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Penteado AB, de Oliveira Ribeiro G, Lima Araújo EL, Kato RB, de Melo Freire CC, de Araújo JMG, da Luz Wallau G, Salvato RS, de Jesus R, Bosco GG, Franz HF, da Silva PEA, de Souza Leal E, Goulart Trossini GH, de Lima Neto DF. Binding Evolution of the Dengue Virus Envelope Against DC-SIGN: A Combined Approach of Phylogenetics and Molecular Dynamics Analyses Over 30 Years of Dengue Virus in Brazil. J Mol Biol 2024; 436:168577. [PMID: 38642883 DOI: 10.1016/j.jmb.2024.168577] [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: 01/09/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
The Red Queen Hypothesis (RQH), derived from Lewis Carroll's "Through the Looking-Glass", postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time.
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MESH Headings
- Dengue Virus/genetics
- Dengue Virus/metabolism
- Receptors, Cell Surface/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/chemistry
- Phylogeny
- Molecular Dynamics Simulation
- Humans
- Cell Adhesion Molecules/metabolism
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/chemistry
- Brazil
- Lectins, C-Type/metabolism
- Lectins, C-Type/genetics
- Lectins, C-Type/chemistry
- Evolution, Molecular
- Dengue/virology
- Host-Pathogen Interactions/genetics
- Protein Binding
- Viral Envelope/metabolism
- Receptors, Virus/metabolism
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
- Viral Envelope Proteins/chemistry
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Affiliation(s)
- André Berndt Penteado
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Geovani de Oliveira Ribeiro
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil; Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Attention to Communicable Diseases in Primary Care of the Department of Comprehensive Care Management of the Secretariat of Primary Health Care of the Ministry of Health (CDTAP/DGCI/SAPS-MS), Brazil
| | - Rodrigo Bentes Kato
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Caio Cesar de Melo Freire
- Department of Genetics and Evolution, Centre of Biological and Health Sciences, Federal University of Sao Carlos, PO Box 676, Washington Luis Road, km 235, São Carlos, SP 13565-905, Brazil
| | - Joselio Maria Galvão de Araújo
- Federal University of Rio Grande do Norte, Biosciences Center, Department of Microbiology and Parasitology, Campus Universitário, S/N Lagoa Nova 59078900, Natal, RN, Brazil
| | - Gabriel da Luz Wallau
- Department of Entomology and Bioinformatics Center of the Aggeu Magalhães Institute - FIOCRUZ - IAM, Brazil
| | - Richard Steiner Salvato
- Center for Scientific and Technological Development, State Center for Health Surveillance of Rio Grande do Sul, State Department of Health of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ronaldo de Jesus
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Geraldine Goés Bosco
- University of São Paulo, Faculty of Philosophy Sciences and Letters of Ribeirão Preto. Av. Bandeirantes, 3900 Ribeirão Preto, SP, Brazil
| | - Helena Ferreira Franz
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Pedro Eduardo Almeida da Silva
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Elcio de Souza Leal
- Federal University of Pará, Faculty of Biotechnology, Institute of Biological Sciences, Rua Augusto Corrêa, Guamá, 04039-032 Belem, PA, Brazil
| | - Gustavo Henrique Goulart Trossini
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Daniel Ferreira de Lima Neto
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil.
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Moumbeket Yifomnjou MH, Monamele GC, Modiyinji AF, Njankouo-Ripa M, Onana B, Njouom R. Genetic Diversity of Human Respiratory Syncytial Virus during COVID-19 Pandemic in Yaoundé, Cameroon, 2020-2021. Microorganisms 2024; 12:952. [PMID: 38792782 PMCID: PMC11123827 DOI: 10.3390/microorganisms12050952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/03/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Worldwide, human respiratory syncytial virus (HRSV) is a major cause of severe infections of the lower respiratory system, affecting individuals of all ages. This study investigated the genetic variability of HRSV during the COVID-19 outbreak in Yaoundé; nasopharyngeal samples positive for HRSV were collected from different age groups between July 2020 and October 2021. A semi-nested RT-PCR was performed on the second hypervariable region of the G gene of detected HRSV, followed by sequencing and phylogenetic assessment. Throughout the study, 40 (37.7%) of the 106 HRSV-positive samples successfully underwent G-gene amplification. HRSV A and HRSV B co-circulated at rates of 47.5% and 52.5%, respectively. HRSV A clustered in the GA2.3.5 genetic lineage (ON1) and HRSV B clustered in the GB5.0.5a genetic lineage (BA9). Differences in circulating genotypes were observed between pre- and post-pandemic years for HRSV A. Predictions revealed potential N-glycosylation sites at positions 237-318 of HRSV A and positions 228-232-294 of HRSV B. This study reports the molecular epidemiology of HRSV in Cameroon during the COVID-19 pandemic. It describes the exclusive co-circulation of two genetic lineages. These findings highlight the importance of implementing comprehensive molecular surveillance to prevent the unexpected emergence of other diseases.
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Affiliation(s)
- Moïse Henri Moumbeket Yifomnjou
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
- Laboratory of Microbiology, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Gwladys Chavely Monamele
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Abdou Fatawou Modiyinji
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Mohamadou Njankouo-Ripa
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Boyomo Onana
- Laboratory of Microbiology, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Richard Njouom
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
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Ngoc LTN, Lee YC. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. BIOSENSORS 2024; 14:97. [PMID: 38392016 PMCID: PMC10886876 DOI: 10.3390/bios14020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Ribonucleic acid (RNA) viruses are one of the major classes of pathogens that cause human diseases. The conventional method to detect RNA viruses is real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), but it has some limitations. It is expensive and time-consuming, with infrastructure and trained personnel requirements. Its high throughput requires sophisticated automation and large-scale infrastructure. Isothermal amplification methods have been explored as an alternative to address these challenges. These methods are rapid, user-friendly, low-cost, can be performed in less specialized settings, and are highly accurate for detecting RNA viruses. Microfluidic technology provides an ideal platform for performing virus diagnostic tests, including sample preparation, immunoassays, and nucleic acid-based assays. Among these techniques, nucleic acid isothermal amplification methods have been widely integrated with microfluidic platforms for RNA virus detection owing to their simplicity, sensitivity, selectivity, and short analysis time. This review summarizes some common isothermal amplification methods for RNA viruses. It also describes commercialized devices and kits that use isothermal amplification techniques for SARS-CoV-2 detection. Furthermore, the most recent applications of isothermal amplification-based microfluidic platforms for RNA virus detection are discussed in this article.
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Affiliation(s)
- Le Thi Nhu Ngoc
- Department of Nano Science and Technology Convergence, Gachon University, 1342 Seongnam-Daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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Dorlass EG, Amgarten DE. Bioinformatic Approaches for Comparative Analysis of Viruses. Methods Mol Biol 2024; 2802:395-425. [PMID: 38819566 DOI: 10.1007/978-1-0716-3838-5_13] [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: 06/01/2024]
Abstract
The field of viral genomic studies has experienced an unprecedented increase in data volume. New strains of known viruses are constantly being added to the GenBank database and so are completely new species with little or no resemblance to our databases of sequences. In addition to this, metagenomic techniques have the potential to further increase the number and rate of sequenced genomes. Besides, it is important to consider that viruses have a set of unique features that often break down molecular biology dogmas, e.g., the flux of information from RNA to DNA in retroviruses and the use of RNA molecules as genomes. As a result, extracting meaningful information from viral genomes remains a challenge and standard methods for comparing the unknown and our databases of characterized sequences may need adaptations. Thus, several bioinformatic approaches and tools have been created to address the challenge of analyzing viral data. This chapter offers descriptions and protocols of some of the most important bioinformatic techniques for comparative analysis of viruses. The authors also provide comments and discussion on how viruses' unique features can affect standard analyses and how to overcome some of the major sources of problems. Protocols and topics emphasize online tools (which are more accessible to users) and give the real experience of what most bioinformaticians do in day-by-day work with command-line pipelines. The topics discussed include (1) clustering related genomes, (2) whole genome multiple sequence alignments for small RNA viruses, (3) protein alignment for marker genes and species affiliation, (4) variant calling and annotation, and (5) virome analyses and pathogen identification.
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Sáez C, Kheireddine A, García A, Sifres A, Moreno A, Font-San-Ambrosio MI, Picó B, López C. Further Molecular Diagnosis Determines Lack of Evidence for Real Seed Transmission of Tomato Leaf Curl New Delhi Virus in Cucurbits. PLANTS (BASEL, SWITZERLAND) 2023; 12:3773. [PMID: 37960129 PMCID: PMC10650430 DOI: 10.3390/plants12213773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
Begomoviruses (family Geminiviridae) cause serious diseases in many crop families. Since 2013, the Spanish isolate of tomato leaf curl New Delhi virus (ToLCNDV) has been a limiting factor for cucurbits production in the Mediterranean basin, forcing farmers to adapt new management and control techniques. Although it is well-known that begomoviruses are naturally transmitted by the whitefly Bemisia tabaci, the capacity of these viruses to be vertically transmitted through seeds remains controversial. Clarifying the potential ToLCNDV seed transmission is essential to understand the epidemiology of this threating-for-cucurbits virus and to design appropriate control strategies. We assessed ToLCNDV distribution in the leaves, flowers and seeds of the infected plants of susceptible Cucumis melo accessions and toleration to the infected genotypes of Cucurbita moschata by conventional and quantitative PCR. We analyzed whether the viral particle was transmitted to offspring. We also evaluated ToLCNDV presence in commercial seeds of cucurbits (zucchini (Cucurbita pepo), melon (C. melo), cucumber (Cucumis sativus) and watermelon (Citrullus lanatus)) and in their progenies. As the assayed seedlings remained symptomless, we increased the reliability and accuracy of detection in these samples by searching for replicative forms of ToLCNDV by combining Southern blot hybridization and rolling-circle amplification (RCA). However, integral genomic DNA was not identified in the plants of offspring. Although the seedborne nature of ToLCNDV was confirmed, our results do not support the transmission of this virus from contaminated seeds to progeny.
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Affiliation(s)
- Cristina Sáez
- Institute for the Conservation and Breeding of Valencian Agro-Diversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain; (A.K.); (A.S.); (B.P.)
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28031 Madrid, Spain
| | - Amina Kheireddine
- Institute for the Conservation and Breeding of Valencian Agro-Diversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain; (A.K.); (A.S.); (B.P.)
| | - Arcadio García
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas—Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain;
| | - Alicia Sifres
- Institute for the Conservation and Breeding of Valencian Agro-Diversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain; (A.K.); (A.S.); (B.P.)
| | | | - María Isabel Font-San-Ambrosio
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València (IAM-UPV), Camino de Vera s/n, 46022 Valencia, Spain;
| | - Belén Picó
- Institute for the Conservation and Breeding of Valencian Agro-Diversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain; (A.K.); (A.S.); (B.P.)
| | - Carmelo López
- Institute for the Conservation and Breeding of Valencian Agro-Diversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022 Valencia, Spain; (A.K.); (A.S.); (B.P.)
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Yu R, Abdullah SMU, Sun Y. HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses. Brief Bioinform 2023; 24:bbad264. [PMID: 37478372 PMCID: PMC10516367 DOI: 10.1093/bib/bbad264] [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: 03/25/2023] [Revised: 06/05/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023] Open
Abstract
Access to accurate viral genomes is important to downstream data analysis. Third-generation sequencing (TGS) has recently become a popular platform for virus sequencing because of its long read length. However, its per-base error rate, which is higher than next-generation sequencing, can lead to genomes with errors. Polishing tools are thus needed to correct errors either before or after sequence assembly. Despite promising results of available polishing tools, there is still room to improve the error correction performance to perform more accurate genome assembly. The errors, particularly those in coding regions, can hamper analysis such as linage identification and variant monitoring. In this work, we developed a novel pipeline, HMMPolish, for correcting (polishing) errors in protein-coding regions of known RNA viruses. This tool can be applied to either raw TGS reads or the assembled sequences of the target virus. By utilizing profile Hidden Markov Models of protein families/domains in known viruses, HMMPolish can correct errors that are ignored by available polishers. We extensively validated HMMPolish on 34 datasets that covered four clinically important viruses, including HIV-1, influenza-A, norovirus, and severe acute respiratory syndrome coronavirus 2. These datasets contain reads with different properties, such as sequencing depth and platforms (PacBio or Nanopore). The benchmark results against popular/representative polishers show that HMMPolish competes favorably on error correction in coding regions of known RNA viruses.
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Affiliation(s)
- Runzhou Yu
- Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | | | - Yanni Sun
- Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
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Alston JJ, Soranno A, Holehouse AS. Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552128. [PMID: 37609146 PMCID: PMC10441348 DOI: 10.1101/2023.08.06.552128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Intrinsically disordered regions (IDRs) are critical for cellular function, yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. We focussed here on the first two domains of coronavirus nucleocapsid proteins, the disordered N-terminal domain (NTD) followed by the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system to explore the interplay between an IDR adjacent to a folded domain, and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved fuzzy RNA:protein complex is found across nucleocapsid protein orthologs, despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.
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Nourinejhad Zarghani S, Al Kubrusli R, Iancev S, Jalkanen R, Büttner C, von Bargen S. Molecular Population Genetics of Aspen Mosaic-Associated Virus in Finland and Sweden. Viruses 2023; 15:1678. [PMID: 37632020 PMCID: PMC10460043 DOI: 10.3390/v15081678] [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: 07/20/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Aspen mosaic-associated virus (AsMaV) is a newly identified Emaravirus, in the family Fimoviridae, Bunyavirales, associated with mosaic symptoms in aspen trees (Populus tremula). Aspen trees are widely distributed in Europe and understanding the population structure of AsMaV may aid in the development of better management strategies. The virus genome consists of five negative-sense single-stranded RNA (-ssRNA) molecules. To investigate the genetic diversity and population parameters of AsMaV, different regions of the genome were amplified and analyzed and full-length sequence of the divergent isolates were cloned and sequenced. The results show that RNA3 or nucleoprotein is a good representative for studying genetic diversity in AsMaV. Developed RT-PCR-RFLP was able to identify areas with a higher number of haplotypes and could be applied for screening the large number of samples. In general, AsMaV has a conserved genome and based on the phylogenetic studies, geographical structuring was observed in AsMaV isolates from Sweden and Finland, which could be attributed to founder effects. The genome of AsMaV is under purifying selection but not distributed uniformly on genomic RNAs. Distant AsMaV isolates displayed amino acid sequence variations compared to other isolates, and bioinformatic analysis predicted potential post-translational modification sites in some viral proteins.
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Affiliation(s)
- Shaheen Nourinejhad Zarghani
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Serghei Iancev
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | | | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
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Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Stefani E, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Migheli Q, Vloutoglou I, Maiorano A, Pautasso M, Reignault PL. Pest categorisation of the avocado sunblotch viroid. EFSA J 2023; 21:e08116. [PMID: 37485255 PMCID: PMC10357502 DOI: 10.2903/j.efsa.2023.8116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
The EFSA Panel on Plant Health conducted a pest categorisation of the avocado sunblotch viroid (ASBVd) for the EU. The identity of ASBVd, a member of the genus Avsunviroid (family Avsunviroidae) is clearly defined and detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. ASBVd has been reported in Australia, Ghana, Guatemala, Israel, Mexico, Peru, South Africa, USA (California, Florida) and Venezuela. In the EU, it has been reported in Greece (Crete Island) and Spain. The pathogen could establish in the EU wherever avocado (Persea americana) is grown. The only known natural host of ASBVd is avocado to which it causes the severe 'avocado sunblotch' disease, characterised by white, yellow, red or necrotic depressed areas or scars on the fruit surface, bleached veins and petioles of the leaf, and rectangular cracking patterns in the bark of the old branches. Fruit yield and quality are severely diminished. ASBVd infects under experimental conditions a few more species in the family Lauraceae. The viroid is naturally transmitted at an extremely high rate by seeds (up to 100% in asymptomatically infected trees), but with a low efficiency by pollen (only to the produced seeds), and possibly through root grafts. Plants for planting, including seeds, and fresh avocado fruits were identified as the most relevant pathways for further entry of ASBVd into the EU. Avocado crops are cultivated in southern EU countries. Should the pest further enter and establish in the EU, impact on the production of avocado is expected. Phytosanitary measures are available to prevent entry and spread of the viroid in the EU. ASBVd fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.
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Howe-Kerr LI, Grupstra CGB, Rabbitt KM, Conetta D, Coy SR, Klinges JG, Maher RL, McConnell KM, Meiling SS, Messyasz A, Schmeltzer ER, Seabrook S, Sims JA, Veglia AJ, Thurber AR, Thurber RLV, Correa AMS. Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape. ISME COMMUNICATIONS 2023; 3:27. [PMID: 37009785 PMCID: PMC10068613 DOI: 10.1038/s43705-023-00227-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 02/17/2023] [Accepted: 03/01/2023] [Indexed: 05/31/2023]
Abstract
Viruses can affect coral health by infecting their symbiotic dinoflagellate partners (Symbiodiniaceae). Yet, viral dynamics in coral colonies exposed to environmental stress have not been studied at the reef scale, particularly within individual viral lineages. We sequenced the viral major capsid protein (mcp) gene of positive-sense single-stranded RNA viruses known to infect symbiotic dinoflagellates ('dinoRNAVs') to analyze their dynamics in the reef-building coral, Porites lobata. We repeatedly sampled 54 colonies harboring Cladocopium C15 dinoflagellates, across three environmentally distinct reef zones (fringing reef, back reef, and forereef) around the island of Moorea, French Polynesia over a 3-year period and spanning a reef-wide thermal stress event. By the end of the sampling period, 28% (5/18) of corals in the fringing reef experienced partial mortality versus 78% (14/18) of corals in the forereef. Over 90% (50/54) of colonies had detectable dinoRNAV infections. Reef zone influenced the composition and richness of viral mcp amino acid types ('aminotypes'), with the fringing reef containing the highest aminotype richness. The reef-wide thermal stress event significantly increased aminotype dispersion, and this pattern was strongest in the colonies that experienced partial mortality. These findings demonstrate that dinoRNAV infections respond to environmental fluctuations experienced in situ on reefs. Further, viral productivity will likely increase as ocean temperatures continue to rise, potentially impacting the foundational symbiosis underpinning coral reef ecosystems.
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Affiliation(s)
| | - Carsten G B Grupstra
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Biology, Boston University, Boston, MA, USA
| | - Kristen M Rabbitt
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA, USA
| | - Dennis Conetta
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Samantha R Coy
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Oceanography, Texas A & M University, College Station, TX, USA
| | - J Grace Klinges
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, USA
| | - Rebecca L Maher
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | | | - Sonora S Meiling
- University of the Virgin Islands, St. Thomas, US Virgin Islands, USA
| | - Adriana Messyasz
- Rutgers School of Environmental and Biological Sciences, New Brunswick, NJ, USA
| | | | - Sarah Seabrook
- Oregon State University, Corvallis, OR, USA
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Jordan A Sims
- Department of BioSciences, Rice University, Houston, TX, USA
- Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Alex J Veglia
- Department of BioSciences, Rice University, Houston, TX, USA
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11
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Zhu X, Jiang Y, Zhang H, Li C, Xing D, Guo X, Zhao T. An alternating transmission model between mice and mosquitoes for genetic study of dengue virus. Acta Trop 2023; 239:106834. [PMID: 36646237 DOI: 10.1016/j.actatropica.2023.106834] [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: 11/30/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Rapidly increased incidence and prevalence of dengue virus serotype 2 (DENV-2) in recent decades highlight the need for better understanding of the selective pressures that drive genetic and phenotypic changes in this virus. We simulated the transfer of DENV-2 between human hosts and mosquito vectors by horizontally transmitting the virus between suckling mice and Aedes aegypti (Linnaeus, Diptera: Culicidae). A total of 3 cycles of alternating transmission were performed and 3 passages of virus population were harvested from the infected sucking mice. The viral titer in mice brain and infectivity to mosquitoes of theses viral populations were tested. The genome of the viruses was also sequenced. Results showed that viral titer were similar and infection rate in the mosquitoes were not significantly different among those 3 passages. This in vivo model could be utilized to explore virus evolution and genetic variance in alternating transmission.
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Affiliation(s)
- Xiaojuan Zhu
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China; NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Yuting Jiang
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China
| | - Hengduan Zhang
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China
| | - Chunxiao Li
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China
| | - Dan Xing
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China
| | - Xiaoxia Guo
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China.
| | - Tongyan Zhao
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China.
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12
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Sarry M, Caignard G, Dupré J, Zientara S, Vitour D, Bakkali Kassimi L, Blaise-Boisseau S. Host-Specific Interplay between Foot-and-Mouth Disease Virus 3D Polymerase and the Type-I Interferon Pathway. Viruses 2023; 15:666. [PMID: 36992375 PMCID: PMC10054395 DOI: 10.3390/v15030666] [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: 12/20/2022] [Revised: 02/17/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious viral disease affecting cloven-hoofed animals. One of the issues related to this disease is the persistence of its causative agent, foot-and-mouth disease virus (FMDV). While the mechanisms of FMDV persistence remain unclear, there are clues that it may be related to protein-protein interactions (PPI) between viral proteins and cellular proteins involved in the interferon (IFN) response. Since FMDV persistence has been described in cattle, sheep and goats but not in swine, we screened PPI involving FMDV proteins and sixteen major type-I IFN pathway proteins from these four species by nanoluciferase-2-hybrid complementation assay, in order to identify new PPI and determine their host specificity. As the results concerning the 3Dpol were the most interesting in view of the limited data concerning its role in immune escape, we decided to focus particularly on this protein. The identified PPI were confirmed by GST pull-down. We identified PPI between 3Dpol and seven IFN pathway proteins, namely, IKKα, IKKε, IRF3, IRF7, NEMO, MDA5 and MAVS. These PPI are conserved among the four studied species, with the exception of the one between 3Dpol and MAVS, which was only found with the swine protein. We also showed, using luciferase reporter assays, that 3Dpol could inhibit the induction phase of the IFN pathway. These results demonstrate, for the first time, a putative role for 3Dpol in FMDV innate immune escape.
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Affiliation(s)
- Morgan Sarry
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France; (G.C.); (J.D.); (S.Z.); (D.V.); (L.B.K.)
- AgroParistech, 16 Rue Claude Bernard, 75005 Paris, France
| | - Grégory Caignard
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France; (G.C.); (J.D.); (S.Z.); (D.V.); (L.B.K.)
| | - Juliette Dupré
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France; (G.C.); (J.D.); (S.Z.); (D.V.); (L.B.K.)
| | - Stephan Zientara
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France; (G.C.); (J.D.); (S.Z.); (D.V.); (L.B.K.)
| | - Damien Vitour
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France; (G.C.); (J.D.); (S.Z.); (D.V.); (L.B.K.)
| | - Labib Bakkali Kassimi
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France; (G.C.); (J.D.); (S.Z.); (D.V.); (L.B.K.)
| | - Sandra Blaise-Boisseau
- UMR VIROLOGIE, INRAE, École Nationale Vétérinaire d’Alfort, ANSES Laboratoire de Santé Animale, Université Paris-Est, 94700 Maisons-Alfort, France; (G.C.); (J.D.); (S.Z.); (D.V.); (L.B.K.)
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13
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Bader W, Delerce J, Aherfi S, La Scola B, Colson P. Quasispecies Analysis of SARS-CoV-2 of 15 Different Lineages during the First Year of the Pandemic Prompts Scratching under the Surface of Consensus Genome Sequences. Int J Mol Sci 2022; 23:15658. [PMID: 36555300 PMCID: PMC9779826 DOI: 10.3390/ijms232415658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
The tremendous majority of SARS-CoV-2 genomic data so far neglected intra-host genetic diversity. Here, we studied SARS-CoV-2 quasispecies based on data generated by next-generation sequencing (NGS) of complete genomes. SARS-CoV-2 raw NGS data had been generated for nasopharyngeal samples collected between March 2020 and February 2021 by the Illumina technology on a MiSeq instrument, without prior PCR amplification. To analyze viral quasispecies, we designed and implemented an in-house Excel file (“QuasiS”) that can characterize intra-sample nucleotide diversity along the genomes using data of the mapping of NGS reads. We compared intra-sample genetic diversity and global genetic diversity available from Nextstrain. Hierarchical clustering of all samples based on the intra-sample genetic diversity was performed and visualized with the Morpheus web application. NGS mapping data from 110 SARS-CoV-2-positive respiratory samples characterized by a mean depth of 169 NGS reads/nucleotide position and for which consensus genomes that had been obtained were classified into 15 viral lineages were analyzed. Mean intra-sample nucleotide diversity was 0.21 ± 0.65%, and 5357 positions (17.9%) exhibited significant (>4%) diversity, in ≥2 genomes for 1730 (5.8%) of them. ORF10, spike, and N genes had the highest number of positions exhibiting diversity (0.56%, 0.34%, and 0.24%, respectively). Nine hot spots of intra-sample diversity were identified in the SARS-CoV-2 NSP6, NSP12, ORF8, and N genes. Hierarchical clustering delineated a set of six genomes of different lineages characterized by 920 positions exhibiting intra-sample diversity. In addition, 118 nucleotide positions (0.4%) exhibited diversity at both intra- and inter-patient levels. Overall, the present study illustrates that the SARS-CoV-2 consensus genome sequences are only an incomplete and imperfect representation of the entire viral population infecting a patient, and that quasispecies analysis may allow deciphering more accurately the viral evolutionary pathways.
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Affiliation(s)
- Wahiba Bader
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jeremy Delerce
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sarah Aherfi
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
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14
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COVID-19 vs. Cancer Immunosurveillance: A Game of Thrones within an Inflamed Microenviroment. Cancers (Basel) 2022; 14:cancers14174330. [PMID: 36077865 PMCID: PMC9455004 DOI: 10.3390/cancers14174330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
The COVID-19 pandemic accounts for more than 500 million confirmed infections and over 6 million deaths worldwide in the last 2 years. SARS-CoV-2 causes a highly complex form of inflammation that affects the human organism both acutely and chronically. In the same line, cancer as an inflammation-induced and immune-editing disease appears to cross-react with immune system at different levels including early interactions during carcinogenesis and later cross-talks within the tumor microenvironment. With all that in mind, a reasonable question one might address is whether the SARS-CoV-2 infection and the derived "long lasting inflammatory status" that is frequently observed in patients, might affect the cancer immunosurveillance mechanisms and consequently their risk of developing cancer, as well as the tumor and immune cell behaviors within the inflamed microenvironment. On this context, this review intends to outline and discuss the existing knowledge on SARS-CoV-2-mediated immunomodulation under the prism of changes that might be able to interfere with cancer cell immunoescape and the overall tumor progression and response to conventional therapeutics. Our goal is to highlight a potential interplay between the COVID-19 immunopathology and cancer immune-microenvironment that may pave the way for thorough investigation in the future.
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15
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Khalid AM, Hosny KM, Mirjalili S. COVIDOA: a novel evolutionary optimization algorithm based on coronavirus disease replication lifecycle. Neural Comput Appl 2022; 34:22465-22492. [PMID: 36043205 PMCID: PMC9411047 DOI: 10.1007/s00521-022-07639-x] [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: 10/14/2021] [Accepted: 07/18/2022] [Indexed: 11/13/2022]
Abstract
This paper presents a novel bio-inspired optimization algorithm called Coronavirus Optimization Algorithm (COVIDOA). COVIDOA is an evolutionary search strategy that mimics the mechanism of coronavirus when hijacking human cells. COVIDOA is inspired by the frameshifting technique used by the coronavirus for replication. The proposed algorithm is tested using 20 standard benchmark optimization functions with different parameter values. Besides, we utilized five IEEE Congress of Evolutionary Computation (CEC) benchmark test functions (CECC06, 2019 Competition) and five CEC 2011 real-world problems to prove the proposed algorithm's efficiency. The proposed algorithm is compared to eight of the most popular and recent metaheuristic algorithms from the state-of-the-art in terms of best cost, average cost (AVG), corresponding standard deviation (STD), and convergence speed. The results demonstrate that COVIDOA is superior to most existing metaheuristics.
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16
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Ranking the effectiveness of non-pharmaceutical interventions to counter COVID-19 in UK universities with vaccinated population. Sci Rep 2022; 12:13039. [PMID: 35906452 PMCID: PMC9336164 DOI: 10.1038/s41598-022-16532-5] [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: 12/08/2021] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Several universities around the world have resumed in-person teaching after successful vaccination campaigns have covered 70/80% of the population. In this study, we combine a new compartmental model with an optimal control formulation to discover, among different non-pharmaceutical interventions, the best prevention strategy to maximize on-campus activities while keeping spread under control. Composed of two interconnected Susceptible-Exposed-Infected-Quarantined-Recovered (SEIQR) structures, the model enables staff-to-staff infections, student-to-staff cross infections, student-to-student infections, and environment-to-individual infections. Then, we model input variables representing the implementation of different non-pharmaceutical interventions and formulate and solve optimal control problems for four desired scenarios: minimum number of cases, minimum intervention, minimum non-quarantine intervention, and minimum quarantine intervention. Our results reveal the particular significance of mask wearing and social distancing in universities with vaccinated population (with proportions according to UK data). The study also reveals that quarantining infected students has a higher importance than quarantining staff. In contrast, other measures such as environmental disinfection seems to be less important.
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17
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Shin DH, Gillard A, Van Wieren A, Gomez-Manzano C, Fueyo J. Remission of Liquid Tumors and SARS-CoV-2 Infection: a Literature Review. Mol Ther Oncolytics 2022; 26:135-140. [PMID: 35702422 PMCID: PMC9186532 DOI: 10.1016/j.omto.2022.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has produced a new global challenge for patients with cancer. The disease and the immunosuppression induced by cancer therapies have generated a perfect storm of conditions to increase the severity of the symptoms and worsen the prognosis. However, a few clinical reports showcased the power of viruses to induce remission in some patients suffering from liquid tumors. Here, we reviewed six cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that resulted in cancer remission, simultaneously highlighting the strengths and the unique challenges of oncolytic virotherapy. Virotherapy has become a special case of cancer immunotherapy. This paradigm-shifting concept suggests that oncolytic viruses are not only promising agents to combat particularly immunologically suppressed, immunotherapy-resistant tumors but also that the trigger of local inflammation, such as SARS-CoV-2 infection of the respiratory pathways, may trigger an abscopal effect sufficient to induce the remission of systemic cancer.
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Affiliation(s)
- Dong Ho Shin
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Andrew Gillard
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Arie Van Wieren
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Candelaria Gomez-Manzano
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Corresponding author Candelaria Gomez-Manzano, MD, Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Juan Fueyo
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Corresponding author Juan Fueyo, MD, FAAAS, FAAN, Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Abstract
The debate over whether viruses are living organisms tends to be paradigmatically determined. The metabolic paradigm denies that they are, while new research evidences the opposite. The purpose of this paper is to deliver a generic model for viral contexts that explains why viruses are alive. It will take a systems biology approach, with a qualitative part (using metacybernetics) to provide deeper explanations of viral contexts, and a quantitative part (using Fisher Information deriving from the variational principle of Extreme Physical Information) which is in principle able to take measurements and predict outcomes. The modelling process provides an extended view of the epigenetic processes of viruses. The generic systems biology model will depict viruses as autonomous entities with metaphysical processes of autopoietic self-organisation and adaptation, enabling them to maintain their physical viability and hence, within their populations, mutate and evolve. The autopoietic epigenetic processes are shown to describe their capability to change, and these are both qualitatively and quantitatively explored, the latter providing an approach to make measurements of physical phenomena under uncertainty. Viruses maintain their fitness when they are able to maintain their stability, and this is indicated by information flow efficacy. A brief case study is presented on the COVID-19 virus from the perspective that it is a living system, and this includes outcome predictions given Fisher Information conditions for known contexts.
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Kadoya SS, Urayama SI, Nunoura T, Hirai M, Takaki Y, Kitajima M, Nakagomi T, Nakagomi O, Okabe S, Nishimura O, Sano D. The Intrapopulation Genetic Diversity of RNA Virus May Influence the Sensitivity of Chlorine Disinfection. Front Microbiol 2022; 13:839513. [PMID: 35668760 PMCID: PMC9163991 DOI: 10.3389/fmicb.2022.839513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
RNA virus populations are not clonal; rather, they comprise a mutant swarm in which sequences are slightly different from the master sequence. Genetic diversity within a population (intrapopulation genetic diversity) is critical for RNA viruses to survive under environmental stresses. Disinfection has become an important practice in the control of pathogenic viruses; however, the impact of intrapopulation genetic diversity on the sensitivity of disinfection, defined as -log10 (postdisinfected infectious titer/predisinfected titer), has not been elucidated. In this study, we serially passaged populations of rhesus rotavirus. We demonstrated that populations with reduced chlorine sensitivity emerged at random and independently of chlorine exposure. Sequencing analysis revealed that compared with sensitive populations, less-sensitive ones had higher non-synonymous genetic diversity of the outer capsid protein gene, suggesting that changes in the amino acid sequences of the outer capsid protein were the main factors influencing chlorine sensitivity. No common mutations were found among less-sensitive populations, indicating that rather than specific mutations, the diversity of the outer capsid protein itself was associated with the disinfection sensitivity and that the disinfection sensitivity changed stochastically. Simulation results suggest that the disinfection sensitivity of a genetically diverse population is destabilized if cooperative viral clusters including multiple sequences are formed. These results advocate that any prevention measures leading to low intrapopulation genetic diversity are important to prevent the spread and evolution of pathogenic RNA viruses in society.
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Affiliation(s)
- Syun-suke Kadoya
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| | - Syun-ichi Urayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Miho Hirai
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Toyoko Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Osamu Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Osamu Nishimura
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Japan
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Antiretroviral Drug-Resistance Mutations on the Gag Gene: Mutation Dynamics during Analytic Treatment Interruption among Individuals Experiencing Virologic Failure. Pathogens 2022; 11:pathogens11050534. [PMID: 35631055 PMCID: PMC9145614 DOI: 10.3390/pathogens11050534] [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: 04/08/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
We describe drug-resistance mutation dynamics of the gag gene among individuals under antiretroviral virologic failure who underwent analytical treatment interruption (ATI). These mutations occur in and around the cleavage sites that form the particles that become the mature HIV-1 virus. The study involved a 12-week interruption in antiretroviral therapy (ART) and sequencing of the gag gene in 38 individuals experiencing virologic failure and harboring triple-class resistant HIV strains. Regions of the gag gene surrounding the NC-p2 and p1-p6 cleavage sites were sequenced at baseline before ATI and after 12 weeks from plasma HIV RNA using population-based Sanger sequencing. Fourteen of the sixteen patients sequenced presented at least one mutation in the gag gene at baseline, with an average of 4.93 mutations per patient. All the mutations had reverted to the wild type by the end of the study. Mutations in the gag gene complement mutations in the pol gene to restore HIV fitness. Those mutations around cleavage sites and within substrates contribute to protease inhibitor resistance and difficulty in re-establishing effective virologic suppression. ART interruption in the presence of antiretroviral resistant HIV strains was used here as a practical measure for more adapted HIV profiles in the absence of ART selective pressure.
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Sakamoto K, Satoh Y, Takahashi KI, Wakimoto H, Kitagawa Y, Gotoh B, Ayata M, Itoh M. Upregulation of viral RNA polymerase activity promotes adaptation of SSPE virus to neuronal cells. Virology 2022; 573:1-11. [DOI: 10.1016/j.virol.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022]
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22
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Quer J, Colomer-Castell S, Campos C, Andrés C, Piñana M, Cortese MF, González-Sánchez A, Garcia-Cehic D, Ibáñez M, Pumarola T, Rodríguez-Frías F, Antón A, Tabernero D. Next-Generation Sequencing for Confronting Virus Pandemics. Viruses 2022; 14:v14030600. [PMID: 35337007 PMCID: PMC8950049 DOI: 10.3390/v14030600] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.
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Affiliation(s)
- Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence: (J.Q.); (A.A.)
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Cristina Andrés
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Piñana
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Francesca Cortese
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Alejandra González-Sánchez
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Marta Ibáñez
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
| | - Tomàs Pumarola
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence: (J.Q.); (A.A.)
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Microbiology Departments, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
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23
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Luo X, Kang X, Schönhuth A. Strainline: full-length de novo viral haplotype reconstruction from noisy long reads. Genome Biol 2022; 23:29. [PMID: 35057847 PMCID: PMC8771625 DOI: 10.1186/s13059-021-02587-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/17/2021] [Indexed: 12/02/2022] Open
Abstract
Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Strainline, a novel approach to assemble viral haplotypes from noisy long reads without a reference genome. Strainline is the first approach to provide strain-resolved, full-length de novo assemblies of viral quasispecies from noisy third-generation sequencing data. Benchmarking on simulated and real datasets of varying complexity and diversity confirm this novelty and demonstrate the superiority of Strainline.
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24
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Xiao Y, Lidsky PV, Shirogane Y, Aviner R, Wu CT, Li W, Zheng W, Talbot D, Catching A, Doitsh G, Su W, Gekko CE, Nayak A, Ernst JD, Brodsky L, Brodsky E, Rousseau E, Capponi S, Bianco S, Nakamura R, Jackson PK, Frydman J, Andino R. A defective viral genome strategy elicits broad protective immunity against respiratory viruses. Cell 2021; 184:6037-6051.e14. [PMID: 34852237 PMCID: PMC8598942 DOI: 10.1016/j.cell.2021.11.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022]
Abstract
RNA viruses generate defective viral genomes (DVGs) that can interfere with replication of the parental wild-type virus. To examine their therapeutic potential, we created a DVG by deleting the capsid-coding region of poliovirus. Strikingly, intraperitoneal or intranasal administration of this genome, which we termed eTIP1, elicits an antiviral response, inhibits replication, and protects mice from several RNA viruses, including enteroviruses, influenza, and SARS-CoV-2. While eTIP1 replication following intranasal administration is limited to the nasal cavity, its antiviral action extends non-cell-autonomously to the lungs. eTIP1 broad-spectrum antiviral effects are mediated by both local and distal type I interferon responses. Importantly, while a single eTIP1 dose protects animals from SARS-CoV-2 infection, it also stimulates production of SARS-CoV-2 neutralizing antibodies that afford long-lasting protection from SARS-CoV-2 reinfection. Thus, eTIP1 is a safe and effective broad-spectrum antiviral generating short- and long-term protection against SARS-CoV-2 and other respiratory infections in animal models.
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Affiliation(s)
- Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuta Shirogane
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Ranen Aviner
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Chien-Ting Wu
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Weiyi Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Weihao Zheng
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Dale Talbot
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Aleph Therapeutics, Inc., Stanford, CA 94305, USA
| | - Adam Catching
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gilad Doitsh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Weiheng Su
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; School of Life Sciences, Jilin University, Changchun, China
| | - Colby E Gekko
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Arabinda Nayak
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joel D Ernst
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center and Department of Evolutionary & Environmental Biology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | | | - Elsa Rousseau
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Sara Capponi
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Simone Bianco
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | | | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
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25
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Rodríguez-Frías F, Quer J, Tabernero D, Cortese MF, Garcia-Garcia S, Rando-Segura A, Pumarola T. Microorganisms as Shapers of Human Civilization, from Pandemics to Even Our Genomes: Villains or Friends? A Historical Approach. Microorganisms 2021; 9:2518. [PMID: 34946123 PMCID: PMC8708650 DOI: 10.3390/microorganisms9122518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Universal history is characterized by continuous evolution, in which civilizations are born and die. This evolution is associated with multiple factors, among which the role of microorganisms is often overlooked. Viruses and bacteria have written or decisively contributed to terrible episodes of history, such as the Black Death in 14th century Europe, the annihilation of pre-Columbian American civilizations, and pandemics such as the 1918 Spanish flu or the current COVID-19 pandemic caused by the coronavirus SARS-CoV-2. Nevertheless, it is clear that we could not live in a world without these tiny beings. Endogenous retroviruses have been key to our evolution and for the regulation of gene expression, and the gut microbiota helps us digest compounds that we could not otherwise process. In addition, we have used microorganisms to preserve or prepare food for millennia and more recently to obtain drugs such as antibiotics or to develop recombinant DNA technologies. Due to the enormous importance of microorganisms for our survival, they have significantly influenced the population genetics of different human groups. This paper will review the role of microorganisms as "villains" who have been responsible for tremendous mortality throughout history but also as "friends" who help us survive and evolve.
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Affiliation(s)
- Francisco Rodríguez-Frías
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Maria Francesca Cortese
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Selene Garcia-Garcia
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Ariadna Rando-Segura
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
- Department of Microbiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Tomas Pumarola
- Department of Microbiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
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26
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Ray AM, Davis SL, Rasgon JL, Grozinger CM. Simulated vector transmission differentially influences dynamics of two viral variants of deformed wing virus in honey bees ( Apis mellifera). J Gen Virol 2021; 102. [PMID: 34816791 PMCID: PMC8742989 DOI: 10.1099/jgv.0.001687] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Understanding how vectors alter the interactions between viruses and their hosts is a fundamental question in virology and disease ecology. In honey bees, transmission of deformed wing virus (DWV) by parasitic Varroa mites has been associated with elevated disease and host mortality, and Varroa transmission has been hypothesized to lead to increased viral titres or select for more virulent variants. Here, we mimicked Varroa transmission by serially passaging a mixed population of two DWV variants, A and B, by injection through in vitro reared honey bee pupae and tracking these viral populations through five passages. The DWV-A and DWV-B variant proportions shifted dynamically through passaging, with DWV-B outcompeting DWV-A after one passage, but levels of both variants becoming equivalent by Passage 5. Sequencing analysis revealed a dominant, recombinant DWV-B strain (DWV-A derived 5′ IRES region with the rest of the genome DWV-B), with low nucleotide diversity that decreased through passaging. DWV-A populations had higher nucleotide diversity compared to DWV-B, but this also decreased through passaging. Selection signatures were found across functional regions of the DWV-A and DWV-B genomes, including amino acid mutations in the putative capsid protein region. Simulated vector transmission differentially impacted two closely related viral variants which could influence viral interactions with the host, demonstrating surprising plasticity in vector-host-viral dynamics.
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Affiliation(s)
- Allyson M Ray
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.,Department of Entomology, Center for Infectious Disease Dynamics, Center for Pollinator Research, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Sheldon L Davis
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Jason L Rasgon
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.,Department of Entomology, Center for Infectious Disease Dynamics, Center for Pollinator Research, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Christina M Grozinger
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.,Department of Entomology, Center for Infectious Disease Dynamics, Center for Pollinator Research, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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27
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Kikuti M, Sanhueza J, Vilalta C, Paploski IAD, VanderWaal K, Corzo CA. Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry. PLoS One 2021; 16:e0259531. [PMID: 34797830 PMCID: PMC8604284 DOI: 10.1371/journal.pone.0259531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus genotype 2 (PRRSV-2) genetic diversity in the U.S. was assessed using a database comprising 10 years’ worth of sequence data obtained from swine production systems routine monitoring and outbreak investigations. A total of 26,831 ORF5 PRRSV-2 sequences from 34 production systems were included in this analysis. Within group mean genetic distance (i.e. mean proportion of nucleotide differences within ORF5) per year according to herd type was calculated for all PRRSV-2 sequences. The percent nucleotide difference between each sequence and the ORF5 sequences from four commercially available PRRSV-2 vaccines (Ingelvac PRRS MLV, Ingelvac PRRS ATP, Fostera PRRS, and Prevacent PRRS) within the same lineage over time was used to classify sequences in wild-type or vaccine-like. The mean ORF5 genetic distance fluctuated from 0.09 to 0.13, being generally smaller in years in which there was a relative higher frequency of dominant lineage. Vaccine-like sequences comprised about one fourth of sequences obtained through routine monitoring of PRRS. We found that lineage 5 sequences were mostly Ingelvac PRRS MLV-like. Lineage 8 sequences up to 2011 were 62.9% Ingelvac PRRS ATP-like while the remaining were wild-type viruses. From 2012 onwards, 51.9% of lineage 8 sequences were Ingelvac PRRS ATP-like, 45.0% were Fostera PRRS-like, and only 3.2% were wild-type. For lineage 1 sequences, 0.1% and 1.7% of the sequences were Prevacent PRRS-like in 2009–2018 and 2019, respectively. These results suggest that repeated introductions of vaccine-like viruses through use of modified live vaccines might decrease within-lineage viral diversity as vaccine-like strains become more prevalent. Overall, this compilation of private data from routine monitoring provides valuable information on PRRSV viral diversity.
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Affiliation(s)
- Mariana Kikuti
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Juan Sanhueza
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States of America
- Facultad de Recursos Naturales, Departamento de Ciencias Veterinarias y Salud Pública, Universidad Católica de Temuco, Temuco, Araucanía, Chile
| | - Carles Vilalta
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States of America
- Upnorth Analytics, Barcelona, Spain
| | | | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States of America
| | - Cesar A. Corzo
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States of America
- * E-mail:
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28
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Kikuti M, Paploski IAD, Pamornchainavakul N, Picasso-Risso C, Schwartz M, Yeske P, Leuwerke B, Bruner L, Murray D, Roggow BD, Thomas P, Feldmann L, Allerson M, Hensch M, Bauman T, Sexton B, Rovira A, VanderWaal K, Corzo CA. Emergence of a New Lineage 1C Variant of Porcine Reproductive and Respiratory Syndrome Virus 2 in the United States. Front Vet Sci 2021; 8:752938. [PMID: 34733906 PMCID: PMC8558496 DOI: 10.3389/fvets.2021.752938] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/22/2021] [Indexed: 12/02/2022] Open
Abstract
We report an ongoing regional outbreak of an emerging porcine reproductive and respiratory syndrome virus (PRRSV2) variant within Lineage 1C affecting 154 breeding and grow-finishing sites in the Midwestern U.S. Transmission seemed to have occurred in two waves, with the first peak of weekly cases occurring between October and December 2020 and the second starting in April 2021. Most of cases occurred within a 120 km radius. Both orf5 and whole genome sequencing results suggest that this represents the emergence of a new variant within Lineage 1C distinct from what has been previously circulating. A case-control study was conducted with 50 cases (sites affected with the newly emerged variant) and 58 controls (sites affected with other PRRSV variants) between October and December 2020. Sites that had a market vehicle that was not exclusive to the production system had 0.04 times the odds of being a case than a control. A spatial cluster (81.42 km radius) with 1.68 times higher the number of cases than controls was found. The average finishing mortality within the first 4 weeks after detection was higher amongst cases (4.50%) than controls (0.01%). The transmission of a highly similar virus between different farms carrying on trough spring rises concerns for the next high transmission season of PRRS.
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Affiliation(s)
- Mariana Kikuti
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Igor A D Paploski
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Nakarin Pamornchainavakul
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Catalina Picasso-Risso
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Mark Schwartz
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States.,Schwartz Farms Inc., Sleepy Eye, MN, United States
| | - Paul Yeske
- Swine Vet Center, St. Peter, MN, United States
| | | | | | | | | | - Pete Thomas
- Iowa Select Farms, Iowa Falls, IA, United States
| | | | | | | | | | | | - Albert Rovira
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Cesar A Corzo
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
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29
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Hunter JR, dos Santos DEM, Munerato P, Janini LM, Castelo A, Sucupira MC, Truong HHM, Diaz RS. Fitness Cost of Antiretroviral Drug Resistance Mutations on the pol Gene during Analytical Antiretroviral Treatment Interruption among Individuals Experiencing Virological Failure. Pathogens 2021; 10:pathogens10111425. [PMID: 34832581 PMCID: PMC8622617 DOI: 10.3390/pathogens10111425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
HIV cure studies require patients to enter an analytical treatment interruption (ATI). Here, we describe previously unanalyzed data that sheds light on ATI dynamics in PLHIV (People Living with HIV). We present drug resistance mutation dynamics on the pol gene among individuals with antiretroviral virological failure who underwent ATI. The study involved a 12-week interruption in antiretroviral therapy (ART), monitoring of viral load, CD4+/CD8+ T cell counts, and sequencing of the pol gene from 38 individuals experiencing virological failure and harboring 3-class resistant HIV strains: nucleoside reverse transcriptase inhibitors (NRTI) non-nucleoside inhibitors (NNRTI), and protease inhibitors (PI). Protease and reverse transcriptase regions of the pol gene were sequenced at baseline before ATI and every four weeks thereafter from PBMCs and at baseline and after 12 weeks from plasma HIV RNA using population-based Sanger sequencing. Average viral load increased 0.559 log10 copies per milliliter. CD4+ T cell count decreased as soon as ART was withdrawn, an average loss of 99.0 cells/mL. Forty-three percent of the mutations associated with antiretroviral resistance in PBMCs disappeared and fifty-seven percent of the mutations in plasma reverted to wild type, which was less than the 100% reversion expected. In PBMC, the PI mutations reverted more slowly than reverse transcriptase mutations. The patients were projected to need an average of 33.7 weeks for PI to revert compared with 20.9 weeks for NRTI and 19.8 weeks for NNRTI. Mutations in the pol gene can cause virological failure and difficulty in re-establishing effective virological suppression.
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Affiliation(s)
- James R. Hunter
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Domingos E. Matos dos Santos
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Patricia Munerato
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Luiz Mario Janini
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Adauto Castelo
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Maria Cecilia Sucupira
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
| | - Hong-Ha M. Truong
- Department of Medicine, University of California, San Francisco, CA 94158, USA;
| | - Ricardo Sobhie Diaz
- Department of Medicine, Federal University of São Paulo, São Paulo 04039-032, Brazil; (J.R.H.); (D.E.M.d.S.); (P.M.); (L.M.J.); (A.C.); (M.C.S.)
- Correspondence:
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Reduced subgenomic RNA expression is a molecular indicator of asymptomatic SARS-CoV-2 infection. COMMUNICATIONS MEDICINE 2021; 1:33. [PMID: 35602196 PMCID: PMC9053197 DOI: 10.1038/s43856-021-00034-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/02/2021] [Indexed: 01/12/2023] Open
Abstract
Background It is estimated that up to 80% of infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are asymptomatic and asymptomatic patients can still effectively transmit the virus and cause disease. While much of the effort has been placed on decoding single nucleotide variation in SARS-CoV-2 genomes, considerably less is known about their transcript variation and any correlation with clinical severity in human hosts, as defined here by the presence or absence of symptoms. Methods To assess viral genomic signatures of disease severity, we conducted a systematic characterization of SARS-CoV-2 transcripts and genetic variants in 81 clinical specimens collected from symptomatic and asymptomatic individuals using multi-scale transcriptomic analyses including amplicon-seq, short-read metatranscriptome and long-read Iso-seq. Results Here we show a highly coordinated and consistent pattern of sgRNA expression from individuals with robust SARS-CoV-2 symptomatic infection and their expression is significantly repressed in the asymptomatic infections. We also observe widespread inter- and intra-patient variants in viral RNAs, known as quasispecies frequently found in many RNA viruses. We identify unique sets of deletions preferentially found primarily in symptomatic individuals, with many likely to confer changes in SARS-CoV-2 virulence and host responses. Moreover, these frequently occurring structural variants in SARS-CoV-2 genomes serve as a mechanism to further induce SARS-CoV-2 proteome complexity. Conclusions Our results indicate that differential sgRNA expression and structural mutational burden are highly correlated with the clinical severity of SARS-CoV-2 infection. Longitudinally monitoring sgRNA expression and structural diversity could further guide treatment responses, testing strategies, and vaccine development. Wong and Ngan et al. characterize the expression and structural variation of SARS-CoV-2 subgenomic RNAs (sgRNAs) in diagnostic specimens from symptomatic and asymptomatic COVID-19 patients. In a series of genomic and transcriptomic analyses, the authors observe reduced sgRNA expression and a distinct set of structural deletions in asymptomatic infections compared with symptomatic infections. Infection with SARS-CoV-2 can lead to symptoms of different severity, with some individuals remaining entirely asymptomatic but still responsible for much of the viral transmission. Here, we sought to identify markers of the severity of symptoms of SARS-CoV-2 infection, as defined by the presence or absence of symptoms. We used a combination of methods to study SARS-CoV-2 genes and their readouts, known as transcripts, in clinical samples from people with symptomatic and asymptomatic infections. We demonstrate that transcripts responsible for making viral proteins are seen at lower levels in asymptomatic infections. We also identify structural changes in the viral genes and transcripts that potentially influence the host’s response to the virus. Our study defines potential markers of symptom severity that may ultimately guide risk mitigation and testing strategies.
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DeLong JP, Al-Sammak MA, Al-Ameeli ZT, Dunigan DD, Edwards KF, Fuhrmann JJ, Gleghorn JP, Li H, Haramoto K, Harrison AO, Marston MF, Moore RM, Polson SW, Ferrell BD, Salsbery ME, Schvarcz CR, Shirazi J, Steward GF, Van Etten JL, Wommack KE. Towards an integrative view of virus phenotypes. Nat Rev Microbiol 2021; 20:83-94. [PMID: 34522049 DOI: 10.1038/s41579-021-00612-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 12/25/2022]
Abstract
Understanding how phenotypes emerge from genotypes is a foundational goal in biology. As challenging as this task is when considering cellular life, it is further complicated in the case of viruses. During replication, a virus as a discrete entity (the virion) disappears and manifests itself as a metabolic amalgam between the virus and the host (the virocell). Identifying traits that unambiguously constitute a virus's phenotype is straightforward for the virion, less so for the virocell. Here, we present a framework for categorizing virus phenotypes that encompasses both virion and virocell stages and considers functional and performance traits of viruses in the context of fitness. Such an integrated view of virus phenotype is necessary for comprehensive interpretation of viral genome sequences and will advance our understanding of viral evolution and ecology.
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Affiliation(s)
- John P DeLong
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Maitham A Al-Sammak
- Tropical Biological Research Unit, College of Science, University of Baghdad, Baghdad, Iraq.,Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Zeina T Al-Ameeli
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Medical Technical Institutes, Middle Technical University, Baghdad, Iraq
| | - David D Dunigan
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Jeffry J Fuhrmann
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Jason P Gleghorn
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Hanqun Li
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Kona Haramoto
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Amelia O Harrison
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Marcia F Marston
- Department of Biology and Marine Biology, Roger Williams University, Bristol, RI, USA
| | - Ryan M Moore
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Shawn W Polson
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Barbra D Ferrell
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Miranda E Salsbery
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Jasmine Shirazi
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Grieg F Steward
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA. .,Department of Biological Sciences, University of Delaware, Newark, DE, USA. .,Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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Huang X, Zhang F, Zhu K, Lin W, Ma W. dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Virus Res 2021; 304:198530. [PMID: 34363850 PMCID: PMC8339451 DOI: 10.1016/j.virusres.2021.198530] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/26/2022]
Abstract
Fast evolving of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has caused the spreading of COVID-19 disease rapidly around the globe. The mutation, especially in the gene encoding spike protein has helped the virus adapt and evade human immune system, as well as affect the efficacy of the immunizations and treatments. SARS-CoV-2 variant carrying D614G amino acid change at the spike protein is the most dominant strain in the pandemic. Therefore, efficient detection of the SARS-CoV-2 variants including D614G mutation is critical to control the COVID-19 pandemic. Herein, we report a dual synthetic mismatches CRISPR/Cas12a (dsmCRISPR) method to detect the SARS-CoV-2 D614G mutation with high sensitivity and specificity. By targeting SARS-CoV-2 D614G mutation, synthetic mismatch crRNAs were designed from -3 to +3 position around the mutation site. To improve the sensitivity and specificity, a synthetic mismatch primer with a 3'-terminal base complementary to the D614G point mutation and a mismatch next to 3'-terminal base was used to specifically amplify the D614G mutation site with higher annealing temperature. Using synthetic mismatch crRNA-(-1), a higher ratio (13.45) of the fluorescence between G614 and D614 was observed. When combined with mismatch primer to amplify D614G mutation, the fluorescence ratio of G614/D164 template detected was increased by 73.53% to 23.12. This method can detect the SARS-CoV-2 D614G mutation nucleic acid with high sensitivity, which was validated with synthetic SARS-CoV-2 D614G RNA. Therefore, the dsmCRIPSR method has significant potential to serve as a sensitive and specific assay for SARS-CoV-2 D614G detection and could be further extended for the detection of other SARS-CoV-2 variants of interest.
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Affiliation(s)
- Xiaoming Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Fuming Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Kun Zhu
- Beijing Origingene-tech biotechnology Co., Ltd., Beijing, China
| | - Wanjun Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Wenzhe Ma
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
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Bhatia S, Narayanan N, Nagpal S, Nair DT. Antiviral therapeutics directed against RNA dependent RNA polymerases from positive-sense viruses. Mol Aspects Med 2021; 81:101005. [PMID: 34311994 DOI: 10.1016/j.mam.2021.101005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/18/2023]
Abstract
Viruses with positive-sense single stranded RNA (+ssRNA) genomes are responsible for different diseases and represent a global health problem. In addition to developing new vaccines that protect against severe illness on infection, it is imperative to identify new antiviral molecules to treat infected patients. The genome of these RNA viruses generally codes for an enzyme with RNA dependent RNA polymerase (RdRP) activity. This molecule is centrally involved in the duplication of the RNA genome. Inhibition of this enzyme by small molecules will prevent duplication of the RNA genome and thus reduce the viral titer. An overview of the different therapeutic strategies used to inhibit RdRPs from +ssRNA viruses is provided, along with an analysis of these enzymes to highlight new binding sites for inhibitors.
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Affiliation(s)
- Sonam Bhatia
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Shilpi Nagpal
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Deepak T Nair
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India.
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Wu S, Li X, Wang G. tRNA-like structures and their functions. FEBS J 2021; 289:5089-5099. [PMID: 34117728 DOI: 10.1111/febs.16070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 06/10/2021] [Indexed: 11/27/2022]
Abstract
tRNA-like structures (TLSs) were first identified in the RNA genomes of turnip yellow mosaic virus. Since then, TLSs have been found in many other species including mammals, and the RNAs harboring these structures range from viral genomic RNAs to mRNAs and noncoding RNAs. Some progress has also been made on understanding their functions that include regulation of RNA replication, translation enhancement, RNA-protein interaction, and more. In this review, we summarize the current knowledge about the regulations and functions of these TLSs. Possible future directions of the field are also briefly discussed.
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Affiliation(s)
- Sipeng Wu
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Xiang Li
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Geng Wang
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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Ebrahimi S, Nonacs P. Genetic diversity through social heterosis can increase virulence in RNA viral infections and cancer progression. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202219. [PMID: 34035948 PMCID: PMC8097216 DOI: 10.1098/rsos.202219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/12/2021] [Indexed: 05/04/2023]
Abstract
In viral infections and cancer tumours, negative health outcomes often correlate with increasing genetic diversity. Possible evolutionary processes for such relationships include mutant lineages escaping host control or diversity, per se, creating too many immune system targets. Another possibility is social heterosis where mutations and replicative errors create clonal lineages varying in intrinsic capability for successful dispersal; improved environmental buffering; resource extraction or effective defence against immune systems. Rather than these capabilities existing in one genome, social heterosis proposes complementary synergies occur across lineages in close proximity. Diverse groups overcome host defences as interacting 'social genomes' with group genetic tool kits exceeding limited individual plasticity. To assess the possibility of social heterosis in viral infections and cancer progression, we conducted extensive literature searches for examples consistent with general and specific predictions from the social heterosis hypothesis. Numerous studies found supportive patterns in cancers across multiple tissues and in several families of RNA viruses. In viruses, social heterosis mechanisms probably result from long coevolutionary histories of competition between pathogen and host. Conversely, in cancers, social heterosis is a by-product of recent mutations. Investigating how social genomes arise and function in viral quasi-species swarms and cancer tumours may lead to new therapeutic approaches.
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Affiliation(s)
- Saba Ebrahimi
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90024, USA
| | - Peter Nonacs
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90024, USA
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Geraghty RJ, Aliota MT, Bonnac LF. Broad-Spectrum Antiviral Strategies and Nucleoside Analogues. Viruses 2021; 13:v13040667. [PMID: 33924302 PMCID: PMC8069527 DOI: 10.3390/v13040667] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/18/2023] Open
Abstract
The emergence or re-emergence of viruses with epidemic and/or pandemic potential, such as Ebola, Zika, Middle East Respiratory Syndrome (MERS-CoV), Severe Acute Respiratory Syndrome Coronavirus 1 and 2 (SARS and SARS-CoV-2) viruses, or new strains of influenza represents significant human health threats due to the absence of available treatments. Vaccines represent a key answer to control these viruses. However, in the case of a public health emergency, vaccine development, safety, and partial efficacy concerns may hinder their prompt deployment. Thus, developing broad-spectrum antiviral molecules for a fast response is essential to face an outbreak crisis as well as for bioweapon countermeasures. So far, broad-spectrum antivirals include two main categories: the family of drugs targeting the host-cell machinery essential for virus infection and replication, and the family of drugs directly targeting viruses. Among the molecules directly targeting viruses, nucleoside analogues form an essential class of broad-spectrum antiviral drugs. In this review, we will discuss the interest for broad-spectrum antiviral strategies and their limitations, with an emphasis on virus-targeted, broad-spectrum, antiviral nucleoside analogues and their mechanisms of action.
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Affiliation(s)
- Robert J. Geraghty
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA;
| | - Laurent F. Bonnac
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence:
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Nchinda GW, Al-Atoom N, Coats MT, Cameron JM, Waffo AB. Uniqueness of RNA Coliphage Qβ Display System in Directed Evolutionary Biotechnology. Viruses 2021; 13:v13040568. [PMID: 33801772 PMCID: PMC8067240 DOI: 10.3390/v13040568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
Phage display technology involves the surface genetic engineering of phages to expose desirable proteins or peptides whose gene sequences are packaged within phage genomes, thereby rendering direct linkage between genotype with phenotype feasible. This has resulted in phage display systems becoming invaluable components of directed evolutionary biotechnology. The M13 is a DNA phage display system which dominates this technology and usually involves selected proteins or peptides being displayed through surface engineering of its minor coat proteins. The displayed protein or peptide’s functionality is often highly reduced due to harsh treatment of M13 variants. Recently, we developed a novel phage display system using the coliphage Qβ as a nano-biotechnology platform. The coliphage Qβ is an RNA phage belonging to the family of Leviviridae, a long investigated virus. Qβ phages exist as a quasispecies and possess features making them comparatively more suitable and unique for directed evolutionary biotechnology. As a quasispecies, Qβ benefits from the promiscuity of its RNA dependent RNA polymerase replicase, which lacks proofreading activity, and thereby permits rapid variant generation, mutation, and adaptation. The minor coat protein of Qβ is the readthrough protein, A1. It shares the same initiation codon with the major coat protein and is produced each time the ribosome translates the UGA stop codon of the major coat protein with the of misincorporation of tryptophan. This misincorporation occurs at a low level (1/15). Per convention and definition, A1 is the target for display technology, as this minor coat protein does not play a role in initiating the life cycle of Qβ phage like the pIII of M13. The maturation protein A2 of Qβ initiates the life cycle by binding to the pilus of the F+ host bacteria. The extension of the A1 protein with a foreign peptide probe recognizes and binds to the target freely, while the A2 initiates the infection. This avoids any disturbance of the complex and the necessity for acidic elution and neutralization prior to infection. The combined use of both the A1 and A2 proteins of Qβ in this display system allows for novel bio-panning, in vitro maturation, and evolution. Additionally, methods for large library size construction have been improved with our directed evolutionary phage display system. This novel phage display technology allows 12 copies of a specific desired peptide to be displayed on the exterior surface of Qβ in uniform distribution at the corners of the phage icosahedron. Through the recently optimized subtractive bio-panning strategy, fusion probes containing up to 80 amino acids altogether with linkers, can be displayed for target selection. Thus, combined uniqueness of its genome, structure, and proteins make the Qβ phage a desirable suitable innovation applicable in affinity maturation and directed evolutionary biotechnology. The evolutionary adaptability of the Qβ phage display strategy is still in its infancy. However, it has the potential to evolve functional domains of the desirable proteins, glycoproteins, and lipoproteins, rendering them superior to their natural counterparts.
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Affiliation(s)
- Godwin W. Nchinda
- Laboratory of Vaccinology and Biobanking, International Reference Centre CIRCB), BP 3077 Yaoundé, Cameroon;
- Department of Pharmaceutical Microbiology & Biotechnology, Nnamdi Azikiwe University, 420110 Awka, Nigeria
| | - Nadia Al-Atoom
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL 36088, USA;
| | - Mamie T. Coats
- Clinical and Diagnostic Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Jacqueline M. Cameron
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Alain B. Waffo
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Correspondence: ; Tel.: +1-317-274-9640
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Genome Number and Size Polymorphism in Zika Virus Infectious Units. J Virol 2021; 95:JVI.00787-20. [PMID: 33328311 PMCID: PMC8094933 DOI: 10.1128/jvi.00787-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022] Open
Abstract
The arthropod-borne Zika virus (ZIKV) infects humans and can cause severe neurological sequelae, particularly in fetuses infected in utero. How this virus has been able to spread across vast geological ranges and evolve in new host populations is not yet understood. Zika virus (ZIKV; Flaviviridae, Flavivirus) is an arthropod-borne infection that can result in severe outcomes, particularly in fetuses infected in utero. It has been assumed that infection by ZIKV, as well as other viruses, is largely initiated by individual virus particles binding to and entering a cell. However, recent studies have demonstrated that multiple virus particles are frequently delivered to a cell simultaneously and that this collective particle delivery enhances infection. ZIKV is maintained in nature between Aedes aegypti mosquitos and vertebrate hosts, including humans. Human infection is initiated through the injection of a relatively small initial inoculum comprised of a genetically complex virus population. Since most mutations decrease virus fitness, collective particle transmission could benefit ZIKV and other arthropod-borne diseases by facilitating the maintenance of genetic complexity and adaptability during infection or through other mechanisms. Therefore, we utilized a barcoded ZIKV to quantify the number of virus genomes that initiate a plaque. We found that individual plaques contain a mean of 10 infecting viral genomes (range, 1 to 212). Few plaques contained more than two dominant genomes. To determine whether multigenome infectious units consist of collectively transmitting virions, infectious units of ZIKV were then separated mechanically by centrifugation, and heavier fractions were found to contain more genomes per plaque-forming unit, with larger diameters. Finally, larger/heavier infectious units reformed after removal. These data suggest that ZIKV populations consist of a variety of infectious unit sizes, likely mostly made up of aggregates, and only rarely begin with a single virus genome. IMPORTANCE The arthropod-borne Zika virus (ZIKV) infects humans and can cause severe neurological sequelae, particularly in fetuses infected in utero. How this virus has been able to spread across vast geological ranges and evolve in new host populations is not yet understood. This research demonstrates a novel mechanism of ZIKV transmission through multigenome aggregates, providing insight into ZIKV evolution, immunologic evasion, and better future therapeutic design. This study shows that ZIKV plaques result from collections of genomes rather than individual genomes, increasing the potential for interactions between ZIKV genotypes.
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Maheden K, Todd B, Gordon CJ, Tchesnokov EP, Götte M. Inhibition of viral RNA-dependent RNA polymerases with clinically relevant nucleotide analogs. Enzymes 2021; 49:315-354. [PMID: 34696837 PMCID: PMC8517576 DOI: 10.1016/bs.enz.2021.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The treatment of viral infections remains challenging, in particular in the face of emerging pathogens. Broad-spectrum antiviral drugs could potentially be used as a first line of defense. The RNA-dependent RNA polymerase (RdRp) of RNA viruses serves as a logical target for drug discovery and development efforts. Herein we discuss compounds that target RdRp of poliovirus, hepatitis C virus, influenza viruses, respiratory syncytial virus, and the growing data on coronaviruses. We focus on nucleotide analogs and mechanisms of action and resistance.
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Affiliation(s)
- Kieran Maheden
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Brendan Todd
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Institute of Virology at University of Alberta, Edmonton, AB, Canada.
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Polymerase Fidelity Contributes to Foot-and-Mouth Disease Virus Pathogenicity and Transmissibility In Vivo. J Virol 2020; 95:JVI.01569-20. [PMID: 33028719 DOI: 10.1128/jvi.01569-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
The low fidelity of foot-and-mouth disease virus (FMDV) RNA-dependent RNA polymerase allows FMDV to exhibit high genetic diversity. Previously, we showed that the genetic diversity of FMDV plays an important role in virulence in suckling mice. Here, we mutated the amino acid residue Phe257, located in the finger domain of FMDV polymerase and conserved across FMDV serotypes, to a cysteine (F257C) to study the relationship between viral genetic diversity, virulence, and transmissibility in natural hosts. The single amino acid substitution in FMDV polymerase resulted in a high-fidelity virus variant, rF257C, with growth kinetics indistinguishable from those of wild-type (WT) virus in cell culture, but it displayed smaller plaques and impaired fitness in direct competition assays. Furthermore, we found that rF257C was attenuated in vivo in both suckling mice and pigs (one of its natural hosts). Importantly, contact exposure experiments showed that the rF257C virus exhibited reduced transmissibility compared to that of wild-type FMDV in the porcine model. This study provides evidence that FMDV genetic diversity is important for viral virulence and transmissibility in susceptible animals. Given that type O FMDV exhibits the highest genetic diversity among all seven serotypes of FMDV, we propose that the lower polymerase fidelity of the type O FMDV could contribute to its dominance worldwide.IMPORTANCE Among the seven serotypes of FMDV, serotype O FMDV have the broadest distribution worldwide, which could be due to their high virulence and transmissibility induced by high genetic diversity. In this paper, we generated a single amino acid substitution FMDV variant with a high-fidelity polymerase associated with viral fitness, virulence, and transmissibility in a natural host. The results highlight that maintenance of viral population diversity is essential for interhost viral spread. This study provides evidence that higher genetic diversity of type O FMDV could increase both virulence and transmissibility, thus leading to their dominance in the global epidemic.
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Andrés C, Garcia-Cehic D, Gregori J, Piñana M, Rodriguez-Frias F, Guerrero-Murillo M, Esperalba J, Rando A, Goterris L, Codina MG, Quer S, Martín MC, Campins M, Ferrer R, Almirante B, Esteban JI, Pumarola T, Antón A, Quer J. Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients. Emerg Microbes Infect 2020; 9:1900-1911. [PMID: 32752979 PMCID: PMC8284971 DOI: 10.1080/22221751.2020.1806735] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site (PRRAR/S), generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We suggest that natural selection has favoured a "Don't burn down the house" strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.
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Affiliation(s)
- Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics SL, Sant Cugat del Valles, Barcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Mercedes Guerrero-Murillo
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Juliana Esperalba
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Ariadna Rando
- Microbiology Department, Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Lidia Goterris
- Microbiology Department, Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Maria Gema Codina
- Microbiology Department, Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Susanna Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Maria Carmen Martín
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Magda Campins
- Preventive Medicine, Hospital Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Ricard Ferrer
- Intensive Care Department. Shock, Disfunció Orgànica i Ressuscitació (SODIR) Research Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Benito Almirante
- Infectious Diseases Department. Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Tomás Pumarola
- Universitat Autònoma de Barcelona, Bellaterra, Spain
- Microbiology Department, Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Spain
- Andrés Antón Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain Universitat Autònoma de Barcelona, 08193Bellaterra, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Josep Quer Liver Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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42
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Petushkova AI, Zamyatnin AA. Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations. Pharmaceuticals (Basel) 2020; 13:E277. [PMID: 32998368 PMCID: PMC7601131 DOI: 10.3390/ph13100277] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/26/2020] [Accepted: 09/26/2020] [Indexed: 12/23/2022] Open
Abstract
Papain-like proteases (PLpro) of coronaviruses (CoVs) support viral reproduction and suppress the immune response of the host, which makes CoV PLpro perspective pharmaceutical targets. Their inhibition could both prevent viral replication and boost the immune system of the host, leading to the speedy recovery of the patient. Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the third CoV outbreak in the last 20 years. Frequent mutations of the viral genome likely lead to the emergence of more CoVs. Inhibitors for CoV PLpro can be broad-spectrum and can diminish present and prevent future CoV outbreaks as PLpro from different CoVs have conservative structures. Several inhibitors have been developed to withstand SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV). This review summarizes the structural features of CoV PLpro, the inhibitors that have been identified over the last 20 years, and the compounds that have the potential to become novel effective therapeutics against CoVs in the near future.
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Affiliation(s)
- Anastasiia I. Petushkova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
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43
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Furuse Y, Oshitani H. Viruses That Can and Cannot Coexist With Humans and the Future of SARS-CoV-2. Front Microbiol 2020; 11:583252. [PMID: 33042101 PMCID: PMC7530166 DOI: 10.3389/fmicb.2020.583252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/19/2020] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a worldwide pandemic. Many projections concerning the outbreak, such as the estimated number of cases and deaths in upcoming months, have been made available. However, what happens to the virus after the pandemic subsides has not been fully explored. In this article, we discuss the ways that past and present human viruses have emerged via zoonotic transmission, the mechanisms that they have acquired the ability for effective transmission among humans, the process to sustain a chain of transmission to coexist with humans, and the factors important for complete containment leading to eradication of viruses. These aspects of viral disease may provide clues for the future path that SARS-CoV-2 might take in relation to human infection.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
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44
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Kadoya SS, Urayama SI, Nunoura T, Hirai M, Takaki Y, Kitajima M, Nakagomi T, Nakagomi O, Okabe S, Nishimura O, Sano D. Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain. J Virol 2020; 94:e02083-19. [PMID: 32132235 PMCID: PMC7199400 DOI: 10.1128/jvi.02083-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/21/2020] [Indexed: 12/24/2022] Open
Abstract
RNA viruses form a dynamic distribution of mutant swarms (termed "quasispecies") due to the accumulation of mutations in the viral genome. The genetic diversity of a viral population is affected by several factors, including a bottleneck effect. Human-to-human transmission exemplifies a bottleneck effect, in that only part of a viral population can reach the next susceptible hosts. In the present study, two lineages of the rhesus rotavirus (RRV) strain of rotavirus A were serially passaged five times at a multiplicity of infection (MOI) of 0.1 or 0.001, and three phenotypes (infectious titer, cell binding ability, and specific growth rate) were used to evaluate the impact of a bottleneck effect on the RRV population. The specific growth rate values of lineages passaged under the stronger bottleneck (MOI of 0.001) were higher after five passages. The nucleotide diversity also increased, which indicated that the mutant swarms of the lineages under the stronger bottleneck effect were expanded through the serial passages. The random distribution of synonymous and nonsynonymous substitutions on rotavirus genome segments indicated that almost all mutations were selectively neutral. Simple simulations revealed that the presence of minor mutants could influence the specific growth rate of a population in a mutant frequency-dependent manner. These results indicate a stronger bottleneck effect can create more sequence spaces for minor sequences.IMPORTANCE In this study, we investigated a bottleneck effect on an RRV population that may drastically affect the viral population structure. RRV populations were serially passaged under two levels of a bottleneck effect, which exemplified human-to-human transmission. As a result, the genetic diversity and specific growth rate of RRV populations increased under the stronger bottleneck effect, which implied that a bottleneck created a new space in a population for minor mutants originally existing in a hidden layer, which includes minor mutations that cannot be distinguished from a sequencing error. The results of this study suggest that the genetic drift caused by a bottleneck in human-to-human transmission explains the random appearance of new genetic lineages causing viral outbreaks, which can be expected according to molecular epidemiology using next-generation sequencing in which the viral genetic diversity within a viral population is investigated.
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Affiliation(s)
- Syun-Suke Kadoya
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Syun-Ichi Urayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Toyoko Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Osamu Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Osamu Nishimura
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
- Department of Environmental Studies, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
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45
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Kum DB, Mishra N, Vrancken B, Thibaut HJ, Wilder-Smith A, Lemey P, Neyts J, Dallmeier K. Limited evolution of the yellow fever virus 17d in a mouse infection model. Emerg Microbes Infect 2020; 8:1734-1746. [PMID: 31797751 PMCID: PMC6896426 DOI: 10.1080/22221751.2019.1694394] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
By infecting mice with the yellow fever virus vaccine strain 17D (YFV-17D; Stamaril®), the dose dependence and evolutionary consequences of neurotropic yellow fever infection was assessed. Highly susceptible AG129 mice were used to allow for a maximal/unlimited expansion of the viral populations. Infected mice uniformly developed neurotropic disease; the virus was isolated from their brains, plaque purified and sequenced. Viral RNA populations were overall rather homogenous [Shannon entropies 0−0.15]. The remaining, yet limited intra-host population diversity (0−11 nucleotide exchanges per genome) appeared to be a consequence of pre-existing clonal heterogeneities (quasispecies) of Stamaril®. In parallel, mice were infected with a molecular clone of YFV-17D which was in vivo launched from a plasmid. Such plasmid-launched YFV-17D had a further reduced and almost clonal evolution. The limited intra-host evolution during unrestricted expansion in a highly susceptible host is relevant for vaccine and drug development against flaviviruses in general. Firstly, a propensity for limited evolution even upon infection with a (very) low inoculum suggests that fractional dosing as implemented in current YF-outbreak control may pose only a limited risk of reversion to pathogenic vaccine-derived virus variants. Secondly, it also largely lowers the chance of antigenic drift and development of resistance to antivirals.
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Affiliation(s)
- Dieudonné Buh Kum
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium.,Aligos Belgium, Leuven, Belgium
| | - Niraj Mishra
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Bram Vrancken
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Annelies Wilder-Smith
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
| | - Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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46
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Leber MF, Hoyler B, Prien S, Neault S, Engeland CE, Förster JM, Bossow S, Springfeld C, von Kalle C, Jäger D, Bell JC, Ungerechts G. Sequencing of serially passaged measles virus affirms its genomic stability and reveals a nonrandom distribution of consensus mutations. J Gen Virol 2020; 101:399-409. [PMID: 32053093 DOI: 10.1099/jgv.0.001395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Oncolytic virotherapy is an emerging treatment option for numerous cancers, with several virus families currently being evaluated in clinical trials. More specifically, vaccine-strain measles virus has arisen as a promising candidate for the treatment of different tumour types in several early clinical trials. Replicating viruses, and especially RNA viruses without proofreading polymerases, can rapidly adapt to varying environments by selecting quasispecies with advantageous genetic mutations. Subsequently, these genetic alterations could potentially weaken the safety profile of virotherapy. In this study, we demonstrate that, following an extended period of virus replication in producer or cancer cell lines, the quasispecies consensus sequence of vaccine strain-derived measles virus accrues a remarkably small number of mutations throughout the nonsegmented negative-stranded RNA genome. Interestingly, we detected a nonrandom distribution of genetic alterations within the genome, with an overall decreasing frequency of mutations from the 3' genome start to its 5' end. Comparing the serially passaged viruses to the parental virus on producer cells, we found that the acquired consensus mutations did not drastically change viral replication kinetics or cytolytic potency. Collectively, our data corroborate the genomic stability and excellent safety profile of oncolytic measles virus, thus supporting its continued development and clinical translation as a promising viro-immunotherapeutic.
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Affiliation(s)
- Mathias Felix Leber
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
| | - Birgit Hoyler
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefanie Prien
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Serge Neault
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
| | - Christine E Engeland
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Judith M Förster
- Heidelberg University, Faculty of Biosciences, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sascha Bossow
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Christoph Springfeld
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Christof von Kalle
- Sidra Medical and Research Center, Al Luqta Street, Education City, North Campus, 26999, Doha, Qatar.,Berlin Institute of Health and Charité, Universitätsmedizin, Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany.,German Cancer Research Center (DKFZ), Division of Translational Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Dirk Jäger
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - John C Bell
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
| | - Guy Ungerechts
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada.,Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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47
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Rubio L, Galipienso L, Ferriol I. Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution. FRONTIERS IN PLANT SCIENCE 2020; 11:1092. [PMID: 32765569 PMCID: PMC7380168 DOI: 10.3389/fpls.2020.01092] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/02/2020] [Indexed: 05/04/2023]
Abstract
Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable.
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Affiliation(s)
- Luis Rubio
- Centro de Protección Vegetal y Biotecnology, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
- *Correspondence: Luis Rubio,
| | - Luis Galipienso
- Centro de Protección Vegetal y Biotecnology, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Inmaculada Ferriol
- Plant Responses to Stress Programme, Centre for Research in Agricultural Genomics (CRAG-CSIC_UAB-UB) Cerdanyola del Vallès, Barcelona, Spain
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48
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Paploski IAD, Corzo C, Rovira A, Murtaugh MP, Sanhueza JM, Vilalta C, Schroeder DC, VanderWaal K. Temporal Dynamics of Co-circulating Lineages of Porcine Reproductive and Respiratory Syndrome Virus. Front Microbiol 2019; 10:2486. [PMID: 31736919 PMCID: PMC6839445 DOI: 10.3389/fmicb.2019.02486] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/15/2019] [Indexed: 02/05/2023] Open
Abstract
Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009–2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sub-lineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non- synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact.
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Affiliation(s)
| | - Cesar Corzo
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Albert Rovira
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Michael P Murtaugh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Juan Manuel Sanhueza
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Carles Vilalta
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States.,School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
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Tyr82 Amino Acid Mutation in PB1 Polymerase Induces an Influenza Virus Mutator Phenotype. J Virol 2019; 93:JVI.00834-19. [PMID: 31462570 DOI: 10.1128/jvi.00834-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/19/2019] [Indexed: 01/16/2023] Open
Abstract
In various positive-sense single-stranded RNA viruses, a low-fidelity viral RNA-dependent RNA polymerase (RdRp) confers attenuated phenotypes by increasing the mutation frequency. We report a negative-sense single-stranded RNA virus RdRp mutant strain with a mutator phenotype. Based on structural data of RdRp, rational targeting of key residues, and screening of fidelity variants, we isolated a novel low-fidelity mutator strain of influenza virus that harbors a Tyr82-to-Cys (Y82C) single-amino-acid substitution in the PB1 polymerase subunit. The purified PB1-Y82C polymerase indeed showed an increased frequency of misincorporation compared with the wild-type PB1 in an in vitro biochemical assay. To further investigate the effects of position 82 on PB1 polymerase fidelity, we substituted various amino acids at this position. As a result, we isolated various novel mutators other than PB1-Y82C with higher mutation frequencies. The structural model of influenza virus polymerase complex suggested that the Tyr82 residue, which is located at the nucleoside triphosphate entrance tunnel, may influence a fidelity checkpoint. Interestingly, although the PB1-Y82C variant replicated with wild-type PB1-like kinetics in tissue culture, the 50% lethal dose of the PB1-Y82C mutant was 10 times lower than that of wild-type PB1 in embryonated chicken eggs. In conclusion, our data indicate that the Tyr82 residue of PB1 has a crucial role in regulating polymerase fidelity of influenza virus and is closely related to attenuated pathogenic phenotypes in vivo IMPORTANCE Influenza A virus rapidly acquires antigenic changes and antiviral drug resistance, which limit the effectiveness of vaccines and drug treatments, primarily owing to its high rate of evolution. Virus populations formed by quasispecies can contain resistance mutations even before a selective pressure is applied. To study the effects of the viral mutation spectrum and quasispecies, high- and low-fidelity variants have been isolated for several RNA viruses. Here, we report the discovery of a low-fidelity RdRp variant of influenza A virus that contains a substitution at Tyr82 in PB1. Viruses containing the PB1-Y82C substitution showed growth kinetics and viral RNA synthesis levels similar to those of the wild-type virus in cell culture; however, they had significantly attenuated phenotypes in a chicken egg infection experiment. These data demonstrated that decreased RdRp fidelity attenuates influenza A virus in vivo, which is a desirable feature for the development of safer live attenuated vaccine candidates.
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50
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Predictive Water Virology: Hierarchical Bayesian Modeling for Estimating Virus Inactivation Curve. WATER 2019. [DOI: 10.3390/w11102187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hazard analysis and critical control point (HACCP) are a series of actions to be taken to ensure product consumption safety. In food poisoning risk management, researchers in the field of predictive microbiology calculate the values that provide minimum stress (e.g., temperature and contact time in heating) for sufficient microbe inactivation based on mathematical models. HACCP has also been employed for health risk management in sanitation safety planning (SSP), but the application of predictive microbiology to water-related pathogens is difficult because the variety of pathogen types and the complex composition of the wastewater matrix does not allow us to make a simple mathematical model to predict inactivation efficiency. In this study, we performed a systematic review and meta-analysis to construct predictive inactivation curves using free chlorine for enteric viruses based on a hierarchical Bayesian model using parameters such as water quality. Our model considered uncertainty among virus disinfection tests and difference in genotype-dependent sensitivity of a virus to disinfectant. The proposed model makes it possible to identify critical disinfection stress capable of reducing virus concentration that is below the tolerable concentration to ensure human health.
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