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Desingu PA, Rubeni TP, Nagarajan K, Sundaresan NR. Molecular evolution of 2022 multi-country outbreak-causing monkeypox virus Clade IIb. iScience 2024; 27:108601. [PMID: 38188513 PMCID: PMC10770499 DOI: 10.1016/j.isci.2023.108601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/16/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
The monkeypox virus (Mpoxv) Clade IIb viruses that caused an outbreak in 2017-18 in Nigeria and its genetically related viruses have been detected in many countries and caused multi-country outbreak in 2022. Since the pandemic-causing Mpoxv Clade IIb viruses are closely related to Clade IIa viruses which mostly cause endemic, the Clade IIb Mpoxv might have certain specific genetic variations that are still largely unknown. Here, we have systematically analyzed genetic alterations in different clades of Mpox viruses. The results suggest that the Mpoxv Clade IIb have genetic variations in terms of genomic gaps, frameshift mutations, in-frame nonsense mutations, amino acid tandem repeats, and APOBEC3 mutations. Further, we observed specific genetic variations in the multiple genes specific for Clade I and Clade IIb, and exclusive genetic variations for Clade IIa and Clade IIb. Collectively, findings shed light on the evolution and genetic variations in the outbreak of 2022 causing Mpoxv Clade IIb.
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Affiliation(s)
- Perumal Arumugam Desingu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | | | - K. Nagarajan
- Department of Veterinary Pathology, Madras Veterinary College, Vepery, Chennai 600007, Tamil Nadu
- Veterinary and Animal Sciences University (TANUVAS)
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2
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Brüssow H. Pandemic potential of poxviruses: From an ancient killer causing smallpox to the surge of monkeypox. Microb Biotechnol 2023; 16:1723-1735. [PMID: 37335284 PMCID: PMC10443337 DOI: 10.1111/1751-7915.14294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 06/04/2023] [Indexed: 06/21/2023] Open
Abstract
Smallpox caused by the variola virus (VARV) was one of the greatest infectious killers of mankind. Historical records trace back smallpox for at least a millennium while phylogenetic analysis dated the ancestor of VARV circulating in the 20th century into the 19th century. The discrepancy was solved by the detection of distinct VARV sequences first in 17th-century mummies and then in human skeletons dated to the 7th century. The historical records noted marked variability in VARV virulence which scientists tentatively associated with gene losses occurring when broad-host poxviruses narrow their host range to a single host. VARV split from camel and gerbil poxviruses and had no animal reservoir, a prerequisite for its eradication led by WHO. The search for residual pockets of VARV led to the discovery of the monkeypox virus (MPXV); followed by the detection of endemic smallpox-like monkeypox (mpox) disease in Africa. Mpox is caused by less virulent clade 2 MPXV in West Africa and more virulent clade 1 MPXV in Central Africa. Exported clade 2 mpox cases associated with the pet animal trade were observed in 2003 in the USA. In 2022 a world-wide mpox epidemic infecting more than 80,000 people was noted, peaking in August 2022 although waning rapidly. The cases displayed particular epidemiological characteristics affecting nearly exclusively young men having sex with men (MSM). In contrast, mpox in Africa mostly affects children by non-sexual transmission routes possibly from uncharacterized animal reservoirs. While African children show a classical smallpox picture, MSM mpox cases show few mostly anogenital lesions, low-hospitalization rates and 140 fatal cases worldwide. MPXV strains from North America and Europe are closely related, derived from clade 2 African MPXV. Distinct transmission mechanisms are more likely causes for the epidemiological and clinical differences between endemic African cases and the 2022 epidemic cases than viral traits.
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Affiliation(s)
- Harald Brüssow
- Laboratory of Gene Technology, Department of BiosystemsKU LeuvenLeuvenBelgium
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3
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Kumar P, Chaudhary B, Yadav N, Devi S, Pareek A, Alla S, Kajal F, Nowrouzi-Kia B, Chattu VK, Gupta MM. Recent Advances in Research and Management of Human Monkeypox Virus: An Emerging Global Health Threat. Viruses 2023; 15:v15040937. [PMID: 37112916 PMCID: PMC10146223 DOI: 10.3390/v15040937] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/01/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
In 2003, the United States saw an epidemic of monkeypox that was later traced back to rodents of West Africa infected with the monkeypox virus (MPXV). Disease in the United States seemed less severe than the smallpox-like disease in the Democratic Republic of the Congo (DRC). In this study, researchers analyzed data from Central Africa: two distinct MPXV clades were confirmed by sequencing the genomes of MPXV isolates from Western Africa, the United States, and Central Africa. By comparing open reading frames across MPXV clades, scientists can infer which virus proteins might account for the observed variation in pathogenicity in humans. Monkeypox can be prevented and controlled with a better understanding of MPXV's molecular etiology and epidemiological and clinical features. In light of the current outbreaks worldwide, we provide updated information on monkeypox for medical professionals in this review.
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Affiliation(s)
- Parveen Kumar
- Shri Ram College of Pharmacy, Karnal 132116, Haryana, India
| | - Benu Chaudhary
- Guru Gobind Singh College of Pharmacy, Yamunanagar 135001, Haryana, India
| | - Nishant Yadav
- B.S. Anangpuria Institute of Pharmacy, Faridabad 121004, Haryana, India
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India
| | - Sushma Devi
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India
| | - Ashutosh Pareek
- Department of Pharmacy, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India
| | - Sujatha Alla
- Department of Engineering Management & Systems Engineering, Frank Batten College of Engineering, Old Dominion University, Norfolk, VA 23529, USA
- Center for Technology and Innovations, Global Health Research and Innovations Canada, Toronto, ON M1J 2W8, Canada
| | - Fnu Kajal
- Department of Health Promotion Sciences, University of Arizona, Tucson, AZ 85719, USA
| | - Behdin Nowrouzi-Kia
- Department of Occupational Science and Occupational Therapy, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
| | - Vijay Kumar Chattu
- Department of Occupational Science and Occupational Therapy, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada
- Department of Community Medicine, Faculty of Medicine, Datta Meghe Institute of Medical Sciences, Wardha 442107, Maharashtra, India
- Center for Transdisciplinary Research, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Madan Mohan Gupta
- School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, St. Augustine 3303, Trinidad and Tobago
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4
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Shchelkunova GA, Shchelkunov SN. Smallpox, Monkeypox and Other Human Orthopoxvirus Infections. Viruses 2022; 15:103. [PMID: 36680142 PMCID: PMC9865299 DOI: 10.3390/v15010103] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
Considering that vaccination against smallpox with live vaccinia virus led to serious adverse effects in some cases, the WHO, after declaration of the global eradication of smallpox in 1980, strongly recommended to discontinue the vaccination in all countries. This led to the loss of immunity against not only smallpox but also other zoonotic orthopoxvirus infections in humans over the past years. An increasing number of human infections with zoonotic orthopoxviruses and, first of all, monkeypox, force us to reconsider a possible re-emergence of smallpox or a similar disease as a result of natural evolution of these viruses. The review contains a brief analysis of the results of studies on genomic organization and evolution of human pathogenic orthopoxviruses, development of modern methods for diagnosis, vaccination, and chemotherapy of smallpox, monkeypox, and other zoonotic human orthopoxvirus infections.
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Affiliation(s)
| | - Sergei N. Shchelkunov
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, 630559 Novosibirsk, Russia
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5
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Lvov DK, Alkhovsky SV, Zhirnov OP. [130th anniversary of virology]. Vopr Virusol 2022; 67:357-384. [PMID: 36515283 DOI: 10.36233/0507-4088-140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Indexed: 06/17/2023]
Abstract
130 years ago, in 1892, our great compatriot Dmitry Iosifovich Ivanovsky (18641920) discovered a new type of pathogen viruses. Viruses have existed since the birth of life on Earth and for more than three billion years, as the biosphere evolved, they are included in interpopulation interactions with representatives of all kingdoms of life: archaea, bacteria, protozoa, algae, fungi, plants, invertebrates, and vertebrates, including the Homo sapiens (Hominidae, Homininae). Discovery of D.I. Ivanovsky laid the foundation for a new science virology. The rapid development of virology in the 20th century was associated with the fight against emerging and reemerging infections, epidemics (epizootics) and pandemics (panzootics) of which posed a threat to national and global biosecurity (tick-borne and other encephalitis, hemorrhagic fevers, influenza, smallpox, poliomyelitis, HIV, parenteral hepatitis, coronaviral and other infections). Fundamental research on viruses created the basis for the development of effective methods of diagnostics, vaccine prophylaxis, and antiviral drugs. Russian virologists continue to occupy leading positions in some priority areas of modern virology in vaccinology, environmental studies oz zoonotic viruses, studies of viral evolution in various ecosystems, and several other areas. A meaningful combination of theoretical approaches to studying the evolution of viruses with innovative methods for studying their molecular genetic properties and the creation of new generations of vaccines and antiviral drugs on this basis will significantly reduce the consequences of future pandemics or panzootics. The review presents the main stages in the formation and development of virology as a science in Russia with an emphasis on the most significant achievements of soviet and Russian virologists in the fight against viral infectious diseases.
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Affiliation(s)
- D K Lvov
- D.I. Ivanovsky Institute of Virology of N.F Gamaleya National Research Center of Epidemiology and Microbiology of Ministry of Health of the Russian Federation
| | - S V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F Gamaleya National Research Center of Epidemiology and Microbiology of Ministry of Health of the Russian Federation
| | - O P Zhirnov
- D.I. Ivanovsky Institute of Virology of N.F Gamaleya National Research Center of Epidemiology and Microbiology of Ministry of Health of the Russian Federation
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6
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Sprygin A, Mazloum A, van Schalkwyk A, Babiuk S. Capripoxviruses, leporipoxviruses, and orthopoxviruses: Occurrences of recombination. Front Microbiol 2022; 13:978829. [PMID: 36274700 PMCID: PMC9584655 DOI: 10.3389/fmicb.2022.978829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Poxviruses are double-stranded DNA viruses with several members displaying restricted host ranges. They are genetically stable with low nucleotide mutation rates compared to other viruses, due to the poxviral high-fidelity DNA polymerase. Despite the low accumulation of mutations per replication cycle, poxvirus genomes can recombine with each other to generate genetically rearranged viruses through recombination, a process directly associated with replication and the aforementioned DNA polymerase. Orthopoxvirus replication is intimately tethered to high frequencies of homologous recombination between co-infecting viruses, duplicated sequences of the same virus, and plasmid DNA transfected into poxvirus-infected cells. Unfortunately, the effect of these genomic alterations on the cellular context for all poxviruses across the family Poxviridae remains elusive. However, emerging sequence data on currently circulating and archived poxviruses, such as the genera orthopoxviruses and capripoxviruses, display a wide degree of divergence. This genetic variability cannot be explained by clonality or genetic drift alone, but are probably a result of significant genomic alterations, such as homologous recombination, gene loss and gain, or gene duplications as the major selection forces acting on viral progeny. The objective of this review is to cross-sectionally overview the currently available findings on natural and laboratory observations of recombination in orthopoxviruses, capripoxviruses, and leporipoxviruses, as well as the possible mechanisms involved. Overall, the reviewed available evidence allows us to conclude that the current state of knowledge is limited in terms of the relevance of genetic variations across even a genus of poxviruses as well as fundamental features governing and precipitating intrinsic gene flow and recombination events.
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Affiliation(s)
- Alexander Sprygin
- Federal Center for Animal Health, Vladimir, Russia
- *Correspondence: Alexander Sprygin,
| | - Ali Mazloum
- Federal Center for Animal Health, Vladimir, Russia
| | | | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
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Shchelkunov SN, Shchelkunova GA. [We should be prepared to smallpox re-emergence.]. Vopr Virusol 2021; 64:206-214. [PMID: 32167685 DOI: 10.36233/0507-4088-2019-64-5-206-214] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022]
Abstract
The review contains a brief analysis of the results of investigations conducted during 40 years after smallpox eradication and directed to study genomic organization and evolution of variola virus (VARV) and development of modern diagnostics, vaccines and chemotherapies of smallpox and other zoonotic orthopoxviral infections of humans. Taking into account that smallpox vaccination in several cases had adverse side effects, WHO recommended ceasing this vaccination after 1980 in all countries of the world. The result of this decision is that the mankind lost the collective immunity not only to smallpox, but also to other zoonotic orthopoxvirus infections. The ever more frequently recorded human cases of zoonotic orthopoxvirus infections force to renew consideration of the problem of possible smallpox reemergence resulting from natural evolution of these viruses. Analysis of the available archive data on smallpox epidemics, the history of ancient civilizations, and the newest data on the evolutionary relationship of orthopoxviruses has allowed us to hypothesize that VARV could have repeatedly reemerged via evolutionary changes in a zoonotic ancestor virus and then disappeared because of insufficient population size of isolated ancient civilizations. Only the historically last smallpox pandemic continued for a long time and was contained and stopped in the 20th century thanks to the joint efforts of medics and scientists from many countries under the aegis of WHO. Thus, there is no fundamental prohibition on potential reemergence of smallpox or a similar human disease in future in the course of natural evolution of the currently existing zoonotic orthopoxviruses. Correspondingly, it is of the utmost importance to develop and widely adopt state-of-the-art methods for efficient and rapid species-specific diagnosis of all orthopoxvirus species pathogenic for humans, VARV included. It is also most important to develop new safe methods for prevention and therapy of human orthopoxvirus infections.
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Affiliation(s)
- S N Shchelkunov
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk region, 630559, Russia
| | - G A Shchelkunova
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk region, 630559, Russia
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8
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Ferrari G, Neukamm J, Baalsrud HT, Breidenstein AM, Ravinet M, Phillips C, Rühli F, Bouwman A, Schuenemann VJ. Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190572. [PMID: 33012235 PMCID: PMC7702794 DOI: 10.1098/rstb.2019.0572] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2020] [Indexed: 12/15/2022] Open
Abstract
Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Helle T. Baalsrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
| | - Abagail M. Breidenstein
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Carina Phillips
- The Royal College of Surgeons of England, 35-43 Lincoln's Inn Fields, London WC2A 3PE, UK
| | - Frank Rühli
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Abigail Bouwman
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Verena J. Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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9
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Lvov DK, Gulyukin MI, Zaberezhniy AD, Gulyukin AM. Formation of population gene pools of zoonotic viruses, potentially threatening biosafety. ACTA ACUST UNITED AC 2020; 65:243-258. [DOI: 10.36233/0507-4088-2020-65-5-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/14/2020] [Indexed: 12/14/2022]
Affiliation(s)
- D. K. Lvov
- D.I. Ivanovsky Institute of Virology. N.F Gamaleya National Research Center of Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Russian Federation
| | - M. I. Gulyukin
- Federal State Budget Scientific Institution «Federal Scientific Center VIEV»
| | - A. D. Zaberezhniy
- Federal State Budget Scientific Institution «Federal Scientific Center VIEV»
| | - A. M. Gulyukin
- Federal State Budget Scientific Institution «Federal Scientific Center VIEV»
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10
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Why were the UK and USA unprepared for the COVID-19 pandemic? The systemic weaknesses of neoliberalism: a comparison between the UK, USA, Germany, and South Korea. ACTA ACUST UNITED AC 2020. [DOI: 10.13169/jglobfaul.7.1.0009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
The last case of natural smallpox was recorded in October, 1977. It took humanity almost 20 years to achieve that feat after the World Health Organization had approved the global smallpox eradication program. Vaccination against smallpox was abolished, and, during the past 40 years, the human population has managed to lose immunity not only to smallpox, but to other zoonotic orthopoxvirus infections as well. As a result, multiple outbreaks of orthopoxvirus infections in humans in several continents have been reported over the past decades. The threat of smallpox reemergence as a result of evolutionary transformations of these zoonotic orthopoxviruses exists. Modern techniques for the diagnostics, prevention, and therapy of smallpox and other orthopoxvirus infections are being developed today.
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Olson VA, Shchelkunov SN. Are We Prepared in Case of a Possible Smallpox-Like Disease Emergence? Viruses 2017; 9:E242. [PMID: 32962316 PMCID: PMC5618008 DOI: 10.3390/v9090242] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 12/16/2022] Open
Abstract
Smallpox was the first human disease to be eradicated, through a concerted vaccination campaign led by the World Health Organization. Since its eradication, routine vaccination against smallpox has ceased, leaving the world population susceptible to disease caused by orthopoxviruses. In recent decades, reports of human disease from zoonotic orthopoxviruses have increased. Furthermore, multiple reports of newly identified poxviruses capable of causing human disease have occurred. These facts raise concerns regarding both the opportunity for these zoonotic orthopoxviruses to evolve and become a more severe public health issue, as well as the risk of Variola virus (the causative agent of smallpox) to be utilized as a bioterrorist weapon. The eradication of smallpox occurred prior to the development of the majority of modern virological and molecular biological techniques. Therefore, there is a considerable amount that is not understood regarding how this solely human pathogen interacts with its host. This paper briefly recounts the history and current status of diagnostic tools, vaccines, and anti-viral therapeutics for treatment of smallpox disease. The authors discuss the importance of further research to prepare the global community should a smallpox-like virus emerge.
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Affiliation(s)
- Victoria A. Olson
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Sergei N. Shchelkunov
- Department of Genomic Research and Development of DNA Diagnostics of Poxviruses, State Research Center of Virology and Biotechnology VECTOR, Koltsovo, 630559 Novosibirsk Region, Russia
- Department of Molecular Biology, Novosibirsk State University, 630090 Novosibirsk, Russia
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13
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Pajer P, Dresler J, Kabíckova H, Písa L, Aganov P, Fucik K, Elleder D, Hron T, Kuzelka V, Velemínsky P, Klimentova J, Fucikova A, Pejchal J, Hrabakova R, Benes V, Rausch T, Dundr P, Pilin A, Cabala R, Hubalek M, Stríbrny J, Antwerpen MH, Meyer H. Characterization of Two Historic Smallpox Specimens from a Czech Museum. Viruses 2017; 9:E200. [PMID: 28749451 PMCID: PMC5580457 DOI: 10.3390/v9080200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 11/25/2022] Open
Abstract
Although smallpox has been known for centuries, the oldest available variola virus strains were isolated in the early 1940s. At that time, large regions of the world were already smallpox-free. Therefore, genetic information of these strains can represent only the very last fraction of a long evolutionary process. Based on the genomes of 48 strains, two clades are differentiated: Clade 1 includes variants of variola major, and clade 2 includes West African and variola minor (Alastrim) strains. Recently, the genome of an almost 400-year-old Lithuanian mummy was determined, which fell basal to all currently sequenced strains of variola virus on phylogenetic trees. Here, we determined two complete variola virus genomes from human tissues kept in a museum in Prague dating back 60 and 160 years, respectively. Moreover, mass spectrometry-based proteomic, chemical, and microscopic examinations were performed. The 60-year-old specimen was most likely an importation from India, a country with endemic smallpox at that time. The genome of the 160-year-old specimen is related to clade 2 West African and variola minor strains. This sequence likely represents a new endemic European variant of variola virus circulating in the midst of the 19th century in Europe.
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Affiliation(s)
- Petr Pajer
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Jiri Dresler
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Hana Kabíckova
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Libor Písa
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Pavel Aganov
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Karel Fucik
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Daniel Elleder
- Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Tomas Hron
- Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Vitezslav Kuzelka
- National Museum, Department of Anthropology, Václavské náměstí 68, 115 79 Praha 1, Czech Republic.
| | - Petr Velemínsky
- National Museum, Department of Anthropology, Václavské náměstí 68, 115 79 Praha 1, Czech Republic.
| | - Jana Klimentova
- Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 500 01 Hradec Králové, Czech Republic.
| | - Alena Fucikova
- Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 500 01 Hradec Králové, Czech Republic.
| | - Jaroslav Pejchal
- Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 500 01 Hradec Králové, Czech Republic.
| | - Rita Hrabakova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 277 21 Liběchov, Czech Republic.
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Tobias Rausch
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Pavel Dundr
- Institute of Pathology of the First Faculty of Medicine and General Teaching Hospital, Studničkova 2, 128 00 Prague, Czech Republic.
| | - Alexander Pilin
- Institute of Forensic Medicine and Toxicology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 4, 128 21, Praha 2, Czech Republic.
| | - Radomir Cabala
- Institute of Forensic Medicine and Toxicology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 4, 128 21, Praha 2, Czech Republic.
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 542/2, 166 10 Praha 6, Czech Republic.
| | - Jan Stríbrny
- Military Institute of Forensic Medicine, Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6.
| | - Markus H Antwerpen
- Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
| | - Hermann Meyer
- Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
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Abstract
Smallpox is considered among the most devastating of human diseases. Its spread in populations, initiated for thousands of years following a probable transmission from an animal host, was concomitant with movements of people across regions and continents, trade and wars. Literature permitted to retrace the occurrence of epidemics from ancient times to recent human history, smallpox having affected all levels of past society including famous monarchs. The disease was officially declared eradicated in 1979 following intensive vaccination campaigns.Paleomicrobiology dedicated to variola virus is restricted to few studies, most unsuccessful, involving ancient material. Only one recent approach allowed the identification of viral DNA fragments from lung tissue of a 300-year-old body excavated from permafrost in Eastern Siberia; phylogenetic analysis revealed that this ancient strain was distinct from those described during the 20th century.
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17 th Century Variola Virus Reveals the Recent History of Smallpox. Curr Biol 2016; 26:3407-3412. [PMID: 27939314 PMCID: PMC5196022 DOI: 10.1016/j.cub.2016.10.061] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 11/23/2022]
Abstract
Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1-4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4-9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4-6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20th century VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18th and 19th centuries, concomitant with the development of modern vaccination.
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Abstract
Smallpox has shaped human history, from the earliest human civilizations well into the 20th century. With high mortality rates, rapid transmission, and serious long-term effects on survivors, smallpox was a much-feared disease. The eradication of smallpox represents an unprecedented medical victory for the lasting benefit of human health and prosperity. Concerns remain, however, about the development and use of the smallpox virus as a biological weapon, which necessitates the need for continued vaccine development. Smallpox vaccine development is thus a much-reviewed topic of high interest. This review focuses on the current state of smallpox vaccines and their context in biodefense efforts.
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Affiliation(s)
- Emily A Voigt
- a Mayo Vaccine Research Group , Mayo Clinic , Rochester , MN , USA
| | | | - Gregory A Poland
- a Mayo Vaccine Research Group , Mayo Clinic , Rochester , MN , USA
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18
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Le Loc'h G, Bertagnoli S, Ducatez MF. Time scale evolution of avipoxviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 35:75-81. [PMID: 26231721 PMCID: PMC7106339 DOI: 10.1016/j.meegid.2015.07.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/16/2015] [Accepted: 07/24/2015] [Indexed: 01/19/2023]
Abstract
Avipoxviruses are divided into three clades: canarypox-like viruses, fowlpox-like viruses, and psittacinepox-like viruses. Several molecular clock and demographic models available in the BEAST package were compared on three avipoxvirus genes (P4b, cnpv186 and DNA polymerase genes), which enabled to determine that avipoxviruses evolved at a rate of 2-8×10(-5)substitution/site/year, in the range of poxviruses previously reported evolution rates. In addition, the date of mean time of divergence of avipoxviruses from a common ancestor was extrapolated to be about 10,000-30,000years ago, at the same period as modern poxvirus species. Our findings will facilitate epidemiological investigations on avipoxviruses' spread, origin and circulation.
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Affiliation(s)
- Guillaume Le Loc'h
- RENECO Wildlife Consultants LLC, Abu Dhabi, United Arab Emirates; Université de Toulouse, INP, ENVT, UMR1225, IHAP, F-31076 Toulouse, France; INRA, UMR1225, IHAP, F-31076 Toulouse, France.
| | - Stéphane Bertagnoli
- Université de Toulouse, INP, ENVT, UMR1225, IHAP, F-31076 Toulouse, France; INRA, UMR1225, IHAP, F-31076 Toulouse, France
| | - Mariette F Ducatez
- INRA, UMR1225, IHAP, F-31076 Toulouse, France; Université de Toulouse, INP, ENVT, UMR1225, IHAP, F-31076 Toulouse, France
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Wurtz N, Grobusch MP, Raoult D. Negative impact of laws regarding biosecurity and bioterrorism on real diseases. Clin Microbiol Infect 2015; 20:507-15. [PMID: 24909400 DOI: 10.1111/1469-0691.12709] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/28/2014] [Accepted: 06/02/2014] [Indexed: 11/28/2022]
Abstract
Research on highly pathogenic microorganisms in biosafety level 3 and 4 laboratories is very important for human public health, as it provides opportunities for the development of vaccines and novel therapeutics as well as diagnostic methods to prevent epidemics. However, in recent years, after the anthrax and World Trade Center attacks in 2001 in the USA, the threat of bioterrorism has grown for both the public and the authorities. As a result, technical and physical containment measures and biosafety and biosecurity practices have been implemented in laboratories handling these dangerous pathogens. Working with selected biological agents and toxins is now highly regulated, owing to their potential to pose a threat to public health and safety, despite the fact that the anthrax attack was found to be the result of a lack of security at a US Army laboratory. Thus, these added regulations have been associated with a large amount of fruitless investment. Herein, we describe the limitations of research in these facilities, and the multiple consequences of the increased regulations. These limitations have seriously negatively impacted on the number of collaborations, the size of research projects, and, more generally, scientific research on microbial pathogens. Clearly, the actual number of known victims and fatalities caused by the intentional use of microorganisms has been negligible as compared with those caused by naturally acquired human infections.
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Affiliation(s)
- N Wurtz
- URMITE, CNRS UMR 7278, IRD 198, Inserm 1095, Aix Marseille Université, Marseille, France
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Babkin IV, Babkina IN. The origin of the variola virus. Viruses 2015; 7:1100-12. [PMID: 25763864 PMCID: PMC4379562 DOI: 10.3390/v7031100] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/14/2015] [Accepted: 02/26/2015] [Indexed: 11/16/2022] Open
Abstract
The question of the origin of smallpox, one of the major menaces to humankind, is a constant concern for the scientific community. Smallpox is caused by the agent referred to as the variola virus (VARV), which belongs to the genus Orthopoxvirus. In the last century, smallpox was declared eradicated from the human community; however, the mechanisms responsible for the emergence of new dangerous pathogens have yet to be unraveled. Evolutionary analyses of the molecular biological genomic data of various orthopoxviruses, involving a wide range of epidemiological and historical information about smallpox, have made it possible to date the emergence of VARV. Comparisons of the VARV genome to the genomes of the most closely related orthopoxviruses and the examination of the distribution their natural hosts' ranges suggest that VARV emerged 3000 to 4000 years ago in the east of the African continent. The VARV evolution rate has been estimated to be approximately 2 × 10-6 substitutions/site/year for the central conserved genomic region and 4 × 10-6 substitutions/site/year for the synonymous substitutions in the genome. Presumably, the introduction of camels to Africa and the concurrent changes to the climate were the particular factors that triggered the divergent evolution of a cowpox-like ancestral virus and thereby led to the emergence of VARV.
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Affiliation(s)
- Igor V Babkin
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
| | - Irina N Babkina
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
- JSC VECTOR-BEST, Novosibirsk 630559, Russia.
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Kugelman JR, Johnston SC, Mulembakani PM, Kisalu N, Lee MS, Koroleva G, McCarthy SE, Gestole MC, Wolfe ND, Fair JN, Schneider BS, Wright LL, Huggins J, Whitehouse CA, Wemakoy EO, Muyembe-Tamfum JJ, Hensley LE, Palacios GF, Rimoin AW. Genomic variability of monkeypox virus among humans, Democratic Republic of the Congo. Emerg Infect Dis 2014; 20:232-9. [PMID: 24457084 PMCID: PMC3901482 DOI: 10.3201/eid2002.130118] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Monkeypox virus is a zoonotic virus endemic to Central Africa. Although active disease surveillance has assessed monkeypox disease prevalence and geographic range, information about virus diversity is lacking. We therefore assessed genome diversity of viruses in 60 samples obtained from humans with primary and secondary cases of infection from 2005 through 2007. We detected 4 distinct lineages and a deletion that resulted in gene loss in 10 (16.7%) samples and that seemed to correlate with human-to-human transmission (p = 0.0544). The data suggest a high frequency of spillover events from the pool of viruses in nonhuman animals, active selection through genomic destabilization and gene loss, and increased disease transmissibility and severity. The potential for accelerated adaptation to humans should be monitored through improved surveillance.
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Affiliation(s)
| | | | - Prime M. Mulembakani
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Neville Kisalu
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Michael S. Lee
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Galina Koroleva
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Sarah E. McCarthy
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Marie C. Gestole
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Nathan D. Wolfe
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Joseph N. Fair
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Bradley S. Schneider
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Linda L. Wright
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - John Huggins
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Chris A. Whitehouse
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Emile Okitolonda Wemakoy
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Jean Jacques Muyembe-Tamfum
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Lisa E. Hensley
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
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Haller SL, Peng C, McFadden G, Rothenburg S. Poxviruses and the evolution of host range and virulence. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2014; 21:15-40. [PMID: 24161410 PMCID: PMC3945082 DOI: 10.1016/j.meegid.2013.10.014] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 10/15/2013] [Accepted: 10/15/2013] [Indexed: 11/22/2022]
Abstract
Poxviruses as a group can infect a large number of animals. However, at the level of individual viruses, even closely related poxviruses display highly diverse host ranges and virulence. For example, variola virus, the causative agent of smallpox, is human-specific and highly virulent only to humans, whereas related cowpox viruses naturally infect a broad spectrum of animals and only cause relatively mild disease in humans. The successful replication of poxviruses depends on their effective manipulation of the host antiviral responses, at the cellular-, tissue- and species-specific levels, which constitutes a molecular basis for differences in poxvirus host range and virulence. A number of poxvirus genes have been identified that possess host range function in experimental settings, and many of these host range genes target specific antiviral host pathways. Herein, we review the biology of poxviruses with a focus on host range, zoonotic infections, virulence, genomics and host range genes as well as the current knowledge about the function of poxvirus host range factors and how their interaction with the host innate immune system contributes to poxvirus host range and virulence. We further discuss the evolution of host range and virulence in poxviruses as well as host switches and potential poxvirus threats for human and animal health.
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Affiliation(s)
- Sherry L Haller
- Laboratory for Host-Specific Virology, Division of Biology, Kansas State University, KS 66506, USA
| | - Chen Peng
- Laboratory for Host-Specific Virology, Division of Biology, Kansas State University, KS 66506, USA
| | - Grant McFadden
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Stefan Rothenburg
- Laboratory for Host-Specific Virology, Division of Biology, Kansas State University, KS 66506, USA.
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Abstract
On May 8, 1980, the World Health Assembly at its 33rd session solemnly declared that the world and all its peoples had won freedom from smallpox and recommended ceasing the vaccination of the population against smallpox. Currently, a larger part of the world population has no immunity not only against smallpox but also against other zoonotic orthopoxvirus infections. Recently, recorded outbreaks of orthopoxvirus diseases not only of domestic animals but also of humans have become more frequent. All this indicates a new situation in the ecology and evolution of zoonotic orthopoxviruses. Analysis of state-of-the-art data on the phylogenetic relationships, ecology, and host range of orthopoxviruses—etiological agents of smallpox (variola virus, VARV), monkeypox (MPXV), cowpox (CPXV), vaccinia (VACV), and camelpox (CMLV)—as well as the patterns of their evolution suggests that a VARV-like virus could emerge in the course of natural evolution of modern zoonotic orthopoxviruses. Thus, there is an insistent need for organization of the international control over the outbreaks of zoonotic orthopoxvirus infections in various countries to provide a rapid response and prevent them from developing into epidemics.
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Affiliation(s)
- Sergei N. Shchelkunov
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk Oblast, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail: ,
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Harper KN, Armelagos GJ. Genomics, the origins of agriculture, and our changing microbe-scape: time to revisit some old tales and tell some new ones. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152 Suppl 57:135-52. [PMID: 24249593 PMCID: PMC7159788 DOI: 10.1002/ajpa.22396] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Though agriculture is often viewed as one of humanity's crowning achievements, skeletal evidence indicates that dependence on domesticated plants and animals was accompanied by an increase in infectious disease. Scientists have proposed that many important infections emerged in the period following the advent of agriculture, as a result of newly dense populations and novel proximity to domestic animals that served as reservoirs for novel pathogens. Here, we review genomic evidence regarding pathogen origins, analyzing these data using the epidemiological transition framework. Genetic information has forced us to reconsider how and when many important pathogens emerged; it appears that a number of infections thought to result from contact with domesticated animals arose much earlier than agriculture was adopted. We also consider the broader effect of agriculture upon the microbiome, exploring potential consequences for human health. We end by discussing the changes in the human microbe-scape we are likely to see in the future.
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Affiliation(s)
- Kristin N Harper
- Department of Environmental Health Sciences, Columbia University, New York, NY, 10032
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Babkin IV, Babkina IN. A retrospective study of the orthopoxvirus molecular evolution. INFECTION GENETICS AND EVOLUTION 2012; 12:1597-604. [PMID: 22878096 DOI: 10.1016/j.meegid.2012.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/14/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
The data on the structure of conserved genes of the Old and New World orthopoxviruses and unclassified Yoka poxvirus were used for a Bayesian dating of their independent evolution. This reconstruction estimates the time when an orthopoxvirus ancestor was transferred to the North American continent as approximately 50 thousand years ago (TYA) and allows for relation of this time interval with the global climate changes (with one of the short-term warmings during the Last Ice Age). The onset of the Yoka poxvirus evolution was assessed as approximately 90TYA. Availability of a large number of genome sequences of various cowpox virus strains provided for a comprehensive analysis of the orthopoxvirus evolutionary history. Such a study is especially topical in view of the postulated role of this virus in the evolution of various orthopoxviruses, namely, as an progenitor virus. The computations have demonstrated that the orthopoxviruses diverged from the ancestor virus to form the extant species about 10TYA, while the forbear of horsepox virus separated about 3TYA. An independent evolution of taterapox, camelpox, and variola viruses commenced approximately 3.5TYA. Study of the geographic distribution areas of the hosts of these three orthopoxviruses suggests the hypothesis on the region of their origin. It is likely that these viruses first emerged in Africa, in the region of the Horn of Africa, and that the introduction of camels to East Africa induced their divergent evolution.
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Affiliation(s)
- Igor V Babkin
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.
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Orthopoxvirus genes that mediate disease virulence and host tropism. Adv Virol 2012; 2012:524743. [PMID: 22899927 PMCID: PMC3413996 DOI: 10.1155/2012/524743] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 05/31/2012] [Indexed: 12/16/2022] Open
Abstract
In the course of evolution, viruses have developed various molecular mechanisms to evade the defense reactions of the host organism. When understanding the mechanisms used by viruses to overcome manifold defense systems of the animal organism, represented by molecular factors and cells of the immune system, we would not only comprehend better but also discover new patterns of organization and function of these most important reactions directed against infectious agents. Here, study of the orthopoxviruses pathogenic for humans, such as variola (smallpox), monkeypox, cowpox, and vaccinia viruses, may be most important. Analysis of the experimental data, presented in this paper, allows to infer that variola virus and other orthopoxviruses possess an unexampled set of genes whose protein products efficiently modulate the manifold defense mechanisms of the host organisms compared with the viruses from other families.
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Shchelkunov SN. Emergence and reemergence of smallpox: the need for development of a new generation smallpox vaccine. Vaccine 2011; 29 Suppl 4:D49-53. [PMID: 22185833 DOI: 10.1016/j.vaccine.2011.05.037] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 04/13/2011] [Accepted: 05/13/2011] [Indexed: 11/16/2022]
Abstract
The review summarizes the archive data on smallpox, history of ancient civilizations, and the most recent data on the genome organization of orthopoxviruses, their evolutionary relationships, and the time points of smallpox emergence. The performed analysis provides the grounds for the hypothesis that smallpox could have emerged several times as a result of evolutionary changes in the zoonotic ancestor virus and disappeared due to insufficient population size of ancient civilizations. Smallpox reemerged in the Indian subcontinent approximately 2500-3000 years before present, which resulted in endemization of this anthroponotic infection, which had been preserved until the smallpox eradication in the 20th century AD. The conclusion suggests a potential possibility of future variola virus reemergence, presenting a great menace for mankind, as well as the need for development of new safe smallpox vaccines, design of anti-smallpox drugs, and activation of the control of zoonotic human orthopoxvirus infections.
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Affiliation(s)
- Sergei N Shchelkunov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
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Shchelkunov SN, Shcherbakov DN, Maksyutov RA, Gavrilova EV. Species-specific identification of variola, monkeypox, cowpox, and vaccinia viruses by multiplex real-time PCR assay. J Virol Methods 2011; 175:163-9. [DOI: 10.1016/j.jviromet.2011.05.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/26/2011] [Accepted: 05/03/2011] [Indexed: 01/13/2023]
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Abstract
In 2011, the World Health Organization will recommend the fate of existing smallpox stockpiles, but circumstances have changed since the complete destruction of these cultures was first proposed. Recent studies suggest that variola and its experimental surrogate, vaccinia, have a remarkable ability to modify the human immune response through complex mechanisms that scientists are only just beginning to unravel. Further study that might require intact virus is essential. Moreover, modern science now has the capability to recreate smallpox or a smallpox-like organism in the laboratory in addition to the risk of nature re-creating it as it did once before. These factors strongly suggest that relegating smallpox to the autoclave of extinction would be ill advised.
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Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, Rambaut A. Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol 2010; 27:2038-51. [PMID: 20363828 PMCID: PMC3107591 DOI: 10.1093/molbev/msq088] [Citation(s) in RCA: 228] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Double-stranded (ds) DNA viruses are often described as evolving through long-term codivergent associations with their hosts, a pattern that is expected to be associated with low rates of nucleotide substitution. However, the hypothesis of codivergence between dsDNA viruses and their hosts has rarely been rigorously tested, even though the vast majority of nucleotide substitution rate estimates for dsDNA viruses are based upon this assumption. It is therefore important to estimate the evolutionary rates of dsDNA viruses independent of the assumption of host-virus codivergence. Here, we explore the use of temporally structured sequence data within a Bayesian framework to estimate the evolutionary rates for seven human dsDNA viruses, including variola virus (VARV) (the causative agent of smallpox) and herpes simplex virus-1. Our analyses reveal that although the VARV genome is likely to evolve at a rate of approximately 1 x 10(-5) substitutions/site/year and hence approaching that of many RNA viruses, the evolutionary rates of many other dsDNA viruses remain problematic to estimate. Synthetic data sets were constructed to inform our interpretation of the substitution rates estimated for these dsDNA viruses and the analysis of these demonstrated that given a sequence data set of appropriate length and sampling depth, it is possible to use time-structured analyses to estimate the substitution rates of many dsDNA viruses independently from the assumption of host-virus codivergence. Finally, the discovery that some dsDNA viruses may evolve at rates approaching those of RNA viruses has important implications for our understanding of the long-term evolutionary history and emergence potential of this major group of viruses.
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Affiliation(s)
- Cadhla Firth
- Department of Biology, The Pennsylvania State University, USA.
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