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Liu T, Reiser WK, Tan TJC, Lv H, Rivera-Cardona J, Heimburger K, Wu NC, Brooke CB. Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin. Virus Evol 2024; 10:veae046. [PMID: 38915760 PMCID: PMC11196192 DOI: 10.1093/ve/veae046] [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: 03/19/2024] [Revised: 05/30/2024] [Accepted: 06/12/2024] [Indexed: 06/26/2024] Open
Abstract
The antigenic evolution of the influenza A virus hemagglutinin (HA) gene poses a major challenge for the development of vaccines capable of eliciting long-term protection. Prior efforts to understand the mechanisms that govern viral antigenic evolution mainly focus on HA in isolation, ignoring the fact that HA must act in concert with the viral neuraminidase (NA) during replication and spread. Numerous studies have demonstrated that the degree to which the receptor-binding avidity of HA and receptor-cleaving activity of NA are balanced with each other influences overall viral fitness. We recently showed that changes in NA activity can significantly alter the mutational fitness landscape of HA in the context of a lab-adapted virus strain. Here, we test whether natural variation in relative NA activity can influence the evolutionary potential of HA in the context of the seasonal H1N1 lineage (pdmH1N1) that has circulated in humans since the 2009 pandemic. We observed substantial variation in the relative activities of NA proteins encoded by a panel of H1N1 vaccine strains isolated between 2009 and 2019. We comprehensively assessed the effect of NA background on the HA mutational fitness landscape in the circulating pdmH1N1 lineage using deep mutational scanning and observed pronounced epistasis between NA and residues in or near the receptor-binding site of HA. To determine whether NA variation could influence the antigenic evolution of HA, we performed neutralizing antibody selection experiments using a panel of monoclonal antibodies targeting different HA epitopes. We found that the specific antibody escape profiles of HA were highly contingent upon NA background. Overall, our results indicate that natural variation in NA activity plays a significant role in governing the evolutionary potential of HA in the currently circulating pdmH1N1 lineage.
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Affiliation(s)
- Tongyu Liu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - William K Reiser
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huibin Lv
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joel Rivera-Cardona
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kyle Heimburger
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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2
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Tawfeeq MT, Voordeckers K, van den Berg P, Govers SK, Michiels J, Verstrepen KJ. Mutational robustness and the role of buffer genes in evolvability. EMBO J 2024; 43:2294-2307. [PMID: 38719995 PMCID: PMC11183146 DOI: 10.1038/s44318-024-00109-1] [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: 11/08/2023] [Revised: 03/19/2024] [Accepted: 04/17/2024] [Indexed: 06/19/2024] Open
Abstract
Organisms rely on mutations to fuel adaptive evolution. However, many mutations impose a negative effect on fitness. Cells may have therefore evolved mechanisms that affect the phenotypic effects of mutations, thus conferring mutational robustness. Specifically, so-called buffer genes are hypothesized to interact directly or indirectly with genetic variation and reduce its effect on fitness. Environmental or genetic perturbations can change the interaction between buffer genes and genetic variation, thereby unmasking the genetic variation's phenotypic effects and thus providing a source of variation for natural selection to act on. This review provides an overview of our understanding of mutational robustness and buffer genes, with the chaperone gene HSP90 as a key example. It discusses whether buffer genes merely affect standing variation or also interact with de novo mutations, how mutational robustness could influence evolution, and whether mutational robustness might be an evolved trait or rather a mere side-effect of complex genetic interactions.
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Affiliation(s)
- Mohammed T Tawfeeq
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Karin Voordeckers
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Pieter van den Berg
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Jan Michiels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.
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3
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Oliver JE, Rotenberg D, Agosto-Shaw K, McInnes HA, Lahre KA, Mulot M, Adkins S, Whitfield AE. Multigenic Hairpin Transgenes in Tomato Confer Resistance to Multiple Orthotospoviruses Including Sw-5 Resistance-Breaking Tomato Spotted Wilt Virus. PHYTOPATHOLOGY 2024; 114:1137-1149. [PMID: 37856697 DOI: 10.1094/phyto-07-23-0256-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Tomato spotted wilt virus (TSWV) and related thrips-borne orthotospoviruses are a threat to food and ornamental crops. Orthotospoviruses have the capacity for rapid genetic change by genome segment reassortment and mutation. Genetic resistance is one of the most effective strategies for managing orthotospoviruses, but there are multiple examples of resistance gene breakdown. Our goal was to develop effective multigenic, broad-spectrum resistance to TSWV and other orthotospoviruses. The most conserved sequences for each open reading frame (ORF) of the TSWV genome were identified, and comparison with other orthotospoviruses revealed sequence conservation within virus clades; some overlapped with domains with well-documented biological functions. We made six hairpin constructs, each of which incorporated sequences matching portions of all five ORFs. Tomato plants expressing the hairpin transgene were challenged with TSWV by thrips and leaf-rub inoculation, and four constructs provided strong protection against TSWV in foliage and fruit. To determine if the hairpin constructs provided protection against other emerging orthotospoviruses, we challenged the plants with tomato chlorotic spot virus and resistance-breaking TSWV and found that the same constructs also provided resistance to these related viruses. Antiviral hairpin constructs are an effective way to protect plants from multiple orthotospoviruses and are an important strategy in the fight against resistance-breaking TSWV and emerging viruses. Targeting of all five viral ORFs is expected to increase the durability of resistance, and combining them with other resistance genes could further extend the utility of this disease control strategy. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jonathan E Oliver
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502
| | - Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Karolyn Agosto-Shaw
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Holly A McInnes
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Kirsten A Lahre
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Michaël Mulot
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Scott Adkins
- U.S. Department of Agriculture-Agricultural Research Service-USHRL, Fort Pierce, FL 34945
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
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4
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Warghane A, Saini R, Shri M, Andankar I, Ghosh DK, Chopade BA. Application of nanoparticles for management of plant viral pathogen: Current status and future prospects. Virology 2024; 592:109998. [PMID: 38301447 DOI: 10.1016/j.virol.2024.109998] [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: 10/14/2023] [Revised: 12/29/2023] [Accepted: 01/18/2024] [Indexed: 02/03/2024]
Abstract
Plant viruses are responsible for nearly 47 % of all crop losses brought by plant diseases, which have a considerable negative impact on agricultural output. Nanoparticles have the potential to greatly raise agricultural output due to their wonderful applications in the fields of highly sensitive biomolecular detection, disease diagnostics, antimicrobials, and therapeutic compounds. The application of nanotechnology in plant virology is known as nanophytovirology, and it involves biostimulation, drug transport, genetic manipulation, therapeutic agents, and induction of plant defenses. The inactivation and denaturation of capsid protein, nucleic acids (RNA or DNA), and other protein constituents are involved in the underlying mechanism. To determine the precise mechanism by which nanoparticles affect viral mobility, reproduction, encapsidation, and transmission, more research is however required. Nanoparticles can be used to precisely detect plant viruses using nanobiosensors or as biostimulants. The varieties of nanoparticles employed in plant virus control and their methods of virus suppression are highlighted in this review.
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Affiliation(s)
- Ashish Warghane
- School of Applied Sciences and Technology (SAST), Gujarat Technological University, Ahmedabad, Gujarat, India.
| | - Rashmi Saini
- Department of Zoology, Gargi College, University of Delhi, Delhi, India.
| | - Manju Shri
- School of Applied Sciences and Technology (SAST), Gujarat Technological University, Ahmedabad, Gujarat, India
| | - Isha Andankar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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5
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Liu T, Reiser WK, Tan TJC, Lv H, Rivera-Cardona J, Heimburger K, Wu NC, Brooke CB. Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585603. [PMID: 38562808 PMCID: PMC10983940 DOI: 10.1101/2024.03.18.585603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The antigenic evolution of the influenza A virus hemagglutinin (HA) gene poses a major challenge for the development of vaccines capable of eliciting long-term protection. Prior efforts to understand the mechanisms that govern viral antigenic evolution mainly focus on HA in isolation, ignoring the fact that HA must act in concert with the viral neuraminidase (NA) during replication and spread. Numerous studies have demonstrated that the degree to which the receptor binding avidity of HA and receptor cleaving activity of NA are balanced with each other influences overall viral fitness. We recently showed that changes in NA activity can significantly alter the mutational fitness landscape of HA in the context of a lab-adapted virus strain. Here, we test whether natural variation in relative NA activity can influence the evolutionary potential of HA in the context of the seasonal H1N1 lineage (pdmH1N1) that has circulated in humans since the 2009 pandemic. We observed substantial variation in the relative activities of NA proteins encoded by a panel of H1N1 vaccine strains isolated between 2009 and 2019. We comprehensively assessed the effect of NA background on the HA mutational fitness landscape in the circulating pdmH1N1 lineage using deep mutational scanning and observed pronounced epistasis between NA and residues in or near the receptor binding site of HA. To determine whether NA variation could influence the antigenic evolution of HA, we performed neutralizing antibody selection experiments using a panel of monoclonal antibodies targeting different HA epitopes. We found that the specific antibody escape profiles of HA were highly contingent upon NA background. Overall, our results indicate that natural variation in NA activity plays a significant role in governing the evolutionary potential of HA in the currently circulating pdmH1N1 lineage.
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6
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Shvartzman B, Ram Y. Self-replicating artificial neural networks give rise to universal evolutionary dynamics. PLoS Comput Biol 2024; 20:e1012004. [PMID: 38547320 PMCID: PMC11003675 DOI: 10.1371/journal.pcbi.1012004] [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: 08/01/2023] [Revised: 04/09/2024] [Accepted: 03/17/2024] [Indexed: 04/11/2024] Open
Abstract
In evolutionary models, mutations are exogenously introduced by the modeler, rather than endogenously introduced by the replicator itself. We present a new deep-learning based computational model, the self-replicating artificial neural network (SeRANN). We train it to (i) copy its own genotype, like a biological organism, which introduces endogenous spontaneous mutations; and (ii) simultaneously perform a classification task that determines its fertility. Evolving 1,000 SeRANNs for 6,000 generations, we observed various evolutionary phenomena such as adaptation, clonal interference, epistasis, and evolution of both the mutation rate and the distribution of fitness effects of new mutations. Our results demonstrate that universal evolutionary phenomena can naturally emerge in a self-replicator model when both selection and mutation are implicit and endogenous. We therefore suggest that SeRANN can be applied to explore and test various evolutionary dynamics and hypotheses.
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Affiliation(s)
- Boaz Shvartzman
- School of Zoology, Faculty of Life Sciences, Tel Aviv University; Tel Aviv, Israel
- School of Computer Science, Reichman University; Herzliya, Israel
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University; Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University; Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University; Tel Aviv, Israel
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7
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Giancotti R, Lomoio U, Puccio B, Tradigo G, Vizza P, Torti C, Veltri P, Guzzi PH. The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics. BIOLOGY 2024; 13:90. [PMID: 38392308 PMCID: PMC10886209 DOI: 10.3390/biology13020090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
The SARS-CoV-2 virus, which is a major threat to human health, has undergone many mutations during the replication process due to errors in the replication steps and modifications in the structure of viral proteins. The XBB variant was identified for the first time in Singapore in the fall of 2022. It was then detected in other countries, including the United States, Canada, and the United Kingdom. We study the impact of sequence changes on spike protein structure on the subvariants of XBB, with particular attention to the velocity of variant diffusion and virus activity with respect to its diffusion. We examine the structural and functional distinctions of the variants in three different conformations: (i) spike glycoprotein in complex with ACE2 (1-up state), (ii) spike glycoprotein (closed-1 state), and (iii) S protein (open-1 state). We also estimate the affinity binding between the spike protein and ACE2. The market binding affinity observed in specific variants raises questions about the efficacy of current vaccines in preparing the immune system for virus variant recognition. This work may be useful in devising strategies to manage the ongoing COVID-19 pandemic. To stay ahead of the virus evolution, further research and surveillance should be carried out to adjust public health measures accordingly.
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Affiliation(s)
- Raffaele Giancotti
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Ugo Lomoio
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Barbara Puccio
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | | | - Patrizia Vizza
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Carlo Torti
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Pierangelo Veltri
- Department of Computer Engineering, Modelling, Electronics and System, University of Calabria, 87036 Rende, Italy
| | - Pietro Hiram Guzzi
- Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
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8
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Jeronimo PMC, Aksenen CF, Duarte IO, Lins RD, Miyajima F. Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation. J Virol 2024; 98:e0140423. [PMID: 38088350 PMCID: PMC10804945 DOI: 10.1128/jvi.01404-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Coronaviruses are large RNA viruses that can infect and spread among humans and animals. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019, has evolved since its first detection in December 2019. Deletions are a common occurrence in SARS-CoV-2 evolution, particularly in specific genomic sites, and may be associated with the emergence of highly competent lineages. While deletions typically have a negative impact on viral fitness, some persist and become fixed in viral populations, indicating that they may confer advantageous benefits for the virus's adaptive evolution. This work presents a literature review and data analysis on structural losses in the SARS-CoV-2 genome and the potential relevance of specific signatures for enhanced viral fitness and spread.
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Affiliation(s)
| | - Cleber Furtado Aksenen
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Igor Oliveira Duarte
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Roberto D. Lins
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Pernambuco, Recife, Brazil
| | - Fabio Miyajima
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
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Illingworth CJR, Guerra-Assuncao JA, Gregg S, Charles O, Pang J, Roy S, Abdelnabi R, Neyts J, Breuer J. Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus Evol 2024; 10:veae001. [PMID: 38486802 PMCID: PMC10939363 DOI: 10.1093/ve/veae001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 11/23/2023] [Accepted: 01/03/2024] [Indexed: 03/17/2024] Open
Abstract
Mutagenic antiviral drugs have shown promise against multiple viruses, but concerns have been raised about whether their use might promote the emergence of new and harmful viral variants. Recently, genetic signatures associated with molnupiravir use have been identified in the global SARS-COV-2 population. Here, we examine the consequences of using favipiravir and molnupiravir to treat SARS-CoV-2 infection in a hamster model, comparing viral genome sequence data collected from (1) untreated hamsters, and (2) from hamsters receiving effective and suboptimal doses of treatment. We identify a broadly linear relationship between drug dose and the extent of variation in treated viral populations, with a high proportion of this variation being composed of variants at frequencies of less than 1 per cent, below typical thresholds for variant calling. Treatment with an effective dose of antiviral drug was associated with a gain of between 7 and 10 variants per viral genome relative to drug-free controls: even after a short period of treatment a population founded by a transmitted virus could contain multiple sequence differences to that of the original host. Treatment with a suboptimal dose of drug showed intermediate gains of variants. No dose-dependent signal was identified in the numbers of single-nucleotide variants reaching frequencies in excess of 5 per cent. We did not find evidence to support the emergence of drug resistance or of novel immune phenotypes. Our study suggests that where onward transmission occurs, a short period of treatment with mutagenic drugs may be sufficient to generate a significant increase in the number of viral variants transmitted.
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Affiliation(s)
| | - Jose A Guerra-Assuncao
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH, UK
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Samuel Gregg
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Oscar Charles
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH, UK
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Juanita Pang
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Sunando Roy
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Leuven B-3000, Belgium
- The VirusBank Platform, Gaston Geenslaan, Leuven B-3000, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Leuven B-3000, Belgium
- The VirusBank Platform, Gaston Geenslaan, Leuven B-3000, Belgium
| | - Judith Breuer
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH, UK
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
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Lezcano OM, Fuhrmann L, Ramakrishnan G, Beerenwinkel N, Huynen MA, van Rij RP. Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster. Virus Evol 2023; 9:vead074. [PMID: 38162315 PMCID: PMC10757409 DOI: 10.1093/ve/vead074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
Virus evolution is strongly affected by antagonistic co-evolution of virus and host. Host immunity positively selects for viruses that evade the immune response, which in turn may drive counter-adaptations in host immune genes. We investigated how host immune pressure shapes virus populations, using the fruit fly Drosophila melanogaster and its natural pathogen Drosophila C virus (DCV), as a model. We performed an experimental evolution study in which DCV was serially passaged for ten generations in three fly genotypes differing in their antiviral RNAi response: wild-type flies and flies in which the endonuclease gene Dicer-2 was either overexpressed or inactivated. All evolved virus populations replicated more efficiently in vivo and were more virulent than the parental stock. The number of polymorphisms increased in all three host genotypes with passage number, which was most pronounced in Dicer-2 knockout flies. Mutational analysis showed strong parallel evolution, as mutations accumulated in a specific region of the VP3 capsid protein in every lineage in a host genotype-independent manner. The parental tyrosine at position ninety-five of VP3 was substituted with either one of five different amino acids in fourteen out of fifteen lineages. However, no consistent amino acid changes were observed in the viral RNAi suppressor gene 1A, nor elsewhere in the genome in any of the host backgrounds. Our study indicates that the RNAi response restricts the sequence space that can be explored by viral populations. Moreover, our study illustrates how evolution towards higher virulence can be a highly reproducible, yet unpredictable process.
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Affiliation(s)
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel 4056, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
| | - Gayatri Ramakrishnan
- Department of Medical BioSciences, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel 4056, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
- Department of Medical Microbiology, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
| | | | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, P.O. Box 9101, Nijmegen 6500 HB, The Netherlands
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11
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Hyug Choi J, Sook Jun M, Yong Jeon J, Kim HS, Kyung Kim Y, Ho Jeon C, Hwan Choi S, Sun Kim D, Han MH, Won Oh J. Global lineage evolution pattern of sars-cov-2 in Africa, America, Europe, and Asia: A comparative analysis of variant clusters and their relevance across continents. J Transl Int Med 2023; 11:410-422. [PMID: 38130632 PMCID: PMC10732492 DOI: 10.2478/jtim-2023-0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Objective The objective of this study is to provide a comparative analysis of variant clusters and their relevance across Africa, America, Europe, and Asia, in order to understand the evolutionary patterns of the virus across different regions and to inform the development of targeted interventions and genomic surveillance eforts. Methods The study analyzed the global lineage evolution pattern of 74, 075 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from 32 countries across four continents, focusing on variant clusters and their relevance across regions. Variants were weighted according to their hierarchical level. The correlation between variants was visualized through Dimensionality reduction analysis and Pairwise Pearson's correlation. We presented a reconstructed phylogenetic tree based on correlation analysis and variant weights. Results The analysis revealed that each continent had distinct variant clusters and different evolutionary patterns. The Americas had two clustered variants before lineage divergence and a downstream confluence lineage, Europe had bifurcation into two global lineages with an early occurrence of certain cluster while Asia had a downstream confluence of two large lineages diverging by two distinct clusters. Based on the cluster patterns of shared variants of the SARS-CoV-2 virus, Africa demonstrated a relatively clear distinction among three distinct regions. Conclusions The study provides insights into the evolutionary patterns of SARS-CoV-2 and highlights the importance of international collaboration in tracking and responding to emerging variants. The study found that the global pandemic was driven by Omicron variants that evolved with significant differences between countries and regions, and with different patterns across continents.
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Affiliation(s)
- June Hyug Choi
- Department of Anatomy, BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Mee Sook Jun
- Department of Internal Medicine, Chungbuk National University, Cheongju, Yonsei University-Industry Foundation, Seoul, Republic of Korea
| | | | - Hae-Suk Kim
- Theragen Bio Co., Ltd., Seongnam-si, Republic of Korea
| | - Yu Kyung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Ho Jeon
- Department of Laboratory Medicine, Catholic University of Daegu School of Medicine, Daegu, Republic of Korea
| | - Seock Hwan Choi
- Department of Urology, School of Medicine, BioMedical Research Institute, Kyungpook National University Hospital, Kyungpook National University, Daegu, Republic of Korea
| | - Dong Sun Kim
- Department of Anatomy, BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Man-Hoon Han
- Department of Pathology, School of Medicine, BioMedical Research Institute, Kyungpook National University Hospital, Kyungpook National University, Daegu, Republic of Korea
| | - Ji Won Oh
- Department of Anatomy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
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12
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Lorenzo-Redondo R, de Sant’Anna Carvalho AM, Hultquist JF, Ozer EA. SARS-CoV-2 genomics and impact on clinical care for COVID-19. J Antimicrob Chemother 2023; 78:ii25-ii36. [PMID: 37995357 PMCID: PMC10667012 DOI: 10.1093/jac/dkad309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/02/2023] [Indexed: 11/25/2023] Open
Abstract
The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that had been previously applied on a more limited basis to other viral pathogens, such as HIV and influenza viruses. The need for WGS was driven in part by the low mutation rate of SARS-CoV-2, which necessitated measuring variation along the entire genome sequence to effectively differentiate lineages and characterize viral evolution. Several WGS approaches designed to maximize throughput and accuracy were quickly adopted by surveillance labs around the world. These broad-based SARS-CoV-2 genomic sequencing efforts revealed ongoing evolution of the virus, highlighted by the successive emergence of new viral variants throughout the course of the pandemic. These genomic insights were instrumental in characterizing the effects of viral mutations on transmissibility, immune escape and viral tropism, which in turn helped guide public health policy, the use of monoclonal antibody therapeutics and vaccine development strategies. As the use of direct-acting antivirals for the treatment of COVID-19 became more widespread, the potential for emergence of antiviral resistance has driven ongoing efforts to delineate resistance mutations and to monitor global sequence databases for their emergence. Given the critical role of viral genomics in the international effort to combat the COVID-19 pandemic, coordinated efforts should be made to expand global genomic surveillance capacity and infrastructure towards the anticipation and prevention of future pandemics.
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Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Alexandre Machado de Sant’Anna Carvalho
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
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13
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Abstract
Understanding the factors that shape viral evolution is critical for developing effective antiviral strategies, accurately predicting viral evolution, and preventing pandemics. One fundamental determinant of viral evolution is the interplay between viral protein biophysics and the host machineries that regulate protein folding and quality control. Most adaptive mutations in viruses are biophysically deleterious, resulting in a viral protein product with folding defects. In cells, protein folding is assisted by a dynamic system of chaperones and quality control processes known as the proteostasis network. Host proteostasis networks can determine the fates of viral proteins with biophysical defects, either by assisting with folding or by targeting them for degradation. In this review, we discuss and analyze new discoveries revealing that host proteostasis factors can profoundly shape the sequence space accessible to evolving viral proteins. We also discuss the many opportunities for research progress proffered by the proteostasis perspective on viral evolution and adaptation.
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Affiliation(s)
- Jimin Yoon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Jessica E Patrick
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - C Brandon Ogbunugafor
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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14
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Svoboda P, Haviernik J, Bednar P, Matkovic M, Cervantes Rincón T, Keeffe J, Palus M, Salat J, Agudelo M, Nussenzweig MC, Cavalli A, Robbiani DF, Ruzek D. A combination of two resistance mechanisms is critical for tick-borne encephalitis virus escape from a broadly neutralizing human antibody. Cell Rep 2023; 42:113149. [PMID: 37715951 PMCID: PMC10591882 DOI: 10.1016/j.celrep.2023.113149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/26/2023] [Accepted: 08/31/2023] [Indexed: 09/18/2023] Open
Abstract
Tick-borne encephalitis virus (TBEV) is a flavivirus that causes human neuroinfections and represents a growing health problem. The human monoclonal antibody T025 targets envelope protein domain III (EDIII) of TBEV and related tick-borne flaviviruses, potently neutralizing TBEV in vitro and in preclinical models, representing a promising candidate for clinical development. We demonstrate that TBEV escape in the presence of T025 or T028 (another EDIII-targeting human monoclonal antibody) results in virus variants of reduced pathogenicity, characterized by distinct sets of amino acid changes in EDII and EDIII that are jointly needed to confer resistance. EDIII substitution K311N impairs formation of a salt bridge critical for T025-epitope interaction. EDII substitution E230K is not on the T025 epitope but likely induces quaternary rearrangements of the virus surface because of repulsion of positively charged residues on the adjacent EDI. A combination of T025 and T028 prevents virus escape and improves neutralization.
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Affiliation(s)
- Pavel Svoboda
- Veterinary Research Institute, Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno, Czech Republic
| | - Jan Haviernik
- Veterinary Research Institute, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Bednar
- Veterinary Research Institute, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Milos Matkovic
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Tomás Cervantes Rincón
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | | | - Martin Palus
- Veterinary Research Institute, Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Jiri Salat
- Veterinary Research Institute, Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, New York, NY, USA
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Davide F Robbiani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.
| | - Daniel Ruzek
- Veterinary Research Institute, Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Japan.
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15
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Si Y, Wu W, Xue X, Sun X, Qin Y, Li Y, Qiu C, Li Y, Zhuo Z, Mi Y, Zheng P. The evolution of SARS-CoV-2 and the COVID-19 pandemic. PeerJ 2023; 11:e15990. [PMID: 37701824 PMCID: PMC10493083 DOI: 10.7717/peerj.15990] [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: 03/21/2023] [Accepted: 08/08/2023] [Indexed: 09/14/2023] Open
Abstract
Scientists have made great efforts to understand the evolution of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) to provide crucial information to public health experts on strategies to control this viral pathogen. The pandemic of the coronavirus disease that began in 2019, COVID-19, lasted nearly three years, and nearly all countries have set different epidemic prevention policies for this virus. The continuous evolution of SARS-CoV-2 alters its pathogenicity and infectivity in human hosts, thus the policy and treatments have been continually adjusted. Based on our previous study on the dynamics of binding ability prediction between the COVID-19 spike protein and human ACE2, the present study mined over 10 million sequences and epidemiological data of SARS-CoV-2 during 2020-2022 to understand the evolutionary path of SARS-CoV-2. We analyzed and predicted the mutation rates of the whole genome and main proteins of SARS-CoV-2 from different populations to understand the adaptive relationship between humans and COVID-19. Our study identified a correlation of the mutation rates from each protein of SARS-CoV-2 and various human populations. Overall, this analysis provides a scientific basis for developing data-driven strategies to confront human pathogens.
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Affiliation(s)
- Yuanfang Si
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Weidong Wu
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xia Xue
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiangdong Sun
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Yaping Qin
- School of Basic Medical Sciences, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ya Li
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Chunjing Qiu
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Yingying Li
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Ziran Zhuo
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Mi
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Pengyuan Zheng
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Cente, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Department of Gastroenterology, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China
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16
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Lomoio U, Puccio B, Tradigo G, Guzzi PH, Veltri P. SARS-CoV-2 protein structure and sequence mutations: Evolutionary analysis and effects on virus variants. PLoS One 2023; 18:e0283400. [PMID: 37471335 PMCID: PMC10358949 DOI: 10.1371/journal.pone.0283400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023] Open
Abstract
The structure and sequence of proteins strongly influence their biological functions. New models and algorithms can help researchers in understanding how the evolution of sequences and structures is related to changes in functions. Recently, studies of SARS-CoV-2 Spike (S) protein structures have been performed to predict binding receptors and infection activity in COVID-19, hence the scientific interest in the effects of virus mutations due to sequence, structure and vaccination arises. However, there is the need for models and tools to study the links between the evolution of S protein sequence, structure and functions, and virus transmissibility and the effects of vaccination. As studies on S protein have been generated a large amount of relevant information, we propose in this work to use Protein Contact Networks (PCNs) to relate protein structures with biological properties by means of network topology properties. Topological properties are used to compare the structural changes with sequence changes. We find that both node centrality and community extraction analysis can be used to relate protein stability and functionality with sequence mutations. Starting from this we compare structural evolution to sequence changes and study mutations from a temporal perspective focusing on virus variants. Finally by applying our model to the Omicron variant we report a timeline correlation between Omicron and the vaccination campaign.
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Affiliation(s)
- Ugo Lomoio
- Department of Surgical and Medical Sciences, University of Catanzaro, Catanzaro, Italy
| | - Barbara Puccio
- Department of Surgical and Medical Sciences, University of Catanzaro, Catanzaro, Italy
| | | | - Pietro Hiram Guzzi
- Department of Surgical and Medical Sciences, University of Catanzaro, Catanzaro, Italy
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17
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Mu S, Zou X, Wang Y, Deng X, Cui D, Liu S, Cao B. The combined effect of oseltamivir and favipiravir on influenza a virus evolution in patients hospitalized with severe influenza. Antiviral Res 2023:105657. [PMID: 37369282 DOI: 10.1016/j.antiviral.2023.105657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/14/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023]
Abstract
Our previous study shows favipiravir and oseltamivir combination therapy may accelerate clinical recovery compared to oseltamivir monotherapy in severe influenza, but its effect on virological evolution and resistance mutation against oseltamivir is still unknown. In this study, we collected longitudinal respiratory samples from influenza patients who underwent combination therapy and applied them to next generation sequencing of the whole genome of the influenza A virus (IAV). We also included a cohort untreated with any antivirals to serve as the control. In total, 62 samples from 19 patients treated with combination therapy and 20 samples from 20 patients untreated were successfully sequenced. The nucleotide diversity in the whole genome of IAV in the combination group showed no difference compared to that in the control group (P > 0.05). Moreover, we observed 174 kinds of nonsynonymous nucleotide substitutions in patients with combination therapy, mostly in NA (n = 44) and HA (n = 43). Of them, the G→A transition was the dominant variant type (27%) and 46/174 (26%) was reported to have biological effects, such as increased pathogenicity and polymerase activity. Among the 29 mutations conferring reduction in oseltamivir sensitivity we investigated, H275Y was the only mutation detected in the 4 samples from 1 of 19 patients and demonstrated increasing frequency during the treatment. Mutations conferring favipiravir resistance were not observed. Our studies showed combination therapy of favipiravir and oseltamivir has little effect on virus nucleotide diversity, nor prevents the increase of oseltamivir-resistant variants.
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Affiliation(s)
- Shengrui Mu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China.
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaoyan Deng
- Tsinghua University School of Medicine, Beijing, China
| | - Dan Cui
- Harbin Medical University, Harbin, Heilongjiang, China
| | - Shuai Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, Shandong, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Tsinghua University School of Medicine, Beijing, China; Harbin Medical University, Harbin, Heilongjiang, China.
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18
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Wei H, Kumthip K, Khamrin P, Yodmeeklin A, Jampanil N, Phengma P, Xie Z, Ukarapol N, Ushijima H, Maneekarn N. Triple Intergenotype Recombination of Human Astrovirus 5, Human Astrovirus 8, and Human Astrovirus 1 in the Open Reading Frame 1a, Open Reading Frame 1b, and Open Reading Frame 2 Regions of the Human Astrovirus Genome. Microbiol Spectr 2023; 11:e0488822. [PMID: 37017548 PMCID: PMC10269785 DOI: 10.1128/spectrum.04888-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/08/2023] [Indexed: 04/06/2023] Open
Abstract
Human astrovirus (HAstV) strains exhibit high levels of genetic diversity, and many recombinant strains with different recombination patterns have been reported. The aims of the present study were to investigate the emergence of HAstV recombinant strains and to characterize the recombination patterns of the strains detected in pediatric patients admitted to the hospital with acute gastroenteritis in Chiang Mai, Thailand. A total of 92 archival HAstV strains detected in 2011 to 2020 were characterized regarding their open reading frame 1a (ORF1a) genotypes in comparison with their ORF1b genotypes to identify recombinant strains. The recombination breakpoints of the putative recombinant strains were determined by whole-genome sequencing and were analyzed by SimPlot and RDP software. Three HAstV strains (CMH-N178-12, CMH-S059-15, and CMH-S062-15) were found to be recombinant strains of three different HAstV genotypes, i.e., HAstV5, HAstV8, and HAstV1 within the ORF1a, ORF1b, and ORF2 regions, respectively. The CMH-N178-12 strain displayed recombination breakpoints at nucleotide positions 2681 and 4357 of ORF1a and ORF1b, respectively, whereas the other two recombinant strains, CMH-S059-15 and CMH-S062-15, displayed recombination breakpoints at nucleotide positions 2612 and 4357 of ORF1a and ORF1b, respectively. This is the first study to reveal nearly full-length genome sequences of HAstV recombinant strains with a novel recombination pattern of ORF1a-ORF1b-ORF2 genotypes. This finding may be useful as a guideline for identifying other recombinant HAstV strains in other geographical regions and may provide a better understanding of their genetic diversity, as well as basic knowledge regarding virus evolution. IMPORTANCE Recombination is one of the mechanisms that plays a crucial role in the genetic diversity and evolution of HAstV. We wished to investigate the emergence of HAstV recombinant strains and to analyze the whole-genome sequences of the putative HAstV recombinant strains detected in pediatric patients with acute gastroenteritis in 2011 to 2020. We reported 3 novel intergenotype recombinant strains of HAstV5-HAstV8-HAstV1 at the ORF1a-ORF1b-ORF2 regions of the HAstV genome. The hot spots of recombination occur frequently near the ORF1a-ORF1b and ORF1b-ORF2 junctions of the HAstV genome. The findings indicate that intergenotype recombination of HAstV occurs frequently in nature. The emergence of a novel recombinant strain allows the new virus to adapt and successfully escape from the host immune system, eventually emerging as the predominant genotype to infect human populations that lack herd immunity against novel recombinant strains. The virus may cause an outbreak and needs to be monitored continually.
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Affiliation(s)
- Hongyu Wei
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phitchakorn Phengma
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Zhenfeng Xie
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Nuthapong Ukarapol
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
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19
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Kariithi HM, Volkening JD, Chiwanga GH, Pantin-Jackwood MJ, Msoffe PLM, Suarez DL. Genome Sequences and Characterization of Chicken Astrovirus and Avian Nephritis Virus from Tanzanian Live Bird Markets. Viruses 2023; 15:1247. [PMID: 37376547 DOI: 10.3390/v15061247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The enteric chicken astrovirus (CAstV) and avian nephritis virus (ANV) are the type species of the genus Avastrovirus (AAstV; Astroviridae family), capable of causing considerable production losses in poultry. Using next-generation sequencing of a cloacal swab from a backyard chicken in Tanzania, we assembled genome sequences of ANV and CAstV (6918 nt and 7318 nt in length, respectively, excluding poly(A) tails, which have a typical AAstV genome architecture (5'-UTR-ORF1a-ORF1b-ORF2-'3-UTR). They are most similar to strains ck/ANV/BR/RS/6R/15 (82.72%) and ck/CAstV/PL/G059/14 (82.23%), respectively. Phylogenetic and sequence analyses of the genomes and the three open reading frames (ORFs) grouped the Tanzanian ANV and CAstV strains with Eurasian ANV-5 and CAstV-Aii viruses, respectively. Compared to other AAstVs, the Tanzanian strains have numerous amino acid variations (substitutions, insertions and deletions) in the spike region of the capsid protein. Furthermore, CAstV-A has a 4018 nt recombinant fragment in the ORF1a/1b genomic region, predicted to be from Eurasian CAstV-Bi and Bvi parental strains. These data should inform future epidemiological studies and options for AAstV diagnostics and vaccines.
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Affiliation(s)
- Henry M Kariithi
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kaptagat Rd, Nairobi P.O. Box 57811-00200, Kenya
| | | | - Gaspar H Chiwanga
- Tanzania Veterinary Laboratory Agency, South Zone, Mtwara P.O. Box 186, Tanzania
| | - Mary J Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA
| | - Peter L M Msoffe
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Chuo Kikuu, Morogoro P.O. Box 3000, Tanzania
| | - David L Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA
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20
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Groza C, Totschnig D, Wenisch C, Atamaniuk J, Zoufaly A. A retrospective analysis of clinical features of patients hospitalized with SARS-CoV-2 Omicron variants BA.1 and BA.2. Sci Rep 2023; 13:7896. [PMID: 37193727 DOI: 10.1038/s41598-023-34712-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/05/2023] [Indexed: 05/18/2023] Open
Abstract
The causative agent of the ongoing Corona virus disease 2019 (COVID-19) pandemic, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has acquired a considerable amount of mutations, leading to changes in clinical manifestations and increased transmission. Recent studies based on animal disease models and data from the general population were reporting a higher pathogenicity of the BA.2 sublineage compared to BA.1. The aim of this study was to provide real world data on patients with the SARS-CoV-2 Omicron BA.1 and BA.2 subvariants treated at our center, highlighting similarities and differences in the clinical disease course. We retrospectively collected and analyzed the data of adult patients admitted with confirmed SARS-CoV-2 infection at the Department for Infectious Diseases and Tropical Medicine, Klinik Favoriten, Vienna, Austria. Patient characteristics including age, underlying diseases, vaccination status and outcome were compared between patients with the BA.1 and BA.2 subvariants. Between January 2022 and May 2022 we included 168 patients infected with Omicron BA.1 and 100 patients with BA.2. Patients admitted with BA.2 were significantly older, more often fully immunized and required less dexamethasone than patients with BA.1. No substantial differences were identified between patients infected with BA.1 and BA.2 regarding BMI, laboratory findings, need for supplemental oxygen, mortality and other evaluated comorbidities excepting active malignancies. The significantly larger percentage of fully immunized patients admitted with BA.2 is pointing to an increased transmissibility of this subvariant, while the comparable outcome of a somewhat older and sicker patient population might be indicative of reduced virulence.
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Affiliation(s)
- Cristina Groza
- Department of Medicine IV, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria.
- Faculty of Medicine, Sigmund Freud University, Vienna, Austria.
| | - David Totschnig
- Department of Medicine IV, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria
| | - Christoph Wenisch
- Department of Medicine IV, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria
| | - Johanna Atamaniuk
- Faculty of Medicine, Sigmund Freud University, Vienna, Austria
- Department of Laboratory Medicine, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria
| | - Alexander Zoufaly
- Department of Medicine IV, Klinik Favoriten, Vienna Healthcare Group, Kundratstraße 3, 1100, Vienna, Austria
- Faculty of Medicine, Sigmund Freud University, Vienna, Austria
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21
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Kosidło JW, Wolszczak-Biedrzycka B, Matowicka-Karna J, Dymicka-Piekarska V, Dorf J. Clinical Significance and Diagnostic Utility of NLR, LMR, PLR and SII in the Course of COVID-19: A Literature Review. J Inflamm Res 2023; 16:539-562. [PMID: 36818192 PMCID: PMC9930576 DOI: 10.2147/jir.s395331] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/18/2023] [Indexed: 02/12/2023] Open
Abstract
Nowadays, society is increasingly struggling with infectious diseases that are characterized by severe course and even death. Recently, the whole world has faced the greatest epidemiological threat, which is COVID-19 caused by SARS CoV-2 virus. SARS CoV-2 infection is often accompanied by severe inflammation, which can lead to the development of different complications. Consequently, clinicians need easily interpreted and effective markers of inflammation that can predict the efficacy of the treatment and patient prognosis. Inflammation is associated with changes in many biochemical and hematological parameters, including leukocyte counts and their populations. In COVID-19, changes in leukocytes count populations such as neutrophils, lymphocytes or monocytes are observed. The numerous research confirm that indicators like neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), platelets-to-lymphocyte ratio (PLR) and systemic inflammatory index (SII) may prove effective in assessment patient prognosis and choosing optimal therapy. Therefore, in this review, we would like to summarize the latest knowledge about the diagnostic utility of systemic inflammatory ratios - NLR, LMR, PLR and SII in patients with COVID-19. We focused on the papers evaluating the diagnostic utility of inflammatory ratios using ROC curve published in the recent 3 years. Identification of biomarkers associated with inflammation would help the selection of patients with severe course of COVID-19 and high risk of death.
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Affiliation(s)
- Jakub Wiktor Kosidło
- Students’ Scientific Club at the Department of Clinical Laboratory Diagnostics, Medical University of Bialystok, Bialystok, Poland
| | - Blanka Wolszczak-Biedrzycka
- Department of Psychology and Sociology of Health and Public Health, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland,Warmia and Mazury Oncology Center of the Hospital of the Ministry of the Interior and Administration, Olsztyn, Poland
| | - Joanna Matowicka-Karna
- Department of Clinical Laboratory Diagnostics, Medical University of Bialystok, Bialystok, Poland
| | | | - Justyna Dorf
- Department of Clinical Laboratory Diagnostics, Medical University of Bialystok, Bialystok, Poland,Correspondence: Justyna Dorf, Department of Clinical Laboratory Diagnostics, Medical University of Bialystok, Waszyngtona 15a St., 15-269, Bialystok, Poland, Tel +48 85 8 31 87 16, Email
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22
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Shannon A, Canard B. Kill or corrupt: Mechanisms of action and drug-resistance of nucleotide analogues against SARS-CoV-2. Antiviral Res 2023; 210:105501. [PMID: 36567022 PMCID: PMC9773703 DOI: 10.1016/j.antiviral.2022.105501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Nucleoside/tide analogues (NAs) have long been used in the fight against viral diseases, and now present a promising option for the treatment of COVID-19. Once activated to the 5'-triphosphate state, NAs act by targeting the viral RNA-dependent RNA-polymerase for incorporation into the viral RNA genome. Incorporated analogues can either 'kill' (terminate) synthesis, or 'corrupt' (genetically or chemically) the RNA. Against coronaviruses, the use of NAs has been further complicated by the presence of a virally encoded exonuclease domain (nsp14) with proofreading and repair capacities. Here, we describe the mechanism of action of four promising anti-COVID-19 NAs; remdesivir, molnupiravir, favipiravir and bemnifosbuvir. Their distinct mechanisms of action best exemplify the concept of 'killers' and 'corruptors'. We review available data regarding their ability to be incorporated and excised, and discuss the specific structural features that dictate their overall potency, toxicity, and mutagenic potential. This should guide the synthesis of novel analogues, lend insight into the potential for resistance mutations, and provide a rational basis for upcoming combinations therapies.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France.
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23
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Li Q, Shah T, Wang B, Qu L, Wang R, Hou Y, Baloch Z, Xia X. Cross-species transmission, evolution and zoonotic potential of coronaviruses. Front Cell Infect Microbiol 2023; 12:1081370. [PMID: 36683695 PMCID: PMC9853062 DOI: 10.3389/fcimb.2022.1081370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Coronaviruses (CoVs) continuously evolve, crossing species barriers and spreading across host ranges. Over the last two decades, several CoVs (HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2) have emerged in animals and mammals, causing significant economic and human life losses. Due to CoV cross-species transmission and the evolution of novel viruses, it is critical to identify their natural reservoiurs and the circumstances under which their transmission occurs. In this review, we use genetic and ecological data to disentangle the evolution of various CoVs in wildlife, humans, and domestic mammals. We thoroughly investigate several host species and outline the epidemiology of CoVs toward specific hosts. We also discuss the cross-species transmission of CoVs at the interface of wildlife, animals, and humans. Clarifying the epidemiology and diversity of species reservoirs will significantly impact our ability to respond to the future emergence of CoVs in humans and domestic animals.
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Affiliation(s)
- Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,The First Affiliated Hospital & Clinical Medical College, Dali University, Dali, Yunnan, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Linyu Qu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Rui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,*Correspondence: Xueshan Xia,
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24
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Petrof O, Fajgenblat M, Neyens T, Molenberghs G, Faes C. The doubling effect of COVID-19 cases on key health indicators. PLoS One 2022; 17:e0275523. [PMID: 36417418 PMCID: PMC9683546 DOI: 10.1371/journal.pone.0275523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/19/2022] [Indexed: 11/25/2022] Open
Abstract
From the beginning of the COVID-19 pandemic, researchers advised policy makers to make informed decisions towards the adoption of mitigating interventions. Key easy-to-interpret metrics applied over time can measure the public health impact of epidemic outbreaks. We propose a novel method which quantifies the effect of hospitalizations or mortality when the number of COVID-19 cases doubles. Two analyses are used, a country-by-country analysis and a multi-country approach which considers all countries simultaneously. The new measure is applied to several European countries, where the presence of different variants, vaccination rates and intervention measures taken over time leads to a different risk. Based on our results, the vaccination campaign has a clear effect for all countries analyzed, reducing the risk over time. However, the constant emergence of new variants combined with distinct intervention measures impacts differently the risk per country.
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Affiliation(s)
- Oana Petrof
- I-Biostat, DSI, Hasselt University, Diepenbeek, Belgium
- * E-mail:
| | - Maxime Fajgenblat
- Laboratory of Freshwater Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Thomas Neyens
- I-Biostat, DSI, Hasselt University, Diepenbeek, Belgium
- Leuven Biostatistics and Statistical Bioinformatics Centre (L-BioStat), KU Leuven, Leuven, Belgium
| | - Geert Molenberghs
- I-Biostat, DSI, Hasselt University, Diepenbeek, Belgium
- I-BioStat, KU Leuven University of Leuven, Leuven, Belgium
| | - Christel Faes
- I-Biostat, DSI, Hasselt University, Diepenbeek, Belgium
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25
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Molecular Detection of Southern Tomato Amalgavirus Prevalent in Tomatoes and Its Genomic Characterization with Global Evolutionary Dynamics. Viruses 2022; 14:v14112481. [PMID: 36366579 PMCID: PMC9693158 DOI: 10.3390/v14112481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynamics of STV. We found that STV prevailed across China and Pakistan, with a maximum average rate of infection of 43.19% in Beijing, China, and 40.08% in Punjab, Pakistan. Subsequently, we amplified, cloned, and annotated the complete genome sequences of STV isolates from Solanum lycopersicum L. in China (OP548653 and OP548652) and Pakistan (MT066231) using Sanger and next-generation sequencing (NGS). These STV isolates displayed close evolutionary relationships with others from Asia, America, and Europe. Whole-genome-based molecular diversity analysis showed that STV populations had 33 haplotypes with a gene diversity (Hd) of 0.977 and a nucleotide diversity (π) of 0.00404. The genetic variability of RNA-dependent RNA-polymerase (RdRp) was higher than that of the putative coat protein (CP) p42. Further analysis revealed that STV isolates were likely to be recombinant but with a lower-to-moderate level of confidence. With a variable distribution pattern of positively and negatively selected sites, negative selection pressure predominantly acted on p42 and RdRp. These findings elaborated on the molecular variability and evolutionary trends among STV populations across major tomato-producing regions of the world.
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26
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Sharma P, Kumar M, Tripathi MK, Gupta D, Vishwakarma P, Das U, Kaur P. Genomic and structural mechanistic insight to reveal the differential infectivity of omicron and other variants of concern. Comput Biol Med 2022; 150:106129. [PMID: 36195045 PMCID: PMC9493144 DOI: 10.1016/j.compbiomed.2022.106129] [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: 04/28/2022] [Revised: 09/04/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND The genome of SARS-CoV-2, is mutating rapidly and continuously challenging the management and preventive measures adopted and recommended by healthcare agencies. The spike protein is the main antigenic site that binds to the host receptor hACE-2 and is recognised by antibodies. Hence, the mutations in this site were analysed to assess their role in differential infectivity of lineages having these mutations, rendering the characterisation of these lineages as variants of concern (VOC) and variants of interest (VOI). METHODS In this work, we examined the genome sequence of SARS-CoV-2 VOCs and their phylogenetic relationships with the other PANGOLIN lineages. The mutational landscape of WHO characterized variants was determined and mutational diversity was compared amongst the different severity groups. We then computationally studied the structural impact of the mutations in receptor binding domain of the VOCs. The binding affinity was quantitatively determined by molecular dynamics simulations and free energy calculations. RESULTS The mutational frequency, as well as phylogenetic distance, was maximum in the case of omicron followed by the delta variant. The maximum binding affinity was for delta variant followed by the Omicron variant. The increased binding affinity of delta strain followed by omicron as compared to other variants and wild type advocates high transmissibility and quick spread of these two variants and high severity of delta variant. CONCLUSION This study delivers a foundation for discovering the improved binding knacks and structural features of SARS-CoV-2 variants to plan novel therapeutics and vaccine candidates against the virus.
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Affiliation(s)
- Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Manish Kumar Tripathi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Poorvi Vishwakarma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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27
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Abstract
The virus-encoded RNA-dependent RNA polymerase (RdRp) is responsible for viral replication, and its fidelity is closely related to viral diversity, pathogenesis, virulence, and fitness. Hepatitis C virus (HCV) and the second human pegivirus (HPgV-2) belong to the family Flaviviridae and share some features, including similar viral genome structure. Unlike HCV, HPgV-2 preserves a highly conserved genome sequence and low intrahost variation. However, the underlying mechanism remains to be elucidated. In this study, we evaluated the fidelity of HPgV-2 and HCV RdRp in an in vitro RNA polymerase reaction system. The results showed higher fidelity of HPgV-2 RdRp than HCV NS5B with respect to the misincorporation rate due to their difference in recognizing nucleoside triphosphate (NTP) substrates. Furthermore, HPgV-2 RdRp showed lower sensitivity than HCV to sofosbuvir, a nucleotide inhibitor against HCV RdRp, which explained the insusceptibility of HPgV-2 to direct-acting antiviral (DAA) therapy against HCV infection. Our results indicate that HPgV-2 could be an excellent model for studying the mechanisms involved in viral polymerase fidelity as well as RNA virus diversity and evolution. IMPORTANCE RNA viruses represent the most important pathogens for humans and animals and exhibit rapid evolution and high adaptive capacity, which is due to the high mutation rates for using the error-prone RNA-dependent RNA polymerase (RdRp) during replication. The fidelity of RdRp is closely associated with viral diversity, fitness, and pathogenesis. Previous studies have shown that the second human pegivirus (HPgV-2) exhibits a highly conserved genome sequence and low intrahost variation, which might be due to the fidelity of HPgV-2 RdRp. In this work, we used a series of in vitro RNA polymerase assays to evaluate the in vitro fidelity of HPgV-2 RdRp and compared it with that of HCV RdRp. The results indicated that HPgV-2 RdRp preserves significantly higher fidelity than HCV RdRp, which might contribute to the conservation of the HPgV-2 genome. The unique feature of HPgV-2 RdRp fidelity provides a new model for investigation of viral RdRp fidelity.
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28
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Liu T, Wang Y, Tan TJC, Wu NC, Brooke CB. The evolutionary potential of influenza A virus hemagglutinin is highly constrained by epistatic interactions with neuraminidase. Cell Host Microbe 2022; 30:1363-1369.e4. [PMID: 36150395 PMCID: PMC9588755 DOI: 10.1016/j.chom.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/27/2022] [Accepted: 09/02/2022] [Indexed: 11/03/2022]
Abstract
Antigenic evolution of the influenza A virus (IAV) hemagglutinin (HA) gene limits efforts to effectively control the spread of the virus in the population. Efforts to understand the mechanisms governing HA antigenic evolution typically examine the HA gene in isolation. This can ignore the importance of balancing HA receptor binding activities with the receptor-destroying activities of the viral neuraminidase (NA) to maintain viral fitness. We hypothesize that the need to maintain functional balance with NA significantly constrains the evolutionary potential of the HA. We use deep mutational scanning and show that variation in NA activity significantly reshapes the HA fitness landscape by modulating the overall mutational robustness of HA. Consistent with this, we observe that different NA backgrounds support the emergence of distinct repertoires of HA escape variants under neutralizing antibody pressure. Our results reveal a critical role for intersegment epistasis in influencing the evolutionary potential of the HA gene.
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Affiliation(s)
- Tongyu Liu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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29
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Rotrattanadumrong R, Yokobayashi Y. Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning. Nat Commun 2022; 13:4847. [PMID: 35977956 PMCID: PMC9385714 DOI: 10.1038/s41467-022-32538-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
A neutral network connects all genotypes with equivalent phenotypes in a fitness landscape and plays an important role in the mutational robustness and evolvability of biomolecules. In contrast to earlier theoretical works, evidence of large neutral networks has been lacking in recent experimental studies of fitness landscapes. This suggests that evolution could be constrained globally. Here, we demonstrate that a deep learning-guided evolutionary algorithm can efficiently identify neutral genotypes within the sequence space of an RNA ligase ribozyme. Furthermore, we measure the activities of all 216 variants connecting two active ribozymes that differ by 16 mutations and analyze mutational interactions (epistasis) up to the 16th order. We discover an extensive network of neutral paths linking the two genotypes and reveal that these paths might be predicted using only information from lower-order interactions. Our experimental evaluation of over 120,000 ribozyme sequences provides important empirical evidence that neutral networks can increase the accessibility and predictability of the fitness landscape. Neutral networks, which are sets of genotypes connected via single mutations that share the same phenotype, are important for evolvability. Here, the authors provide experimental evidence of a neutral network in an RNA enzyme using a high-throughput assay and deep learning.
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Affiliation(s)
- Rachapun Rotrattanadumrong
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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30
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Yeung J, Routh AL. ViReMaShiny: an interactive application for analysis of viral recombination data. Bioinformatics 2022; 38:4420-4422. [PMID: 35904541 PMCID: PMC9477530 DOI: 10.1093/bioinformatics/btac522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/15/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Recombination is an essential driver of virus evolution and adaption, giving rise to new chimeric viruses, structural variants, sub-genomic RNAs and defective RNAs. Next-generation sequencing (NGS) of virus samples, either from experimental or clinical settings, has revealed a complex distribution of recombination events that contributes to intrahost diversity. We and others have previously developed alignment tools to discover and map these diverse recombination events in NGS data. However, there is no standard for data visualization to contextualize events of interest, and downstream analysis often requires bespoke coding. RESULTS We present ViReMaShiny, a web-based application built using the R Shiny framework to allow interactive exploration and point-and-click visualization of viral recombination data provided in BED format generated by computational pipelines such as ViReMa (Viral-Recombination-Mapper). AVAILABILITY AND IMPLEMENTATION The application is hosted at https://routhlab.shinyapps.io/ViReMaShiny/ with associated documentation at https://jayeung12.github.io/. Code is available at https://github.com/routhlab/ViReMaShiny. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jason Yeung
- John Sealy School of Medicine, The University of Texas Medical Branch, Galveston, TX 77550, USA
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31
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Johnson MS, Desai MM. Mutational robustness changes during long-term adaptation in laboratory budding yeast populations. eLife 2022; 11:76491. [PMID: 35880743 PMCID: PMC9355567 DOI: 10.7554/elife.76491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
As an adapting population traverses the fitness landscape, its local neighborhood (i.e., the collection of fitness effects of single-step mutations) can change shape because of interactions with mutations acquired during evolution. These changes to the distribution of fitness effects can affect both the rate of adaptation and the accumulation of deleterious mutations. However, while numerous models of fitness landscapes have been proposed in the literature, empirical data on how this distribution changes during evolution remains limited. In this study, we directly measure how the fitness landscape neighborhood changes during laboratory adaptation. Using a barcode-based mutagenesis system, we measure the fitness effects of 91 specific gene disruption mutations in genetic backgrounds spanning 8000–10,000 generations of evolution in two constant environments. We find that the mean of the distribution of fitness effects decreases in one environment, indicating a reduction in mutational robustness, but does not change in the other. We show that these distribution-level patterns result from differences in the relative frequency of certain patterns of epistasis at the level of individual mutations, including fitness-correlated and idiosyncratic epistasis.
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Affiliation(s)
- Milo S Johnson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
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32
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Nunes DBSM, Vieira C, Sá JM, Araújo GC, Caruso IP, Souza FP. M2-2 gene as a new alternative molecular marker for phylogenetic, phylodynamic, and evolutionary studies of hRSV. Virus Res 2022; 318:198850. [PMID: 35750131 DOI: 10.1016/j.virusres.2022.198850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 10/18/2022]
Abstract
The human Respiratory Syncytial Virus (hRSV) is the main causative agent of acute respiratory infections (ARI), such as pneumonia and bronchiolitis. One of the factors that lead to success in viral replication is the interaction of the M2-2 protein with the ribosomal complex. This interaction is responsible for the phase change of viral activity, acting as an inhibitor or inducer of viral replication, according to the concentration of mRNA. Based on the importance of M2-2 gene and protein have to viral physiology, we performed here evaluations of genetic diversity, phylogenetic reconstructions, phylodynamics, and selection test. Our results suggested an alternative way of classifying this virus in clades A and B, based on a new phylogenetic marker, the M2-2 gene. Therefore, our study is the first one to investigate the dynamics of the evolutionary diversification process of hRSV from the perspective of the M2-2 viral gene. In our study was also identified that the M2-2 gene is under the effect of purifying selection originated by population genetic bottlenecks. Therefore, the M2-2 gene demonstrated an interesting potential to be applied in evolutionary studies involving hRSV, recovering phylogenetic signals and traits of natural selection under the evolution of this virus.
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Affiliation(s)
- Denis Bruno S M Nunes
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), Campus A.C. Simões, AL, Brazil
| | - Camila Vieira
- Department of Basic Sciences, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, SP, Brazil
| | - Jéssica M Sá
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil
| | - Gabriela C Araújo
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil
| | - Icaro P Caruso
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil; Institute of Medical Biochemistry Leopoldo de Meis and National Center for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| | - Fátima P Souza
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil.
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Piazza M, Di Cicco M, Pecoraro L, Ghezzi M, Peroni D, Comberiati P. Long COVID-19 in Children: From the Pathogenesis to the Biologically Plausible Roots of the Syndrome. Biomolecules 2022; 12:556. [PMID: 35454144 PMCID: PMC9024951 DOI: 10.3390/biom12040556] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
Long Coronavirus disease-19 (COVID-19) refers to the persistence of symptoms related to the infection with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). This condition is described as persistent and can manifest in various combinations of signs and symptoms, such as fatigue, headache, dyspnea, depression, cognitive impairment, and altered perception of smells and tastes. Long COVID-19 may be due to long-term damage to different organs-such as lung, brain, kidney, and heart-caused by persisting viral-induced inflammation, immune dysregulation, autoimmunity, diffuse endothelial damage, and micro thrombosis. In this review, we discuss the potential and biologically plausible role of some vitamins, essential elements, and functional foods based on the hypothesis that an individual's dietary status may play an important adjunctive role in protective immunity against COVID-19 and possibly against its long-term consequences.
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Affiliation(s)
- Michele Piazza
- Department of Surgery, Dentistry, Pediatrics and Gynecology, University of Verona, 37126 Verona, Italy; (M.P.); (L.P.)
| | - Maria Di Cicco
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, 56126 Pisa, Italy; (M.D.C.); (P.C.)
| | - Luca Pecoraro
- Department of Surgery, Dentistry, Pediatrics and Gynecology, University of Verona, 37126 Verona, Italy; (M.P.); (L.P.)
| | - Michele Ghezzi
- Allergology and Pneumology Unit, V. Buzzi Children’s Hospital, 20154 Milan, Italy;
| | - Diego Peroni
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, 56126 Pisa, Italy; (M.D.C.); (P.C.)
| | - Pasquale Comberiati
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, 56126 Pisa, Italy; (M.D.C.); (P.C.)
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Hwang J, Jung Y, Moon S, Yu S, Oh H, Kim S, Kim KW, Yoon JH, Chun J, Kim SJ, Chung WJ, Kweon DH. Nanodisc-Mediated Conversion of Virustatic Antiviral Antibody to Disrupt Virus Envelope in Infected Cells. SMALL METHODS 2022; 6:e2101516. [PMID: 35107214 DOI: 10.1002/smtd.202101516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Many antibody-based antivirals, including broadly neutralizing antibodies (bnAbs) against various influenza virus strains, suffer from limited potency. A booster of the antiviral activity of an antibody is expected to facilitate development of antiviral therapeutics. In this study, a nanodisc (ND), a discoidal lipid bilayer encircled by membrane scaffold proteins, is engineered to provide virucidal properties to antibodies, thereby augmenting their antiviral activity. NDs carrying the Fc-binding peptide sequence form an antibody-ND complex (ANC), which can co-endocytose into cells infected with influenza virus. ANC efficiently inhibits endosome escape of viral RNA by dual complimentary mode of action. While the antibody moiety in an ANC inhibits hemagglutinin-mediated membrane fusion, its ND moiety destroys the viral envelope using free hemagglutinins that are not captured by antibodies. Providing virus-infected host cells with the ability to self-eliminate by the synergistic effect of ANC components dramatically amplifies the antiviral efficacy of a bnAb against influenza virus. When the efficacy of ANC is assessed in mouse models, administration of ANCs dramatically reduces morbidity and mortality compared to bnAb alone. This study is the first to demonstrate the novel nanoparticle ANC and its role in combating viral infections, suggesting that ANC is a versatile platform applicable to various viruses.
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Affiliation(s)
- Jaehyeon Hwang
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Younghun Jung
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seokoh Moon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seokhyeon Yu
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyunseok Oh
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Soomin Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Kyeong Won Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jeong Hyeon Yoon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jihwan Chun
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sang Jick Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Woo-Jae Chung
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Dae-Hyuk Kweon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
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Transcriptome and Small RNA Profiling of Potato Virus Y Infected Potato Cultivars, Including Systemically Infected Russet Burbank. Viruses 2022; 14:v14030523. [PMID: 35336930 PMCID: PMC8952017 DOI: 10.3390/v14030523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 02/06/2023] Open
Abstract
Potatoes are the world’s most produced non-grain crops and an important food source for billions of people. Potatoes are susceptible to numerous pathogens that reduce yield, including Potato virus Y (PVY). Genetic resistance to PVY is a sustainable way to limit yield and quality losses due to PVY infection. Potato cultivars vary in their susceptibility to PVY and include susceptible varieties such as Russet Burbank, and resistant varieties such as Payette Russet. Although the loci and genes associated with PVY-resistance have been identified, the genes and mechanisms involved in limiting PVY during the development of systemic infections have yet to be fully elucidated. To increase our understanding of PVY infection, potato antiviral responses, and resistance, we utilized RNA sequencing to characterize the transcriptomes of two potato cultivars. Since transcriptional responses associated with the extreme resistance response occur soon after PVY contact, we analyzed the transcriptome and small RNA profile of both the PVY-resistant Payette Russet cultivar and PVY-susceptible Russet Burbank cultivar 24 h post-inoculation. While hundreds of genes, including terpene synthase and protein kinase encoding genes, exhibited increased expression, the majority, including numerous genes involved in plant pathogen interactions, were downregulated. To gain greater understanding of the transcriptional changes that occur during the development of systemic PVY-infection, we analyzed Russet Burbank leaf samples one week and four weeks post-inoculation and identified similarities and differences, including higher expression of genes involved in chloroplast function, photosynthesis, and secondary metabolite production, and lower expression of defense response genes at those time points. Small RNA sequencing identified different populations of 21- and 24-nucleotide RNAs and revealed that the miRNA profiles in PVY-infected Russet Burbank plants were similar to those observed in other PVY-tolerant cultivars and that during systemic infection ~32% of the NLR-type disease resistance genes were targeted by 21-nt small RNAs. Analysis of alternative splicing in PVY-infected potato plants identified splice variants of several hundred genes, including isoforms that were more dominant in PVY-infected plants. The description of the PVYN-Wi-associated transcriptome and small RNA profiles of two potato cultivars described herein adds to the body of knowledge regarding differential outcomes of infection for specific PVY strain and host cultivar pairs, which will help further understanding of the mechanisms governing genetic resistance and/or virus-limiting responses in potato plants.
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Kopanke J, Carpenter M, Lee J, Reed K, Rodgers C, Burton M, Lovett K, Westrich JA, McNulty E, McDermott E, Barbera C, Cavany S, Rohr JR, Perkins TA, Mathiason CK, Stenglein M, Mayo C. Bluetongue Research at a Crossroads: Modern Genomics Tools Can Pave the Way to New Insights. Annu Rev Anim Biosci 2022; 10:303-324. [PMID: 35167317 DOI: 10.1146/annurev-animal-051721-023724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bluetongue virus (BTV) is an arthropod-borne, segmented double-stranded RNA virus that can cause severe disease in both wild and domestic ruminants. BTV evolves via several key mechanisms, including the accumulation of mutations over time and the reassortment of genome segments.Additionally, BTV must maintain fitness in two disparate hosts, the insect vector and the ruminant. The specific features of viral adaptation in each host that permit host-switching are poorly characterized. Limited field studies and experimental work have alluded to the presence of these phenomena at work, but our understanding of the factors that drive or constrain BTV's genetic diversification remains incomplete. Current research leveraging novel approaches and whole genome sequencing applications promises to improve our understanding of BTV's evolution, ultimately contributing to the development of better predictive models and management strategies to reduce future impacts of bluetongue epizootics.
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Affiliation(s)
- Jennifer Kopanke
- Office of the Campus Veterinarian, Washington State University, Spokane, Washington, USA;
| | - Molly Carpenter
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Justin Lee
- Genomic Sequencing Laboratory, Centers for Disease Control and Prevention, Atlanta, Georgia, USA;
| | - Kirsten Reed
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Case Rodgers
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Mollie Burton
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Kierra Lovett
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Joseph A Westrich
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Erin McNulty
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Emily McDermott
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, Arkansas, USA;
| | - Carly Barbera
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Sean Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Jason R Rohr
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Candace K Mathiason
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Mark Stenglein
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Christie Mayo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
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Parallel profiling of antigenicity alteration and immune escape of SARS-CoV-2 Omicron and other variants. Signal Transduct Target Ther 2022; 7:42. [PMID: 35136040 PMCID: PMC8826850 DOI: 10.1038/s41392-022-00910-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 variants have evolved a variety of critical mutations, leading to antigenicity changes and immune escape. The recent emerging SARS-CoV-2 Omicron variant attracted global attention due to its significant resistance to current antibody therapies and vaccines. Here, we profiled the mutations of Omicron and other various circulating SARS-CoV-2 variants in parallel by computational interface analysis and in vitro experimental assays. We identified critical mutations that lead to antigenicity changes and diminished neutralization efficiency of a panel of 14 antibodies due to diverse molecular mechanisms influencing the antigen-antibody interaction. Our study identified that Omicron exhibited extraordinary potency in immune escape compared to the other variants of concern, and explores the application of computational interface analysis in SARS-CoV-2 mutation surveillance and demonstrates its potential for the early identification of concerning variants, providing preliminary guidance for neutralizing antibody therapy.
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COLSON P, PAROLA P, RAOULT D. The emergence, dynamics and significance of SARS-CoV-2 variants. New Microbes New Infect 2022; 45:100962. [PMID: 35127101 PMCID: PMC8806113 DOI: 10.1016/j.nmni.2022.100962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/21/2022] [Indexed: 11/07/2022] Open
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Ghosh U, Ahammed KS, Mishra S, Bhaumik A. The Emerging Roles of Silver nanoparticles to Target Viral Life-Cycle and Detect Viral Pathogens. Chem Asian J 2022; 17:e202101149. [PMID: 35020270 PMCID: PMC9011828 DOI: 10.1002/asia.202101149] [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: 10/04/2021] [Revised: 01/05/2022] [Indexed: 11/26/2022]
Abstract
Along the line of recent vaccine advancements, new antiviral therapeutics are compelling to combat viral infection‐related public health crises. Several properties of silver nanoparticles (AgNPs) such as low level of cytotoxicity, ease of tunability of the AgNPs in the ultra‐small nanoscale size and shape through different convenient bottom‐up chemistry approaches, high penetration of the composite with drug formulations into host cells has made AgNPs, a promising candidate for developing antivirals. In this review, we have highlighted the recent advancements in the AgNPs based nano‐formulations to target cellular mechanisms of viral propagation, immune modulation of the host, and the ability to synergistically enhance the activity of existing antiviral drugs. On the other hand, we have discussed the recent advancements on AgNPs based detection of viral pathogens from clinical samples using inherent physicochemical properties. This article will provide an overview of our current knowledge on AgNPs based formulations that has promising potential for developing a counteractive strategy against emerging and existing viruses.
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Affiliation(s)
- Ujjyini Ghosh
- CSIR-Indian Institute of Chemical Biology: Indian Institute of Chemical Biology CSIR, Cancer & Inflammatory Disorder Division, INDIA
| | - Khondakar Sayef Ahammed
- CSIR-Indian Institute of Chemical Biology: Indian Institute of Chemical Biology CSIR, Cancer & Inflammatory Disorder Division, INDIA
| | - Snehasis Mishra
- CSIR-Indian Institute of Chemical Biology: Indian Institute of Chemical Biology CSIR, Cancer & Inflammatory Disorder Division, INDIA
| | - Asim Bhaumik
- Indian Association for the Cultivation of Science, Department of Materials Science, 2A & B Raja S. C. Mullick Road, Jadavpur, 700032, Kolkata, INDIA
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40
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Diaz Arenas C, Ardaševa A, Miller J, Mikheyev AS, Yokobayashi Y. Ribozyme Mutagenic Evolution: Mechanisms of Survival. ORIGINS LIFE EVOL B 2022; 51:321-339. [PMID: 34994918 DOI: 10.1007/s11084-021-09617-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
Primeval populations replicating at high error rates required a mechanism to overcome the accumulation of mutations and information deterioration. Known strategies to overcome mutation pressures include RNA processivity, epistasis, selection, and quasispecies. We investigated the mechanism by which small molecular ribozyme populations can survive under high error rates by propagating several lineages under different mutagen concentrations. We found that every population that evolved without mutagen went extinct, while those subjected to mutagenic evolution survived. To understand how they survived, we characterized the evolved genotypic diversity, the formation of genotype-genotype interaction networks, the fitness of the most common mutants for each enzymatic step, and changes in population size along the course of evolution. We found that the elevated mutation rate was necessary for the populations to survive in the novel environment, in which all the steps of the metabolism worked to promote the survival of even less catalytically efficient ligases. Besides, an increase in population size and the mutational coupling of genotypes in close-knit networks, which helped maintain or recover lost genotypes making their disappearance transient, prevented Muller's ratchet and extinction.
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Affiliation(s)
- Carolina Diaz Arenas
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan. .,Yale University, New Haven, CT, USA.
| | - Aleksandra Ardaševa
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Jonathan Miller
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan.,Evolutionary Genomics Lab, Research School of Biology, Australian National University, Canberra, Australia
| | - Yohei Yokobayashi
- Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa Prefecture, Japan
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Gurevich Y, Ram Y, Hadany L. Modeling the evolution of SARS-CoV-2 under non-pharmaceutical interventions and testing. Evol Med Public Health 2022; 10:179-188. [PMID: 35498119 PMCID: PMC9046092 DOI: 10.1093/emph/eoac013] [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: 12/02/2021] [Accepted: 04/06/2022] [Indexed: 11/28/2022] Open
Abstract
Background and objectives Social and behavioral non-pharmaceutical interventions (NPIs), such as mask-wearing, social distancing and travel restrictions, as well as diagnostic tests, have been broadly implemented in response to the COVID-19 pandemic. Epidemiological models and data analysis affirm that wide adoption of NPIs helps to control the pandemic. However, SARS-CoV-2 has extensively demonstrated its ability to evolve. Therefore, it is crucial to examine how NPIs may affect the evolution of the virus. Such evolution could have important effects on the spread and impact of the pandemic. Methodology We used evo-epidemiological models to examine the effect of NPIs and testing on two evolutionary trajectories for SARS-CoV-2: attenuation and test evasion. Results Our results show that when stronger measures are taken, selection may act to reduce disease severity. Additionally, the timely application of NPIs could significantly affect the competition between viral strains, favoring the milder strain. Furthermore, a higher testing rate can select for a test-evasive viral strain, even if that strain is less infectious than the detectable competing strain. Importantly, if a less detectable strain evolves, epidemiological metrics such as confirmed daily cases may distort our assessment of the pandemic. Conclusions and implications Our results highlight the important implications NPIs can have on the evolution of SARS-CoV-2. Lay Summary We used evo-epidemiological models to examine the effect of non-pharmaceutical interventions and testing on two evolutionary trajectories for SARS-CoV-2: attenuation and test evasion. Our results show that when stronger measures are taken, selection may act to reduce disease severity.
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Affiliation(s)
- Yael Gurevich
- Faculty of Life Sciences, School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Yoav Ram
- Faculty of Life Sciences, School of Zoology, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Lilach Hadany
- Faculty of Life Sciences, School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Corresponding author. Faculty of Life Sciences, School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv 6997801, Israel; Tel: +972-3-640-9831; E-mail:
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Durand M, Thibault P, Lévesque S, Brault A, Carignan A, Valiquette L, Martin P, Labbé S. Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its first variants in fourplex real-time quantitative reverse transcription-PCR assays. MICROBIAL CELL (GRAZ, AUSTRIA) 2022; 9:1-20. [PMID: 35083313 PMCID: PMC8717086 DOI: 10.15698/mic2022.01.767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022]
Abstract
The early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is required to identify and isolate contagious patients to prevent further transmission of SARS-CoV-2. In this study, we present a multitarget real-time TaqMan reverse transcription PCR (rRT-PCR) assay for the quantitative detection of SARS-CoV-2 and some of its circulating variants harboring mutations that give the virus a selective advantage. Seven different primer-probe sets that included probes containing locked nucleic acid (LNA) nucleotides were designed to amplify specific wild-type and mutant sequences in Orf1ab, Envelope (E), Spike (S), and Nucleocapsid (N) genes. Furthermore, a newly developed primer-probe set targeted human β2-microglobulin (B2M) as a highly sensitive internal control for RT efficacy. All singleplex and fourplex assays detected ≤ 14 copies/reaction of quantified synthetic RNA transcripts, with a linear amplification range of nine logarithmic orders. Primer-probe sets for detection of SARS-CoV-2 exhibited no false-positive amplifications with other common respiratory pathogens, including human coronaviruses NL63, 229E, OC43, and HKU-1. Fourplex assays were evaluated using 160 clinical samples positive for SARS-CoV-2. Results showed that SARS-CoV-2 viral RNA was detected in all samples, including viral strains harboring mutations in the Spike coding sequence that became dominant in the pandemic. Given the emergence of SARS-CoV-2 variants and their rapid spread in some populations, fourplex rRT-PCR assay containing four primer-probe sets represents a reliable approach to allow quicker detection of circulating relevant variants in a single reaction.
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Affiliation(s)
- Mathieu Durand
- Plateforme RNomique et de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Philippe Thibault
- Plateforme RNomique et de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Simon Lévesque
- Département de Microbiologie et d'Infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Laboratoire de Microbiologie, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) de l'Estrie, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Ariane Brault
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alex Carignan
- Département de Microbiologie et d'Infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Louis Valiquette
- Département de Microbiologie et d'Infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Philippe Martin
- Département de Microbiologie et d'Infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Simon Labbé
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
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Role of Selenium in Viral Infections with a Major Focus on SARS-CoV-2. Int J Mol Sci 2021; 23:ijms23010280. [PMID: 35008706 PMCID: PMC8745607 DOI: 10.3390/ijms23010280] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 02/06/2023] Open
Abstract
Viral infections have afflicted human health and despite great advancements in scientific knowledge and technologies, continue to affect our society today. The current coronavirus (COVID-19) pandemic has put a spotlight on the need to review the evidence on the impact of nutritional strategies to maintain a healthy immune system, particularly in instances where there are limited therapeutic treatments. Selenium, an essential trace element in humans, has a long history of lowering the occurrence and severity of viral infections. Much of the benefits derived from selenium are due to its incorporation into selenocysteine, an important component of proteins known as selenoproteins. Viral infections are associated with an increase in reactive oxygen species and may result in oxidative stress. Studies suggest that selenium deficiency alters immune response and viral infection by increasing oxidative stress and the rate of mutations in the viral genome, leading to an increase in pathogenicity and damage to the host. This review examines viral infections, including the novel SARS-CoV-2, in the context of selenium, in order to inform potential nutritional strategies to maintain a healthy immune system.
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N-terminal domain mutations of the spike protein are structurally implicated in epitope recognition in emerging SARS-CoV-2 strains. Comput Struct Biotechnol J 2021; 19:5556-5567. [PMID: 34630935 PMCID: PMC8489513 DOI: 10.1016/j.csbj.2021.10.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/16/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022] Open
Abstract
During the past two years, the world has been ravaged by a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Acquired mutations in the SARS-CoV-2 genome affecting virus infectivity and/or immunogenicity have led to a number of novel strains with higher transmissibility compared to the original Wuhan strain. Mutations in the receptor binding domain (RBD) of the SARS-CoV-2 spike protein have been extensively studied in this context. However, mutations and deletions within the N-terminal domain (NTD) located adjacent to the RBD are less studied. Many of these are found within certain β sheet-linking loops, which are surprisingly long in SARS-CoV-2 in comparison to SARS-CoV and other related β coronaviruses. Here, we perform a structural and epidemiological study of novel strains carrying mutations and deletions within these loops. We identify short and long-distance interactions that stabilize the NTD loops and form a critical epitope that is essential for the recognition by a wide variety of neutralizing antibodies from convalescent plasma. Among the different mutations/deletions found in these loops, Ala 67 and Asp 80 mutations as well as His 69/Val 70 and Tyr 144 deletions have been identified in different fast-spreading strains. Similarly, deletions in amino acids 241-243 and 246-252 have been found to affect the network of NTD loops in strains with high transmissibility. Our structural findings provide insight regarding the role of these mutations/deletions in altering the epitope structure and thus affecting the immunoreactivity of the NTD region of spike protein.
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45
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Paradowska E, Studzińska M, Jabłońska A, Lozovski V, Rusinchuk N, Mukha I, Vitiuk N, Leśnikowski ZJ. Antiviral Effect of Nonfunctionalized Gold Nanoparticles against Herpes Simplex Virus Type-1 (HSV-1) and Possible Contribution of Near-Field Interaction Mechanism. Molecules 2021; 26:molecules26195960. [PMID: 34641506 PMCID: PMC8512028 DOI: 10.3390/molecules26195960] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
The antiviral activity of nonfunctionalized gold nanoparticles (AuNPs) against herpes simplex virus type-1 (HSV-1) in vitro was revealed in this study. We found that AuNPs are capable of reducing the cytopathic effect (CPE) of HSV-1 in Vero cells in a dose- and time-dependent manner when used in pretreatment mode. The demonstrated antiviral activity was within the nontoxic concentration range of AuNPs. Interestingly, we noted that nanoparticles with smaller sizes reduced the CPE of HSV-1 more effectively than larger ones. The observed phenomenon can be tentatively explained by the near-field action of nanoparticles at the virus envelope. These results show that AuNPs can be considered as potential candidates for the treatment of HSV-1 infections.
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Affiliation(s)
- Edyta Paradowska
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Łódź, Poland; (E.P.); (M.S.); (A.J.)
| | - Mirosława Studzińska
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Łódź, Poland; (E.P.); (M.S.); (A.J.)
| | - Agnieszka Jabłońska
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Łódź, Poland; (E.P.); (M.S.); (A.J.)
| | - Valeri Lozovski
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, 64/13 Volodymyrska St., 01033 Kyiv, Ukraine;
- Correspondence: (V.L.); (Z.J.L.)
| | - Natalia Rusinchuk
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, 64/13 Volodymyrska St., 01033 Kyiv, Ukraine;
| | - Iuliia Mukha
- Chuiko Institute of Surface Chemistry of National Academy of Sciences of Ukraine, 17 General Naumov St., 03164 Kyiv, Ukraine; (I.M.); (N.V.)
| | - Nadiia Vitiuk
- Chuiko Institute of Surface Chemistry of National Academy of Sciences of Ukraine, 17 General Naumov St., 03164 Kyiv, Ukraine; (I.M.); (N.V.)
| | - Zbigniew J. Leśnikowski
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Łódź, Poland; (E.P.); (M.S.); (A.J.)
- Correspondence: (V.L.); (Z.J.L.)
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The nucleotide addition cycle of the SARS-CoV-2 polymerase. Cell Rep 2021; 36:109650. [PMID: 34433083 PMCID: PMC8367775 DOI: 10.1016/j.celrep.2021.109650] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/10/2021] [Accepted: 08/11/2021] [Indexed: 12/29/2022] Open
Abstract
Coronaviruses have evolved elaborate multisubunit machines to replicate and transcribe their genomes. Central to these machines are the RNA-dependent RNA polymerase subunit (nsp12) and its intimately associated cofactors (nsp7 and nsp8). We use a high-throughput magnetic-tweezers approach to develop a mechanochemical description of this core polymerase. The core polymerase exists in at least three catalytically distinct conformations, one being kinetically consistent with incorporation of incorrect nucleotides. We provide evidence that the RNA-dependent RNA polymerase (RdRp) uses a thermal ratchet instead of a power stroke to transition from the pre- to post-translocated state. Ultra-stable magnetic tweezers enable the direct observation of coronavirus polymerase deep and long-lived backtracking that is strongly stimulated by secondary structures in the template. The framework we present here elucidates one of the most important structure-dynamics-function relationships in human health today and will form the grounds for understanding the regulation of this complex.
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Van Eyndhoven LC, Singh A, Tel J. Decoding the dynamics of multilayered stochastic antiviral IFN-I responses. Trends Immunol 2021; 42:824-839. [PMID: 34364820 DOI: 10.1016/j.it.2021.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/11/2021] [Accepted: 07/11/2021] [Indexed: 12/11/2022]
Abstract
Type I Interferon (IFN-I) responses were first recognized for their role in antiviral immunity, but it is now widely appreciated that IFN-Is have many immunomodulatory functions, influencing antitumor responses, autoimmune manifestations, and antimicrobial defenses. Given these pivotal roles, it may be surprising that multilayered stochastic events create highly heterogeneous, but tightly regulated, all-or-nothing cellular decisions. Recently, mathematical models have provided crucial insights into the stochastic nature of antiviral IFN-I responses, which we critically evaluate in this review. In this context, we emphasize the need for innovative single-cell technologies combined with mathematical models to further reveal, understand, and predict the complexity of the IFN-I system in physiological and pathological conditions that may be relevant to a plethora of diseases.
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Affiliation(s)
- Laura C Van Eyndhoven
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands; Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, USA
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands; Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands.
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49
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Winston DS, Boehr DD. Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity. Enzymes 2021; 49:149-193. [PMID: 34696831 DOI: 10.1016/bs.enz.2021.06.001] [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] [Indexed: 06/13/2023]
Abstract
All RNA viruses encode an RNA-dependent RNA polymerase (RdRp) responsible for genome replication. It is now recognized that enzymes in general, and RdRps specifically, are dynamic macromolecular machines such that their moving parts, including active site loops, play direct functional roles. While X-ray crystallography has provided deep insight into structural elements important for RdRp function, this methodology generally provides only static snapshots, and so is limited in its ability to report on dynamic fluctuations away from the lowest energy conformation. Nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations and other biophysical techniques have brought new insight into RdRp function by their ability to characterize the trajectories, kinetics and thermodynamics of conformational motions. In particular, these methodologies have identified coordinated motions among conserved structural motifs necessary for nucleotide selection and incorporation. Disruption of these motions through amino acid substitutions or inhibitor binding impairs RdRp function. Understanding and re-engineering these motions thus provides exciting new avenues for anti-viral strategies. This chapter outlines the basics of these methodologies, summarizes the dynamic motions observed in different RdRps important for nucleotide selection and incorporation, and illustrates how this information can be leveraged towards rational vaccine strain development and anti-viral drug design.
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Affiliation(s)
- Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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Shapiro JT, Víquez-R L, Leopardi S, Vicente-Santos A, Mendenhall IH, Frick WF, Kading RC, Medellín RA, Racey P, Kingston T. Setting the Terms for Zoonotic Diseases: Effective Communication for Research, Conservation, and Public Policy. Viruses 2021; 13:1356. [PMID: 34372562 PMCID: PMC8310020 DOI: 10.3390/v13071356] [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: 06/04/2021] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 12/19/2022] Open
Abstract
Many of the world's most pressing issues, such as the emergence of zoonotic diseases, can only be addressed through interdisciplinary research. However, the findings of interdisciplinary research are susceptible to miscommunication among both professional and non-professional audiences due to differences in training, language, experience, and understanding. Such miscommunication contributes to the misunderstanding of key concepts or processes and hinders the development of effective research agendas and public policy. These misunderstandings can also provoke unnecessary fear in the public and have devastating effects for wildlife conservation. For example, inaccurate communication and subsequent misunderstanding of the potential associations between certain bats and zoonoses has led to persecution of diverse bats worldwide and even government calls to cull them. Here, we identify four types of miscommunication driven by the use of terminology regarding bats and the emergence of zoonotic diseases that we have categorized based on their root causes: (1) incorrect or overly broad use of terms; (2) terms that have unstable usage within a discipline, or different usages among disciplines; (3) terms that are used correctly but spark incorrect inferences about biological processes or significance in the audience; (4) incorrect inference drawn from the evidence presented. We illustrate each type of miscommunication with commonly misused or misinterpreted terms, providing a definition, caveats and common misconceptions, and suggest alternatives as appropriate. While we focus on terms specific to bats and disease ecology, we present a more general framework for addressing miscommunication that can be applied to other topics and disciplines to facilitate more effective research, problem-solving, and public policy.
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Affiliation(s)
- Julie Teresa Shapiro
- Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva 8410501, Israel
| | - Luis Víquez-R
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, 89069 Ulm, Germany;
| | - Stefania Leopardi
- Laboratory of Emerging Viral Zoonoses, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy;
| | - Amanda Vicente-Santos
- Graduate Program in Population Biology, Ecology and Evolution, Emory University, Atlanta, GA 30322, USA;
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore;
| | - Winifred F. Frick
- Bat Conservation International, Austin, TX 78746, USA;
- Department of Ecology and Evolution, University of California, Santa Cruz, CA 95060, USA
| | - Rebekah C. Kading
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA;
| | - Rodrigo A. Medellín
- Institute of Ecology, National Autonomous University of Mexico (UNAM), Mexico City 04510, Mexico;
| | - Paul Racey
- The Centre for Ecology and Conservation, University of Exeter, Exeter TR10 9FE, UK;
| | - Tigga Kingston
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
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