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Agol VI. Existence and significance of viral nonreplicative RNA recombination. PLoS Biol 2023; 21:e3002216. [PMID: 37490454 PMCID: PMC10368251 DOI: 10.1371/journal.pbio.3002216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/26/2023] [Indexed: 07/27/2023] Open
Abstract
In response to a recent article, this Formal Comment discusses nonreplicative joining of fragments of viral RNAs, a class of reactions which might be widespread in nature, contributing to conservation and evolution not only of viruses but of cellular organisms as well.
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Affiliation(s)
- Vadim I Agol
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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2
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Fixsen SM, Cone KR, Goldstein SA, Sasani TA, Quinlan AR, Rothenburg S, Elde NC. Poxviruses capture host genes by LINE-1 retrotransposition. eLife 2022; 11:63332. [PMID: 36069526 PMCID: PMC9578705 DOI: 10.7554/elife.63332] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Horizontal gene transfer (HGT) provides a major source of genetic variation. Many viruses, including poxviruses, encode genes with crucial functions directly gained by gene transfer from hosts. The mechanism of transfer to poxvirus genomes is unknown. Using genome analysis and experimental screens of infected cells, we discovered a central role for Long Interspersed Nuclear Element-1 retrotransposition in HGT to virus genomes. The process recapitulates processed pseudogene generation, but with host messenger RNA directed into virus genomes. Intriguingly, hallmark features of retrotransposition appear to favor virus adaption through rapid duplication of captured host genes on arrival. Our study reveals a previously unrecognized conduit of genetic traffic with fundamental implications for the evolution of many virus classes and their hosts.
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Affiliation(s)
- Sarah M Fixsen
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Kelsey R Cone
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Stephen A Goldstein
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, United States
| | - Nels C Elde
- Department of Human Genetics, University of Utah, Salt Lake City, United States
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3
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Pröll J, Paar C, Taylor N, Skocic M, Freystetter A, Blaimschein A, Mayr R, Niklas N, Atzmüller S, Raml E, Wechselberger C. New aspects of the Virus Life Cycle and Clinical Utility of Next Generation Sequencing based HIV-1 Resistance Testing in the Genomic, the Proviral and the Viral Reservoir of Peripheral Blood Mononuclear Cells. Curr HIV Res 2022; 20:213-221. [PMID: 35331114 DOI: 10.2174/1570162x20666220324111418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 12/07/2021] [Accepted: 01/28/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Typically, genotypic resistance testing is recommended at the start of antiretroviral therapy and is even mandatory in cases of virologic failure. The material of choice is plasma viral RNA. However, in patients with low viremia (viral load < 500 copies/ml), resistance testing by population-based sequencing is very difficult. OBJECTIVE Therefore, we aimed to investigate whether next generation sequencing (NGS) from proviral DNA and RNA could be an alternative. MATERIAL AND METHODS EDTA blood samples (n = 36) from routine clinical viral load testing were used for the study. Viral loads ranged from 96 to 390,000 copies/mL, with 100% of samples having low viremia. Distribution of subtypes A (n = 2), B (n = 16), C (n = 4), D (n = 2), G (1), CRF02 AG (n = 5), CRF01 AE (n = 5), undefined/mixed (n = 4). The extracted consensus sequences were uploaded to the Stanford HIV Drug Resistance Data Base and Geno2pheno for online analysis of drug resistance mutations and resistance factors. RESULTS A total of 2476 variants or drug resistance mutations (DRMs) were detected with Sanger sequencing, compared with 2892 variants with NGS. An average of 822/1008 variants were identified in plasma viral RNA by Sanger or NGS sequencing, 834/956 in cellular viral RNA, and 820/928 in cellular viral DNA. CONCLUSIONS Both methods are well suited for the detection of HIV substitutions or drug resistance mutations. Our results suggest that cellular RNA or cellular viral DNA is an informative alternative to plasma viral RNA for variant detection in patients with low viremia, as shown by the high correlation of variants in the different viral pools. And we show that by using UDS, a plus of two DRMs per patient becomes visible and that can make a big difference in the assessment of the expected resistance behavior of the virus.
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Affiliation(s)
- Johannes Pröll
- Center for Medical Research, Medical Faculty Johannes Kepler University, Medical Faculty, Krankenhausstraße 5, A-4020 Linz, Austria
| | - Christian Paar
- Institute of Laboratory Medicine, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Ninon Taylor
- Department of Dermatology, University Hospital of the Paracelsus Medical University, Müllner Hauptstraße 48, A-5020 Salzburg, Austria
| | - Matthias Skocic
- Department of Dermatology, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Andrea Freystetter
- Institute of Laboratory Medicine, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Anna Blaimschein
- Institute of Laboratory Medicine, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Roland Mayr
- Institute of Laboratory Medicine, Kepler Universitätsklinikum, Med Campus III, Krankenhausstraße 9, A-4020 Linz, Austria
| | - Norbert Niklas
- Red Cross Transfusion Center for Upper Austria, Krankenhausstraße 7, A-4020, Austria
| | - Sabine Atzmüller
- Center for Medical Research, Medical Faculty Johannes Kepler University, Medical Faculty, Krankenhausstraße 5, A-4020 Linz, Austria
| | - Edeltraud Raml
- Center for Medical Research, Medical Faculty Johannes Kepler University, Medical Faculty, Krankenhausstraße 5, A-4020 Linz, Austria
| | - Christian Wechselberger
- Division of Pathophysiology, Institute for Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University, ADM Building, Krankenhausstraße 5, A-4020 Linz, Austria
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Viral dUTPases: Modulators of Innate Immunity. Biomolecules 2022; 12:biom12020227. [PMID: 35204728 PMCID: PMC8961515 DOI: 10.3390/biom12020227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Most free-living organisms encode for a deoxyuridine triphosphate nucleotidohydrolase (dUTPase; EC 3.6.1.23). dUTPases represent a family of metalloenzymes that catalyze the hydrolysis of dUTP to dUMP and pyrophosphate, preventing dUTP from being incorporated into DNA by DNA polymerases, maintaining a low dUTP/dTTP pool ratio and providing a necessary precursor for dTTP biosynthesis. Thus, dUTPases are involved in maintaining genomic integrity by preventing the uracilation of DNA. Many DNA-containing viruses, which infect mammals also encode for a dUTPase. This review will summarize studies demonstrating that, in addition to their classical enzymatic activity, some dUTPases possess novel functions that modulate the host innate immune response.
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Nikolaidis M, Markoulatos P, Van de Peer Y, Oliver SG, Amoutzias GD. The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes. Mol Biol Evol 2022; 39:msab292. [PMID: 34638137 PMCID: PMC8549283 DOI: 10.1093/molbev/msab292] [Citation(s) in RCA: 23] [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: 12/16/2022] Open
Abstract
Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain-through nonhomologous recombination-accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.
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Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Grigorios D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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Amoutzias GD, Nikolaidis M, Tryfonopoulou E, Chlichlia K, Markoulatos P, Oliver SG. The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2. Viruses 2022; 14:78. [PMID: 35062282 PMCID: PMC8778387 DOI: 10.3390/v14010078] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/22/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics in humans that were of zoonotic origin, highlights the importance of studying the evolution of the entire CoV subfamily in order to understand how novel strains emerge and which molecular processes affect their adaptation, transmissibility, host/tissue tropism, and patho non-homologous genicity. In this review, we focus on studies over the last two years that reveal the impact of point mutations, insertions/deletions, and intratypic/intertypic homologous and non-homologous recombination events on the evolution of CoVs. We discuss whether the next generations of CoV vaccines should be directed against other CoV proteins in addition to or instead of spike. Based on the observed patterns of molecular evolution for the entire subfamily, we discuss five scenarios for the future evolutionary path of SARS-CoV-2 and the COVID-19 pandemic. Finally, within this evolutionary context, we discuss the recently emerged Omicron (B.1.1.529) VoC.
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Affiliation(s)
- Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Eleni Tryfonopoulou
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece; (E.T.); (K.C.)
| | - Katerina Chlichlia
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece; (E.T.); (K.C.)
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Stephen G. Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Koonin EV, Krupovic M. A life LINE for large viruses. eLife 2022; 11:83488. [PMID: 36282171 PMCID: PMC9596153 DOI: 10.7554/elife.83488] [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: 11/13/2022] Open
Abstract
As long suspected, poxviruses capture host genes through a reverse-transcription process now shown to be mediated by retrotransposons.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Institutes of HealthBethesdaUnited States
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology UnitParisFrance
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Mirza AZ, Shamshad H, Osra FA, Habeebullah TM, Morad M. An overview of viruses discovered over the last decades and drug development for the current pandemic. Eur J Pharmacol 2021; 890:173746. [PMID: 33221318 PMCID: PMC8711773 DOI: 10.1016/j.ejphar.2020.173746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 01/06/2023]
Abstract
Since the discovery of the yellow fever virus in 1901, thus far, two hundred nineteen viral species are recognized as human pathogens. Each year, the number of viruses causing infections in humans increases, triggering epidemics and pandemics, such as the current COVID-19 pandemic. Pointing to bats as the natural host, in 2019, a genome highly identical to a bat coronavirus (COVID-19) spread all over the world, and the World Health Organization (WHO) officially confirmed it as a pandemic. The virus mainly spreads through the respiratory tract, uses angiotensin-converting enzyme 2 (ACE2) as a receptor, and is characterized by symptoms of fever, cough, and fatigue. Antivirals and vaccines have provided improvements in some cases, but the discovery of a new and diverse variety of viruses with outbreaks has posed a challenge in timely treatments for medical scientists. Currently, few specific antiviral strategies are being used, and many of the effective antiviral drugs and reported active molecules are under vital exploration. In this review, with the details of viral diseases, we summarize the current attempts in drug development, epidemiology, and the latest treatments and scientific advancements to combat the COVID-19 epidemic. Moreover, we discuss ways to reduce epidemics and pandemics in the near future.
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Affiliation(s)
- Agha Zeeshan Mirza
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Hina Shamshad
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, University of Karachi, Karachi, 75270, Pakistan
| | | | - Turki M Habeebullah
- Department of Environment and Health Research, Custodian of Two Holy Mosques Institute for Hajj and Umrah Research, Umm-Al-Qura University, Makkah, Saudi Arabia
| | - Moataz Morad
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
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Krupovic M, Yutin N, Koonin E. Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase. Virus Evol 2020; 6:veaa059. [PMID: 33686356 DOI: 10.1093/ve/veaa059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The diverse viruses in the phylum Nucleocytoviricota (also known as NLCDVs, Nucleo-cytoplasmic Large DNA Viruses) typically possess large icosahedral virions. However, in several families of Nucleocytoviricota, the icosahedral capsid was replaced by irregular particle shapes, most notably, the amphora-like virions of pandoraviruses and pithoviruses, the largest known virus particles in the entire virosphere. Pandoraviruses appear to be the most highly derived viruses in this phylum because their evolution involved not only the change in the virion shape, but also, the actual loss of the gene encoding double-jelly roll major capsid protein (DJR MCP), the main building block of icosahedral capsids in this virus assemblage. Instead, pandoravirus virions are built of unrelated abundant proteins. Here we show that the second most abundant virion protein of pandoraviruses, major virion protein 2 (MVP2), evolved from an inactivated derivative of a bacterial glycoside hydrolase of the GH16 family. The ancestral form of MVP2 was apparently acquired early in the evolution of the Nucleocytoviricota, to become a minor virion protein. After a duplication in the common ancestor of pandoraviruses and molliviruses, one of the paralogs displaces DJR MCP in pandoraviruses, conceivably, opening the way for a major increase in the size of the virion and the genome. Exaptation of a carbohydrate-binding protein for the function of the MVP is a general trend in virus evolution and might underlie the transformation of the virion shape in other groups of the Nucleocytoviricota as well.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Archaeal Virology Unit, Institut Pasteur, Paris 75015, France
| | - Natalya Yutin
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene Koonin
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
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11
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Campillo-Balderas JA, Lazcano A, Becerra A. Viral Genome Size Distribution Does not Correlate with the Antiquity of the Host Lineages. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00143] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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