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Ning X, Xia B, Wang J, Gao R, Ren H. Host-adaptive mutations in Chikungunya virus genome. Virulence 2024; 15:2401985. [PMID: 39263937 DOI: 10.1080/21505594.2024.2401985] [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] [Received: 05/09/2024] [Revised: 08/08/2024] [Accepted: 08/31/2024] [Indexed: 09/13/2024] Open
Abstract
Chikungunya virus (CHIKV) is the causative agent of chikungunya fever (CHIKF), and its primary vectors are the mosquitoes Aedes aegypti and Aedes albopictus. CHIKV was initially endemic to Africa but has spread globally in recent years and affected millions of people. According to a risk assessment by the World Health Organization, CHIKV has the potential seriously impact public health. A growing body of research suggests that mutations in the CHIKV gene that enhance viral fitness in the host are contributing to the expansion of the global CHIKF epidemic. In this article, we review the host-adapted gene mutations in CHIKV under natural evolution and laboratory transmission conditions, which can help improve our understanding of the adaptive evolution of CHIKV and provide a basis for monitoring and early warning of future CHIKV outbreaks.
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Affiliation(s)
- Xinhang Ning
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, People's Republic of China
| | - Binghui Xia
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, People's Republic of China
| | - Jiaqi Wang
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, People's Republic of China
| | - Rong Gao
- Department of Respiratory Medicine, The People's Liberation Army Joint Logistic Support Force 943 Hospital, Wuwei, Gansu, People's Republic of China
| | - Hao Ren
- Department of Microbiology, Faculty of Naval Medicine, Shanghai Key Laboratory of Medical Biodefense, Naval Medical University, Shanghai, People's Republic of China
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2
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Smith SC, Krystofiak E, Ogden KM. Mammalian orthoreovirus can exit cells in extracellular vesicles. PLoS Pathog 2024; 20:e1011637. [PMID: 38206991 PMCID: PMC10807757 DOI: 10.1371/journal.ppat.1011637] [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: 08/25/2023] [Revised: 01/24/2024] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
Several egress pathways have been defined for many viruses. Among these pathways, extracellular vesicles (EVs) have been shown to function as vehicles of non-lytic viral egress. EVs are heterogenous populations of membrane-bound structures released from cells as a form of intercellular communication. EV-mediated viral egress may enable immune evasion and collective viral transport. Strains of nonenveloped mammalian orthoreovirus (reovirus) differ in cell lysis phenotypes, with T3D disrupting cell membranes more efficiently than T1L. However, mechanisms of reovirus egress and the influence of transport strategy on infection are only partially understood. To elucidate reovirus egress mechanisms, we infected murine fibroblasts (L cells) and non-polarized human colon epithelial (Caco-2) cells with T1L or T3D reovirus and enriched cell culture supernatants for large EVs, medium EVs, small EVs, and free reovirus. We found that both reovirus strains exit cells in association with large and medium EVs and as free virus particles, and that EV-enriched fractions are infectious. While reovirus visually associates with large and medium EVs, only medium EVs offer protection from antibody-mediated neutralization. EV-mediated protection from neutralization is virus strain- and cell type-specific, as medium EVs enriched from L cell supernatants protect T1L and T3D, while medium EVs enriched from Caco-2 cell supernatants largely fail to protect T3D and only protect T1L efficiently. Using genetically barcoded reovirus, we provide evidence that large and medium EVs can convey multiple particles to recipient cells. Finally, T1L or T3D infection increases the release of all EV sizes from L cells. Together, these findings suggest that in addition to exiting cells as free particles, reovirus promotes egress from distinct cell types in association with large and medium EVs during lytic or non-lytic infection, a mode of exit that can mediate multiparticle infection and, in some cases, protection from antibody neutralization.
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Affiliation(s)
- Sydni Caet Smith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Evan Krystofiak
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kristen M. Ogden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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3
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Catching A, Te Yeh M, Bianco S, Capponi S, Andino R. A tradeoff between enterovirus A71 particle stability and cell entry. Nat Commun 2023; 14:7450. [PMID: 37978288 PMCID: PMC10656440 DOI: 10.1038/s41467-023-43029-0] [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: 09/07/2022] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
A central role of viral capsids is to protect the viral genome from the harsh extracellular environment while facilitating initiation of infection when the virus encounters a target cell. Viruses are thought to have evolved an optimal equilibrium between particle stability and efficiency of cell entry. In this study, we genetically perturb this equilibrium in a non-enveloped virus, enterovirus A71 to determine its structural basis. We isolate a single-point mutation variant with increased particle thermotolerance and decreased efficiency of cell entry. Using cryo-electron microscopy and molecular dynamics simulations, we determine that the thermostable native particles have acquired an expanded conformation that results in a significant increase in protein dynamics. Examining the intermediate states of the thermostable variant reveals a potential pathway for uncoating. We propose a sequential release of the lipid pocket factor, followed by internal VP4 and ultimately the viral RNA.
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Affiliation(s)
- Adam Catching
- Department of Microbiology and Immunology, University of California in San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Biophysics, University of California in San Francisco, San Francisco, CA, 94158, USA
| | - Ming Te Yeh
- Department of Microbiology and Immunology, University of California in San Francisco, San Francisco, CA, 94158, USA
| | - Simone Bianco
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA, 95120, USA
- Center for Cellular Construction, San Francisco, CA, 94158, USA
- Altos Labs, Redwood City, CA, 94022, USA
| | - Sara Capponi
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA, 95120, USA.
- Center for Cellular Construction, San Francisco, CA, 94158, USA.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California in San Francisco, San Francisco, CA, 94158, USA.
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4
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Lequime S. The sociality continuum of viruses: a commentary on Leeks et al. 2023. J Evol Biol 2023; 36:1568-1570. [PMID: 37975506 DOI: 10.1111/jeb.14247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Affiliation(s)
- Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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5
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Bou JV, Taguwa S, Matsuura Y. Trick-or-Trap: Extracellular Vesicles and Viral Transmission. Vaccines (Basel) 2023; 11:1532. [PMID: 37896936 PMCID: PMC10611016 DOI: 10.3390/vaccines11101532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/15/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Extracellular vesicles (EVs) are lipid membrane-enclosed particles produced by most cells, playing important roles in various biological processes. They have been shown to be involved in antiviral mechanisms such as transporting antiviral molecules, transmitting viral resistance, and participating in antigen presentation. While viral transmission was traditionally thought to occur through independent viral particles, the process of viral infection is complex, with multiple barriers and challenges that viruses must overcome for successful infection. As a result, viruses exploit the intercellular communication pathways of EVs to facilitate cluster transmission, increasing their chances of infecting target cells. Viral vesicle transmission offers two significant advantages. Firstly, it enables the collective transmission of viral genomes, increasing the chances of infection and promoting interactions between viruses in subsequent generations. Secondly, the use of vesicles as vehicles for viral transmission provides protection to viral particles against environmental factors, while also expanding the cell tropism allowing viruses to reach cells in a receptor-independent manner. Understanding the role of EVs in viral transmission is crucial for comprehending virus evolution and developing innovative antiviral strategies, therapeutic interventions, and vaccine approaches.
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Affiliation(s)
- Juan-Vicente Bou
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuhei Taguwa
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Center for Advanced Modalities and DDS, Osaka University, 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Center for Advanced Modalities and DDS, Osaka University, 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
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Smith SC, Krystofiak E, Ogden KM. Mammalian orthoreovirus can exit cells in extracellular vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555250. [PMID: 37693509 PMCID: PMC10491149 DOI: 10.1101/2023.08.29.555250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Several egress pathways have been defined for many viruses. Among these pathways, extracellular vesicles (EVs) have been shown to function as vehicles of non-lytic viral egress. EVs are heterogenous populations of membrane-bound structures released from cells as a form of intercellular communication. EV-mediated viral egress may enable immune evasion and collective viral transport. Strains of nonenveloped mammalian orthoreovirus (reovirus) differ in cell lysis phenotypes, with T3D disrupting cell membranes more efficiently than T1L. However, mechanisms of reovirus egress and the influence of transport strategy on infection are only partially understood. To elucidate reovirus egress mechanisms, we infected murine fibroblasts (L cells) and non-polarized human colon epithelial (Caco-2) cells with T1L or T3D reovirus and enriched cell culture supernatants for large EVs, medium EVs, small EVs, and free reovirus. We found that both reovirus strains exit cells in association with large and medium EVs and as free virus particles, and that EV-enriched fractions are infectious. While reovirus visually associates with large and medium EVs, only medium EVs offer protection from antibody-mediated neutralization. EV-mediated protection from neutralization is virus strain- and cell type-specific, as medium EVs enriched from L cell supernatants protect T1L and T3D, while medium EVs enriched from Caco-2 cell supernatants largely fail to protect T3D and only protect T1L efficiently. Using genetically barcoded reovirus, we provide evidence that large and medium EVs can convey multiple particles to recipient cells. Finally, T1L or T3D infection increases the release of all EV sizes from L cells. Together, these findings suggest that in addition to exiting cells as free particles, reovirus promotes egress from distinct cell types in association with large and medium EVs during lytic or non-lytic infection, a mode of exit that can mediate multiparticle infection and, in some cases, protection from antibody neutralization.
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Affiliation(s)
- Sydni Caet Smith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Evan Krystofiak
- Department of Cell & Developmental Biology, Vanderbilt University
| | - Kristen M. Ogden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
- Department of Pediatrics, Vanderbilt University Medical Center
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Nyirakanani C, Tamisier L, Bizimana JP, Rollin J, Nduwumuremyi A, Bigirimana VDP, Selmi I, Lasois L, Vanderschuren H, Massart S. Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda. Virus Evol 2023; 9:vead053. [PMID: 37692897 PMCID: PMC10491861 DOI: 10.1093/ve/vead053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/14/2023] [Accepted: 08/20/2023] [Indexed: 09/12/2023] Open
Abstract
Cassava Brown Streak Disease (CBSD), which is caused by cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), represents one of the most devastating threats to cassava production in Africa, including in Rwanda where a dramatic epidemic in 2014 dropped cassava yield from 3.3 million to 900,000 tonnes (1). Studying viral genetic diversity at the genome level is essential in disease management, as it can provide valuable information on the origin and dynamics of epidemic events. To fill the current lack of genome-based diversity studies of UCBSV, we performed a nationwide survey of cassava ipomovirus genomic sequences in Rwanda by high-throughput sequencing (HTS) of pools of plants sampled from 130 cassava fields in thirteen cassava-producing districts, spanning seven agro-ecological zones with contrasting climatic conditions and different cassava cultivars. HTS allowed the assembly of a nearly complete consensus genome of UCBSV in twelve districts. The phylogenetic analysis revealed high homology between UCBSV genome sequences, with a maximum of 0.8 per cent divergence between genomes at the nucleotide level. An in-depth investigation based on Single Nucleotide Polymorphisms (SNPs) was conducted to explore the genome diversity beyond the consensus sequences. First, to ensure the validity of the result, a panel of SNPs was confirmed by independent reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing. Furthermore, the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNP patterns identified three different UCBSV haplotypes geographically clustered. The haplotype 2 (H2) was restricted to the central regions, where the NAROCAS 1 cultivar is predominantly farmed. RT-PCR and Sanger sequencing of individual NAROCAS1 plants confirmed their association with H2. Haplotype 1 was widely spread, with a 100 per cent occurrence in the Eastern region, while Haplotype 3 was only found in the Western region. These haplotypes' associations with specific cultivars or regions would need further confirmation. Our results prove that a much more complex picture of genetic diversity can be deciphered beyond the consensus sequences, with practical implications on virus epidemiology, evolution, and disease management. Our methodology proposes a high-resolution analysis of genome diversity beyond the consensus between and within samples. It can be used at various scales, from individual plants to pooled samples of virus-infected plants. Our findings also showed how subtle genetic differences could be informative on the potential impact of agricultural practices, as the presence and frequency of a virus haplotype could be correlated with the dissemination and adoption of improved cultivars.
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Affiliation(s)
- Chantal Nyirakanani
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Crop Sciences, School of Agriculture and Food Sciences, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze 210, Rwanda
| | - Lucie Tamisier
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Jean Pierre Bizimana
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Research, Rwanda Agriculture and Animal Resources Development Board, Huye 5016, Rwanda
| | - Johan Rollin
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Research, DNAVision, Gosselies, Charleroi 6041, Belgium
| | - Athanase Nduwumuremyi
- Department of Research, Rwanda Agriculture and Animal Resources Development Board, Huye 5016, Rwanda
| | - Vincent de Paul Bigirimana
- Department of Crop Sciences, School of Agriculture and Food Sciences, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze 210, Rwanda
| | - Ilhem Selmi
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Ludivine Lasois
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Hervé Vanderschuren
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Tropical Crop Improvement Laboratory, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven 3001, Belgium
| | - Sébastien Massart
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
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8
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Rollin J, Bester R, Brostaux Y, Caglayan K, De Jonghe K, Eichmeier A, Foucart Y, Haegeman A, Koloniuk I, Kominek P, Maree H, Onder S, Posada Céspedes S, Roumi V, Šafářová D, Schumpp O, Ulubas Serce C, Sõmera M, Tamisier L, Vainio E, van der Vlugt RAA, Massart S. Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies. PeerJ 2023; 11:e15816. [PMID: 37601254 PMCID: PMC10439718 DOI: 10.7717/peerj.15816] [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] [Received: 02/20/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.
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Affiliation(s)
- Johan Rollin
- Laboratory of Plant Pathology—TERRA—Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachelle Bester
- Citrus Research International, Matieland, South Africa
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Yves Brostaux
- Laboratory of Statistics, Computer Science and Modelling Applied to Bioengineering, TERRA, Gembloux Agro-Bio Tech, Teaching and Research Centre, University of Liège, Gembloux, Belgium
| | - Kadriye Caglayan
- Plant Protection Department, Agricultural Faculty, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Kris De Jonghe
- Fisheries and Food (ILVO), Plant Sciences Unit, Flanders Research Institute for Agriculture, Merelbeke, Belgium
| | - Ales Eichmeier
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czech Republic
| | - Yoika Foucart
- Fisheries and Food (ILVO), Plant Sciences Unit, Flanders Research Institute for Agriculture, Merelbeke, Belgium
| | - Annelies Haegeman
- Fisheries and Food (ILVO), Plant Sciences Unit, Flanders Research Institute for Agriculture, Merelbeke, Belgium
| | - Igor Koloniuk
- Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Hans Maree
- Citrus Research International, Matieland, South Africa
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Serkan Onder
- Department of Plant Protection, Faculty of Agriculture, Eskişehir Osmangazi University, Eskişehir, Turkey
| | - Susana Posada Céspedes
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Vahid Roumi
- Plant Protection Department, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | - Dana Šafářová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | | | - Cigdem Ulubas Serce
- Plant Production and Technologies Department, Ayhan Şahenk Faculty of Agricultural Science and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Lucie Tamisier
- Pathologie Végétale, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Montfavet, France
- GAFL, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Montfavet, France
| | - Eeva Vainio
- Natural Resources Institute Finland, Helsinki, Finland
| | | | - Sebastien Massart
- Laboratory of Plant Pathology—TERRA—Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Saeki K, Sasaki A. Cell-to-cell transmission promotes the emergence of double-drug resistance. Virus Evol 2023; 9:vead017. [PMID: 37744652 PMCID: PMC10517696 DOI: 10.1093/ve/vead017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/13/2023] [Accepted: 03/08/2023] [Indexed: 09/26/2023] Open
Abstract
The use of multiple antivirals in a single patient increases the risk of emergence of multidrug-resistant viruses, posing a public health challenge and limiting management options. Cell-to-cell viral transmission allows a pair of viruses that are each resistant to a single drug to persist for a prolonged period of passages although neither can survive alone under double-drug treatment. This pair should then persist until they accumulate a second mutation to generate resistance to both drugs. Accordingly, we here propose a hypothesis that viruses have a much higher probability of developing double-drug resistance when they are transmitted via a cell-to-cell mode than when they are transmitted via a cell-free mode through released virions. By using a stochastic model describing the changes in the frequencies of viral genotypes over successive infections, we analytically demonstrate that the emergence probability of double resistance is approximately the square of the number of viral genomes that establish infection times greater in cell-to-cell transmission than in cell-free transmission. Our study suggests the importance of inhibiting cell-to-cell transmission during multidrug treatment.
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Affiliation(s)
- Koichi Saeki
- Department of Computational Biology and Medical Sciences, Graduate School for Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0885, Japan
| | - Akira Sasaki
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Kanagawa 240-0193, Japan
- Evolution and Ecology Program, International Institute for Applied Systems Analysis, Laxenburg A-2361, Austria
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10
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Guo J, He Y, Wang X, Merits A, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Gao Q, Sun D, Tian B, Cheng A, Chen S. Attenuation of Avian Flavivirus by Rewiring the Leucine and Serine Codons of Its E-NS1 Protein toward Stop Mutation To Redirect Virus Evolution. Microbiol Spectr 2023; 11:e0292122. [PMID: 36625643 PMCID: PMC9927255 DOI: 10.1128/spectrum.02921-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/21/2022] [Indexed: 01/11/2023] Open
Abstract
Recently, a new strategy for attenuating RNA viruses by redirecting their evolution in sequence space was confirmed for Enterovirus and Influenza viruses. Using avian flavivirus as a model, the 69 serine and 53 leucine codons on the E-NS1 genes were modified to change evolutionary direction of the viral sequence space. This means that all codons encoding serine or leucine residues were substituted with codons that are only one base different from the three stop codons, resulting in the initial position of the virus genome in sequence space being closer to the detrimental areas to achieve attenuation by reducing viral adaptability. The growth curve and plaque size of CQW1-one-to-stop (CQW1-OTS) were similar to those of CQW1-wild type (CQW1-WT) in vitro, but attenuated proliferation was detected when treated with a mutagenic reagent (ribavirin). However, comparably high CQW1-OTS and CQW1-WT lethality rates were detected in 9-day-old duck embryos and 5-day-old ducklings, suggesting that this strategy works but with limitations. With that in mind, homologous hosts in nonsensitive age (25-day-old ducks) and heterologous hosts (3-week-old Kunming mice) were employed to investigate if CQW1-OTS was attenuated under host selection pressure. Minimal attenuation of CQW1-OTS in elder ducks and apparent attenuation in mice were reported, providing reduced viral titers, mild clinical signs, and lower specific infectivity. Collectively, we experimentally demonstrate that the attenuation strategy of redirecting virus evolution in sequence space works for flavivirus. Redirection of the virus is attenuated only under some outside pressure, such as heterologous hosts or antiviral drugs treatment, limiting its usage in flaviviruses. IMPORTANCE Flaviviruses are medically important arboviruses that threaten public health, but no approved treatments are currently available. Vaccines prevent flavivirus infection. We employed duck Tembusu virus (TMUV), a mosquito-borne flavivirus, to evaluate virus redirection. TMUV is native to birds and could infect mice by intracerebral injection, making it an experimental animal model to study flavivirus characteristics in vivo. The 69 serine and 53 leucine codons on the E-NS1 proteins of CQW1 were synonymously substituted to change evolutionary direction of the virus in sequence space. In vitro mutagen reagent treatment suppressed CQW1-OTS viral multiplication, but in vivo attenuation depended on host selective pressure. CQW1-OTS viral attenuation was observed in older ducks but not sensitive ducklings; considerable attenuation was also observed in heterogenous host (mice), which provides more selective pressure on viruses. Collectively, these data indicated that there are very important preconditions for application of evaluating whether this strategy shows application prospects in novel flavivirus vaccine development.
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Affiliation(s)
- Jiaqi Guo
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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11
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Xia B, Pan X, Luo RH, Shen X, Li S, Wang Y, Zuo X, Wu Y, Guo Y, Xiao G, Li Q, Long XY, He XY, Zheng HY, Lu Y, Pang W, Zheng YT, Li J, Zhang LK, Gao Z. Extracellular vesicles mediate antibody-resistant transmission of SARS-CoV-2. Cell Discov 2023; 9:2. [PMID: 36609376 PMCID: PMC9821354 DOI: 10.1038/s41421-022-00510-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/13/2022] [Indexed: 01/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. Antibody resistance dampens neutralizing antibody therapy and threatens current global Coronavirus (COVID-19) vaccine campaigns. In addition to the emergence of resistant SARS-CoV-2 variants, little is known about how SARS-CoV-2 evades antibodies. Here, we report a novel mechanism of extracellular vesicle (EV)-mediated cell-to-cell transmission of SARS-CoV-2, which facilitates SARS-CoV-2 to escape from neutralizing antibodies. These EVs, initially observed in SARS-CoV-2 envelope protein-expressing cells, are secreted by various SARS-CoV-2-infected cells, including Vero E6, Calu-3, and HPAEpiC cells, undergoing infection-induced pyroptosis. Various SARS-CoV-2-infected cells produce similar EVs characterized by extra-large sizes (1.6-9.5 μm in diameter, average diameter > 4.2 μm) much larger than previously reported virus-generated vesicles. Transmission electron microscopy analysis and plaque assay reveal that these SARS-CoV-2-induced EVs contain large amounts of live virus particles. In particular, the vesicle-cloaked SARS-CoV-2 virus is resistant to neutralizing antibodies and able to reinfect naïve cells independent of the reported receptors and cofactors. Consistently, the constructed 3D images show that intact EVs could be taken up by recipient cells directly, supporting vesicle-mediated cell-to-cell transmission of SARS-CoV-2. Our findings reveal a novel mechanism of receptor-independent SARS-CoV-2 infection via cell-to-cell transmission, provide new insights into antibody resistance of SARS-CoV-2 and suggest potential targets for future antiviral therapeutics.
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Affiliation(s)
- Bingqing Xia
- grid.9227.e0000000119573309Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyan Pan
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei China
| | - Rong-Hua Luo
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Xurui Shen
- grid.9227.e0000000119573309Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Shuangqu Li
- grid.9227.e0000000119573309Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Yi Wang
- grid.9227.e0000000119573309Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Zuo
- grid.9227.e0000000119573309Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yan Wu
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei China
| | - Yingqi Guo
- grid.9227.e0000000119573309Public Technology Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Gengfu Xiao
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei China
| | - Qiguang Li
- grid.9227.e0000000119573309Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Yan Long
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Xiao-Yan He
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Hong-Yi Zheng
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Ying Lu
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Wei Pang
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Yong-Tang Zheng
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Jia Li
- grid.9227.e0000000119573309Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309Zhongshan Institute for Drug Research, Institution for Drug Discovery Innovation, Chinese Academy of Science, Zhongshan, Guangdong China
| | - Lei-Ke Zhang
- grid.9227.e0000000119573309State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei China
| | - Zhaobing Gao
- grid.9227.e0000000119573309Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309Zhongshan Institute for Drug Research, Institution for Drug Discovery Innovation, Chinese Academy of Science, Zhongshan, Guangdong China ,grid.8547.e0000 0001 0125 2443School of Pharmacy, Fudan University, Shanghai, China
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12
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Allman B, Koelle K, Weissman D. Heterogeneity in viral populations increases the rate of deleterious mutation accumulation. Genetics 2022; 222:6673144. [PMID: 35993909 PMCID: PMC9526070 DOI: 10.1093/genetics/iyac127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
RNA viruses have high mutation rates, with the majority of mutations being deleterious. We examine patterns of deleterious mutation accumulation over multiple rounds of viral replication, with a focus on how cellular coinfection and heterogeneity in viral output affect these patterns. Specifically, using agent-based intercellular simulations we find, in agreement with previous studies, that coinfection of cells by viruses relaxes the strength of purifying selection, and thereby increases the rate of deleterious mutation accumulation. We further find that cellular heterogeneity in viral output exacerbates the rate of deleterious mutation accumulation, regardless of whether this heterogeneity in viral output is stochastic or is due to variation in cellular multiplicity of infection. These results highlight the need to consider the unique life histories of viruses and their population structure to better understand observed patterns of viral evolution.
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Affiliation(s)
- Brent Allman
- Graduate Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, Georgia 30322, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Daniel Weissman
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA.,Department of Physics, Emory University, Atlanta, Georgia 30322, USA
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13
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Miura T, Kadoya SS, Takino H, Sano D, Akiba M. Temporal variations of human and animal Rotavirus A genotypes in surface water used for drinking water production. Front Microbiol 2022; 13:912147. [PMID: 36016785 PMCID: PMC9395708 DOI: 10.3389/fmicb.2022.912147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Rotavirus is a major cause of gastroenteritis among infants and children. In this study, nested PCR assays were developed to amplify partial regions of the VP7, VP4, and VP6 genes of Rotavirus A (RVA) for amplicon-based Illumina MiSeq sequencing to investigate RVA genotypes in environmental water samples. Eight sets of inner primers were first designed and screened for use in the nested PCR assays, and four sets of them could produce amplicons. Six sets of outer primers were then designed and combined with the four sets of inner primers that worked. The assays were evaluated for sensitivity using raw water samples collected from one drinking water treatment plant between April 2019 and March 2020 (Sample Set 1; N = 12) and seven DWTPs between 2018 and 2020 (Sample Set 2; N = 18). In total, 43 amplicons from Set 1 were sequenced and diverse sequences from human, porcine, bovine, equine, and feline RVA were observed. Human G8, G3, and G2 genotypes were obtained, with G8 predominant (relative abundance, 36–87%) in samples taken during the rotavirus epidemic season between April and June. Porcine G5, G11, and G4, and bovine G10 and G6 genotypes were also detected. VP4 sequence analysis revealed that the human P[8] genotype was present throughout the year, whereas P[4] and P[9] were present only in the epidemic season. The vaccine strains P[5] and P[8] (RotaTeq®) were also detected. Our approach enables the identification of prevalent human and animal RVA genotypes and their host species that potentially caused fecal contamination in water sources.
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Affiliation(s)
- Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
- *Correspondence: Takayuki Miura,
| | - Syun-suke Kadoya
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
- Department of Urban Engineering, The University of Tokyo, Bunkyo, Japan
| | - Hiroyuki Takino
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
| | - Michihiro Akiba
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
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14
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Kadoya SS, Urayama SI, Nunoura T, Hirai M, Takaki Y, Kitajima M, Nakagomi T, Nakagomi O, Okabe S, Nishimura O, Sano D. The Intrapopulation Genetic Diversity of RNA Virus May Influence the Sensitivity of Chlorine Disinfection. Front Microbiol 2022; 13:839513. [PMID: 35668760 PMCID: PMC9163991 DOI: 10.3389/fmicb.2022.839513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
RNA virus populations are not clonal; rather, they comprise a mutant swarm in which sequences are slightly different from the master sequence. Genetic diversity within a population (intrapopulation genetic diversity) is critical for RNA viruses to survive under environmental stresses. Disinfection has become an important practice in the control of pathogenic viruses; however, the impact of intrapopulation genetic diversity on the sensitivity of disinfection, defined as -log10 (postdisinfected infectious titer/predisinfected titer), has not been elucidated. In this study, we serially passaged populations of rhesus rotavirus. We demonstrated that populations with reduced chlorine sensitivity emerged at random and independently of chlorine exposure. Sequencing analysis revealed that compared with sensitive populations, less-sensitive ones had higher non-synonymous genetic diversity of the outer capsid protein gene, suggesting that changes in the amino acid sequences of the outer capsid protein were the main factors influencing chlorine sensitivity. No common mutations were found among less-sensitive populations, indicating that rather than specific mutations, the diversity of the outer capsid protein itself was associated with the disinfection sensitivity and that the disinfection sensitivity changed stochastically. Simulation results suggest that the disinfection sensitivity of a genetically diverse population is destabilized if cooperative viral clusters including multiple sequences are formed. These results advocate that any prevention measures leading to low intrapopulation genetic diversity are important to prevent the spread and evolution of pathogenic RNA viruses in society.
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Affiliation(s)
- Syun-suke Kadoya
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| | - Syun-ichi Urayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Miho Hirai
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Toyoko Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Osamu Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Osamu Nishimura
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Japan
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15
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Zheng M. ACE2 and COVID-19 Susceptibility and Severity. Aging Dis 2022; 13:360-372. [PMID: 35371596 PMCID: PMC8947832 DOI: 10.14336/ad.2021.0805] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/05/2021] [Indexed: 11/11/2022] Open
Abstract
Sick, male, and older populations are more vulnerable to COVID-19. However, it remains unclear whether a common mechanism exists across different demographic characteristics. SARS-CoV-2 infection is initiated by the specific binding of the viral spike protein to angiotensin-converting enzyme 2 (ACE2). This study analyzed the demographics of pulmonary ACE2 expression, Mendelian randomization (MR) of ACE2 and COVID-19, and comparative tropism of SARS-CoV-2. The key features of SARS-CoV-2 tropism, including pulmonary ACE2 expression and ACE2-expressing cell types, showed distinct subphenotypes associated with the demographics of vulnerable COVID-19 populations, suggesting a hypothesis centered on “ACE2” to explain their interplay. Next, by integrating multiple COVID-19 cohorts of genome-wide association studies (GWASs) and cis-expression quantitative trait loci (cis-eQTLs) of ACE2, MR analysis demonstrated that ACE2 played a causal role in COVID-19 susceptibility and severity, suggesting ACE2 as a promising target for early COVID-19 treatment. Next, by analyzing the expression of host cell receptors using single-cell RNA sequencing (scRNA-seq) data of human lung tissues, comparative tropism analysis showed that SARS-CoV-2 and other respiratory viruses, but not non-respiratory viruses, had remarkably overlapping and enriched cellular tropism in alveolar type 2 (AT2) cells. This finding indicates the possibility of coinfection with SARS-CoV-2 and other respiratory viruses, perhaps implying sociovirology at the cellular level. Moreover, the binding of viral entry proteins to the compatible host cell receptors is under strong natural selection pressure. Therefore, comparative tropism might reveal the footprint of natural selection that shapes the virus population, which provides a novel perspective for understanding zoonotic spillover events.
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Affiliation(s)
- Ming Zheng
- 1Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing, China.,2Beijing Institute of Basic Medical Sciences, Beijing, China
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16
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Wang Y, Tang CY, Wan XF. Antigenic characterization of influenza and SARS-CoV-2 viruses. Anal Bioanal Chem 2022; 414:2841-2881. [PMID: 34905077 PMCID: PMC8669429 DOI: 10.1007/s00216-021-03806-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.
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Affiliation(s)
- Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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17
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Pathak AK, Mishra GP, Uppili B, Walia S, Fatihi S, Abbas T, Banu S, Ghosh A, Kanampalliwar A, Jha A, Fatma S, Aggarwal S, Dhar MS, Marwal R, Radhakrishnan VS, Ponnusamy K, Kabra S, Rakshit P, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Thukral L, Raghav SK, Mukerji M. Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. Nucleic Acids Res 2022; 50:1551-1561. [PMID: 35048970 PMCID: PMC8860616 DOI: 10.1093/nar/gkab1297] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.
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Affiliation(s)
- Ankit K Pathak
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Bharathram Uppili
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Safal Walia
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Saman Fatihi
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tahseen Abbas
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sofia Banu
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Arup Ghosh
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | | | - Atimukta Jha
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Sana Fatma
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Shifu Aggarwal
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mahesh Shanker Dhar
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | | | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Sandhya Kabra
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Partha Rakshit
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Rahul C Bhoyar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Abhinav Jain
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohit Kumar Divakar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohamed Imran
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohammed Faruq
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Divya Tej Sowpati
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Lipi Thukral
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Sunil K Raghav
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mitali Mukerji
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Indian Institute of Technology (IIT), Jodhpur, India
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18
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Abstract
Bats are a key reservoir of coronaviruses (CoVs), including the agent of the severe acute respiratory syndrome, SARS-CoV-2, responsible for the recent deadly viral pneumonia pandemic. However, understanding how bats can harbor several microorganisms without developing illnesses is still a matter under discussion. Viruses and other pathogens are often studied as stand-alone entities, despite that, in nature, they mostly live in multispecies associations called biofilms-both externally and within the host. Microorganisms in biofilms are enclosed by an extracellular matrix that confers protection and improves survival. Previous studies have shown that viruses can secondarily colonize preexisting biofilms, and viral biofilms have also been described. In this review, we raise the perspective that CoVs can persistently infect bats due to their association with biofilm structures. This phenomenon potentially provides an optimal environment for nonpathogenic and well-adapted viruses to interact with the host, as well as for viral recombination. Biofilms can also enhance virion viability in extracellular environments, such as on fomites and in aquatic sediments, allowing viral persistence and dissemination. Moreover, understanding the biofilm lifestyle of CoVs in reservoirs might contribute to explaining several burning questions as to persistence and transmissibility of highly pathogenic emerging CoVs.
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Affiliation(s)
- Rafael Gomes Von Borowski
- Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, Rennes, France
| | - Danielle Silva Trentin
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Brazil
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19
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Cubas-Gaona LL, Flageul A, Courtillon C, Briand FX, Contrant M, Bougeard S, Lucas P, Quenault H, Leroux A, Keita A, Amelot M, Grasland B, Blanchard Y, Eterradossi N, Brown PA, Soubies SM. Genome Evolution of Two Genetically Homogeneous Infectious Bursal Disease Virus Strains During Passages in vitro and ex vivo in the Presence of a Mutagenic Nucleoside Analog. Front Microbiol 2021; 12:678563. [PMID: 34177862 PMCID: PMC8226269 DOI: 10.3389/fmicb.2021.678563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
The avibirnavirus infectious bursal disease virus (IBDV) is responsible for a highly contagious and sometimes lethal disease of chickens (Gallus gallus). IBDV genetic variation is well-described for both field and live-attenuated vaccine strains, however, the dynamics and selection pressures behind this genetic evolution remain poorly documented. Here, genetically homogeneous virus stocks were generated using reverse genetics for a very virulent strain, rvv, and a vaccine-related strain, rCu-1. These viruses were serially passaged at controlled multiplicities of infection in several biological systems, including primary chickens B cells, the main cell type targeted by IBDV in vivo. Passages were also performed in the absence or presence of a strong selective pressure using the antiviral nucleoside analog 7-deaza-2'-C-methyladenosine (7DMA). Next Generation Sequencing (NGS) of viral genomes after the last passage in each biological system revealed that (i) a higher viral diversity was generated in segment A than in segment B, regardless 7DMA treatment and viral strain, (ii) diversity in segment B was increased by 7DMA treatment in both viruses, (iii) passaging of IBDV in primary chicken B cells, regardless of 7DMA treatment, did not select cell-culture adapted variants of rvv, preserving its capsid protein (VP2) properties, (iv) mutations in coding and non-coding regions of rCu-1 segment A could potentially associate to higher viral fitness, and (v) a specific selection, upon 7DMA addition, of a Thr329Ala substitution occurred in the viral polymerase VP1. The latter change, together with Ala270Thr change in VP2, proved to be associated with viral attenuation in vivo. These results identify genome sequences that are important for IBDV evolution in response to selection pressures. Such information will help tailor better strategies for controlling IBDV infection in chickens.
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Affiliation(s)
- Liliana L Cubas-Gaona
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Alexandre Flageul
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Céline Courtillon
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Francois-Xavier Briand
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Maud Contrant
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Stephanie Bougeard
- Epidemiology, Animal Health and Welfare Unit (EPISABE), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Pierrick Lucas
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Hélène Quenault
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Aurélie Leroux
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Alassane Keita
- Experimental Poultry Unit (SELEAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Michel Amelot
- Experimental Poultry Unit (SELEAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Béatrice Grasland
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Yannick Blanchard
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Nicolas Eterradossi
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Paul Alun Brown
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
| | - Sébastien Mathieu Soubies
- Avian and Rabbit Virology, Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Ploufragan, France
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20
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Geisler A, Hazini A, Heimann L, Kurreck J, Fechner H. Coxsackievirus B3-Its Potential as an Oncolytic Virus. Viruses 2021; 13:v13050718. [PMID: 33919076 PMCID: PMC8143167 DOI: 10.3390/v13050718] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
Oncolytic virotherapy represents one of the most advanced strategies to treat otherwise untreatable types of cancer. Despite encouraging developments in recent years, the limited fraction of patients responding to therapy has demonstrated the need to search for new suitable viruses. Coxsackievirus B3 (CVB3) is a promising novel candidate with particularly valuable features. Its entry receptor, the coxsackievirus and adenovirus receptor (CAR), and heparan sulfate, which is used for cellular entry by some CVB3 variants, are highly expressed on various cancer types. Consequently, CVB3 has broad anti-tumor activity, as shown in various xenograft and syngeneic mouse tumor models. In addition to direct tumor cell killing the virus induces a strong immune response against the tumor, which contributes to a substantial increase in the efficiency of the treatment. The toxicity of oncolytic CVB3 in healthy tissues is variable and depends on the virus strain. It can be abrogated by genetic engineering the virus with target sites of microRNAs. In this review, we present an overview of the current status of the development of CVB3 as an oncolytic virus and outline which steps still need to be accomplished to develop CVB3 as a therapeutic agent for clinical use in cancer treatment.
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Affiliation(s)
- Anja Geisler
- Department of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; (A.G.); (L.H.); (J.K.)
| | - Ahmet Hazini
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK;
| | - Lisanne Heimann
- Department of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; (A.G.); (L.H.); (J.K.)
| | - Jens Kurreck
- Department of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; (A.G.); (L.H.); (J.K.)
| | - Henry Fechner
- Department of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; (A.G.); (L.H.); (J.K.)
- Correspondence: ; Tel.: +49-30-31-47-21-81
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21
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Dey R, Folkins MA, Ashbolt NJ. Extracellular amoebal-vesicles: potential transmission vehicles for respiratory viruses. NPJ Biofilms Microbiomes 2021; 7:25. [PMID: 33731696 PMCID: PMC7969602 DOI: 10.1038/s41522-021-00201-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/18/2021] [Indexed: 12/29/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is a major cause of acute respiratory tract infections in children and immunocompromised adults worldwide. Here we report that amoebae-release respirable-sized vesicles containing high concentrations of infectious RSV that persisted for the duration of the experiment. Given the ubiquity of amoebae in moist environments, our results suggest that extracellular amoebal-vesicles could contribute to the environmental persistence of respiratory viruses, including potential resistance to disinfection processes and thereby offering novel pathways for viral dissemination and transmission.
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Affiliation(s)
- Rafik Dey
- School of Public Health, University of Alberta, Edmonton, AB, Canada. .,Dept. Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada.
| | - Melanie A Folkins
- Dept. Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Nicholas J Ashbolt
- School of Public Health, University of Alberta, Edmonton, AB, Canada.,Dept. Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada.,School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, Australia
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22
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Asok Kumar N, Muraleedharan Suma S, Kunnakkadan U, Nag J, Koolaparambil Mukesh R, Lyles DS, Johnson JB. Functional Dissection of the Dominant Role of CD55 in Protecting Vesicular Stomatitis Virus against Complement-Mediated Neutralization. Viruses 2021; 13:v13030373. [PMID: 33652918 PMCID: PMC7996768 DOI: 10.3390/v13030373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/05/2021] [Accepted: 02/19/2021] [Indexed: 11/16/2022] Open
Abstract
The human complement system is an important part of the innate immune system. Its effector pathways largely mediate virus neutralization. Vesicular stomatitis virus (VSV) activates the classical pathway of the complement, leading to virus neutralization by lysis. Two host-derived membrane-associated regulators of complement activation (RCA), CD55 and CD46, which are incorporated into the VSV envelope during egress, confer protection by delaying/resisting complement-mediated neutralization. We showed previously that CD55 is more effective than CD46 in the inhibition of neutralization. In this study, we identified that, at the protein level, VSV infection resulted in the down-regulation of CD46 but not CD55. The mRNA of both the RCAs was significantly down-regulated by VSV, but it was delayed in the case of CD55. The immunoblot analysis of the levels of RCAs in the progeny virion harvested at three specific time intervals, points to an equal ratio of its distribution relative to viral proteins. Besides reconfirming the dominant role of CD55 over CD46 in shielding VSV from complement, our results also highlight the importance of the subtle modulation in the expression pattern of RCAs in a system naturally expressing them.
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Affiliation(s)
- Nisha Asok Kumar
- Pathogen Biology, Virology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala 695014, India; (N.A.K.); (S.M.S.); (U.K.); (J.N.); (R.K.M.)
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sreenath Muraleedharan Suma
- Pathogen Biology, Virology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala 695014, India; (N.A.K.); (S.M.S.); (U.K.); (J.N.); (R.K.M.)
| | - Umerali Kunnakkadan
- Pathogen Biology, Virology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala 695014, India; (N.A.K.); (S.M.S.); (U.K.); (J.N.); (R.K.M.)
- Department of Biotechnology, University of Kerala, Thiruvananthapuram, Kerala 695581, India
| | - Joydeep Nag
- Pathogen Biology, Virology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala 695014, India; (N.A.K.); (S.M.S.); (U.K.); (J.N.); (R.K.M.)
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Reshma Koolaparambil Mukesh
- Pathogen Biology, Virology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala 695014, India; (N.A.K.); (S.M.S.); (U.K.); (J.N.); (R.K.M.)
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Douglas S. Lyles
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA;
| | - John Bernet Johnson
- Pathogen Biology, Virology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala 695014, India; (N.A.K.); (S.M.S.); (U.K.); (J.N.); (R.K.M.)
- Correspondence:
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23
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Dolan PT, Taguwa S, Rangel MA, Acevedo A, Hagai T, Andino R, Frydman J. Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells. eLife 2021; 10:e61921. [PMID: 33491648 PMCID: PMC7880689 DOI: 10.7554/elife.61921] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 01/24/2021] [Indexed: 01/11/2023] Open
Abstract
Dengue virus (DENV) cycles between mosquito and mammalian hosts. To examine how DENV populations adapt to these different host environments, we used serial passage in human and mosquito cell lines and estimated fitness effects for all single-nucleotide variants in these populations using ultra-deep sequencing. This allowed us to determine the contributions of beneficial and deleterious mutations to the collective fitness of the population. Our analysis revealed that the continuous influx of a large burden of deleterious mutations counterbalances the effect of rare, host-specific beneficial mutations to shape the path of adaptation. Beneficial mutations preferentially map to intrinsically disordered domains in the viral proteome and cluster to defined regions in the genome. These phenotypically redundant adaptive alleles may facilitate host-specific DENV adaptation. Importantly, the evolutionary constraints described in our simple system mirror trends observed across DENV and Zika strains, indicating it recapitulates key biophysical and biological constraints shaping long-term viral evolution.
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Affiliation(s)
- Patrick T Dolan
- Stanford University, Department of BiologyStanfordUnited States
- University of California, Microbiology and Immunology, San FranciscoSan FranciscoUnited States
| | - Shuhei Taguwa
- Stanford University, Department of BiologyStanfordUnited States
| | | | - Ashley Acevedo
- University of California, Microbiology and Immunology, San FranciscoSan FranciscoUnited States
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel AvivIsrael
| | - Raul Andino
- University of California, Microbiology and Immunology, San FranciscoSan FranciscoUnited States
| | - Judith Frydman
- Stanford University, Department of BiologyStanfordUnited States
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24
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Abstract
Many animal viruses replicate and are released from cells in close association to membranes. However, whether this is a passive process or is controlled by the virus remains poorly understood. Importantly, the genetic basis and evolvability of membrane-associated viral shedding have not been investigated. To address this, we performed a directed evolution experiment using coxsackievirus B3, a model enterovirus, in which we repeatedly selected the free-virion or the fast-sedimenting membrane-associated viral subpopulations. The virus responded to this selection regime by reproducibly fixing a series of mutations that altered the extent of membrane-associated viral shedding, as revealed by full-genome ultra-deep sequencing. Specifically, using site-directed mutagenesis, we showed that substitution N63H in the viral capsid protein VP3 reduced the ratio of membrane-associated to free viral particles by 2 orders of magnitude. These findings open new avenues for understanding the mechanisms and implications of membrane-associated viral transmission.
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Affiliation(s)
- Juan-Vicente Bou
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, València, Spain
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25
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Jones JE, Le Sage V, Lakdawala SS. Viral and host heterogeneity and their effects on the viral life cycle. Nat Rev Microbiol 2020; 19:272-282. [PMID: 33024309 PMCID: PMC7537587 DOI: 10.1038/s41579-020-00449-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2020] [Indexed: 02/08/2023]
Abstract
Traditionally, the viral replication cycle is envisioned as a single, well-defined loop with four major steps: attachment and entry into a target cell, replication of the viral genome, maturation of viral proteins and genome packaging into infectious progeny, and egress and dissemination to the next target cell. However, for many viruses, a growing body of evidence points towards extreme heterogeneity in each of these steps. In this Review, we reassess the major steps of the viral replication cycle by highlighting recent advances that show considerable variability during viral infection. First, we discuss heterogeneity in entry receptors, followed by a discussion on error-prone and low-fidelity polymerases and their impact on viral diversity. Next, we cover the implications of heterogeneity in genome packaging and assembly on virion morphology. Last, we explore alternative egress mechanisms, including tunnelling nanotubes and host microvesicles. In summary, we discuss the implications of viral phenotypic, morphological and genetic heterogeneity on pathogenesis and medicine. This Review highlights common themes and unique features that give nuance to the viral replication cycle.
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Affiliation(s)
- Jennifer E Jones
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Valerie Le Sage
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Seema S Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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26
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Coronavirus hemagglutinin-esterase and spike proteins coevolve for functional balance and optimal virion avidity. Proc Natl Acad Sci U S A 2020; 117:25759-25770. [PMID: 32994342 DOI: 10.1073/pnas.2006299117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human coronaviruses OC43 and HKU1 are respiratory pathogens of zoonotic origin that have gained worldwide distribution. OC43 apparently emerged from a bovine coronavirus (BCoV) spillover. All three viruses attach to 9-O-acetylated sialoglycans via spike protein S with hemagglutinin-esterase (HE) acting as a receptor-destroying enzyme. In BCoV, an HE lectin domain promotes esterase activity toward clustered substrates. OC43 and HKU1, however, lost HE lectin function as an adaptation to humans. Replaying OC43 evolution, we knocked out BCoV HE lectin function and performed forced evolution-population dynamics analysis. Loss of HE receptor binding selected for second-site mutations in S, decreasing S binding affinity by orders of magnitude. Irreversible HE mutations led to cooperativity in virus swarms with low-affinity S minority variants sustaining propagation of high-affinity majority phenotypes. Salvageable HE mutations induced successive second-site substitutions in both S and HE. Apparently, S and HE are functionally interdependent and coevolve to optimize the balance between attachment and release. This mechanism of glycan-based receptor usage, entailing a concerted, fine-tuned activity of two envelope protein species, is unique among CoVs, but reminiscent of that of influenza A viruses. Apparently, general principles fundamental to virion-sialoglycan interactions prompted convergent evolution of two important groups of human and animal pathogens.
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27
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Single-Point Mutations within the Coxsackie B Virus Receptor-Binding Site Promote Resistance against Soluble Virus Receptor Traps. J Virol 2020; 94:JVI.00952-20. [PMID: 32669334 PMCID: PMC7495374 DOI: 10.1128/jvi.00952-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/18/2020] [Indexed: 12/28/2022] Open
Abstract
Coxsackie B viruses (CVB) cause a wide spectrum of diseases, ranging from mild respiratory syndromes and hand, foot, and mouth disease to life-threatening conditions, such as pancreatitis, myocarditis, and encephalitis. Previously, we and others found that the soluble virus receptor trap sCAR-Fc strongly attenuates CVB3 infection in mice. In this study, we investigated whether treatment with sCAR-Fc results in development of resistance by CVB3. Two CVB3 strains (CVB3-H3 and CVB3 Nancy) were passaged in HeLa cells in the presence of sCAR-Fc. The CVB3-H3 strain did not develop resistance, whereas two populations of CVB3 Nancy mutants emerged, one with complete (CVB3M) and one with partial (CVB3K) resistance. DNA sequence alignment of the resistant virus variant CVB3M with CVB3 Nancy revealed an amino acid exchange from Asn(N) to Ser(S) at position 139 of the CVB3 capsid protein VP2 (N2139S), an amino acid predicted to be involved in the virus's interaction with its cognate receptor CAR. Insertion of the N2139S mutation into CVB3-H3 by site-directed mutagenesis promoted resistance of the engineered CVB3-H3N2139S to sCAR-Fc. Interestingly, development of resistance by CVB3-H3N2139S and the exemplarily investigated CVB3M-clone 2 (CVB3M2) against soluble CAR did not compromise the use of cellular CAR for viral infection. Infection of HeLa cells showed that sCAR-Fc resistance, however, negatively affected both virus stability and viral replication compared to that of the parental strains. These data demonstrate that during sCAR-Fc exposure, CVB3 can develop resistance against sCAR-Fc by single-amino-acid exchanges within the virus-receptor binding site, which, however, come at the expense of viral fitness.IMPORTANCE The emergence of resistant viruses is one of the most frequent obstacles preventing successful therapy of viral infections, representing a significant threat to human health. We investigated the emergence of resistant viruses during treatment with sCAR-Fc, a well-studied, highly effective antiviral molecule against CVB infections. Our data show the molecular aspects of resistant CVB3 mutants that arise during repetitive sCAR-Fc usage. However, drug resistance comes at the price of lower viral fitness. These results extend our knowledge of the development of resistance by coxsackieviruses and indicate potential limitations of antiviral therapy using soluble receptor molecules.
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28
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Analysis of Virus Population Profiles within Pigs Infected with Virulent Classical Swine Fever Viruses: Evidence for Bottlenecks in Transmission but Absence of Tissue-Specific Virus Variants. J Virol 2020; 94:JVI.01119-20. [PMID: 32699086 DOI: 10.1128/jvi.01119-20] [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: 06/04/2020] [Accepted: 07/14/2020] [Indexed: 11/20/2022] Open
Abstract
Classical swine fever virus (CSFV) contains a specific motif within the E2 glycoprotein that differs between strains of different virulence. In the highly virulent CSFV strain Koslov, this motif comprises residues S763/L764 in the polyprotein. However, L763/P764 represent the predominant alleles in published CSFV genomes. In this study, changes were introduced into the CSFV strain Koslov (here called vKos_SL) to generate modified CSFVs with substitutions at residues 763 and/or 764 (vKos_LL, vKos_SP, and vKos_LP). The properties of these mutant viruses, in comparison to those of vKos_SL, were determined in pigs. Each of the viruses was virulent and induced typical clinical signs of CSF, but the vKos_LP strain produced them significantly earlier. Full-length CSFV cDNA amplicons (12.3 kb) derived from sera of infected pigs were deep sequenced and cloned to reveal the individual haplotypes that contributed to the single-nucleotide polymorphism (SNP) profiles observed in the virus population. The SNP profiles for vKos_SL and vKos_LL displayed low-level heterogeneity across the entire genome, whereas vKos_SP and vKos_LP displayed limited diversity with a few high-frequency SNPs. This indicated that vKos_SL and vKos_LL exhibited a higher level of fitness in the host and more stability at the consensus level, whereas several consensus changes were observed in the vKos_SP and vKos_LP sequences, pointing to adaptation. For each virus, only a subset of the variants present within the virus inoculums were maintained in the infected pigs. No clear tissue-dependent quasispecies differentiation occurred within inoculated pigs; however, clear evidence for transmission bottlenecks to contact animals was observed, with subsequent loss of sequence diversity.IMPORTANCE The surface-exposed E2 protein of classical swine fever virus is required for its interaction with host cells. A short motif within this protein varies between strains of different virulence. The importance of two particular amino acid residues in determining the properties of a highly virulent strain of the virus has been analyzed. Each of the different viruses tested proved highly virulent, but one of them produced earlier, but not more severe, disease. By analyzing the virus genomes present within infected pigs, it was found that the viruses which replicated within inoculated animals were only a subset of those within the virus inoculum. Furthermore, following contact transmission, it was shown that a very restricted set of viruses had transferred between animals. There were no significant differences in the virus populations present in various tissues of the infected animals. These results indicate mechanisms of virus population change during transmission between animals.
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Elrashdy F, Redwan EM, Uversky VN. Why COVID-19 Transmission Is More Efficient and Aggressive Than Viral Transmission in Previous Coronavirus Epidemics? Biomolecules 2020; 10:E1312. [PMID: 32933047 PMCID: PMC7565143 DOI: 10.3390/biom10091312] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a pandemic of coronavirus disease 2019 (COVID-19). The worldwide transmission of COVID-19 from human to human is spreading like wildfire, affecting almost every country in the world. In the past 100 years, the globe did not face a microbial pandemic similar in scale to COVID-19. Taken together, both previous outbreaks of other members of the coronavirus family (severe acute respiratory syndrome (SARS-CoV) and middle east respiratory syndrome (MERS-CoV)) did not produce even 1% of the global harm already inflicted by COVID-19. There are also four other CoVs capable of infecting humans (HCoVs), which circulate continuously in the human population, but their phenotypes are generally mild, and these HCoVs received relatively little attention. These dramatic differences between infection with HCoVs, SARS-CoV, MERS-CoV, and SARS-CoV-2 raise many questions, such as: Why is COVID-19 transmitted so quickly? Is it due to some specific features of the viral structure? Are there some specific human (host) factors? Are there some environmental factors? The aim of this review is to collect and concisely summarize the possible and logical answers to these questions.
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Affiliation(s)
- Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Kasr Alainy School of Medicine, Cairo University, Cairo 11562, Egypt;
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290 Moscow, Russia
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30
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Sun J, Vera JC, Drnevich J, Lin YT, Ke R, Brooke CB. Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection. PLoS Pathog 2020; 16:e1008671. [PMID: 32614923 PMCID: PMC7363107 DOI: 10.1371/journal.ppat.1008671] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/15/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022] Open
Abstract
Viral infection outcomes are governed by the complex and dynamic interplay between the infecting virus population and the host response. It is increasingly clear that both viral and host cell populations are highly heterogeneous, but little is known about how this heterogeneity influences infection dynamics or viral pathogenicity. To dissect the interactions between influenza A virus (IAV) and host cell heterogeneity, we examined the combined host and viral transcriptomes of thousands of individual cells, each infected with a single IAV virion. We observed complex patterns of viral gene expression and the existence of multiple distinct host transcriptional responses to infection at the single cell level. We show that human H1N1 and H3N2 strains differ significantly in patterns of both viral and host anti-viral gene transcriptional heterogeneity at the single cell level. Our analyses also reveal that semi-infectious particles that fail to express the viral NS can play a dominant role in triggering the innate anti-viral response to infection. Altogether, these data reveal how patterns of viral population heterogeneity can serve as a major determinant of antiviral gene activation.
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Affiliation(s)
- Jiayi Sun
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - J. Cristobal Vera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jenny Drnevich
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yen Ting Lin
- Information Sciences Group, Computer, Computational and Statistical Sciences DIvision (CCS-3), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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31
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Braun T, Bordería AV, Barbezange C, Vignuzzi M, Louzoun Y. Long-term context-dependent genetic adaptation of the viral genetic cloud. Bioinformatics 2020; 35:1907-1915. [PMID: 30346482 DOI: 10.1093/bioinformatics/bty891] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/10/2018] [Accepted: 10/20/2018] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION RNA viruses generate a cloud of genetic variants within each host. This cloud contains high-frequency genotypes, and many rare variants. The dynamics of these variants is crucial to understand viral evolution and their effect on their host. RESULTS We use an experimental evolution system to show that the genetic cloud surrounding the Coxsackie virus master sequence slowly, but steadily, evolves over hundreds of generations. This movement is determined by strong context-dependent mutations, where the frequency and type of mutations are affected by neighboring positions, even in silent mutations. This context-dependent mutation pattern serves as a spearhead for the viral population's movement within the adaptive landscape and affects which new dominant variants will emerge. The non-local mutation patterns affect the mutated dinucleotide distribution, and eventually lead to a non-uniform dinucleotide distribution in the main viral sequence. We tested these results on other RNA viruses with similar conclusions. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tzipi Braun
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Antonio V Bordería
- Institut Pasteur, Viral Populations and Pathogenesis, CNRS UMR 3569, Paris, France
| | - Cyril Barbezange
- Institut Pasteur, Viral Populations and Pathogenesis, CNRS UMR 3569, Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis, CNRS UMR 3569, Paris, France
| | - Yoram Louzoun
- Department of Mathematics and Gonda Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
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32
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Fish I, Stenfeldt C, Palinski RM, Pauszek SJ, Arzt J. Into the Deep (Sequence) of the Foot-and-Mouth Disease Virus Gene Pool: Bottlenecks and Adaptation during Infection in Naïve and Vaccinated Cattle. Pathogens 2020; 9:pathogens9030208. [PMID: 32178297 PMCID: PMC7157448 DOI: 10.3390/pathogens9030208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) infects hosts as a population of closely related viruses referred to as a quasispecies. The behavior of this quasispecies has not been described in detail in natural host species. In this study, virus samples collected from vaccinated and non-vaccinated cattle up to 35 days post-experimental infection with FMDV A24-Cruzeiro were analyzed by deep-sequencing. Vaccination induced significant differences compared to viruses from non-vaccinated cattle in substitution rates, entropy, and evidence for adaptation. Genomic variation detected during early infection reflected the diversity inherited from the source virus (inoculum), whereas by 12 days post infection, dominant viruses were defined by newly acquired mutations. Mutations conferring recognized fitness gain occurred and were associated with selective sweeps. Persistent infections always included multiple FMDV subpopulations, suggesting distinct foci of infection within the nasopharyngeal mucosa. Subclinical infection in vaccinated cattle included very early bottlenecks associated with reduced diversity within virus populations. Viruses from both animal cohorts contained putative antigenic escape mutations. However, these mutations occurred during later stages of infection, at which time transmission is less likely to occur. This study improves upon previously published work by analyzing deep sequences of samples, allowing for detailed characterization of FMDV populations over time within multiple hosts.
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Affiliation(s)
- Ian Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN 37830, USA
| | - Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Rachel M. Palinski
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
| | - Steven J. Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- Correspondence:
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33
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Bouin A, Gretteau PA, Wehbe M, Renois F, N'Guyen Y, Lévêque N, Vu MN, Tracy S, Chapman NM, Bruneval P, Fornes P, Semler BL, Andreoletti L. Enterovirus Persistence in Cardiac Cells of Patients With Idiopathic Dilated Cardiomyopathy Is Linked to 5' Terminal Genomic RNA-Deleted Viral Populations With Viral-Encoded Proteinase Activities. Circulation 2020; 139:2326-2338. [PMID: 30755025 DOI: 10.1161/circulationaha.118.035966] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Group B enteroviruses are common causes of acute myocarditis, which can be a precursor of chronic myocarditis and dilated cardiomyopathy, leading causes of heart transplantation. To date, the specific viral functions involved in the development of dilated cardiomyopathy remain unclear. METHODS Total RNA from cardiac tissue of patients with dilated cardiomyopathy was extracted, and sequences corresponding to the 5' termini of enterovirus RNAs were identified. After next-generation RNA sequencing, viral cDNA clones mimicking the enterovirus RNA sequences found in patient tissues were generated in vitro, and their replication and impact on host cell functions were assessed on primary human cardiac cells in culture. RESULTS Major enterovirus B populations characterized by 5' terminal genomic RNA deletions ranging from 17 to 50 nucleotides were identified either alone or associated with low proportions of intact 5' genomic termini. In situ hybridization and immunohistological assays detected these persistent genomes in clusters of cardiomyocytes. Transfection of viral RNA into primary human cardiomyocytes demonstrated that deleted forms of genomic RNAs displayed early replication activities in the absence of detectable viral plaque formation, whereas mixed deleted and complete forms generated particles capable of inducing cytopathic effects at levels distinct from those observed with full-length forms alone. Moreover, deleted or full-length and mixed forms of viral RNA were capable of directing translation and production of proteolytically active viral proteinase 2A in human cardiomyocytes. CONCLUSIONS We demonstrate that persistent viral forms are composed of B-type enteroviruses harboring a 5' terminal deletion in their genomic RNAs and that these viruses alone or associated with full-length populations of helper RNAs could impair cardiomyocyte functions by the proteolytic activity of viral proteinase 2A in cases of unexplained dilated cardiomyopathy. These results provide a better understanding of the molecular mechanisms that underlie the persistence of EV forms in human cardiac tissues and should stimulate the development of new therapeutic strategies based on specific inhibitors of the coxsackievirus B proteinase 2A activity for acute and chronic cardiac infections.
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Affiliation(s)
- Alexis Bouin
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine (A.B., M.N.V., B.L.S.)
| | - Paul-Antoine Gretteau
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.)
| | - Michel Wehbe
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,Centre AZM pour la recherche en biotechnologie et ses applications, Université Libanaise, Tripoli, Lebanon (M.W.)
| | - Fanny Renois
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,LUNAM University, Oniris, LABERCA, UMR INRA 1329, Nantes, France (F.R.).,CHU Robert Debré, Laboratoire de Virologie Médicale et Moléculaire, Reims, France (F.R., Y.N., N.L., P.F., L.A.)
| | - Yohan N'Guyen
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,CHU Robert Debré, Laboratoire de Virologie Médicale et Moléculaire, Reims, France (F.R., Y.N., N.L., P.F., L.A.)
| | - Nicolas Lévêque
- CHU Robert Debré, Laboratoire de Virologie Médicale et Moléculaire, Reims, France (F.R., Y.N., N.L., P.F., L.A.).,EA-4331 LITEC, Faculty of Medicine and Pharmacy, University Hospital of Poitiers, France (N.L.)
| | - Michelle N Vu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine (A.B., M.N.V., B.L.S.)
| | - Steven Tracy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (S.T., N.M.C.)
| | - Nora M Chapman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (S.T., N.M.C.)
| | - Patrick Bruneval
- Service d'Anatomie Pathologique, Hôpital Européen Georges Pompidou, Paris, France (P.B.)
| | - Paul Fornes
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.)
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine (A.B., M.N.V., B.L.S.)
| | - Laurent Andreoletti
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.)
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Andreu-Moreno I, Sanjuán R. Collective Viral Spread Mediated by Virion Aggregates Promotes the Evolution of Defective Interfering Particles. mBio 2020; 11:e02156-19. [PMID: 31911487 PMCID: PMC6946798 DOI: 10.1128/mbio.02156-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/18/2019] [Indexed: 01/30/2023] Open
Abstract
A growing number of studies report that viruses can spread in groups in so-called collective infectious units. By increasing the cellular multiplicity of infection, collective dispersal may allow for social-like interactions, such as cooperation or cheating. Yet, little is known about how such interactions evolve. In previous work with vesicular stomatitis virus, we showed that virion aggregation accelerates early infection stages in most cell types, providing a short-term fitness benefit to the virus. Here, we examine the effects of virion aggregation over several infection cycles. Flow cytometry, deep sequencing, infectivity assays, reverse transcription-quantitative PCR, and electron microscopy revealed that virion aggregation rapidly promotes the emergence of defective interfering particles. Therefore, virion aggregation provides immediate fitness benefits to the virus but incurs fitness costs after a few viral generations. This suggests that an optimal strategy for the virus is to undergo virion aggregation only episodically, for instance, during interhost transmission.IMPORTANCE Recent insights have revealed that viruses use a highly diverse set of strategies to release multiple viral genomes into the same target cells, allowing the emergence of beneficial, but also detrimental, interactions among viruses inside infected cells. This has prompted interest among microbial ecologists and evolutionary biologists in studying how collective dispersal impacts the outcome of viral infections. Here, we have used vesicular stomatitis virus as a model system to study the evolutionary implications of collective dissemination mediated by viral aggregates, since this virus can spontaneously aggregate in the presence of saliva. We find that saliva-driven aggregation has a dual effect on viral fitness; whereas aggregation tends to increase infectivity in the very short term, virion aggregates are highly susceptible to invasion by noncooperative defective variants after a few viral generations.
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Affiliation(s)
- Iván Andreu-Moreno
- Institute for Integrative Systems Biology (ISysBio), Universitat de Valencia, Valencia, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (ISysBio), Universitat de Valencia, Valencia, Spain
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35
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Shipley MM, Renner DW, Pandey U, Ford B, Bloom DC, Grose C, Szpara ML. Personalized viral genomic investigation of herpes simplex virus 1 perinatal viremic transmission with dual fatality. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004382. [PMID: 31582464 PMCID: PMC6913147 DOI: 10.1101/mcs.a004382] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/04/2019] [Indexed: 11/25/2022] Open
Abstract
Here we present a personalized viral genomics approach to investigating a rare case of perinatal herpes simplex virus 1 (HSV-1) transmission that ended in death of both mother and neonate. We sought to determine whether the virus involved in this rare case had any unusual features that may have contributed to the dire patient outcome. A pregnant woman with negative HerpeSelect antibody test underwent cesarean section at 30 wk gestation and died the same day. The premature newborn died 5 d later. Both individuals were found postmortem to have positive blood HSV-1 PCR tests. Using oligonucleotide enrichment and deep sequencing, we determined that viral transmission from mother to infant was nearly perfect at the consensus genome level. At the virus population level, 77% of minor variants (MVs) in the mother's blood also appeared on the neonate's skin, of which more than half were disseminated into the neonate's blood. We also detected nonmaternal MVs that arose de novo in the neonate's viral populations. Of note, one de novo MV in the neonate's skin virus induced a nonsynonymous mutation in the UL6 protein, which is a component of the portal that allows DNA entry into new progeny capsids. This case suggests that perinatal viremic HSV-1 transmission includes the majority of genetic diversity from the maternal virus population and that new, nonsynonymous mutations can occur after relatively few rounds of replication. This report expands our understanding of viral transmission in humans and may lead to improved diagnostic strategies for neonatal HSV-1 acquisition.
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Affiliation(s)
- Mackenzie M Shipley
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Daniel W Renner
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Utsav Pandey
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Bradley Ford
- Department of Pathology, University of Iowa, Iowa City, Iowa 52242, USA
| | - David C Bloom
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida 32610, USA
| | - Charles Grose
- Division of Infectious Disease/Virology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Moriah L Szpara
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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36
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Weger-Lucarelli J, Carrau L, Levi LI, Rezelj V, Vallet T, Blanc H, Boussier J, Megrian D, Coutermarsh-Ott S, LeRoith T, Vignuzzi M. Host nutritional status affects alphavirus virulence, transmission, and evolution. PLoS Pathog 2019; 15:e1008089. [PMID: 31710653 PMCID: PMC6872174 DOI: 10.1371/journal.ppat.1008089] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 11/21/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022] Open
Abstract
Malnourishment, specifically overweight/obesity and undernourishment, affects more than 2.5 billion people worldwide, with the number affected ever-increasing. Concurrently, emerging viral diseases, particularly those that are mosquito-borne, have spread dramatically in the past several decades, culminating in outbreaks of several viruses worldwide. Both forms of malnourishment are known to lead to an aberrant immune response, which can worsen disease outcomes and reduce vaccination efficacy for viral pathogens such as influenza and measles. Given the increasing rates of malnutrition and spread of arthropod-borne viruses (arboviruses), there is an urgent need to understand the role of host nutrition on the infection, virulence, and transmission of these viruses. To address this gap in knowledge, we infected lean, obese, and undernourished mice with arthritogenic arboviruses from the genus Alphavirus and assessed morbidity, virus replication, transmission, and evolution. Obesity and undernourishment did not consistently influence virus replication in the blood of infected animals except for reductions in virus in obese mice late in infection. However, morbidity was increased in obese mice under all conditions. Using Mayaro virus (MAYV) as a model arthritogenic alphavirus, we determined that both obese and undernourished mice transmit virus less efficiently to mosquitoes than control (lean) mice. In addition, viral genetic diversity and replicative fitness were reduced in virus isolated from obese compared to lean controls. Taken together, nutrition appears to alter the course of alphavirus infection and should be considered as a critical environmental factor during outbreaks. Over- and undernutrition, collectively known as malnutrition, affect over 2.5 billion people worldwide. Associations between malnutrition and mosquito-borne virus infection and resulting disease have been identified in epidemiological studies but have not been explored in controlled studies. Here, we infect obese or undernourished mice with different arthritis inducing viruses in the genus Alphavirus and measure disease symptoms, viral replication, transmission, and evolution. We found that markers of disease, namely weight loss and footpad swelling, were increased in obese mice. We also found that replication differences between mice fed different diets were minimal except late in infection for obese mice when levels of virus dropped significantly. When mosquitoes were allowed to feed on mice fed different diets, we observed reduced infection and transmission rates, depending on the diet. Finally, we found reduced genetic diversity and replicative fitness of virus isolated from obese mice. This study provides insights into the influence of nutrition on alphavirus pathogenesis and evolution.
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Affiliation(s)
- James Weger-Lucarelli
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Paris, France.,Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, United States of America
| | - Lucia Carrau
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Paris, France
| | - Laura I Levi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Paris, France.,Ecole doctorale BioSPC, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Veronica Rezelj
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Paris, France
| | - Thomas Vallet
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Paris, France
| | - Hervé Blanc
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Paris, France
| | - Jérémy Boussier
- Institut Pasteur, Immunobiology of Dendritic Cells, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Daniela Megrian
- Institut Pasteur, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, France
| | - Sheryl Coutermarsh-Ott
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, United States of America
| | - Tanya LeRoith
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, United States of America
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Paris, France
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Zhang L, Sun M, Zhang Q, Wang J, Cao Y, Cui S, Su J. Long-term passage of duck Tembusu virus in BHK-21 cells generates a completely attenuated and immunogenic population with increased genetic diversity. Vaccine 2019; 38:933-941. [PMID: 31708180 DOI: 10.1016/j.vaccine.2019.10.080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/12/2019] [Accepted: 10/25/2019] [Indexed: 12/28/2022]
Abstract
Duck Tembusu virus (TMUV) is an emerging pathogenic flavivirus that causes severe egg-drop and fatal encephalitis in domestic ducks and geese. Although a live-attenuated virus vaccine is effective for disease control, the stability of the attenuation has not been clearly evaluated due to a poor understanding of the attenuation mechanism. Here, a virulent duck TMUV isolate was successively passaged in BHK-21 cells, leading to an approximately 100-fold increase of virus production in cell culture and a complete attenuation of virulence for ducks. The passaged virus induced high titers of TMUV-specific antibody and provided efficient protection against a virulent TMUV challenge after a single-dose vaccination. One hundred and two, and eighteen single-nucleotide polymorphisms (SNPs) at a frequency of >1% were respectively identified in the attenuated virus population and the original isolate by deep sequencing. The increased SNPs numbers suggested that the accumulated variants of virus population may have conferred the phenotypic changes. We cloned and characterized a dominant variant exhibiting similar fitness to the mixed population, and 23 amino acid substitutions were identified across the viral open reading frame. Using reverse genetics, two chimeric viruses were generated by introducing the mutated E or NS5 gene into the backbone of virulent TMUV. We found that mutations in the E gene conferred a fitness advantage in BHK-21 cells and decreased the virus pathogenicity, whereas NS5 mutations reduced the virus infectivity in ducklings without altering the in vitro fitness. In conclusion, increased mutations in a virulent TMUV strain did substantially reduce the virus virulence, and mutations in multiple genes co-contribute to TMUV attenuation.
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Affiliation(s)
- Lijiao Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis, the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Mengxu Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qingshui Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis, the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jun Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yanxin Cao
- Key Laboratory of Animal Epidemiology and Zoonosis, the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Shangjin Cui
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Observation Station for Veterinary Biological Technique, Ministry of Agricultural, Beijing 100193, China.
| | - Jingliang Su
- Key Laboratory of Animal Epidemiology and Zoonosis, the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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Bou JV, Geller R, Sanjuán R. Membrane-Associated Enteroviruses Undergo Intercellular Transmission as Pools of Sibling Viral Genomes. Cell Rep 2019; 29:714-723.e4. [PMID: 31618638 PMCID: PMC6899498 DOI: 10.1016/j.celrep.2019.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 08/02/2019] [Accepted: 09/05/2019] [Indexed: 01/07/2023] Open
Abstract
Some viruses are released from cells as pools of membrane-associated virions. By increasing the multiplicity of infection (MOI), this type of collective dispersal could favor viral cooperation, but also the emergence of cheater-like viruses such as defective interfering particles. To better understand this process, we examined the genetic diversity of membrane-associated coxsackievirus infectious units. We find that infected cells release membranous structures (including vesicles) that contain 8-21 infectious particles on average. However, in most cases (62%-93%), these structures do not promote the co-transmission of different viral genetic variants present in a cell. Furthermore, collective dispersal has no effect on viral population sequence diversity. Our results indicate that membrane-associated collective infectious units typically contain viral particles derived from the same parental genome. Hence, if cooperation occurs, it should probably involve sibling viral particles rather than different variants. As shown by social evolution theory, cooperation among siblings should be robust against cheater invasion.
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Affiliation(s)
- Juan-Vicente Bou
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| | - Ron Geller
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain.
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39
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Cifuente JO, Moratorio G. Evolutionary and Structural Overview of Human Picornavirus Capsid Antibody Evasion. Front Cell Infect Microbiol 2019; 9:283. [PMID: 31482072 PMCID: PMC6710328 DOI: 10.3389/fcimb.2019.00283] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/24/2019] [Indexed: 11/13/2022] Open
Abstract
Picornaviruses constitute one of the most relevant viral groups according to their impact on human and animal health. Etiologic agents of a broad spectrum of illnesses with a clinical presentation that ranges from asymptomatic to fatal disease, they have been the cause of uncountable epidemics throughout history. Picornaviruses are small naked RNA-positive single-stranded viruses that include some of the most important pillars in the development of virology, comprising poliovirus, rhinovirus, and hepatitis A virus. Picornavirus infectious particles use the fecal-oral or respiratory routes as primary modes of transmission. In this regard, successful viral spread relies on the capability of viral capsids to (i) shelter the viral genome, (ii) display molecular determinants for cell receptor recognition, (iii) facilitate efficient genome delivery, and (iv) escape from the immune system. Importantly, picornaviruses display a substantial amount of genetic variability driven by both mutation and recombination. Therefore, the outcome of their replication results in the emergence of a genetically diverse cloud of individuals presenting phenotypic variance. The host humoral response against the capsid protein represents the most active immune pressure and primary weapon to control the infection. Since the preservation of the capsid function is deeply rooted in the virus evolutionary dynamics, here we review the current structural evidence focused on capsid antibody evasion mechanisms from that perspective.
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Affiliation(s)
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
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40
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Henningsson R, Moratorio G, Bordería AV, Vignuzzi M, Fontes M. DISSEQT-DIStribution-based modeling of SEQuence space Time dynamics. Virus Evol 2019; 5:vez028. [PMID: 31392032 PMCID: PMC6680062 DOI: 10.1093/ve/vez028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rapidly evolving microbes are a challenge to model because of the volatile, complex, and dynamic nature of their populations. We developed the DISSEQT pipeline (DIStribution-based SEQuence space Time dynamics) for analyzing, visualizing, and predicting the evolution of heterogeneous biological populations in multidimensional genetic space, suited for population-based modeling of deep sequencing and high-throughput data. The pipeline is openly available on GitHub (https://github.com/rasmushenningsson/DISSEQT.jl, accessed 23 June 2019) and Synapse (https://www.synapse.org/#!Synapse: syn11425758, accessed 23 June 2019), covering the entire workflow from read alignment to visualization of results. Our pipeline is centered around robust dimension and model reduction algorithms for analysis of genotypic data with additional capabilities for including phenotypic features to explore dynamic genotype-phenotype maps. We illustrate its utility and capacity with examples from evolving RNA virus populations, which present one of the highest degrees of genetic heterogeneity within a given population found in nature. Using our pipeline, we empirically reconstruct the evolutionary trajectories of evolving populations in sequence space and genotype-phenotype fitness landscapes. We show that while sequence space is vastly multidimensional, the relevant genetic space of evolving microbial populations is of intrinsically low dimension. In addition, evolutionary trajectories of these populations can be faithfully monitored to identify the key minority genotypes contributing most to evolution. Finally, we show that empirical fitness landscapes, when reconstructed to include minority variants, can predict phenotype from genotype with high accuracy.
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Affiliation(s)
- R Henningsson
- The Centre for Mathematical Sciences, Lund University, Sweden
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- The International Group for Data Analysis, Institut Pasteur, Paris, France
- Division of Clinical Genetics, Lund University, Sweden
| | - G Moratorio
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- Laboratorio de Virología Molecular, Universidad de la República, Montevideo, Uruguay
| | - A V Bordería
- The International Group for Data Analysis, Institut Pasteur, Paris, France
| | - M Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | - M Fontes
- The International Group for Data Analysis, Institut Pasteur, Paris, France
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
- The Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
- Persimune, The Centre of Excellence for Personalized Medicine, Copenhagen, Denmark
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41
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Xiang K, Xiao Y, Li Y, He L, Wang L, Zhuang H, Li T. The Effect of the Hepatitis B Virus Surface Protein Truncated sC69 ∗ Mutation on Viral Infectivity and the Host Innate Immune Response. Front Microbiol 2019; 10:1341. [PMID: 31249567 PMCID: PMC6584109 DOI: 10.3389/fmicb.2019.01341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/29/2019] [Indexed: 12/19/2022] Open
Abstract
Viruses could rapidly diversify into variants, which has long been known to facilitate viral adaption in the host. Recent studies showed that cooperation among variants and wild-type (WT) also increased viral fitness. Here, a mutant of sC69∗ in small hepatitis B surface protein (SHBs) that resulted in premature stop was investigated and the frequency of sC69∗ was 4.37% (19/435), most of which coexisted with the WT (78.95%, 15/19), indicating mixed viral populations. Functional studies showed that sC69∗ mutant was associated with lower viral spread, but could be rescued by coexisting with the WT. The sC69∗ mutant showed to attenuate host innate immune response during infection and poly (I:C) treatment such as IL29, ISG15, and RIG-I (p < 0.05). The lower immune response was not caused by the lower replication of sC69∗ mutant. Our data provide information that sC69∗ coexisting with the WT might facilitate the fitness and persistence of the viral quasispecies in the host.
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Affiliation(s)
- Kuanhui Xiang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yiwei Xiao
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yao Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lingyuan He
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Luwei Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hui Zhuang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Tong Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
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42
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Bertels F, Leemann C, Metzner KJ, Regoes R. Parallel evolution of HIV-1 in a long-term experiment. Mol Biol Evol 2019; 36:2400-2414. [PMID: 31251344 PMCID: PMC6805227 DOI: 10.1093/molbev/msz155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/06/2019] [Accepted: 06/22/2019] [Indexed: 12/15/2022] Open
Abstract
One of the most intriguing puzzles in biology is the degree to which evolution is repeatable. The repeatability of evolution, or parallel evolution, has been studied in a variety of model systems, but has rarely been investigated with clinically relevant viruses. To investigate parallel evolution of HIV-1, we passaged two replicate HIV-1 populations for almost 1 year in each of two human T-cell lines. For each of the four evolution lines, we determined the genetic composition of the viral population at nine time points by deep sequencing the entire genome. Mutations that were carried by the majority of the viral population accumulated continuously over 1 year in each evolution line. Many majority mutations appeared in more than one evolution line, that is, our experiments showed an extreme degree of parallel evolution. In one of the evolution lines, 62% of the majority mutations also occur in another line. The parallelism impairs our ability to reconstruct the evolutionary history by phylogenetic methods. We show that one can infer the correct phylogenetic topology by including minority mutations in our analysis. We also find that mutation diversity at the beginning of the experiment is predictive of the frequency of majority mutations at the end of the experiment.
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Affiliation(s)
- Frederic Bertels
- Department of Environmental Systems Sciences, ETH Zurich, Zurich.,Max-Planck-Institute for Evolutionary Biology, Department of Microbial Population Biology
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich.,Insitute of Medical Virology, University of Zurich, Zurich
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich.,Insitute of Medical Virology, University of Zurich, Zurich
| | - Roland Regoes
- Department of Environmental Systems Sciences, ETH Zurich, Zurich
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43
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Abstract
Many organisms disperse in groups, yet this process is understudied in viruses. Recent work, however, has uncovered different types of collective infectious units, all of which lead to the joint delivery of multiple viral genome copies to target cells, favoring co-infections. Collective spread of viruses can occur through widely different mechanisms, including virion aggregation driven by specific extracellular components, cloaking inside lipid vesicles, encasement in protein matrices, or binding to cell surfaces. Cell-to-cell viral spread, which allows the transmission of individual virions in a confined environment, is yet another mode of clustered virus dissemination. Nevertheless, the selective advantages of dispersing in groups remain poorly understood in most cases. Collective dispersal might have emerged as a means of sharing efficacious viral transmission vehicles. Alternatively, increasing the cellular multiplicity of infection may confer certain short-term benefits to viruses, such as overwhelming antiviral responses, avoiding early stochastic loss of viral components required for initiating infection, or complementing genetic defects present in different viral genomes. However, increasing infection multiplicity may also entail long-term costs, such as mutation accumulation and the evolution of defective particles or other types of cheater viruses. These costs and benefits, in turn, should depend on the genetic relatedness among collective infectious unit members. Establishing the genetic basis of collective viral dispersal and performing controlled experiments to pinpoint fitness effects at different spatial and temporal scales should help us clarify the implications of these spread modes for viral fitness, pathogenicity, and evolution.
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Affiliation(s)
- Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/Catedrático Agustín Escardino 9, Paterna, València, Spain
| | - María-Isabel Thoulouze
- Institut Pasteur, Structural Virology Unit, Biofilm & Viral Transmission Group, Paris, France
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44
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Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission. PLoS Pathog 2019; 15:e1007799. [PMID: 31220188 PMCID: PMC6615636 DOI: 10.1371/journal.ppat.1007799] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 07/09/2019] [Accepted: 04/29/2019] [Indexed: 12/25/2022] Open
Abstract
The development of high-throughput genome sequencing enables accurate measurements of levels of sub-consensus intra-host virus genetic diversity and analysis of the role played by natural selection during cross-species transmission. We analysed the natural and experimental evolution of rabies virus (RABV), an important example of a virus that is able to make multiple host jumps. In particular, we (i) analyzed RABV evolution during experimental host switching with the goal of identifying possible genetic markers of host adaptation, (ii) compared the mutational changes observed during passage with those observed in natura, and (iii) determined whether the colonization of new hosts or tissues requires adaptive evolution in the virus. To address these aims, animal infection models (dog and fox) and primary cell culture models (embryo brain cells of dog and fox) were developed and viral variation was studied in detail through deep genome sequencing. Our analysis revealed a strong unidirectional host evolutionary effect, as dog-adapted rabies virus was able to replicate in fox and fox cells relatively easily, while dogs or neuronal dog cells were not easily susceptible to fox adapted-RABV. This suggests that dog RABV may be able to adapt to some hosts more easily than other host variants, or that when RABV switched from dogs to red foxes it lost its ability to adapt easily to other species. Although no difference in patterns of mutation variation between different host organs was observed, mutations were common following both in vitro and in vivo passage. However, only a small number of these mutations also appeared in natura, suggesting that adaptation during successful cross-species virus transmission is a complex, multifactorial evolutionary process. Understanding the mechanisms that underpin the cross-species transmission and host adaptation of rabies virus (RABV) remains an important part of the ongoing goal to reduce and eliminate rabies. We utilized next-generation sequencing to perform a deep comparative analysis of the genomic evolution of RABV subpopulations during host adaptation in culture and in animals, with the aim of determining the molecular mechanisms involved in the host-species or tissue adaptation of rabies virus. In particular, we aimed to determine whether experimental evolution can recapitulate evolution in nature. Our results suggest that a limited number of mutations that appeared following both in vitro and in vivo passage were observed in natura. This study also suggests that dog RABV may be able to adapt to some hosts more easily than other host variants.
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45
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Bhar S, Jones MK. In Vitro Replication of Human Norovirus. Viruses 2019; 11:v11060547. [PMID: 31212759 PMCID: PMC6630950 DOI: 10.3390/v11060547] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022] Open
Abstract
Human norovirus (HuNoV) infection is a major cause of gastroenteritis all over the world. Despite this, these non-enveloped RNA viruses are poorly characterized due to the lack of robust and widely available HuNoV culture systems. The two published systems (B cell line and stem cell-derived enteroids) support replication of HuNoVs but the levels of replication are not sufficient for the generation of highly purified virus stocks or the development of culture-based quantification assays. Therefore, improvement of HuNoV in vitro replication is still needed. Murine norovirus and other caliciviruses have provided insights into norovirus replication that paved the way for the development of the current HuNoV culture systems and may also aid in the improvement of these systems. This review will highlight ways in which previous research guided and impacted the development of HuNoV culture systems and discuss ways in which more recent discoveries might be utilized to improve the quality of the HuNoV in vitro replication.
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Affiliation(s)
- Sutonuka Bhar
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL 32611, USA.
| | - Melissa K Jones
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL 32611, USA.
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46
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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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47
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Warmbrod KL, Patterson EI, Kautz TF, Stanton A, Rockx-Brouwer D, Kalveram BK, Khanipov K, Thangamani S, Fofanov Y, Forrester NL. Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts. PLoS Pathog 2019; 15:e1007610. [PMID: 30947291 PMCID: PMC6467425 DOI: 10.1371/journal.ppat.1007610] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 04/16/2019] [Accepted: 01/31/2019] [Indexed: 02/06/2023] Open
Abstract
The presence of bottlenecks in the transmission cycle of many RNA viruses leads to a severe reduction of number of virus particles and this occurs multiple times throughout the viral transmission cycle. Viral replication is then necessary for regeneration of a diverse mutant swarm. It is now understood that any perturbation of the mutation frequency either by increasing or decreasing the accumulation of mutations in an RNA virus results in attenuation of the virus. To determine if altering the rate at which a virus accumulates mutations decreases the probability of a successful virus infection due to issues traversing host bottlenecks, a series of mutations in the RNA-dependent RNA polymerase of Venezuelan equine encephalitis virus (VEEV), strain 68U201, were tested for mutation rate changes. All RdRp mutants were attenuated in both the mosquito and vertebrate hosts, while showing no attenuation during in vitro infections. The rescued viruses containing these mutations showed some evidence of change in fidelity, but the phenotype was not sustained following passaging. However, these mutants did exhibit changes in the frequency of specific types of mutations. Using a model of mutation production, these changes were shown to decrease the number of stop codons generated during virus replication. This suggests that the observed mutant attenuation in vivo may be due to an increase in the number of unfit genomes, which may be normally selected against by the accumulation of stop codons. Lastly, the ability of these attenuated viruses to transition through a bottleneck in vivo was measured using marked virus clones. The attenuated viruses showed an overall reduction in the number of marked clones for both the mosquito and vertebrate hosts, as well as a reduced ability to overcome the known bottlenecks in the mosquito. This study demonstrates that any perturbation of the optimal mutation frequency whether through changes in fidelity or by alterations in the mutation frequency of specific nucleotides, has significant deleterious effects on the virus, especially in the presence of host bottlenecks.
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Affiliation(s)
- K. Lane Warmbrod
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Edward I. Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tiffany F. Kautz
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Adam Stanton
- School of Computing and Mathematics, University of Keele, Keele, United Kingdom
| | - Dedeke Rockx-Brouwer
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Birte K. Kalveram
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kamil Khanipov
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Saravanan Thangamani
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yuriy Fofanov
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Naomi L. Forrester
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
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48
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Leeks A, Sanjuán R, West SA. The evolution of collective infectious units in viruses. Virus Res 2019; 265:94-101. [PMID: 30894320 PMCID: PMC6470120 DOI: 10.1016/j.virusres.2019.03.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 12/21/2022]
Abstract
Many viruses disperse in groups, as part of collective infectious units (CIUs). We modelled different factors that could influence the evolution of CIUs. Group infectivity benefits favoured CIUs, especially if CIUs were more efficient. Defective genomes did not favour or disfavour CIUs. Defective interfering genomes disfavoured CIUs.
Viruses frequently spread among cells or hosts in groups, with multiple viral genomes inside the same infectious unit. These collective infectious units can consist of multiple viral genomes inside the same virion, or multiple virions inside a larger structure such as a vesicle. Collective infectious units deliver multiple viral genomes to the same cell simultaneously, which can have important implications for viral pathogenesis, antiviral resistance, and social evolution. However, little is known about why some viruses transmit in collective infectious units, whereas others do not. We used a simple evolutionary approach to model the potential costs and benefits of transmitting in a collective infectious unit. We found that collective infectious units could be favoured if cells infected by multiple viral genomes were significantly more productive than cells infected by just one viral genome, and especially if there were also efficiency benefits to packaging multiple viral genomes inside the same infectious unit. We also found that if some viral sequences are defective, then collective infectious units could evolve to become very large, but that if these defective sequences interfered with wild-type virus replication, then collective infectious units were disfavoured.
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Affiliation(s)
- Asher Leeks
- University of Oxford, Department of Zoology, Zoology Research and Administration, Oxford, OX1 3SZ, United Kingdom.
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain
| | - Stuart A West
- University of Oxford, Department of Zoology, Zoology Research and Administration, Oxford, OX1 3SZ, United Kingdom
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49
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Shirogane Y, Watanabe S, Yanagi Y. Cooperation between different variants: A unique potential for virus evolution. Virus Res 2019; 264:68-73. [PMID: 30822430 DOI: 10.1016/j.virusres.2019.02.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/25/2019] [Indexed: 02/05/2023]
Abstract
RNA viruses exist as quasispecies containing many variants within their populations because of the error prone nature of viral RNA-dependent RNA polymerases. Quasispecies are not a simple collection of individual variants. Instead, internal interactions among variants provide quasispecies with unique evolvability. An example is 'cooperation' between wild-type and defective measles viruses, in which co-existence of a wild-type and a mutant genome produces a new phenotype. Such internal interactions presuppose efficient co-transmission of multiple genomes to the same cell, which is achieved by polyploid virions of some virus families or by a high multiplicity of infection. Recent studies have revealed that multiple viral genomes can also be transmitted simultaneously ('bloc transmission') by other mechanisms, strengthening the concept of internal interactions among viral quasispecies. Elucidation of the mechanisms of virus evolution, including internal interactions and bloc transmission, may provide rational strategies to solve such important problems of virus infections as drug-resistance, immune evasion, and acquisition of the new tropism and host range.
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Affiliation(s)
- Yuta Shirogane
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.
| | - Shumpei Watanabe
- Department of Microbiology, Faculty of Veterinary Medicine, Okayama University of Science, Ehime, 794-0085, Japan
| | - Yusuke Yanagi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.
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50
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Vesicle-Cloaked Virus Clusters Are Optimal Units for Inter-organismal Viral Transmission. Cell Host Microbe 2019; 24:208-220.e8. [PMID: 30092198 DOI: 10.1016/j.chom.2018.07.006] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 06/11/2018] [Accepted: 07/13/2018] [Indexed: 01/29/2023]
Abstract
In enteric viral infections, such as those with rotavirus and norovirus, individual viral particles shed in stool are considered the optimal units of fecal-oral transmission. We reveal that rotaviruses and noroviruses are also shed in stool as viral clusters enclosed within vesicles that deliver a high inoculum to the receiving host. Cultured cells non-lytically release rotaviruses and noroviruses inside extracellular vesicles. In addition, stools of infected hosts contain norovirus and rotavirus within vesicles of exosomal or plasma membrane origin. These vesicles remain intact during fecal-oral transmission and thereby transport multiple viral particles collectively to the next host, enhancing both the MOI and disease severity. Vesicle-cloaked viruses are non-negligible populations in stool and have a disproportionately larger contribution to infectivity than free viruses. Our findings indicate that vesicle-cloaked viruses are highly virulent units of fecal-oral transmission and highlight a need for antivirals targeting vesicles and virus clustering.
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