants is possible and that these mutants are initially replication competent. We, however, observed a progressive loss of mutant viability upon cell culture passaging, which coincided with the rapid accumulation of mutations in exonuclease-deficient viruses. We thus concluded that a lack of DNA proofreading in exonuclease-deficient viruses causes an initially viable but rapidly suicidal hypermutator phenotype and, consequently, the extinction of mutant viruses within few generations following recovery. This would make the absence of exonuclease activity the primary reason for the long-reported difficulties in culturing exonuclease-deficient HSV-1 mutants.
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12
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Abstract
Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.
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Affiliation(s)
- Ignacio de la Higuera
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, United States
| | - Ester Lázaro
- Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz, Spain
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13
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Strobel HM, Stuart EC, Meyer JR. A Trait-Based Approach to Predicting Viral Host-Range Evolvability. Annu Rev Virol 2022; 9:139-156. [PMID: 36173699 DOI: 10.1146/annurev-virology-091919-092003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Predicting the evolution of virus host range has proven to be extremely difficult, in part because of the sheer diversity of viruses, each with unique biology and ecological interactions. We have not solved this problem, but to make the problem more tractable, we narrowed our focus to three traits intrinsic to all viruses that may play a role in host-range evolvability: mutation rate, recombination rate, and phenotypic heterogeneity. Although each trait should increase evolvability, they cannot do so unbounded because fitness trade-offs limit the ability of all three traits to maximize evolvability. By examining these constraints, we can begin to identify groups of viruses with suites of traits that make them especially concerning, as well as ecological and environmental conditions that might push evolution toward accelerating host-range expansion.
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Affiliation(s)
- Hannah M Strobel
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth C Stuart
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
| | - Justin R Meyer
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
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14
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Lansch‐Justen L, Cusseddu D, Schmitz MA, Bank C. The extinction time under mutational meltdown driven by high mutation rates. Ecol Evol 2022; 12:e9046. [PMID: 35813923 PMCID: PMC9257376 DOI: 10.1002/ece3.9046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 01/15/2023] Open
Abstract
Mutational meltdown describes an eco‐evolutionary process in which the accumulation of deleterious mutations causes a fitness decline that eventually leads to the extinction of a population. Possible applications of this concept include medical treatment of RNA virus infections based on mutagenic drugs that increase the mutation rate of the pathogen. To determine the usefulness and expected success of such an antiviral treatment, estimates of the expected time to mutational meltdown are necessary. Here, we compute the extinction time of a population under high mutation rates, using both analytical approaches and stochastic simulations. Extinction is the result of three consecutive processes: (a) initial accumulation of deleterious mutations due to the increased mutation pressure; (b) consecutive loss of the fittest haplotype due to Muller's ratchet; (c) rapid population decline toward extinction. We find accurate analytical results for the mean extinction time, which show that the deleterious mutation rate has the strongest effect on the extinction time. We confirm that intermediate‐sized deleterious selection coefficients minimize the extinction time. Finally, our simulations show that the variation in extinction time, given a set of parameters, is surprisingly small.
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Affiliation(s)
- Lucy Lansch‐Justen
- Instituto Gulbenkian de Ciência Oeiras Portugal
- Institute of Evolution and Ecology University of Edinburgh Edinburgh UK
| | - Davide Cusseddu
- Instituto Gulbenkian de Ciência Oeiras Portugal
- Grupo Física‐Matemática, Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | | | - Claudia Bank
- Instituto Gulbenkian de Ciência Oeiras Portugal
- Institute of Ecology and Evolution University of Bern Bern Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
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15
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A Virus Is a Community: Diversity within Negative-Sense RNA Virus Populations. Microbiol Mol Biol Rev 2022; 86:e0008621. [PMID: 35658541 DOI: 10.1128/mmbr.00086-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Negative-sense RNA virus populations are composed of diverse viral components that interact to form a community and shape the outcome of virus infections. At the genomic level, RNA virus populations consist not only of a homogeneous population of standard viral genomes but also of an extremely large number of genome variants, termed viral quasispecies, and nonstandard viral genomes, which include copy-back viral genomes, deletion viral genomes, mini viral RNAs, and hypermutated RNAs. At the particle level, RNA virus populations are composed of pleomorphic particles, particles missing or having additional genomes, and single particles or particle aggregates. As we continue discovering more about the components of negative-sense RNA virus populations and their crucial functions during virus infection, it will become more important to study RNA virus populations as a whole rather than their individual parts. In this review, we will discuss what is known about the components of negative-sense RNA virus communities, speculate how the components of the virus community interact, and summarize what vaccines and antiviral therapies are being currently developed to target or harness these components.
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16
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Islam E. Development of epitope-based chimeric protein as a vaccine against Lujo virus by utilizing immunoinformatic tools. Future Virol 2022. [DOI: 10.2217/fvl-2021-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Lujo is a modern zoonotic virus that is potentially fatal and spreads by bodily fluids. In this research, immunoinformatic tools are used to build a vaccine. Methodology: The epitopes of cytotoxic T-lymphocytes, helper T-lymphocytes and linear B-lymphocytes were predicted from the most antigenic protein. The designed vaccine's physiochemical properties and 3D structure have been forecasted. Low free energy and strong binding affinity estimated in molecular docking against toll-like receptor 4 (TLR4) and dynamic simulation. Furthermore, in silico cloning in the Escherichia coli K12 host system was performed for high level of expression. Conclusion: Finally, immune simulation was used to determine immune responses to the vaccine that was formulated confirming the developed vaccine as a good candidate against Lujo virus.
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Affiliation(s)
- Enayetul Islam
- Department of Genetic Engineering & Biotechnology, University of Chittagong, Chittagong, Bangladesh
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17
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van Kampen JJA, Dalm VASH, Fraaij PLA, Oude Munnink BB, Schapendonk CME, Izquierdo-Lara RW, Villabruna N, Ettayebi K, Estes MK, Koopmans MPG, de Graaf M. Clinical and In Vitro Evidence Favoring Immunoglobulin Treatment of a Chronic Norovirus Infection in a Patient With Common Variable Immunodeficiency. J Infect Dis 2022; 226:1781-1789. [PMID: 35255136 PMCID: PMC9650502 DOI: 10.1093/infdis/jiac085] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/04/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Immunocompromised individuals can become chronically infected with norovirus, but effective antiviral therapies are not yet available. METHODS Treatments with nitazoxanide, ribavirin, interferon alpha-2a, and nasoduodenally administered immunoglobulins were evaluated sequentially in an immunocompromised patient chronically infected with norovirus. In support, these components were also applied to measure norovirus inhibition in intestinal enteroid cultures in vitro. Viral RNA levels were determined in fecal and plasma samples during each treatment and viral genomes were sequenced. RESULTS None of the antivirals resulted in a reduction of viral RNA levels in feces or plasma. However, during ribavirin treatment, there was an increased accumulation of virus genome mutations. In vitro, an effect of interferon alpha-2a on virus replication was observed and a genetically related strain was neutralized effectively in vitro using immunoglobulins and post-norovirus-infection antiserum. In agreement, after administration of immunoglobulins, the patient cleared the infection. CONCLUSIONS Intestinal enteroid cultures provide a relevant system to evaluate antivirals and the neutralizing potential of immunoglobulins. We successfully treated a chronically infected patient with immunoglobulins, despite varying results reported by others. This case study provides in-depth, multifaceted exploration of norovirus treatment that can be used as a guidance for further research towards norovirus treatments.
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Affiliation(s)
| | | | - Pieter L A Fraaij
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Ray W Izquierdo-Lara
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nele Villabruna
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Khalil Ettayebi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA,Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Correspondence: Miranda de Graaf, PhD, Erasmus University Medical Center, PO Box 1738, 3000 DR Rotterdam, the Netherlands ()
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18
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Gan SKE, Phua SX, Yeo JY. Sagacious epitope selection for vaccines, and both antibody-based therapeutics and diagnostics: tips from virology and oncology. Antib Ther 2022; 5:63-72. [PMID: 35372784 PMCID: PMC8972324 DOI: 10.1093/abt/tbac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/24/2022] [Accepted: 02/12/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
The target of an antibody plays a significant role in the success of antibody-based therapeutics and diagnostics, and vaccine development. This importance is focused on the target binding site—epitope, where epitope selection as a part of design thinking beyond traditional antigen selection using whole cell or whole protein immunization can positively impact success. With purified recombinant protein production and peptide synthesis to display limited/selected epitopes, intrinsic factors that can affect the functioning of resulting antibodies can be more easily selected for. Many of these factors stem from the location of the epitope that can impact accessibility of the antibody to the epitope at a cellular or molecular level, direct inhibition of target antigen activity, conservation of function despite escape mutations, and even non-competitive inhibition sites. By incorporating novel computational methods for predicting antigen changes to model-informed drug discovery and development, superior vaccines and antibody-based therapeutics or diagnostics can be easily designed to mitigate failures. With detailed examples, this review highlights the new opportunities, factors and methods of predicting antigenic changes for consideration in sagacious epitope selection.
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Affiliation(s)
- Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
- APD SKEG Pte Ltd, Singapore 439444, Singapore
| | - Ser-Xian Phua
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
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19
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Morales-Arce AY, Johri P, Jensen JD. Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies. Heredity (Edinb) 2022; 128:79-87. [PMID: 34987185 PMCID: PMC8728706 DOI: 10.1038/s41437-021-00493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022] Open
Abstract
We here propose an analysis pipeline for inferring the distribution of fitness effects (DFE) from either patient-sampled or experimentally-evolved viral populations, that explicitly accounts for non-Wright-Fisher and non-equilibrium population dynamics inherent to pathogens. We examine the performance of this approach via extensive power and performance analyses, and highlight two illustrative applications - one from an experimentally-passaged RNA virus, and the other from a clinically-sampled DNA virus. Finally, we discuss how such DFE inference may shed light on major research questions in virus evolution, ranging from a quantification of the population genetic processes governing genome size, to the role of Hill-Robertson interference in dictating adaptive outcomes, to the potential design of novel therapeutic approaches to eradicate within-patient viral populations via induced mutational meltdown.
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Affiliation(s)
- Ana Y. Morales-Arce
- grid.215654.10000 0001 2151 2636Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ USA
| | - Parul Johri
- grid.215654.10000 0001 2151 2636Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ USA
| | - Jeffrey D. Jensen
- grid.215654.10000 0001 2151 2636Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ USA
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20
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Murer L, Petkidis A, Vallet T, Vignuzzi M, Greber UF. Chemical Evolution of Rhinovirus Identifies Capsid-Destabilizing Mutations Driving Low-pH-Independent Genome Uncoating. J Virol 2022; 96:e0106021. [PMID: 34705560 PMCID: PMC8791267 DOI: 10.1128/jvi.01060-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/20/2021] [Indexed: 12/24/2022] Open
Abstract
Rhinoviruses (RVs) cause recurrent infections of the nasal and pulmonary tracts, life-threatening conditions in chronic respiratory illness patients, predisposition of children to asthmatic exacerbation, and large economic cost. RVs are difficult to treat. They rapidly evolve resistance and are genetically diverse. Here, we provide insight into RV drug resistance mechanisms against chemical compounds neutralizing low pH in endolysosomes. Serial passaging of RV-A16 in the presence of the vacuolar proton ATPase inhibitor bafilomycin A1 (BafA1) or the endolysosomotropic agent ammonium chloride (NH4Cl) promoted the emergence of resistant virus populations. We found two reproducible point mutations in viral proteins 1 and 3 (VP1 and VP3), A2526G (serine 66 to asparagine [S66N]), and G2274U (cysteine 220 to phenylalanine [C220F]), respectively. Both mutations conferred cross-resistance to BafA1, NH4Cl, and the protonophore niclosamide, as identified by massive parallel sequencing and reverse genetics, but not the double mutation, which we could not rescue. Both VP1-S66 and VP3-C220 locate at the interprotomeric face, and their mutations increase the sensitivity of virions to low pH, elevated temperature, and soluble intercellular adhesion molecule 1 receptor. These results indicate that the ability of RV to uncoat at low endosomal pH confers virion resistance to extracellular stress. The data endorse endosomal acidification inhibitors as a viable strategy against RVs, especially if inhibitors are directly applied to the airways. IMPORTANCE Rhinoviruses (RVs) are the predominant agents causing the common cold. Anti-RV drugs and vaccines are not available, largely due to rapid evolutionary adaptation of RVs giving rise to resistant mutants and an immense diversity of antigens in more than 160 different RV types. In this study, we obtained insight into the cell biology of RVs by harnessing the ability of RVs to evolve resistance against host-targeting small chemical compounds neutralizing endosomal pH, an important cue for uncoating of normal RVs. We show that RVs grown in cells treated with inhibitors of endolysosomal acidification evolved capsid mutations yielding reduced virion stability against elevated temperature, low pH, and incubation with recombinant soluble receptor fragments. This fitness cost makes it unlikely that RV mutants adapted to neutral pH become prevalent in nature. The data support the concept of host-directed drug development against respiratory viruses in general, notably at low risk of gain-of-function mutations.
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Affiliation(s)
- Luca Murer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Thomas Vallet
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Department of Virology, CNRS UMR 3569, Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Department of Virology, CNRS UMR 3569, Paris, France
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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21
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Enhancing the Antiviral Potency of Nucleobases for Potential Broad-Spectrum Antiviral Therapies. Viruses 2021; 13:v13122508. [PMID: 34960780 PMCID: PMC8705664 DOI: 10.3390/v13122508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Broad-spectrum antiviral therapies hold promise as a first-line defense against emerging viruses by blunting illness severity and spread until vaccines and virus-specific antivirals are developed. The nucleobase favipiravir, often discussed as a broad-spectrum inhibitor, was not effective in recent clinical trials involving patients infected with Ebola virus or SARS-CoV-2. A drawback of favipiravir use is its rapid clearance before conversion to its active nucleoside-5′-triphosphate form. In this work, we report a synergistic reduction of flavivirus (dengue, Zika), orthomyxovirus (influenza A), and coronavirus (HCoV-OC43 and SARS-CoV-2) replication when the nucleobases favipiravir or T-1105 were combined with the antimetabolite 6-methylmercaptopurine riboside (6MMPr). The 6MMPr/T-1105 combination increased the C-U and G-A mutation frequency compared to treatment with T-1105 or 6MMPr alone. A further analysis revealed that the 6MMPr/T-1105 co-treatment reduced cellular purine nucleotide triphosphate synthesis and increased conversion of the antiviral nucleobase to its nucleoside-5′-monophosphate, -diphosphate, and -triphosphate forms. The 6MMPr co-treatment specifically increased production of the active antiviral form of the nucleobases (but not corresponding nucleosides) while also reducing levels of competing cellular NTPs to produce the synergistic effect. This in-depth work establishes a foundation for development of small molecules as possible co-treatments with nucleobases like favipiravir in response to emerging RNA virus infections.
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22
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Yeo JY, Gan SKE. Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness. Viruses 2021; 13:2276. [PMID: 34835082 PMCID: PMC8622263 DOI: 10.3390/v13112276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-2021 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organization stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and easy cross to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8, its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins, we can be better prepared against H5N8 and other influenza A viruses.
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Affiliation(s)
- Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
- APD SKEG Pte Ltd., Singapore 439444, Singapore
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23
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Adaptation in a heterogeneous environment I: persistence versus extinction. J Math Biol 2021; 83:14. [PMID: 34228185 DOI: 10.1007/s00285-021-01637-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/16/2021] [Accepted: 06/27/2021] [Indexed: 10/20/2022]
Abstract
Understanding how a diversity of plants in agroecosystems affects the adaptation of pathogens is a key issue in agroecology. We analyze PDE systems describing the dynamics of adaptation of two phenotypically structured populations, under the effects of mutation, selection and migration in a two-patch environment, each patch being associated with a different phenotypic optimum. We consider two types of growth functions that depend on the n-dimensional phenotypic trait: either local and linear or nonlocal nonlinear. In both cases, we obtain existence and uniqueness results as well as a characterization of the large-time behaviour of the solution (persistence or extinction) based on the sign of a principal eigenvalue. We show that migration between the two environments decreases the chances of persistence, with in some cases a 'lethal migration threshold' above which persistence is not possible. Comparison with stochastic individual-based simulations shows that the PDE approach accurately captures this threshold. Our results illustrate the importance of cultivar mixtures for disease prevention and control.
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24
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Anastassopoulou C, Manoussopoulos Y, Lampropoulou V, Tsakris A. Glimpses into evolutionary trajectories of SARS-CoV-2: emerging variants and potential immune evasion routes. Future Microbiol 2021; 16:455-459. [PMID: 33960807 PMCID: PMC8111931 DOI: 10.2217/fmb-2020-0300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/24/2021] [Indexed: 11/30/2022] Open
Abstract
Tweetable abstract An opinion on the coronaviruses' evolution paradoxes, the continuing adaptation of the SARS-CoV-2 in humans following the zoonotic transmission, and clues into escape routes from host immune responses.
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Affiliation(s)
- Cleo Anastassopoulou
- Department of Microbiology, Medical School, National
& Kapodistrian University of Athens, Athens, Greece
| | - Yiannis Manoussopoulos
- Department of Microbiology, Medical School, National
& Kapodistrian University of Athens, Athens, Greece
- Laboratory of Virology, Plant Protection Division of
Patras, ELGO-Demeter, Patras, Greece
| | - Vicky Lampropoulou
- Laboratory of Immunobiology, Center for Clinical,
Experimental Surgery & Translational Research, Biomedical Research
Foundation of The Academy of Athens, Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National
& Kapodistrian University of Athens, Athens, Greece
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25
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Yeo JY, Koh DWS, Yap P, Goh GR, Gan SKE. Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types. Int J Mol Sci 2020; 22:E370. [PMID: 33396460 PMCID: PMC7796399 DOI: 10.3390/ijms22010370] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/25/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
While drug resistant mutations in HIV-1 are largely credited to its error prone HIV-1 RT, the time point in the infection cycle that these mutations can arise and if they appear spontaneously without selection pressures both remained enigmatic. Many HIV-1 RT mutational in vitro studies utilized reporter genes (LacZ) as a template to investigate these questions, thereby not accounting for the possible contribution of viral codon usage. To address this gap, we investigated HIV-1 RT mutation rates and biases on its own Gag, protease, and RT p66 genes in an in vitro selection pressure free system. We found rare clinical mutations with a general avoidance of crucial functional sites in the background mutations rates for Gag, protease, and RT p66 at 4.71 × 10-5, 6.03 × 10-5, and 7.09 × 10-5 mutations/bp, respectively. Gag and p66 genes showed a large number of 'A to G' mutations. Comparisons with silently mutated p66 sequences showed an increase in mutation rates (1.88 × 10-4 mutations/bp) and that 'A to G' mutations occurred in regions reminiscent of ADAR neighbor sequence preferences. Mutational free energies of the 'A to G' mutations revealed an avoidance of destabilizing effects, with the natural p66 gene codon usage providing barriers to disruptive amino acid changes. Our study demonstrates the importance of studying mutation emergence in HIV genes in a RT-PCR in vitro selection pressure free system to understand how fast drug resistance can emerge, providing transferable applications to how new viral diseases and drug resistances can emerge.
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Affiliation(s)
- Joshua Yi Yeo
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
| | - Darius Wen-Shuo Koh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
| | - Ping Yap
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
| | - Ghin-Ray Goh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
| | - Samuel Ken-En Gan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; (J.Y.Y.); (D.W.-S.K.); (P.Y.); (G.-R.G.)
- Experimental Drug Development Centre, A*STAR, 10 Biopolis Road Chromos #05-01, Singapore 138670, Singapore
- p53 Laboratory, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore
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26
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Narayanan N, Nair DT. Ritonavir may inhibit exoribonuclease activity of nsp14 from the SARS-CoV-2 virus and potentiate the activity of chain terminating drugs. Int J Biol Macromol 2020; 168:272-278. [PMID: 33309661 PMCID: PMC7724963 DOI: 10.1016/j.ijbiomac.2020.12.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/05/2020] [Accepted: 12/05/2020] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2is the causative agent for the ongoing COVID19 pandemic, and this virus belongs to the Coronaviridae family. The nsp14 protein of SARS-CoV-2 houses a 3' to 5' exoribonuclease activity responsible for removing mismatches that arise during genome duplication. A homology model of nsp10-nsp14 complex was used to carry out in silico screening to identify molecules among natural products, or FDA approved drugs that can potentially inhibit the activity of nsp14. This exercise showed that ritonavir might bind to the exoribonuclease active site of the nsp14 protein. A model of the SARS-CoV-2-nsp10-nsp14 complex bound to substrate RNA showed that the ritonavir binding site overlaps with that of the 3' nucleotide of substrate RNA. A comparison of the calculated energies of binding for RNA and ritonavir suggested that the drug may bind to the active site of nsp14 with significant affinity. It is, therefore, possible that ritonavir may prevent association with substrate RNA and thus inhibit the exoribonuclease activity of nsp14. Overall, our computational studies suggest that ritonavir may serve as an effective inhibitor of the nsp14 protein. nsp14 is known to attenuate the inhibitory effect of drugs that function through premature termination of viral genome replication. Hence, ritonavir may potentiate the therapeutic properties of drugs such as remdesivir, favipiravir and ribavirin.
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Affiliation(s)
- Naveen Narayanan
- Laboratory of Genomic Integrity and Evolution, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India; Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Deepak T Nair
- Laboratory of Genomic Integrity and Evolution, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India.
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Qu F, Zheng L, Zhang S, Sun R, Slot J, Miyashita S. Bottleneck, Isolate, Amplify, Select (BIAS) as a mechanistic framework for intracellular population dynamics of positive-sense RNA viruses. Virus Evol 2020; 6:veaa086. [PMID: 33343926 PMCID: PMC7733609 DOI: 10.1093/ve/veaa086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many positive-sense RNA viruses, especially those infecting plants, are known to experience stringent, stochastic population bottlenecks inside the cells they invade, but exactly how and why these populations become bottlenecked are unclear. A model proposed ten years ago advocates that such bottlenecks are evolutionarily favored because they cause the isolation of individual viral variants in separate cells. Such isolation in turn allows the viral variants to manifest the phenotypic differences they encode. Recently published observations lend mechanistic support to this model and prompt us to refine the model with novel molecular details. The refined model, designated Bottleneck, Isolate, Amplify, Select (BIAS), postulates that these viruses impose population bottlenecks on themselves by encoding bottleneck-enforcing proteins (BNEPs) that function in a concentration-dependent manner. In cells simultaneously invaded by numerous virions of the same virus, BNEPs reach the bottleneck-ready concentration sufficiently early to arrest nearly all internalized viral genomes. As a result, very few (as few as one) viral genomes stochastically escape to initiate reproduction. Repetition of this process in successively infected cells isolates viral genomes with different mutations in separate cells. This isolation prevents mutant viruses encoding defective viral proteins from hitchhiking on sister genome-encoded products, leading to the swift purging of such mutants. Importantly, genome isolation also ensures viral genomes harboring beneficial mutations accrue the cognate benefit exclusively to themselves, leading to the fixation of such beneficial mutations. Further interrogation of the BIAS hypothesis promises to deepen our understanding of virus evolution and inspire new solutions to virus disease mitigation.
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Affiliation(s)
- Feng Qu
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Limin Zheng
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Shaoyan Zhang
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Rong Sun
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | | | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-aoba, Aoba-ku, Sendai 980-0845, Japan
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Jensen JD, Stikeleather RA, Kowalik TF, Lynch M. Imposed mutational meltdown as an antiviral strategy. Evolution 2020; 74:2549-2559. [PMID: 33047822 PMCID: PMC7993354 DOI: 10.1111/evo.14107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/30/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022]
Abstract
Following widespread infections of the most recent coronavirus known to infect humans, SARS‐CoV‐2, attention has turned to potential therapeutic options. With no drug or vaccine yet approved, one focal point of research is to evaluate the potential value of repurposing existing antiviral treatments, with the logical strategy being to identify at least a short‐term intervention to prevent within‐patient progression, while long‐term vaccine strategies unfold. Here, we offer an evolutionary/population‐genetic perspective on one approach that may overwhelm the capacity for pathogen defense (i.e., adaptation) – induced mutational meltdown – providing an overview of key concepts, review of previous theoretical and experimental work of relevance, and guidance for future research. Applied with appropriate care, including target specificity, induced mutational meltdown may provide a general, rapidly implemented approach for the within‐patient eradication of a wide range of pathogens or other undesirable microorganisms.
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Affiliation(s)
- Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Center for Evolution & Medicine, Arizona State University, Tempe, Arizona, 85281
| | - Ryan A Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, 01655
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
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Ferreira C, Viana SD, Reis F. Gut Microbiota Dysbiosis-Immune Hyperresponse-Inflammation Triad in Coronavirus Disease 2019 (COVID-19): Impact of Pharmacological and Nutraceutical Approaches. Microorganisms 2020; 8:E1514. [PMID: 33019592 PMCID: PMC7601735 DOI: 10.3390/microorganisms8101514] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19) is a pandemic infection caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients present a complex clinical picture that, in severe cases, evolves to respiratory, hepatic, gastrointestinal, and neurological complications, and eventually death. The underlying pathophysiological mechanisms are complex and multifactorial and have been summarized as a hyperresponse of the immune system that originates an inflammatory/cytokine storm. In elderly patients, particularly in those with pre-existing cardiovascular, metabolic, renal, and pulmonary disorders, the disease is particularly severe, causing prolonged hospitalization at intensive care units (ICU) and an increased mortality rate. Curiously, the same populations have been described as more prone to a gut microbiota (GM) dysbiosis profile. Intestinal microflora plays a major role in many metabolic and immune functions of the host, including to educate and strengthen the immune system to fight infections, namely of viral origin. Notably, recent studies suggest the existence of GM dysbiosis in COVID-19 patients. This review article highlights the interplay between the triad GM dysbiosis-immune hyperresponse-inflammation in the individual resilience/fragility to SARS-CoV-2 infection and presents the putative impact of pharmacological and nutraceutical approaches on the triumvirate, with focus on GM.
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Affiliation(s)
- Carolina Ferreira
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal;
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-075 Coimbra, Portugal
| | - Sofia D. Viana
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal;
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-075 Coimbra, Portugal
- Polytechnic Institute of Coimbra, ESTESC-Coimbra Health School, Pharmacy, 3046-854 Coimbra, Portugal
| | - Flávio Reis
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal;
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3000-075 Coimbra, Portugal
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30
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Atypical Porcine Pestivirus Circulation and Molecular Evolution within an Affected Swine Herd. Viruses 2020; 12:v12101080. [PMID: 32992946 PMCID: PMC7599615 DOI: 10.3390/v12101080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 01/27/2023] Open
Abstract
Atypical porcine pestivirus (APPV) is a single-stranded RNA virus from the family Flaviviridae, which is linked to congenital tremor (CT) type A-II in newborn piglets. Here, we retrospectively investigated the molecular evolution of APPV on an affected herd between 2013 and 2019. Monitoring was done at regular intervals, and the same genotype of APPV was found during the entire study period, suggesting no introductions from outside the farm. The nucleotide substitutions over time did not show substantial amino acid variation in the structural glycoproteins. Furthermore, the evolution of the virus showed mainly purifying selection, and no positive selection. The limited pressure on the virus to change at immune-dominant regions suggested that the immune pressure at the farm might be low. In conclusion, farms can have circulation of APPV for years, and massive testing and removal of infected animals are not sufficient to clear the virus from affected farms.
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Kempf BJ, Watkins CL, Peersen OB, Barton DJ. An Extended Primer Grip of Picornavirus Polymerase Facilitates Sexual RNA Replication Mechanisms. J Virol 2020; 94:e00835-20. [PMID: 32522851 PMCID: PMC7394906 DOI: 10.1128/jvi.00835-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/02/2020] [Indexed: 11/20/2022] Open
Abstract
Picornaviruses have both asexual and sexual RNA replication mechanisms. Asexual RNA replication mechanisms involve one parental template, whereas sexual RNA replication mechanisms involve two or more parental templates. Because sexual RNA replication mechanisms counteract ribavirin-induced error catastrophe, we selected for ribavirin-resistant poliovirus to identify polymerase residues that facilitate sexual RNA replication mechanisms. We used serial passage in ribavirin, beginning with a variety of ribavirin-sensitive and ribavirin-resistant parental viruses. Ribavirin-sensitive virus contained an L420A polymerase mutation, while ribavirin-resistant virus contained a G64S polymerase mutation. A G64 codon mutation (G64Fix) was used to inhibit emergence of G64S-mediated ribavirin resistance. Revertants (L420) or pseudorevertants (L420V and L420I) were selected from all independent lineages of L420A, G64Fix L420A, and G64S L420A parental viruses. Ribavirin resistance G64S mutations were selected in two independent lineages, and novel ribavirin resistance mutations were selected in the polymerase in other lineages (M299I, M323I, M392V, and T353I). The structural orientation of M392, immediately adjacent to L420 and the polymerase primer grip region, led us to engineer additional polymerase mutations into poliovirus (M392A, M392L, M392V, K375R, and R376K). L420A revertants and pseudorevertants (L420V and L420I) restored efficient viral RNA recombination, confirming that ribavirin-induced error catastrophe coincides with defects in sexual RNA replication mechanisms. Viruses containing M392 mutations (M392A, M392L, and M392V) and primer grip mutations (K375R and R376K) exhibited divergent RNA recombination, ribavirin sensitivity, and biochemical phenotypes, consistent with changes in the fidelity of RNA synthesis. We conclude that an extended primer grip of the polymerase, including L420, M392, K375, and R376, contributes to the fidelity of RNA synthesis and to efficient sexual RNA replication mechanisms.IMPORTANCE Picornaviruses have both asexual and sexual RNA replication mechanisms. Sexual RNA replication shapes picornavirus species groups, contributes to the emergence of vaccine-derived polioviruses, and counteracts error catastrophe. Can viruses distinguish between homologous and nonhomologous partners during sexual RNA replication? We implicate an extended primer grip of the viral polymerase in sexual RNA replication mechanisms. By sensing RNA sequence complementarity near the active site, the extended primer grip of the polymerase has the potential to distinguish between homologous and nonhomologous RNA templates during sexual RNA replication.
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Affiliation(s)
- Brian J Kempf
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Colorado, USA
| | - Colleen L Watkins
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Olve B Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - David J Barton
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Colorado, USA
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32
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Santiago E, Caballero A. The value of targeting recombination as a strategy against coronavirus diseases. Heredity (Edinb) 2020; 125:169-172. [PMID: 32606420 PMCID: PMC7325643 DOI: 10.1038/s41437-020-0337-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 01/10/2023] Open
Affiliation(s)
- Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain.
| | - Armando Caballero
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, As Lagoas, Universidade de Vigo, Marcosende, 36310, Vigo, Spain
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33
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Moderate Amounts of Epistasis are Not Evolutionarily Stable in Small Populations. J Mol Evol 2020; 88:435-444. [PMID: 32350572 DOI: 10.1007/s00239-020-09942-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
Abstract
High mutation rates select for the evolution of mutational robustness where populations inhabit flat fitness peaks with little epistasis, protecting them from lethal mutagenesis. Recent evidence suggests that a different effect protects small populations from extinction via the accumulation of deleterious mutations. In drift robustness, populations tend to occupy peaks with steep flanks and positive epistasis between mutations. However, it is not known what happens when mutation rates are high and population sizes are small at the same time. Using a simple fitness model with variable epistasis, we show that the equilibrium fitness has a minimum as a function of the parameter that tunes epistasis, implying that this critical point is an unstable fixed point for evolutionary trajectories. In agent-based simulations of evolution at finite mutation rate, we demonstrate that when mutations can change epistasis, trajectories with a subcritical value of epistasis evolve to decrease epistasis, while those with supercritical initial points evolve towards higher epistasis. These two fixed points can be identified with mutational and drift robustness, respectively.
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34
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Jensen JD, Lynch M. Considering mutational meltdown as a potential SARS-CoV-2 treatment strategy. Heredity (Edinb) 2020; 124:619-620. [PMID: 32251365 PMCID: PMC7133120 DOI: 10.1038/s41437-020-0314-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/30/2023] Open
Affiliation(s)
- Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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35
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Caldwell HS, Ngo K, Pata JD, Kramer LD, Ciota AT. West Nile Virus fidelity modulates the capacity for host cycling and adaptation. J Gen Virol 2020; 101:410-419. [PMID: 32068528 DOI: 10.1099/jgv.0.001393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The fidelity of flaviviruses is thought to be tightly regulated for optimal fitness within and between hosts. West Nile virus (WNV) high-fidelity (HiFi) mutations V793I and G806R within the RNA-dependent RNA polymerase, and low-fidelity (LoFi) mutation T248I within the methyltransferase, were previously shown to attenuate infectivity and replicative fitness in Culex mosquitoes and Culex tarsalis (CXT) cells but not in mammalian cells. We hypothesized that fidelity alterations would modify adaptation and maintenance in a host-specific manner. To test this hypothesis, wild-type (WT), HiFi (V793I/G806R) and LoFi (T248I) variants were sequentially passaged eight times in avian (PDE) or mosquito cells, or alternately between the two. Initial characterization confirmed that fidelity mutants are attenuated in mosquito, but not avian, cells. Deep sequencing revealed mutations unique to both cell lines and fidelity mutants, including ENV G1378A, a mutation associated with avian cell adaptation. To characterize maintenance and adaptation, viral outputs were monitored throughout passaging and viral fitness was assessed. The results indicate that fidelity mutants can at times recover fitness during mosquito cell passage, but remain attenuated relative to WT. Despite similar initial fitness, LoFi mutants were impaired during sequential passage in avian cells. Conversely, HiFi mutants passaged in avian cells showed increased adaptation, suggesting that increased fidelity may be advantageous in avian hosts. Although some adaptation occurred with individual mutants, the output titres of fidelity mutants were on average lower and were often lost during host switching. These data confirm that arbovirus fidelity is likely fine-tuned to maximize survival in disparate hosts.
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Affiliation(s)
- Haley S Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA.,Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
| | - Kiet Ngo
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA
| | - Janice D Pata
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
| | - Laura D Kramer
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA.,Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
| | - Alexander T Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA.,Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA
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36
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Mirrahimi S, Gandon S. Evolution of Specialization in Heterogeneous Environments: Equilibrium Between Selection, Mutation and Migration. Genetics 2020; 214:479-491. [PMID: 31862866 PMCID: PMC7017023 DOI: 10.1534/genetics.119.302868] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/06/2019] [Indexed: 02/02/2023] Open
Abstract
Adaptation in spatially heterogeneous environments results from the balance between local selection, mutation, and migration. We study the interplay among these different evolutionary forces and demography in a classical two-habitat scenario with asexual reproduction. We develop a new theoretical approach that goes beyond the Adaptive Dynamics framework, and allows us to explore the effect of high mutation rates on the stationary phenotypic distribution. We show that this approach improves the classical Gaussian approximation, and captures accurately the shape of this equilibrium phenotypic distribution in one- and two-population scenarios. We examine the evolutionary equilibrium under general conditions where demography and selection may be nonsymmetric between the two habitats. In particular, we show how migration may increase differentiation in a source-sink scenario. We discuss the implications of these analytic results for the adaptation of organisms with large mutation rates, such as RNA viruses.
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Affiliation(s)
- Sepideh Mirrahimi
- Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, UPS, IMT, 31062 Cedex 9, France
| | - Sylvain Gandon
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, University Paul Valéry, 34293 Montpellier 3, France
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37
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Lavigne F, Martin G, Anciaux Y, Papaïx J, Roques L. When sinks become sources: Adaptive colonization in asexuals*. Evolution 2019; 74:29-42. [DOI: 10.1111/evo.13848] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/09/2019] [Indexed: 01/31/2023]
Affiliation(s)
- F. Lavigne
- BioSPINRA84914 Avignon France
- Aix Marseille Univ, CNRSCentrale MarseilleI2M Marseille France
- ISEM (UMR 5554)CNRS34095 Montpellier France
| | - G. Martin
- ISEM (UMR 5554)CNRS34095 Montpellier France
| | - Y. Anciaux
- ISEM (UMR 5554)CNRS34095 Montpellier France
- BIRC, Aarhus UniversityC.F. Møllers Allé 8 DK‐8000 Aarhus C Denmark
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38
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Abstract
In evolutionary biology, it is generally assumed that evolution occurs in the weak mutation limit, that is, the frequency of multiple mutations simultaneously occurring in the same genome and the same generation is negligible. We employ mathematical modeling to show that, although under the typical parameter values of the evolutionary process the probability of multimutational leaps is indeed low, they might become substantially more likely under stress, when the mutation rate is dramatically elevated. We hypothesize that stress-induced mutagenesis in microbes is an evolvable adaptive strategy. Multimutational leaps might matter also in other cases of substantially increased mutation rate, such as growing tumors or evolution of primordial replicators. Is evolution always gradual or can it make leaps? We examine a mathematical model of an evolutionary process on a fitness landscape and obtain analytic solutions for the probability of multimutation leaps, that is, several mutations occurring simultaneously, within a single generation in 1 genome, and being fixed all together in the evolving population. The results indicate that, for typical, empirically observed combinations of the parameters of the evolutionary process, namely, effective population size, mutation rate, and distribution of selection coefficients of mutations, the probability of a multimutation leap is low, and accordingly the contribution of such leaps is minor at best. However, we show that, taking sign epistasis into account, leaps could become an important factor of evolution in cases of substantially elevated mutation rates, such as stress-induced mutagenesis in microbes. We hypothesize that stress-induced mutagenesis is an evolvable adaptive strategy.
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39
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Tools and systems for evolutionary engineering of biomolecules and microorganisms. ACTA ACUST UNITED AC 2019; 46:1313-1326. [DOI: 10.1007/s10295-019-02191-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/20/2019] [Indexed: 12/28/2022]
Abstract
Abstract
Evolutionary approaches have been providing solutions to various bioengineering challenges in an efficient manner. In addition to traditional adaptive laboratory evolution and directed evolution, recent advances in synthetic biology and fluidic systems have opened a new era of evolutionary engineering. Synthetic genetic circuits have been created to control mutagenesis and enable screening of various phenotypes, particularly metabolite production. Fluidic systems can be used for high-throughput screening and multiplexed continuous cultivation of microorganisms. Moreover, continuous directed evolution has been achieved by combining all the steps of evolutionary engineering. Overall, modern tools and systems for evolutionary engineering can be used to establish the artificial equivalent to natural evolution for various research applications.
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40
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González R, Wu B, Li X, Martínez F, Elena SF. Mutagenesis Scanning Uncovers Evolutionary Constraints on Tobacco Etch Potyvirus Membrane-Associated 6K2 Protein. Genome Biol Evol 2019; 11:1207-1222. [PMID: 30918938 PMCID: PMC6482416 DOI: 10.1093/gbe/evz069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2019] [Indexed: 12/30/2022] Open
Abstract
RNA virus high mutation rate is a double-edged sword. At the one side, most mutations jeopardize proteins functions; at the other side, mutations are needed to fuel adaptation. The relevant question then is the ratio between beneficial and deleterious mutations. To evaluate this ratio, we created a mutant library of the 6K2 gene of tobacco etch potyvirus that contains every possible single-nucleotide substitution. 6K2 protein anchors the virus replication complex to the network of endoplasmic reticulum membranes. The library was inoculated into the natural host Nicotiana tabacum, allowing competition among all these mutants and selection of those that are potentially viable. We identified 11 nonsynonymous mutations that remain in the viral population at measurable frequencies and evaluated their fitness. Some had fitness values higher than the wild-type and some were deleterious. The effect of these mutations in the structure, transmembrane properties, and function of 6K2 was evaluated in silico. In parallel, the effect of these mutations in infectivity, virus accumulation, symptoms development, and subcellular localization was evaluated in the natural host. The α-helix H1 in the N-terminal part of 6K2 turned out to be under purifying selection, while most observed mutations affect the link between transmembrane α-helices H2 and H3, fusing them into a longer helix and increasing its rigidity. In general, these changes are associated with higher within-host fitness and development of milder or no symptoms. This finding suggests that in nature selection upon 6K2 may result from a tradeoff between within-host accumulation and severity of symptoms.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, València, Spain
| | - Beilei Wu
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, València, Spain.,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianghua Li
- Systems Biology Program, Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, PRBB, Barcelona, Spain
| | - Fernando Martínez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, València, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, València, Spain.,The Santa Fe Institute, Santa Fe, New Mexico
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41
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Abstract
Selection of viral mutants resistant to compounds used in therapy is a major determinant of treatment failure, a problem akin to antibiotic resistance in bacteria. In this scenario, mutagenic base and nucleoside analogs have entered the picture because they increase the mutation rate of viral populations to levels incompatible with their survival. This antiviral strategy is termed lethal mutagenesis. It has found a major impulse with the observation that some antiviral agents, which initially were considered only inhibitors of virus multiplication, may in effect exert part of their antiviral activity through mutagenesis. Here, we review the conceptual basis of lethal mutagenesis, the evidence of virus extinction through mutagenic nucleotide analogs and prospects for application in antiviral designs.
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Anciaux Y, Lambert A, Ronce O, Roques L, Martin G. Population persistence under high mutation rate: From evolutionary rescue to lethal mutagenesis. Evolution 2019; 73:1517-1532. [DOI: 10.1111/evo.13771] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/24/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Yoann Anciaux
- Bioinformatics Research Center (BiRC)Aarhus University C.F. Møllers Allé 8 8000 Aarhus Denmark
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050PSL Research University Paris France
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM)Sorbonne Université CNRS UMR 8001 Paris France
| | - Ophélie Ronce
- Institut des Sciences de l'Evolution de MontpellierUniversité de Montpellier, CNRS, IRD, EPHE Montpellier France
| | | | - Guillaume Martin
- Institut des Sciences de l'Evolution de MontpellierUniversité de Montpellier, CNRS, IRD, EPHE Montpellier France
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43
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The effect of genetic complementation on the fitness and diversity of viruses spreading as collective infectious units. Virus Res 2019; 267:41-48. [PMID: 31077765 DOI: 10.1016/j.virusres.2019.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 12/31/2022]
Abstract
Viruses can spread collectively using different types of structures such as extracellular vesicles, virion aggregates, polyploid capsids, occlusion bodies, and even cells that accumulate virions at their surface, such as bacteria and dendritic cells. Despite the mounting evidence for collective spread, its implications for viral fitness and diversity remain poorly understood. It has been postulated that, by increasing the cellular multiplicity of infection, collective spread could enable mutually beneficial interactions among different viral genetic variants. One such interaction is genetic complementation, whereby deleterious mutations carried by different genomes are compensated. Here, we used simulations to evaluate whether complementation is likely to increase the fitness of viruses spreading collectively. We show that complementation among co-spreading viruses initially buffers the deleterious effects of mutations, but has no positive effect on mean population fitness over the long term, and even promotes error catastrophe at high mutation rates. Additionally, we found that collective spread increases the risk of invasion by social cheaters such as defective interfering particles. We also show that mutation accumulation depends on the type of collective infectious units considered. Co-spreading viral genomes produced in the same cell (e.g. extracellular vesicles, polyploid capsids, occlusion bodies) should exhibit higher genetic relatedness than groups formed extracellularly by viruses released from different cells (aggregates, binding to bacterial or dendritic cell surfaces), and we found that increased relatedness limits the adverse effects of complementation as well cheater invasion risk. Finally, we found that the costs of complementation can be offset by recombination. Based on our results, we suggest that alternative factors promoting collective spread should be considered.
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44
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Zhong Z, Liu CC. Probing pathways of adaptation with continuous evolution. CURRENT OPINION IN SYSTEMS BIOLOGY 2019; 14:18-24. [PMID: 31608311 PMCID: PMC6788780 DOI: 10.1016/j.coisb.2019.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ziwei Zhong
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
- Lead Contact
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45
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Chisholm PJ, Busch JW, Crowder DW. Effects of life history and ecology on virus evolutionary potential. Virus Res 2019; 265:1-9. [PMID: 30831177 DOI: 10.1016/j.virusres.2019.02.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 11/28/2022]
Abstract
The life history traits of viruses pose many consequences for viral population structure. In turn, population structure may influence the evolutionary trajectory of a virus. Here we review factors that affect the evolutionary potential of viruses, including rates of mutation and recombination, bottlenecks, selection pressure, and ecological factors such as the requirement for hosts and vectors. Mutation, while supplying a pool of raw genetic material, also results in the generation of numerous unfit mutants. The infection of multiple host species may expand a virus' ecological niche, although it may come at a cost to genetic diversity. Vector-borne viruses often experience a diminished frequency of positive selection and exhibit little diversity, and resistance against vector-borne viruses may thus be more durable than against non-vectored viruses. Evidence indicates that adaptation to a vector is more evolutionarily difficult than adaptation to a host. Overall, a better understanding of how various factors influence viral dynamics in both plant and animal pathosystems will lead to more effective anti-viral treatments and countermeasures.
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Affiliation(s)
- Paul J Chisholm
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164, USA.
| | - David W Crowder
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
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46
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Theodosiou L, Hiltunen T, Becks L. The role of stressors in altering eco‐evolutionary dynamics. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Loukas Theodosiou
- Community Dynamics GroupMax Planck Institute for Evolutionary Biology Plön Germany
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary Biology Plön Germany
| | - Teppo Hiltunen
- Department of MicrobiologyUniversity of Helsinki Helsinki Finland
- Department of BiologyUniversity of Turku Turku Finland
| | - Lutz Becks
- Community Dynamics GroupMax Planck Institute for Evolutionary Biology Plön Germany
- Limnology ‐ Aquatic Ecology and Evolution, Limnological InstituteUniversity of Konstanz Konstanz Germany
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47
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Zhao L, Abbasi AB, Illingworth CJR. Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection. Virus Evol 2019; 5:vez008. [PMID: 31024738 PMCID: PMC6476161 DOI: 10.1093/ve/vez008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mutational load is known to be of importance for the evolution of RNA viruses, the combination of a high mutation rate and large population size leading to an accumulation of deleterious mutations. However, while the effects of mutational load on global viral populations have been considered, its quantitative effects at the within-host scale of infection are less well understood. We here show that even on the rapid timescale of acute disease, mutational load has an effect on within-host viral adaptation, reducing the effective selection acting upon beneficial variants by ∼10 per cent. Furthermore, mutational load induces considerable stochasticity in the pattern of evolution, causing a more than five-fold uncertainty in the effective fitness of a transmitted beneficial variant. Our work aims to bridge the gap between classic models from population genetic theory and the biology of viral infection. In an advance on some previous models of mutational load, we replace the assumption of a constant variant fitness cost with an experimentally-derived distribution of fitness effects. Expanding previous frameworks for evolutionary simulation, we introduce the Wright-Fisher model with continuous mutation, which describes a continuum of possible modes of replication within a cell. Our results advance our understanding of adaptation in the context of strong selection and a high mutation rate. Despite viral populations having large absolute sizes, critical events in viral adaptation, including antigenic drift and the onset of drug resistance, arise through stochastic evolutionary processes.
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Affiliation(s)
- Lei Zhao
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ali B Abbasi
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Christopher J R Illingworth
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
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48
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Nurtay A, Hennessy MG, Sardanyés J, Alsedà L, Elena SF. Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181179. [PMID: 30800366 PMCID: PMC6366233 DOI: 10.1098/rsos.181179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
We investigate the dynamics of a wild-type viral strain which generates mutant strains differing in phenotypic properties for infectivity, virulence and mutation rates. We study, by means of a mathematical model and bifurcation analysis, conditions under which the wild-type and mutant viruses, which compete for the same host cells, can coexist. The coexistence conditions are formulated in terms of the basic reproductive numbers of the strains, a maximum value of the mutation rate and the virulence of the pathogens. The analysis reveals that parameter space can be divided into five regions, each with distinct dynamics, that are organized around degenerate Bogdanov-Takens and zero-Hopf bifurcations, the latter of which gives rise to a curve of transcritical bifurcations of periodic orbits. These results provide new insights into the conditions by which viral populations may contain multiple coexisting strains in a stable manner.
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Affiliation(s)
- Anel Nurtay
- Centre de Recerca Matemàtica, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Parc Científic UV, Paterna, València 46980, Spain
| | - Matthew G. Hennessy
- Centre de Recerca Matemàtica, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
| | - Josep Sardanyés
- Centre de Recerca Matemàtica, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
| | - Lluís Alsedà
- Centre de Recerca Matemàtica, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Barcelona Graduate School of Mathematics (BGSMath), Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Parc Científic UV, Paterna, València 46980, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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49
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Fabreti LG, Castro D, Gorzoni B, Janini LMR, Antoneli F. Stochastic Modeling and Simulation of Viral Evolution. Bull Math Biol 2018; 81:1031-1069. [PMID: 30552628 DOI: 10.1007/s11538-018-00550-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 12/03/2018] [Indexed: 12/11/2022]
Abstract
RNA viruses comprise vast populations of closely related, but highly genetically diverse, entities known as quasispecies. Understanding the mechanisms by which this extreme diversity is generated and maintained is fundamental when approaching viral persistence and pathobiology in infected hosts. In this paper, we access quasispecies theory through a mathematical model based on the theory of multitype branching processes, to better understand the roles of mechanisms resulting in viral diversity, persistence and extinction. We accomplish this understanding by a combination of computational simulations and the theoretical analysis of the model. In order to perform the simulations, we have implemented the mathematical model into a computational platform capable of running simulations and presenting the results in a graphical format in real time. Among other things, we show that the establishment of virus populations may display four distinct regimes from its introduction into new hosts until achieving equilibrium or undergoing extinction. Also, we were able to simulate different fitness distributions representing distinct environments within a host which could either be favorable or hostile to the viral success. We addressed the most used mechanisms for explaining the extinction of RNA virus populations called lethal mutagenesis and mutational meltdown. We were able to demonstrate a correspondence between these two mechanisms implying the existence of a unifying principle leading to the extinction of RNA viruses.
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Affiliation(s)
- Luiza Guimarães Fabreti
- Programa de Pós-Graduação em Infectologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Diogo Castro
- Programa de Pós-Graduação em Infectologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Bruno Gorzoni
- Programa de Pós-Graduação em Infectologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Luiz Mario Ramos Janini
- Departamentos de Microbiologia, Imunologia, Parasitologia and Medicina, Laboratório de Retrovirologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernando Antoneli
- Departamento de Informática em Saúde, Laboratório de Biocomplexidade e Genômica Evolutiva, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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50
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Ravikumar A, Arzumanyan GA, Obadi MKA, Javanpour AA, Liu CC. Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds. Cell 2018; 175:1946-1957.e13. [PMID: 30415839 PMCID: PMC6343851 DOI: 10.1016/j.cell.2018.10.021] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/16/2018] [Accepted: 10/04/2018] [Indexed: 11/17/2022]
Abstract
Directed evolution is a powerful approach for engineering biomolecules and understanding adaptation. However, experimental strategies for directed evolution are notoriously labor intensive and low throughput, limiting access to demanding functions, multiple functions in parallel, and the study of molecular evolution in replicate. We report OrthoRep, an orthogonal DNA polymerase-plasmid pair in yeast that stably mutates ∼100,000-fold faster than the host genome in vivo, exceeding the error threshold of genomic replication that causes single-generation extinction. User-defined genes in OrthoRep continuously and rapidly evolve through serial passaging, a highly straightforward and scalable process. Using OrthoRep, we evolved drug-resistant malarial dihydrofolate reductases (DHFRs) in 90 independent replicates. We uncovered a more complex fitness landscape than previously realized, including common adaptive trajectories constrained by epistasis, rare outcomes that avoid a frequent early adaptive mutation, and a suboptimal fitness peak that occasionally traps evolving populations. OrthoRep enables a new paradigm of routine, high-throughput evolution of biomolecular and cellular function.
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Affiliation(s)
- Arjun Ravikumar
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Garri A Arzumanyan
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Muaeen K A Obadi
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Alex A Javanpour
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Chang C Liu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA.
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