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Ghafari M, Sõmera M, Sarmiento C, Niehl A, Hébrard E, Tsoleridis T, Ball J, Moury B, Lemey P, Katzourakis A, Fargette D. Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses. PLoS Pathog 2024; 20:e1011911. [PMID: 38206964 PMCID: PMC10807823 DOI: 10.1371/journal.ppat.1011911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/24/2024] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.
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Affiliation(s)
- Mahan Ghafari
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annette Niehl
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Theocharis Tsoleridis
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Jonathan Ball
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Denis Fargette
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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2
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Jing S, Jie W, Yongping M, Yan S, Zhi L. Genealogical Diversity of Endogenous Retrovirus in the Jawless Fish Genome. J Microbiol Biotechnol 2023; 33:1412-1419. [PMID: 37583082 DOI: 10.4014/jmb.2306.06028] [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: 06/12/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023]
Abstract
Retroviral integration into ancient vertebrate genomes left traces that can shed light on the early history of viruses. In this study, we explored the early evolution of retroviruses by isolating nine Spuma endogenous retroviruses (ERVs) and one Epsilon ERV from the genomes of Agnatha and Chondrichthyes. Phylogenetic analysis of protein sequences revealed a striking pattern of co-evolution between jawless fish ERV and their host, while shark ERV underwent ancient cross-class viral transmission with jawless fish, ray-finned fish, and amphibians. Nucleotide sequence analysis showed that jawless fish ERV emerged in the Palaeozoic period, relatively later than ray-finned fish ERV. Moreover, codon analysis suggested that the jawless fish ERV employed an infection strategy that mimics the host codon. The genealogical diversity of ERVs in the jawless fish genome highlights the importance of studying different viral species. Overall, our findings provide valuable insights into the evolution of retroviruses and their interactions with their hosts.
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Affiliation(s)
- Song Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, P.R. China
- College of Chemistry and Biological Engineering, Hechi University, Hechi 546300, P.R. China
| | - Wei Jie
- College of Environment and Life Sciences, Weinan Normal University, Weinan 714099, P. R. China
| | - Ma Yongping
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan 750021, P.R. China
| | - Sun Yan
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, P.R. China
| | - Li Zhi
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, P.R. China
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3
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Ji X, Fisher AA, Su S, Thorne JL, Potter B, Lemey P, Baele G, Suchard MA. Scalable Bayesian Divergence Time Estimation With Ratio Transformations. Syst Biol 2023; 72:1136-1153. [PMID: 37458991 PMCID: PMC10636426 DOI: 10.1093/sysbio/syad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 06/13/2023] [Accepted: 06/30/2023] [Indexed: 11/08/2023] Open
Abstract
Divergence time estimation is crucial to provide temporal signals for dating biologically important events from species divergence to viral transmissions in space and time. With the advent of high-throughput sequencing, recent Bayesian phylogenetic studies have analyzed hundreds to thousands of sequences. Such large-scale analyses challenge divergence time reconstruction by requiring inference on highly correlated internal node heights that often become computationally infeasible. To overcome this limitation, we explore a ratio transformation that maps the original $N-1$ internal node heights into a space of one height parameter and $N-2$ ratio parameters. To make the analyses scalable, we develop a collection of linear-time algorithms to compute the gradient and Jacobian-associated terms of the log-likelihood with respect to these ratios. We then apply Hamiltonian Monte Carlo sampling with the ratio transform in a Bayesian framework to learn the divergence times in 4 pathogenic viruses (West Nile virus, rabies virus, Lassa virus, and Ebola virus) and the coralline red algae. Our method both resolves a mixing issue in the West Nile virus example and improves inference efficiency by at least 5-fold for the Lassa and rabies virus examples as well as for the algae example. Our method now also makes it computationally feasible to incorporate mixed-effects molecular clock models for the Ebola virus example, confirms the findings from the original study, and reveals clearer multimodal distributions of the divergence times of some clades of interest.
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Affiliation(s)
- Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, 6823 St. Charles Avenue, New Orleans, LA 70118, USA
| | - Alexander A Fisher
- Department of Statistical Science, Duke University, 214 Old Chemistry, Durham, NC 27708, USA
| | - Shuo Su
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, No. 1 Weigang, Xiaolingwei District, Nanjing, Jiangsu 210095, China
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Ricks Hall, 1 Lampe Dr, Raleigh, NC 27607, USA
| | - Barney Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, 695 Charles E Young Dr S, Los Angeles, CA 90095, USA
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Silcocks M, Dunstan SJ. Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history. Commun Biol 2023; 6:1037. [PMID: 37833496 PMCID: PMC10575886 DOI: 10.1038/s42003-023-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across Eurasia. A lack of ancient samples from tropical East Asia limits the resolution of this model. We consider insight afforded by patterns of variation within the human pathogen Mycobacterium tuberculosis (Mtb) by analysing its phylogeographic signatures jointly with the human Y-chromosome. We demonstrate the Y-chromosome lineages enriched in the traditionally hunter-gatherer groups associated with East Asia's first layer of peopling to display deep roots, low long-term effective population size, and diversity patterns consistent with a southern entry route. These characteristics mirror those of the evolutionarily ancient Mtb lineage 1. The remaining East Asian Y-chromosome lineage is almost entirely absent from traditionally hunter-gatherer groups and displays spatial and temporal characteristics which are incompatible with a southern entry route, and which link it to the development of agriculture in modern-day China. These characteristics mirror those of the evolutionarily modern Mtb lineage 2. This model paves the way for novel host-pathogen coevolutionary research hypotheses in East Asia.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| | - Sarah J Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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Materniak-Kornas M, Kubiś P, Sell B, Pougialis G, Löchelt M, Kuźmak J. An Outbred Calf Model for Determining Innate Immune Sensing and Evolutionary Trajectories of a Cell Culture-Adapted Bovine Foamy Virus Variant. Viruses 2023; 15:1772. [PMID: 37632114 PMCID: PMC10458543 DOI: 10.3390/v15081772] [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: 06/30/2023] [Revised: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Bovine foamy virus (BFVbta) displays a very high degree of cell-associated replication which is unprecedented even among the other known foamy viruses. Interestingly, recent studies have shown that it can in fact adapt in vitro to high-titer (HT) cell-free transmission due to genetic changes acquired during repeated rounds of cell-free BFVbta passages in immortalized bovine MDBK cells. Molecular clones obtained from the HT BFVbta Riems cell-free variant (HT BFVbta Riems) have been thoroughly characterized in MDBK cell cultures However, during recent years, it has become increasingly clear that the source of the host cells used for virus growth and functional studies of virus replication and virus-cell interactions plays a paramount role. Established cell lines, mostly derived from tumors, but occasionally experimentally immortalized and transformed, frequently display aberrant features relating, for example. to growth, metabolism, and genetics. Even state-of-the-art organoid cultures of primary cells cannot replicate the conditions in an authentic host, especially those concerning cell diversity and the role of innate and adaptive immunity. Therefore, to determine the overall replication characteristics of the cloned wt and HT BFVbta Riems variant, we conducted a small-scale animal pilot study. The replication of the original wt BFVbta Riems isolate, as well as that of its HT variant, were analyzed. Both BFVbta variants established infection in calves, with proviruses in peripheral blood mononuclear cells and induced Gag-specific antibodies. In addition, a related pattern in the host innate immune reaction was detected in the peripheral blood leukocytes of the BFV-infected calves. Surprisingly, an analysis of the Gag sequence two weeks post-inoculation revealed that the HT BFVbta variant showed a very high level of genetic reversion to the wild type (parental BFVbta genotype).
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Affiliation(s)
- Magdalena Materniak-Kornas
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Pulawy, Poland; (P.K.); (J.K.)
| | - Piotr Kubiś
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Pulawy, Poland; (P.K.); (J.K.)
| | - Bartosz Sell
- Department of Pharmacology and Toxicology, National Veterinary Research Institute, 24-100 Pulawy, Poland;
| | - Georgios Pougialis
- Division of Viral Transformation Mechanisms, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, 69120 Heidelberg, Germany; (G.P.); (M.L.)
| | - Martin Löchelt
- Division of Viral Transformation Mechanisms, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, 69120 Heidelberg, Germany; (G.P.); (M.L.)
- Division of Virus-Associated Carcinogenesis, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Jacek Kuźmak
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Pulawy, Poland; (P.K.); (J.K.)
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Zhao X, Dai C, Qian S, Tang Q, Li L, Hao Y, Zhou Z, Ge X, Gong C, Yuan J. Viral Diversity and Epidemiology in Critically Endangered Yangtze Finless Porpoises (Neophocaena asiaeorientalis asiaeorientalis). Microbiol Spectr 2023; 11:e0081023. [PMID: 37265414 PMCID: PMC10434060 DOI: 10.1128/spectrum.00810-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
The Yangtze finless porpoise (YFP) (Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered freshwater cetacean, with about 1,249 individuals thought to be left in the wild. However, viral entities and viral diseases of YFPs remain obscure. In this study, anal swabs for virome analysis were collected during the physical examination of YFPs in the Tian-E-Zhou Oxbow (TEO) ex situ reserve. A total of 19 eukaryotic viral species belonging to 9 families, including Papillomaviridae, Herpesviridae, Picornaviridae, Picobirnaviridae, Caliciviridae, Retroviridae, Parvoviridae, Virgaviridae, and Narnaviridae, and other unclassified viruses were identified based on metasequencing. Among these detected viruses, a novel herpesvirus (NaHV), two different kobuviruses (NaKV1-2), and six different papillomaviruses (NaPV1 to -6) were considered potential risks to YFPs and confirmed by PCR or reverse transcription-PCR (RT-PCR). Most YFPs sampled were found to harbor one or more kinds of detected viral genomes (52/58 [89.7%]). Surveillance results demonstrated that kobuvirus and herpesvirus displayed obvious age distribution and PVs showed significant gender difference in YFPs. According to species demarcation criteria in individual genera in Papillomaviridae, two novel species (referred to as Omikronpapillomavirus 2 and 3) and four novel isolates of PV were identified in YFPs. Further evolutionary analysis suggested that NaPVs would occupy the mucosal niche and that virus-host codivergence mixed with duplications and host-switching events drives the evolution of cetacean PVs. Divergence times of PVs in YFP and other cetacean reflect the incipient speciation of YFPs. In summary, our findings revealed the potential viral entities, their prevalence, and their evolutionary history in YFPs, which raises an important issue regarding effects of viral infection on the fitness of YFPs. IMPORTANCE The Yangtze finless porpoise (YFP) is the only cetacean species in freshwater following the functional extinction of the baiji (Lipotes vexillifer). Health management, disease treatment, and other special measures are important for maintaining the existing YFP populations, especially in in situ and ex situ reserves. The discovery of potential viral entities and their prevalence in YFPs raises an important issue regarding the effects of viral infection on the fitness of YFPs and may contribute to the conservation of YFPs. The evolutionary history of papillomaviruses in YFP and other cetaceans reflects the phylogeny of their hosts and supports the status of incipient species, opening a window to investigate the evolutionary adaptation of cetaceans to freshwater as well as their phylogeny to remedy the deficiency of fossil evidence.
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Affiliation(s)
- Xin Zhao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Caijiao Dai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Shiyu Qian
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Qing Tang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Lijuan Li
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, People’s Republic of China
| | - Yujiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhijian Zhou
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Xingyi Ge
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Cheng Gong
- Tian-e-zhou National Reserve for Lipotes Vexillifer, Shishou, People’s Republic of China
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, People’s Republic of China
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7
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Pereson MJ, Sanabria DJ, Torres C, Liotta DJ, Campos RH, Schurr TG, Di Lello FA, Badano I. Evolutionary analysis of JC polyomavirus in Misiones' population yields insight into the population dynamics of the early human dispersal in the Americas. Virology 2023; 585:100-108. [PMID: 37327595 DOI: 10.1016/j.virol.2023.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND JC polyomavirus (JCV) has an ethno-geographical distribution across human populations. OBJECTIVE Study the origins of the population of Misiones (Argentina) by using JCV as genetic marker. METHODS Viral detection and characterization was conducted by PCR amplification and evolutionary analysis of the intergenic region sequences. RESULTS 22 out of 121 samples were positive for JCV, including 5 viral lineages: MY (n = 8), Eu-a (n = 7), B1-c (n = 4), B1-b (n = 2) and Af2 (n = 1). MY sequences clustered within a branch of Native American origin that diverged from its Asian counterpart about 21,914 years ago (HPD 95% interval 15,383-30,177), followed by a sustained demographic expansion around 5000 years ago. CONCLUSIONS JCV in Misiones reflects the multiethnic origin of the current population, with an important Amerindian contribution. Analysis of the MY viral lineage shows a pattern consistent with the arrival of early human migrations to the Americas and a population expansion by the pre-Columbian native societies.
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Affiliation(s)
- Matias J Pereson
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Daiana J Sanabria
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina
| | - Carolina Torres
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Instituto Nacional de Medicina Tropical-ANLIS ''Dr. Malbrán'', Neuquén y Jujuy S/n, N3370, Puerto Iguazú, Misiones, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania. Philadelphia, PA 19104-6398, USA
| | - Federico A Di Lello
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Badano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina; Universidad Nacional de Misiones. Red de Laboratorios. Laboratorio de Antropología Biológica y Bioinformática Aplicada (LABBA). Misiones, Argentina.
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8
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Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
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9
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Ghafari M, Simmonds P, Pybus OG, Katzourakis A. A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses. Curr Biol 2021; 31:4689-4696.e5. [PMID: 34478645 PMCID: PMC8585505 DOI: 10.1016/j.cub.2021.08.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/02/2021] [Accepted: 08/05/2021] [Indexed: 01/16/2023]
Abstract
Estimating viral timescales is fundamental in understanding the evolutionary biology of viruses. Molecular clocks are widely used to reveal the recent evolutionary histories of viruses but may severely underestimate their longer-term origins because of the inverse correlation between inferred rates of evolution and the timescale of their measurement. Here, we provide a predictive mechanistic model that readily explains the rate decay phenomenon over a wide range of timescales and recapitulates the ubiquitous power-law rate decay with a slope of -0.65. We show that standard substitution models fail to correctly estimate divergence times once the most rapidly evolving sites saturate, typically after hundreds of years in RNA viruses and thousands of years in DNA viruses. Our model successfully recreates the observed pattern of decay and explains the evolutionary processes behind the time-dependent rate phenomenon. We then apply our model to re-estimate the date of diversification of genotypes of hepatitis C virus to 423,000 (95% highest posterior density [HPD]: 394,000-454,000) years before present, a time preceding the dispersal of modern humans out of Africa, and show that the most recent common ancestor of sarbecoviruses dates back to 21,000 (95% HPD: 19,000-22,000) years ago, nearly thirty times older than previous estimates. This creates a new perspective for our understanding of the origins of these viruses and also suggests that a substantial revision of evolutionary timescales of other viruses can be similarly achieved.
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Affiliation(s)
- Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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10
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Donohoe O, Zhang H, Delrez N, Gao Y, Suárez NM, Davison AJ, Vanderplasschen A. Genomes of Anguillid Herpesvirus 1 Strains Reveal Evolutionary Disparities and Low Genetic Diversity in the Genus Cyprinivirus. Microorganisms 2021; 9:microorganisms9050998. [PMID: 34063135 PMCID: PMC8148134 DOI: 10.3390/microorganisms9050998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Anguillid herpesvirus 1 (AngHV-1) is a pathogen of eels and a member of the genus Cyprinivirus in the family Alloherpesviridae. We have compared the biological and genomic features of different AngHV-1 strains, focusing on their growth kinetics in vitro and genetic content, diversity, and recombination. Comparisons based on three core genes conserved among alloherpesviruses revealed that AngHV-1 exhibits a slower rate of change and less positive selection than other cypriniviruses. We propose that this may be linked to major differences in host species and corresponding epidemiological circumstances. Efforts to derive evolutionary rate estimates for cypriniviruses under various theoretical models were ultimately unrewarding. We highlight the potential value of future collaborative efforts towards generating short-term evolutionary rate estimates based on known sequence sampling dates. Finally, we revealed that there is significantly less genetic diversity in core gene sequences within cyprinivirus species clades compared to species in the family Herpesviridae. This suggests that cyprinivirus species may have undergone much more vigorous purifying selection post species clade divergence. We discuss whether this may be linked to biological and anthropogenic factors or to sampling bias, and we propose that the comparison of short-term evolutionary rates between species may provide further insights into these differences.
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Affiliation(s)
- Owen Donohoe
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium; (O.D.); (H.Z.); (N.D.); (Y.G.)
- Bioscience Research Institute, Athlone Institute of Technology, Athlone, Co. N37 HD68 Westmeath, Ireland
| | - Haiyan Zhang
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium; (O.D.); (H.Z.); (N.D.); (Y.G.)
| | - Natacha Delrez
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium; (O.D.); (H.Z.); (N.D.); (Y.G.)
| | - Yuan Gao
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium; (O.D.); (H.Z.); (N.D.); (Y.G.)
| | - Nicolás M. Suárez
- MRC-Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; (N.M.S.); (A.J.D.)
| | - Andrew J. Davison
- MRC-Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; (N.M.S.); (A.J.D.)
| | - Alain Vanderplasschen
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium; (O.D.); (H.Z.); (N.D.); (Y.G.)
- Correspondence: ; Tel.: +32-4-366-42-64; Fax: +32-4-366-42-61
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11
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Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P. Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates. Mol Biol Evol 2020; 36:1793-1803. [PMID: 31004175 PMCID: PMC6657730 DOI: 10.1093/molbev/msz094] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Many factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.
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Affiliation(s)
- Jade Vincent Membrebe
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA.,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,Fogarty International Center, National Institutes of Health, Bethesda, MD
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
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12
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Aiewsakun P. Avian and serpentine endogenous foamy viruses, and new insights into the macroevolutionary history of foamy viruses. Virus Evol 2020; 6:vez057. [PMID: 31942244 PMCID: PMC6955096 DOI: 10.1093/ve/vez057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This study reports and characterises two novel distinct lineages of foamy viruses (FVs) in the forms of endogenous retroviruses (ERVs). Several closely related elements were found in the genome of oriental stork (Ciconia boyciana) and other was found in the genome of spine-bellied sea snake (Hydrophis hardwickii), designated ERV-Spuma.N-Cbo (where 'N' runs from one to thirteen) and ERV-Spuma.1-Hha, respectively. This discovery of avian and serpentine endogenous FVs adds snakes, and perhaps more crucially, birds to the list of currently known hosts of FVs, in addition to mammals, reptiles, amphibians, and fish. This indicates that FVs are, or at least were, capable of infecting all major lineages of vertebrates. Moreover, together with other FVs, phylogenetic analyses showed that both of them are most closely related to mammalian FVs. Further examination revealed that reptilian FVs form a deep paraphyletic group that is basal to mammalian and avian FVs, suggesting that there were multiple ancient FV cross-class transmissions among their hosts. Evolutionary timescales of various FV lineages were estimated in this study, in particular, the timescales of reptilian FVs and that of the clade of mammalian, avian, and serpentine FVs. This was accomplished by using the recently established time-dependent rate phenomenon models, inferred using mainly the knowledge of the co-speciation history between FVs and mammals. It was found that the estimated timescales matched very well with those of reptiles. Combined with the observed phylogenetic patterns, these results suggested that FVs likely co-speciated with ancient reptilian animals, but later jumped to a protomammal and/or a bird, which ultimately gave rise to mammalian and avian FVs. These results contribute to our understanding of FV emergence, specifically the emergence of mammalian and avian FVs, and provide new insights into how FVs co-evolved with their non-mammalian vertebrate hosts in the distant past.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, 272, Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand.,Center of Microbial Genomics (CENMIG), Faculty of Science, Mahidol University, 272, Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
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13
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Kraberger S, Fountain-Jones NM, Gagne RB, Malmberg J, Dannemiller NG, Logan K, Alldredge M, Varsani A, Crooks KR, Craft M, Carver S, VandeWoude S. Frequent cross-species transmissions of foamy virus between domestic and wild felids. Virus Evol 2020; 6:vez058. [PMID: 31942245 PMCID: PMC6955097 DOI: 10.1093/ve/vez058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Emerging viral outbreaks resulting from host switching is an area of continued scientific interest. Such events can result in disease epidemics or in some cases, clinically silent outcomes. These occurrences are likely relatively common and can serve as tools to better understand disease dynamics, and may result in changes in behavior, fecundity, and, ultimately survival of the host. Feline foamy virus (FFV) is a common retrovirus infecting domestic cats globally, which has also been documented in the North American puma (Puma concolor). The prevalent nature of FFV in domestic cats and its ability to infect wild felids, including puma, provides an ideal system to study cross-species transmission across trophic levels (positions in the food chain), and evolution of pathogens transmitted between individuals following direct contact. Here we present findings from an extensive molecular analysis of FFV in pumas, focused on two locations in Colorado, and in relation to FFV recovered from domestic cats in this and previous studies. Prevalence of FFV in puma was high across the two regions, ∼77 per cent (urban interface site) and ∼48 per cent (rural site). Comparison of FFV from pumas living across three states; Colorado, Florida, and California, indicates FFV is widely distributed across North America. FFV isolated from domestic cats and pumas was not distinguishable at the host level, with FFV sequences sharing >93 per cent nucleotide similarity. Phylogenetic, Bayesian, and recombination analyses of FFV across the two species supports frequent cross-species spillover from domestic cat to puma during the last century, as well as frequent puma-to-puma intraspecific transmission in Colorado, USA. Two FFV variants, distinguished by significant difference in the surface unit of the envelope protein, were commonly found in both hosts. This trait is also shared by simian foamy virus and may represent variation in cell tropism or a unique immune evasion mechanism. This study elucidates evolutionary and cross-species transmission dynamics of a highly prevalent multi-host adapted virus, a system which can further be applied to model spillover and transmission of pathogenic viruses resulting in widespread infection in the new host.
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Affiliation(s)
- Simona Kraberger
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
| | - Nicholas M Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Ave, Falcon Heights, St Paul, MN 55108, USA
| | - Roderick B Gagne
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer Malmberg
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Nicholas G Dannemiller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Ken Logan
- Colorado Parks and Wildlife, 317 W Prospect Rd, Fort Collins, CO 80526, USA
| | - Mat Alldredge
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery Fort Collins, CO 80523, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Kevin R Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery Fort Collins, CO 80523, USA
| | - Meggan Craft
- Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Ave, Falcon Heights, St Paul, MN 55108, USA
| | - Scott Carver
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Sue VandeWoude
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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14
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Simmonds P, Aiewsakun P, Katzourakis A. Reply to 'Evolutionary stasis of viruses?'. Nat Rev Microbiol 2019; 17:329-330. [PMID: 30814681 DOI: 10.1038/s41579-019-0169-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
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15
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Aiewsakun P, Richard L, Gessain A, Mouinga-Ondémé A, Vicente Afonso P, Katzourakis A. Modular nature of simian foamy virus genomes and their evolutionary history. Virus Evol 2019; 5:vez032. [PMID: 31636999 PMCID: PMC6795992 DOI: 10.1093/ve/vez032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Among all known retroviruses, foamy viruses (FVs) have the most stable virus–host co-speciation history, co-diverging in concert with their vertebrate hosts for hundreds of millions of years. However, detailed molecular analyses indicate that different parts of their genome might have different evolutionary histories. While their polymerase gene displays a robust and straightforward virus–host co-speciation pattern, the evolutionary history of their envelope (env) gene, is much more complicated. Here, we report eleven new FV env sequences in two mandrill populations in Central Africa, geographically separated by the Ogooué River into the North and the South populations. Phylogenetic reconstruction of the polymerase gene shows that the two virus populations are distinct, and each contains two variants of env genes co-existing with one another. The distinction between the two env variants can be mapped to the surface domain, flanked by two recombination hotspots, as previously reported for chimpanzee and gorilla FVs. Our analyses suggest that the two env variants originated during the diversification of Old World monkeys and apes, ∼30 million years ago. We also show that this env gene region forms two phylogenetically distinct clades, each displaying a host co-divergence and geographical separation pattern, while the rest of the genome of the two strains is phylogenetically indistinguishable in each of the host-specific groups. We propose possible evolutionary mechanisms to explain the modular nature of the FV genome.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Léa Richard
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Paris, France.,Université Paris Diderot - Paris7, Sorbonne Paris Cité, Paris, France
| | - Antoine Gessain
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Paris, France
| | - Augustin Mouinga-Ondémé
- Unité des Infections Rétrovirales et Pathologies Associées, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Philippe Vicente Afonso
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Paris, France
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
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16
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Aiewsakun P, Simmonds P, Katzourakis A. The First Co-Opted Endogenous Foamy Viruses and the Evolutionary History of Reptilian Foamy Viruses. Viruses 2019; 11:v11070641. [PMID: 31336856 PMCID: PMC6669660 DOI: 10.3390/v11070641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/17/2022] Open
Abstract
A recent study reported the discovery of an endogenous reptilian foamy virus (FV), termed ERV-Spuma-Spu, found in the genome of tuatara. Here, we report two novel reptilian foamy viruses also identified as endogenous FVs (EFVs) in the genomes of panther gecko (ERV-Spuma-Ppi) and Schlegel’s Japanese gecko (ERV-Spuma-Gja). Their presence indicates that FVs are capable of infecting reptiles in addition to mammals, amphibians, and fish. Numerous copies of full length ERV-Spuma-Spu elements were found in the tuatara genome littered with in-frame stop codons and transposable elements, suggesting that they are indeed endogenous and are not functional. ERV-Spuma-Ppi and ERV-Spuma-Gja, on the other hand, consist solely of a foamy virus-like env gene. Examination of host flanking sequences revealed that they are orthologous, and despite being more than 96 million years old, their env reading frames are fully coding competent with evidence for strong purifying selection to maintain expression and for them likely being transcriptionally active. These make them the oldest EFVs discovered thus far and the first documented EFVs that may have been co-opted for potential cellular functions. Phylogenetic analyses revealed a complex virus–host co-evolutionary history and cross-species transmission routes of ancient FVs.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
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17
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Ali A, Melcher U. Modeling of Mutational Events in the Evolution of Viruses. Viruses 2019; 11:v11050418. [PMID: 31060293 PMCID: PMC6563203 DOI: 10.3390/v11050418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/27/2019] [Accepted: 05/02/2019] [Indexed: 11/24/2022] Open
Abstract
Diverse studies of viral evolution have led to the recognition that the evolutionary rates of viral taxa observed are dependent on the time scale being investigated—with short-term studies giving fast substitution rates, and orders of magnitude lower rates for deep calibrations. Although each of these factors may contribute to this time dependent rate phenomenon, a more fundamental cause should be considered. We sought to test computationally whether the basic phenomena of virus evolution (mutation, replication, and selection) can explain the relationships between the evolutionary and phylogenetic distances. We tested, by computational inference, the hypothesis that the phylogenetic distances between the pairs of sequences are functions of the evolutionary path lengths between them. A Basic simulation revealed that the relationship between simulated genetic and mutational distances is non-linear, and can be consistent with different rates of nucleotide substitution at different depths of branches in phylogenetic trees.
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Affiliation(s)
- Akhtar Ali
- Department of Biological Sciences, University of Tulsa, Tulsa, OK 74104, USA.
| | - Ulrich Melcher
- Department of Biochemistry & Molecular Biology, Oklahoma State University, Stillwater, OK 74078-3035, USA.
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18
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Chen S, Saito N, Encabo JR, Yamada K, Choi IR, Kishima Y. Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution. Genome Biol Evol 2018; 10:2686-2696. [PMID: 30239708 PMCID: PMC6179347 DOI: 10.1093/gbe/evy207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2018] [Indexed: 12/13/2022] Open
Abstract
Endogenous viral sequences in eukaryotic genomes, such as those derived from plant pararetroviruses (PRVs), can serve as genomic fossils to study viral macroevolution. Many aspects of viral evolutionary rates are heterogeneous, including substitution rate differences between genes. However, the evolutionary dynamics of this viral gene rate heterogeneity (GRH) have been rarely examined. Characterizing such GRH may help to elucidate viral adaptive evolution. In this study, based on robust phylogenetic analysis, we determined an ancient endogenous PRV group in Oryza genomes in the range of being 2.41-15.00 Myr old. We subsequently used this ancient endogenous PRV group and three younger groups to estimate the GRH of PRVs. Long-term substitution rates for the most conserved gene and a divergent gene were 2.69 × 10-8 to 8.07 × 10-8 and 4.72 × 10-8 to 1.42 × 10-7 substitutions/site/year, respectively. On the basis of a direct comparison, a long-term GRH of 1.83-fold was identified between these two genes, which is unexpectedly low and lower than the short-term GRH (>3.40-fold) of PRVs calculated using published data. The lower long-term GRH of PRVs was due to the slightly faster rate decay of divergent genes than of conserved genes during evolution. To the best of our knowledge, we quantified for the first time the long-term GRH of viral genes using paleovirological analyses, and proposed that the GRH of PRVs might be heterogeneous on time scales (time-dependent GRH). Our findings provide special insights into viral gene macroevolution and should encourage a more detailed examination of the viral GRH.
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Affiliation(s)
- Sunlu Chen
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Nozomi Saito
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Jaymee R Encabo
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
- Microbiology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Laguna, Philippines
| | - Kanae Yamada
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Il-Ryong Choi
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Yuji Kishima
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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19
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Patiño-Galindo JÁ, González-Candelas F. The substitution rate of HIV-1 subtypes: a genomic approach. Virus Evol 2017; 3:vex029. [PMID: 29942652 PMCID: PMC6007745 DOI: 10.1093/ve/vex029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
HIV-1M causes most infections in the AIDS pandemic. Its genetic diversity is defined by nine pure subtypes and more than sixty recombinant forms. We have performed a comparative analysis of the evolutionary rate of five pure subtypes (A1, B, C, D, and G) and two circulating recombinant forms (CRF01_AE and CRF02 AG) using data obtained from nearly complete genome coding sequences. Times to the most recent common ancestor (tMRCA) and substitution rates of these HIV genomes, and their genomic partitions, were estimated by Bayesian coalescent analyses. Genomic substitution rate estimates were compared between the HIV-1 datasets analyzed by means of randomization tests. Significant differences in the rate of evolution were found between subtypes, with subtypes C and A1 and CRF01_AE displaying the highest rates. On the other hand, CRF02_AG and subtype D were the slowest evolving types. Using a different molecular clock model for each genomic partition led to more precise tMRCA estimates than when linking the same clock along the HIV genome. Overall, the earliest tMRCA corresponded to subtype A1 (median = 1941, 95% HPD = 1943-55), whereas the most recent tMRCA corresponded to subtype G and CRF01_AE subset 3 (median = 1971, 95% HPD = 1967-75 and median = 1972, 95% HPD = 1970-75, respectively). These results suggest that both biological and epidemiological differences among HIV-1M subtypes are reflected in their evolutionary dynamics. The estimates obtained for tMRCAs and substitution rates provide information that can be used as prior distributions in future Bayesian coalescent analyses of specific HIV-1 subtypes/CRFs and genes.
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Affiliation(s)
- Juan Ángel Patiño-Galindo
- Unidad Mixta Infección y Salud Pública FISABIO-Salud Pública/Universitat de València, Institute for Integrative Systems Biology (I2SysBio), CIBERESP, c/Catedratico Jose Beltran, 2, 46980 Paterna, Valencia, Spain
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO-Salud Pública/Universitat de València, Institute for Integrative Systems Biology (I2SysBio), CIBERESP, c/Catedratico Jose Beltran, 2, 46980 Paterna, Valencia, Spain
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20
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Van Doorslaer K, Ruoppolo V, Schmidt A, Lescroël A, Jongsomjit D, Elrod M, Kraberger S, Stainton D, Dugger KM, Ballard G, Ainley DG, Varsani A. Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins. Virus Evol 2017; 3:vex027. [PMID: 29026649 PMCID: PMC5632515 DOI: 10.1093/ve/vex027] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds (n = 5), a fish (n = 1), a snake (n = 1), and turtles (n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet. As part of this study, we isolated a novel papillomavirus from a 16-year-old female Adélie penguin (Pygoscelis adeliae) from Cape Crozier, Ross Island (Antarctica). The new papillomavirus shares ∼64 per cent genome-wide identity to a previously described Adélie penguin papillomavirus. Phylogenetic analyses show that the non-mammalian viruses (expect the python, Morelia spilota, associated papillomavirus) cluster near the base of the papillomavirus evolutionary tree. A papillomavirus isolated from an avian host (Northern fulmar; Fulmarus glacialis), like the two turtle papillomaviruses, lacks a putative E9 protein that is found in all other avian papillomaviruses. Furthermore, the Northern fulmar papillomavirus has an E7 more similar to the mammalian viruses than the other avian papillomaviruses. Typical E6 proteins of mammalian papillomaviruses have two Zinc finger motifs, whereas the sauropsid papillomaviruses only have one such motif. Furthermore, this motif is absent in the fish papillomavirus. Thus, it is highly likely that the most recent common ancestor of the mammalian and sauropsid papillomaviruses had a single motif E6. It appears that a motif duplication resulted in mammalian papillomaviruses having a double Zinc finger motif in E6. We estimated the divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins.
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Affiliation(s)
| | - Valeria Ruoppolo
- Laboratório de Patologia Comparada de Animais Selvagens (LAPCOM), Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Annie Schmidt
- Point Blue Conservation Science, Petaluma, CA 94954, USA
| | - Amelie Lescroël
- Point Blue Conservation Science, Petaluma, CA 94954, USA.,Centre d'Ecologie Fonctionnelle et Evolutive - CNRS, UMR 5175, Montpellier, France
| | | | - Megan Elrod
- Point Blue Conservation Science, Petaluma, CA 94954, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Daisy Stainton
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Katie M Dugger
- U.S. Geological Survey, Oregon Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA
| | - Grant Ballard
- Point Blue Conservation Science, Petaluma, CA 94954, USA
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ 85287, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
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21
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Patiño-Galindo JÁ, Torres-Puente M, Bracho MA, Alastrué I, Juan A, Navarro D, Galindo MJ, Ocete D, Ortega E, Gimeno C, Belda J, Domínguez V, Moreno R, González-Candelas F. The molecular epidemiology of HIV-1 in the Comunidad Valenciana (Spain): analysis of transmission clusters. Sci Rep 2017; 7:11584. [PMID: 28912478 PMCID: PMC5599654 DOI: 10.1038/s41598-017-10286-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/07/2017] [Indexed: 11/09/2022] Open
Abstract
HIV infections are still a very serious concern for public heath worldwide. We have applied molecular evolution methods to study the HIV-1 epidemics in the Comunidad Valenciana (CV, Spain) from a public health surveillance perspective. For this, we analysed 1804 HIV-1 sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2004 and 2014. These sequences were subtyped and subjected to phylogenetic analyses in order to detect transmission clusters. In addition, univariate and multinomial comparisons were performed to detect epidemiological differences between HIV-1 subtypes, and risk groups. The HIV epidemic in the CV is dominated by subtype B infections among local men who have sex with men (MSM). 270 transmission clusters were identified (>57% of the dataset), 12 of which included ≥10 patients; 11 of subtype B (9 affecting MSMs) and one (n = 21) of CRF14, affecting predominately intravenous drug users (IDUs). Dated phylogenies revealed these large clusters to have originated from the mid-80s to the early 00 s. Subtype B is more likely to form transmission clusters than non-B variants and MSMs to cluster than other risk groups. Multinomial analyses revealed an association between non-B variants, which are not established in the local population yet, and different foreign groups.
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Affiliation(s)
- Juan Ángel Patiño-Galindo
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain.,CIBER of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Manoli Torres-Puente
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain
| | - María Alma Bracho
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain.,CIBER of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | | | - Amparo Juan
- Unidad Prevención del SIDA y otras ITS, Valencia, 46017, Spain
| | - David Navarro
- Hospital Clínico Universitario, Valencia, 46010, Spain.,Dpto. Microbiología, Universidad de Valencia, 46080, Valencia, Spain
| | | | - Dolores Ocete
- Consorcio Hospital General Universitario, Valencia, 46014, Spain
| | - Enrique Ortega
- Consorcio Hospital General Universitario, Valencia, 46014, Spain
| | - Concepción Gimeno
- Dpto. Microbiología, Universidad de Valencia, 46080, Valencia, Spain.,Consorcio Hospital General Universitario, Valencia, 46014, Spain
| | - Josefina Belda
- Unidad Prevención del SIDA y otras ITS, Alicante, 03010, Spain
| | | | | | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO-CSISP/Universidad de Valencia-I2SysBio, Valencia, 46180, Spain. .,CIBER of Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid, 28029, Spain.
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22
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Marine origin of retroviruses in the early Palaeozoic Era. Nat Commun 2017; 8:13954. [PMID: 28071651 PMCID: PMC5512871 DOI: 10.1038/ncomms13954] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 11/16/2016] [Indexed: 02/03/2023] Open
Abstract
Very little is known about the ancient origin of retroviruses, but owing to the discovery of their ancient endogenous viral counterparts, their early history is beginning to unfold. Here we report 36 lineages of basal amphibian and fish foamy-like endogenous retroviruses (FLERVs). Phylogenetic analyses reveal that ray-finned fish FLERVs exhibit an overall co-speciation pattern with their hosts, while amphibian FLERVs might not. We also observe several possible ancient viral cross-class transmissions, involving lobe-finned fish, shark and frog FLERVs. Sequence examination and analyses reveal two major lineages of ray-finned fish FLERVs, one of which had gained two novel accessory genes within their extraordinarily large genomes. Our phylogenetic analyses suggest that this major retroviral lineage, and therefore retroviruses as a whole, have an ancient marine origin and originated together with, if not before, their jawed vertebrate hosts >450 million years ago in the Ordovician period, early Palaeozoic Era. Endogenous retroviruses are viruses that have become integrated into the genomes of their hosts. Here, the authors investigate the evolution of foamy-like endogenous retroviruses, and, by taking into account the temporal dynamics of the rate of viral evolution, suggest that retroviruses arose at least 450 million years ago in marine vertebrates.
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23
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Buseyne F, Gessain A, Soares MA, Santos AF, Materniak-Kornas M, Lesage P, Zamborlini A, Löchelt M, Qiao W, Lindemann D, Wöhrl BM, Stoye JP, Taylor IA, Khan AS. Eleventh International Foamy Virus Conference-Meeting Report. Viruses 2016; 8:v8110318. [PMID: 27886074 PMCID: PMC5127032 DOI: 10.3390/v8110318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 11/08/2016] [Accepted: 11/10/2016] [Indexed: 12/11/2022] Open
Abstract
The Eleventh International Foamy Virus Conference took place on 9–10 June 2016 at the Institut Pasteur, Paris, France. The meeting reviewed progress on foamy virus (FV) research, as well as related current topics in retrovirology. FVs are complex retroviruses that are widespread in several animal species. Several research topics on these viruses are relevant to human health: cross-species transmission and viral emergence, vectors for gene therapy, development of antiretroviral drugs, retroviral evolution and its influence on the human genome. In this article, we review the conference presentations on these viruses and highlight the major questions to be answered.
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Affiliation(s)
- Florence Buseyne
- Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, 75015 Paris, France.
- Centre National de la Recherche Scientifique (CNRS), UMR3569, 75015 Paris, France.
| | - Antoine Gessain
- Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, 75015 Paris, France.
- Centre National de la Recherche Scientifique (CNRS), UMR3569, 75015 Paris, France.
| | - Marcelo A Soares
- Department of Genetics, Universidade Federal do Rio de Janeiro, 21949-570 Rio de Janeiro, Brazil.
- Oncovirology Program, Instituto Nacional de Câncer, 20231-050 Rio de Janeiro, Brazil.
| | - André F Santos
- Department of Genetics, Universidade Federal do Rio de Janeiro, 21949-570 Rio de Janeiro, Brazil.
| | | | - Pascale Lesage
- Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Université Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, 75010 Paris, France.
| | - Alessia Zamborlini
- Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Université Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR 7212, 75010 Paris, France.
- Conservatoire National des Arts et Métiers, Laboratoire de Pathologie et Virologie Moléculaire, 75003 Paris, France.
| | - Martin Löchelt
- Department of Molecular Diagnostics of Oncogenic Infections, Research Program Infection, Inflammation and Cancer, 69120 Heidelberg, Germany.
| | - Wentao Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Dirk Lindemann
- Institute of Virology, Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, 01307 Dresden, Germany.
| | - Birgitta M Wöhrl
- University of Bayreuth, Department of Biopolymers, 95447 Bayreuth, Germany.
| | | | | | - Arifa S Khan
- Laboratory of Retroviruses, Division of Viral Products, OVRR, CBER, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA.
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24
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Abstract
Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses. IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.
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25
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Ho SYW, Duchêne S, Molak M, Shapiro B. Time-dependent estimates of molecular evolutionary rates: evidence and causes. Mol Ecol 2016; 24:6007-12. [PMID: 26769402 DOI: 10.1111/mec.13450] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 06/30/2015] [Accepted: 07/17/2015] [Indexed: 12/28/2022]
Abstract
We are writing in response to a recent critique by Emerson & Hickerson (2015), who challenge the evidence of a time-dependent bias in molecular rate estimates. This bias takes the form of a negative relationship between inferred evolutionary rates and the ages of the calibrations on which these estimates are based. Here, we present a summary of the evidence obtained from a broad range of taxa that supports a time-dependent bias in rate estimates, with a consideration of the potential causes of these observed trends. We also describe recent progress in improving the reliability of evolutionary rate estimation and respond to the concerns raised by Emerson & Hickerson (2015) about the validity of rates estimated from time-structured sequence data. In doing so, we hope to dispel some misconceptions and to highlight several research directions that will improve our understanding of time-dependent biases in rate estimates.
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Affiliation(s)
- Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Sebastián Duchêne
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA.,UCSC Genomics Institute, University of California, Santa Cruz, California, USA
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