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Ding Y, Guo H, Hong X, Li Q, Miao Z, Pan Q, Zheng K, Wang W. The distinct spatiotemporal evolutionary landscape of HBV and HDV largely determines the unique epidemic features of HDV globally. Mol Phylogenet Evol 2024; 197:108114. [PMID: 38825156 DOI: 10.1016/j.ympev.2024.108114] [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: 08/21/2023] [Revised: 05/07/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
Chronic infection of hepatitis B virus (HBV) and hepatitis D virus (HDV) causes the most severe form of viral hepatitis. Due to the dependence on HBV, HDV was deemed to co-evolve and co-migrate with HBV. However, we previously found that the naturally occurred HDV/HBV combinations do not always reflect the most efficient virological adaptation (Wang et al., 2021). Moreover, regions with heavy HBV burden do not always correlate with high HDV prevalence (e.g., East Asia), and vice versa (e.g., Central Asia). Herein, we systematically elucidated the spatiotemporal evolutionary landscape of HDV to understand the unique epidemic features of HDV. We found that the MRCA of HDV was from South America around the late 13th century, was globally dispersed mainly via Central Asia, and evolved into eight genotypes from the 19th to 20th century. In contrast, the MRCA of HBV was from Europe ∼23.7 thousand years ago (Kya), globally dispersed mainly via Africa and East Asia, and evolved into eight genotypes ∼1100 years ago. When HDV stepped in, all present-day HBV genotypes had already formed and its global genotypic distribution had stayed stable geographically. Nevertheless, regionalized HDV adapted to local HBV genotypes and human lineages, contributing to the global geographical separation of HDV genotypes. Additionally, a sharp increase in HDV infections was observed after the 20th century. In conclusion, HDV exhibited a distinct spatiotemporal distribution path compared with HBV. This unique evolutionary relationship largely fostered the unique epidemic features we observe nowadays. Moreover, HDV infections may continue to ramp up globally, thus more efforts are urgently needed to combat this disease.
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Affiliation(s)
- Yibo Ding
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China
| | - Hongbo Guo
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
| | - Xinfang Hong
- Second Medical Center of PLA General Hospital, Beijing, China
| | - Qiudi Li
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
| | - Kuiyang Zheng
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
| | - Wenshi Wang
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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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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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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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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Rupprecht CE, Mshelbwala PP, Reeves RG, Kuzmin IV. Rabies in a postpandemic world: resilient reservoirs, redoubtable riposte, recurrent roadblocks, and resolute recidivism. ANIMAL DISEASES 2023; 3:15. [PMID: 37252063 PMCID: PMC10195671 DOI: 10.1186/s44149-023-00078-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/02/2023] [Indexed: 05/31/2023] Open
Abstract
Rabies is an ancient disease. Two centuries since Pasteur, fundamental progress occurred in virology, vaccinology, and diagnostics-and an understanding of pathobiology and epizootiology of rabies in testament to One Health-before common terminological coinage. Prevention, control, selective elimination, and even the unthinkable-occasional treatment-of this zoonosis dawned by the twenty-first century. However, in contrast to smallpox and rinderpest, eradication is a wishful misnomer applied to rabies, particularly post-COVID-19 pandemic. Reasons are minion. Polyhostality encompasses bats and mesocarnivores, but other mammals represent a diverse spectrum of potential hosts. While rabies virus is the classical member of the genus, other species of lyssaviruses also cause the disease. Some reservoirs remain cryptic. Although global, this viral encephalitis is untreatable and often ignored. As with other neglected diseases, laboratory-based surveillance falls short of the notifiable ideal, especially in lower- and middle-income countries. Calculation of actual burden defaults to a flux within broad health economic models. Competing priorities, lack of defined, long-term international donors, and shrinking local champions challenge human prophylaxis and mass dog vaccination toward targets of 2030 for even canine rabies impacts. For prevention, all licensed vaccines are delivered to the individual, whether parenteral or oral-essentially 'one and done'. Exploiting mammalian social behaviors, future 'spreadable vaccines' might increase the proportion of immunized hosts per unit effort. However, the release of replication-competent, genetically modified organisms selectively engineered to spread intentionally throughout a population raises significant biological, ethical, and regulatory issues in need of broader, transdisciplinary discourse. How this rather curious idea will evolve toward actual unconventional prevention, control, or elimination in the near term remains debatable. In the interim, more precise terminology and realistic expectations serve as the norm for diverse, collective constituents to maintain progress in the field.
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Affiliation(s)
- Charles E. Rupprecht
- College of Forestry, Wildlife & Environment, College of Veterinary Medicine, Auburn University, Auburn, AL 36849 USA
| | - Philip P. Mshelbwala
- School of Veterinary Science, University of Queensland, Gatton, Australia
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Abuja, Abuja, Nigeria
| | - R. Guy Reeves
- Max Planck Institut Für Evolutionsbiologie, 24306 Plön, Germany
| | - Ivan V. Kuzmin
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555 USA
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Gupta MK, Vadde R. Next-generation development and application of codon model in evolution. Front Genet 2023; 14:1091575. [PMID: 36777719 PMCID: PMC9911445 DOI: 10.3389/fgene.2023.1091575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.
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9
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Forni D, Cagliani R, Clerici M, Sironi M. Disease-causing human viruses: novelty and legacy. Trends Microbiol 2022; 30:1232-1242. [PMID: 35902319 DOI: 10.1016/j.tim.2022.07.002] [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: 01/26/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023]
Abstract
About 270 viruses are known to infect humans. Some of these viruses have been known for centuries, whereas others have recently emerged. During their evolutionary history, humans have moved out of Africa to populate the world. In historical times, human migrations resulted in the displacement of large numbers of people. All these events determined the movement and dispersal of human-infecting viruses. Technological advances have resulted in the characterization of the genetic variability of human viruses, both in extant and in archaeological samples. Field studies investigated the diversity of viruses hosted by other animals. In turn, these advances provided insight into the evolutionary history of human viruses back in time and defined the key events through which they originated and spread.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
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10
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Havens JL, Calvignac-Spencer S, Merkel K, Burrel S, Boutolleau D, Wertheim JO. Phylogeographic analysis reveals an ancient East African origin of human herpes simplex virus 2 dispersal out-of-Africa. Nat Commun 2022; 13:5477. [PMID: 36115862 PMCID: PMC9482657 DOI: 10.1038/s41467-022-33214-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 09/08/2022] [Indexed: 11/10/2022] Open
Abstract
Human herpes simplex virus 2 (HSV-2) is a ubiquitous, slowly evolving DNA virus. HSV-2 has two primary lineages, one found in West and Central Africa and the other found worldwide. Competing hypotheses have been proposed to explain how HSV-2 migrated out-of-Africa (i)HSV-2 followed human migration out-of-Africa 50-100 thousand years ago, or (ii)HSV-2 migrated via the trans-Atlantic slave trade 150-500 years ago. Limited geographic sampling and lack of molecular clock signal has precluded robust comparison. Here, we analyze newly sequenced HSV-2 genomes from Africa to resolve geography and timing of divergence events within HSV-2. Phylogeographic analysis consistently places the ancestor of worldwide dispersal in East Africa, though molecular clock is too slow to be detected using available data. Rates 4.2 × 10-8-5.6 × 10-8 substitutions/site/year, consistent with previous age estimates, suggest a worldwide dispersal 22-29 thousand years ago. Thus, HSV-2 likely migrated with humans from East Africa and dispersed after the Last Glacial Maximum.
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Affiliation(s)
- Jennifer L Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
| | | | - Kevin Merkel
- Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - Sonia Burrel
- Virology Department, National Reference Center for Herperviruses (Associated Laboratory), AP-HP-Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
- Sorbonne University, INSERM UMR-S 1136, Pierre Louis Institute of Epidemiology and Public Health (IPLESP), Paris, France
| | - David Boutolleau
- Virology Department, National Reference Center for Herperviruses (Associated Laboratory), AP-HP-Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
- Sorbonne University, INSERM UMR-S 1136, Pierre Louis Institute of Epidemiology and Public Health (IPLESP), Paris, France
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
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11
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Li Y, Bletsa M, Zisi Z, Boonen I, Gryseels S, Kafetzopoulou L, Webster JP, Catalano S, Pybus OG, Van de Perre F, Li H, Li Y, Li Y, Abramov A, Lymberakis P, Lemey P, Lequime S. Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History. Mol Biol Evol 2022; 39:6692409. [PMID: 36063436 PMCID: PMC9550988 DOI: 10.1093/molbev/msac190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.
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Affiliation(s)
- Yiqiao Li
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Zafeiro Zisi
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Ine Boonen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium,Belgium Evolutionary Ecology Group, University of Antwerp, 2610 Wilrijk, Belgium
| | - Liana Kafetzopoulou
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium,Virology Department, Belgium Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Joanne P Webster
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Stefano Catalano
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | | | - Haotian Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yaoyao Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yuchun Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Alexei Abramov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
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12
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Gao J, May MR, Rannala B, Moore BR. New Phylogenetic Models Incorporating Interval-Specific Dispersal Dynamics Improve Inference of Disease Spread. Mol Biol Evol 2022; 39:6647827. [PMID: 35861314 PMCID: PMC9384482 DOI: 10.1093/molbev/msac159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Phylodynamic methods reveal the spatial and temporal dynamics of viral geographic spread, and have featured prominently in studies of the COVID-19 pandemic. Virtually all such studies are based on phylodynamic models that assume—despite direct and compelling evidence to the contrary—that rates of viral geographic dispersal are constant through time. Here, we: (1) extend phylodynamic models to allow both the average and relative rates of viral dispersal to vary independently between pre-specified time intervals; (2) implement methods to infer the number and timing of viral dispersal events between areas; and (3) develop statistics to assess the absolute fit of discrete-geographic phylodynamic models to empirical datasets. We first validate our new methods using simulations, and then apply them to a SARS-CoV-2 dataset from the early phase of the COVID-19 pandemic. We show that: (1) under simulation, failure to accommodate interval-specific variation in the study data will severely bias parameter estimates; (2) in practice, our interval-specific discrete-geographic phylodynamic models can significantly improve the relative and absolute fit to empirical data; and (3) the increased realism of our interval-specific models provides qualitatively different inferences regarding key aspects of the COVID-19 pandemic—revealing significant temporal variation in global viral dispersal rates, viral dispersal routes, and the number of viral dispersal events between areas—and alters interpretations regarding the efficacy of intervention measures to mitigate the pandemic.
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Affiliation(s)
- Jiansi Gao
- Department of Evolution and Ecology, University of California, Davis, Storer Hall, Davis, CA 95616, U.S.A
| | - Michael R May
- Department of Evolution and Ecology, University of California, Davis, Storer Hall, Davis, CA 95616, U.S.A.,Department of Integrative Biology, University of California, Berkeley, 3060 VLSB, Berkeley, CA 94720-3140, U.S.A
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, Storer Hall, Davis, CA 95616, U.S.A
| | - Brian R Moore
- Department of Evolution and Ecology, University of California, Davis, Storer Hall, Davis, CA 95616, U.S.A
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13
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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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14
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Kocher A, Papac L, Barquera R, Key FM, Spyrou MA, Hübler R, Rohrlach AB, Aron F, Stahl R, Wissgott A, van Bömmel F, Pfefferkorn M, Mittnik A, Villalba-Mouco V, Neumann GU, Rivollat M, van de Loosdrecht MS, Majander K, Tukhbatova RI, Musralina L, Ghalichi A, Penske S, Sabin S, Michel M, Gretzinger J, Nelson EA, Ferraz T, Nägele K, Parker C, Keller M, Guevara EK, Feldman M, Eisenmann S, Skourtanioti E, Giffin K, Gnecchi-Ruscone GA, Friederich S, Schimmenti V, Khartanovich V, Karapetian MK, Chaplygin MS, Kufterin VV, Khokhlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Tejedor-Rodríguez C, de Lagrán ÍGM, Arcusa-Magallón H, Garrido-Pena R, Royo-Guillén JI, Nováček J, Rottier S, Kacki S, Saintot S, Kaverzneva E, Belinskiy AB, Velemínský P, Limburský P, Kostka M, Loe L, Popescu E, Clarke R, Lyons A, Mortimer R, Sajantila A, de Armas YC, Hernandez Godoy ST, Hernández-Zaragoza DI, Pearson J, Binder D, Lefranc P, Kantorovich AR, Maslov VE, Lai L, Zoledziewska M, Beckett JF, Langová M, Danielisová A, Ingman T, Atiénzar GG, de Miguel Ibáñez MP, Romero A, Sperduti A, Beckett S, Salter SJ, Zilivinskaya ED, Vasil'ev DV, von Heyking K, Burger RL, Salazar LC, Amkreutz L, Navruzbekov M, Rosenstock E, Alonso-Fernández C, Slavchev V, Kalmykov AA, Atabiev BC, Batieva E, Calmet MA, Llamas B, Schultz M, Krauß R, Jiménez-Echevarría J, Francken M, Shnaider S, de Knijff P, Altena E, Van de Vijver K, Fehren-Schmitz L, Tung TA, Lösch S, Dobrovolskaya M, Makarov N, Read C, Van Twest M, Sagona C, Ramsl PC, Akar M, Yener KA, Ballestero EC, Cucca F, Mazzarello V, Utrilla P, Rademaker K, Fernández-Domínguez E, Baird D, Semal P, Márquez-Morfín L, Roksandic M, Steiner H, Salazar-García DC, Shishlina N, Erdal YS, Hallgren F, Boyadzhiev Y, Boyadzhiev K, Küßner M, Sayer D, Onkamo P, Skeates R, Rojo-Guerra M, Buzhilova A, Khussainova E, Djansugurova LB, Beisenov AZ, Samashev Z, Massy K, Mannino M, Moiseyev V, Mannermaa K, Balanovsky O, Deguilloux MF, Reinhold S, Hansen S, Kitov EP, Dobeš M, Ernée M, Meller H, Alt KW, Prüfer K, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 2021; 374:182-188. [PMID: 34618559 DOI: 10.1126/science.abi5658] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Florian van Bömmel
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Maria Pfefferkorn
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France
| | | | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland
| | - Rezeda I Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia
| | - Lyazzat Musralina
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cody Parker
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA
| | - Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | | | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Marina K Karapetian
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir V Kufterin
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey A Chizhevsky
- Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia
| | - Dmitry A Stashenkov
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Anna F Kochkina
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Cristina Tejedor-Rodríguez
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | | | | | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain
| | | | - Jan Nováček
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.,University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany
| | | | - Sacha Kacki
- Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.,Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Sylvie Saintot
- INRAP, ARAR UMR 5138, Maison de l'Orient et de la Méditerranée, Lyon, France
| | | | | | - Petr Velemínský
- Department of Anthropology, The National Museum, Prague, Czech Republic
| | - Petr Limburský
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK
| | | | - Rachel Clarke
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.,Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland
| | | | - Silvia Teresita Hernandez Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | - Diana I Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Didier Binder
- Université Côte d'Azur, CNRS, CEPAM UMR 7264, Nice, France
| | - Philippe Lefranc
- Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA.,Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michaela Langová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Danielisová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tara Ingman
- Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Maria Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.,Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome, Italy.,Dipartimento Asia Africa e Mediterraneo, Università di Napoli L'Orientale, Napoli, Italy
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.,Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK
| | - Susannah J Salter
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Emma D Zilivinskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany
| | - Richard L Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lucy C Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Luc Amkreutz
- National Museum of Antiquities, 2301 EC Leiden, Netherlands
| | | | - Eva Rosenstock
- Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany
| | | | | | | | - Biaslan Ch Atabiev
- Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.,Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.,National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Schultz
- University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.,Institute of Biology, University of Hildeshein, Germany
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Michael Francken
- State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany
| | - Svetlana Shnaider
- ArchaeoZoology in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Center for Archaeological Sciences, University of Leuven, Belgium.,Dienst Archeologie-Stad Mechelen, Belgium
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Chris Read
- Applied Archaeology School of Science, Institute of Technology Sligo, Ireland
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK
| | - Claudia Sagona
- School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia
| | - Peter C Ramsl
- Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria
| | - Murat Akar
- Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Eduardo Carmona Ballestero
- Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.,Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica-CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Pilar Utrilla
- Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lourdes Márquez-Morfín
- Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.,Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools," University of Tübingen, Tübingen, Germany
| | - Hubert Steiner
- South Tyrol Provincial Heritage Service, South Tyrol, Italy
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Natalia Shishlina
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.,State Historical Museum, Moscow, Russia
| | - Yilmaz Selim Erdal
- Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany
| | - Duncan Sayer
- School of Natural Sciences, University of Central Lancashire, Preston, UK
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20500 Turku, Finland
| | - Robin Skeates
- Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Manuel Rojo-Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Arman Z Beisenov
- Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Zainolla Samashev
- Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.,State Historical and Cultural Museum-Reserve "Berel," Katon-Karagay district, East Kazakhstan region, Kazakhstan
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Marcello Mannino
- Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Egor P Kitov
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.,Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Ernée
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Kurt W Alt
- Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.,Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.,Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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15
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Abstract
African apes harbor at least twelve Plasmodium species, some of which have been a source of human infection. It is now well established that Plasmodium falciparum emerged following the transmission of a gorilla parasite, perhaps within the last 10,000 years, while Plasmodium vivax emerged earlier from a parasite lineage that infected humans and apes in Africa before the Duffy-negative mutation eliminated the parasite from humans there. Compared to their ape relatives, both human parasites have greatly reduced genetic diversity and an excess of nonsynonymous mutations, consistent with severe genetic bottlenecks followed by rapid population expansion. A putative new Plasmodium species widespread in chimpanzees, gorillas, and bonobos places the origin of Plasmodium malariae in Africa. Here, we review what is known about the origins and evolutionary history of all human-infective Plasmodium species, the time and circumstances of their emergence, and the diversity, host specificity, and zoonotic potential of their ape counterparts.
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Affiliation(s)
- Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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16
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Abstract
Over the last two decades, the viromes of our closest relatives, the African great apes (AGA), have been intensively studied. Comparative approaches have unveiled diverse evolutionary patterns, highlighting both stable host-virus associations over extended evolutionary timescales and much more recent viral emergence events. In this chapter, we summarize these findings and outline how they have shed a new light on the origins and evolution of many human-infecting viruses. We also show how this knowledge can be used to better understand the evolution of human health in relation to viral infections.
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17
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Lytras S, Arriagada G, Gifford RJ. Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes. Virus Evol 2021; 7:veab012. [PMID: 33747544 PMCID: PMC7955980 DOI: 10.1093/ve/veab012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepadnaviruses (family Hepadnaviviridae) are reverse-transcribing animal viruses that infect vertebrates. DNA sequences derived from ancient hepadnaviruses have been identified in the germline genome of numerous vertebrate species, and these ‘endogenous hepatitis B viruses’ (eHBVs) reveal aspects of the long-term coevolutionary relationship between hepadnaviruses and their vertebrate hosts. Here, we use a novel, data-oriented approach to recover and analyse the complete repertoire of eHBV elements in published animal genomes. We show that germline incorporation of hepadnaviruses is exclusive to a single vertebrate group (Sauria) and that the eHBVs contained in saurian genomes represent a far greater diversity of hepadnaviruses than previously recognized. Through in-depth characterization of eHBV elements, we establish the existence of four distinct subgroups within the genus Avihepadnavirus and trace their evolution through the Cenozoic Era. Furthermore, we provide a completely new perspective on hepadnavirus evolution by showing that the metahepadnaviruses (genus Metahepadnavirus) originated >300 million years ago in the Paleozoic Era and have historically infected a broad range of vertebrates. We also show that eHBVs have been intra-genomically amplified in some saurian lineages, and that eHBVs located at approximately equivalent genomic loci have been acquired in entirely distinct germline integration events. These findings indicate that selective forces have favoured the accumulation of hepadnaviral sequences at specific loci in the saurian germline. Our investigation provides a range of new insights into the long-term evolutionary history of reverse-transcribing DNA viruses and shows that germline incorporation of hepadnaviruses has played a role in shaping the evolution of saurian genomes.
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Affiliation(s)
- Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK
| | - Gloria Arriagada
- FONDAP Center for Genome Regulation.,Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Echaurren 183, Santiago, Chile
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK
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18
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Spadavecchia G, Chiocchio A, Bisconti R, Canestrelli D. Paso doble: A two-step Late Pleistocene range expansion in the Tyrrhenian tree frog Hyla sarda. Gene 2021; 780:145489. [PMID: 33588038 DOI: 10.1016/j.gene.2021.145489] [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: 08/12/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 10/22/2022]
Abstract
The Tyrrhenian tree frog, Hyla sarda, is an amphibian endemic to the Tyrrhenian islands (Western Mediterranean). Previous investigations of its Pleistocene evolutionary history suggested that it colonised the northern portion of its current range, through a spatial diffusion process from the Sardinia island, during the last glaciation. However, southern and northern portions of the species' range experienced markedly different climatic conditions during the Late Pleistocene, suggesting the possibility of an unusual two-step process of demographic expansion. Here, we use Bayesian phylogeographic approaches to locate the ancestral area in Sardinia and to characterise better the demographic component of this expansion event. These analyses located the ancestral area for H. sarda populations along the central-eastern coast of the Sardinia island, within an area previously shown to host suitable bioclimatic conditions for H. sarda populations throughout the Late Pleistocene. Historical demographic reconstructions clearly showed that a two-step process of demographic growth fits well the data, with northern populations expanding later than Sardinia populations. The harsher climatic conditions occurred in northern islands during the glacial epoch, as compared to Sardinia, likely delayed tree frog colonisation of northern territories, and the associated demographic growth.
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Affiliation(s)
- Giada Spadavecchia
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy
| | - Andrea Chiocchio
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy; Department of Biology, Lunds Universitet, Sölvegatan 37, 223 62 Lund, Sweden
| | - Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy.
| | - Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia. Viale dell'Università s.n.c., I-01100 Viterbo, Italy
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19
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Prevalence and evolutionary analyses of human T-cell lymphotropic virus in Guangdong province, China: Transcontinental and Japanese subtype lineages dominate the prevalence. PLoS Negl Trop Dis 2021; 15:e0009043. [PMID: 33539355 PMCID: PMC7888662 DOI: 10.1371/journal.pntd.0009043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 02/17/2021] [Accepted: 12/18/2020] [Indexed: 11/19/2022] Open
Abstract
To systematically characterize the prevalence and evolution of human T-cell lymphotropic virus (HTLV) infection among voluntary blood donors (BDs) in Guangdong province, China. A three-year survey for HTLV epidemiology among BDs was performed in Guangdong during 2016–2018. Anti-HTLV-1/2 was screened by ELISA and ECLIA, and subsequently confirmed by western blot (WB) and nucleic acid testing (NAT). The prevalence of HTLV in donors from different cities was calculated. The identified HTLV-positive cases were phylogenetically genotyped and analyzed in a Bayesian phylogenetic framework. Among 3,262,271 BDs, 59 were confirmed positive for HTLV-1 (1.81 per 100,000) and no HTLV-2 infection was found. The prevalence of HTLV-1 varied significantly among 21 cities in Guangdong province, China. The highest prevalence was found in donors from Shanwei (13.94 per 100,000), which is a coastal city in eastern Guangdong. Viral genomic sequences genotyped from 55 HTLV-1 carriers showed that 39 were transcontinental subtype and 16 were Japanese subtype. Specially, 13 out of 39 transcontinental subtype sequences were characterized with L55P mutation and 21 out of 55 sequences were characterized with L19F mutation in viral gp46 protein. The L55P mutation seemed be specific to eastern Asia since it only presented in the sequences from Japan, mainland China, and Taiwan. Phylogenetic analysis of gp46 gene shows that HTLV-1a may have been introduced to Guangdong through four different introduction events and formed major transmission clusters: clades I(13,602 years ago), II(16, 010 years ago), III(15,639 years ago) and IV(16,517 years ago). In general, Guangdong is considered to be a low-prevalence region for HTLV-1 infection, but the prevalence is significantly higher in Shanwei city. Transcontinental and Japanese subtype lineages dominate the prevalence in Guangdong. In terms of blood safety, HTLV antibody screening for first-time blood donors can effectively reduce the risk of HTLV transmission. Human T-cell lymphotropic virus type 1 distributed all over the world. Since 1988, serological screening has been included in routine blood screening in certain developed countries and regions such as American countries and some parts of Western Europe and East Asia. However, data from some highly populated countries such as China are still not available. We performed a 3-year large-scale blood screening survey to systematically characterize the prevalence of HTLV infection among blood donors in Guangdong province in south China during 2016–2018. In general, Guangdong was considered to be a low-prevalence region for HTLV-1 infection, but the prevalence is significantly higher in Shanwei, a coastal city of eastern Guangdong. Transcontinental and Japanese subtype lineages dominate the prevalence in Guangdong. Moreover, similar molecular characteristics of prevalent HTLV-1 sequences in Mainland China, Taiwan and Japan suggested a same origin of these viruses.
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20
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Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020; 5:1408-1417. [PMID: 32724171 DOI: 10.1101/2020.03.30.015008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/10/2020] [Indexed: 05/22/2023]
Abstract
There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses-the viral subgenus containing SARS-CoV and SARS-CoV-2-undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879-1999), 1969 (95% HPD: 1930-2000) and 1982 (95% HPD: 1948-2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.
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Affiliation(s)
- Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Leuven, Belgium.
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Blair W Perry
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
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21
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Forni D, Cagliani R, Clerici M, Pozzoli U, Sironi M. You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations. Mol Biol Evol 2020; 37:442-454. [PMID: 31593241 DOI: 10.1093/molbev/msz227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise FST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based FST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations.
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Affiliation(s)
- Diego Forni
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Lecco, Italy
| | - Rachele Cagliani
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Lecco, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Uberto Pozzoli
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Lecco, Italy
| | - Manuela Sironi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Lecco, Italy
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22
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Ling J, Hickman RA, Li J, Lu X, Lindahl JF, Lundkvist Å, Järhult JD. Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Viruses 2020; 12:E1026. [PMID: 32937868 PMCID: PMC7551444 DOI: 10.3390/v12091026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. METHODS We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. RESULTS We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10-3 substitutions per year. CONCLUSIONS Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches.
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Affiliation(s)
- Jiaxin Ling
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
| | - Rachel A. Hickman
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
| | - Jinlin Li
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Xi Lu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Johanna F. Lindahl
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
- International Livestock Research Institute, Nairobi 00100, Kenya
- Swedish University of Agricultural Research, SE-750 07 Uppsala, Sweden
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
| | - Josef D. Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, SE-751 23 Uppsala, Sweden;
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23
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Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020; 5:1408-1417. [DOI: 10.1038/s41564-020-0771-4] [Citation(s) in RCA: 568] [Impact Index Per Article: 142.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
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24
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Düx A, Lequime S, Patrono LV, Vrancken B, Boral S, Gogarten JF, Hilbig A, Horst D, Merkel K, Prepoint B, Santibanez S, Schlotterbeck J, Suchard MA, Ulrich M, Widulin N, Mankertz A, Leendertz FH, Harper K, Schnalke T, Lemey P, Calvignac-Spencer S. Measles virus and rinderpest virus divergence dated to the sixth century BCE. Science 2020; 368:1367-1370. [PMID: 32554594 DOI: 10.1126/science.aba9411] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022]
Abstract
Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. Although it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. We sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the divergence date of measles virus and rinderpest virus. This divergence date represents the earliest possible date for the establishment of measles in human populations. Our analyses show that the measles virus potentially arose as early as the sixth century BCE, possibly coinciding with the rise of large cities.
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Affiliation(s)
- Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Sebastian Lequime
- Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Livia Victoria Patrono
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Bram Vrancken
- Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Sengül Boral
- Institute for Pathology, Charité, Berlin, Germany
| | - Jan F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Antonia Hilbig
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany
| | - David Horst
- Institute for Pathology, Charité, Berlin, Germany
| | - Kevin Merkel
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Baptiste Prepoint
- Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany.,Département de Biologie, Ecole Normale Supérieure, PSL Université Paris, Paris, France
| | - Sabine Santibanez
- National Reference Centre for Measles, Mumps, and Rubella, Robert Koch Institute, Berlin, Germany
| | | | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.,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
| | - Markus Ulrich
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany
| | - Navena Widulin
- Berlin Museum of Medical History, Charité, Berlin, Germany
| | - Annette Mankertz
- National Reference Centre for Measles, Mumps, and Rubella, Robert Koch Institute, Berlin, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany
| | - Kyle Harper
- Department of Classics and Letters, University of Oklahoma, Norman, OK, USA
| | | | - Philippe Lemey
- Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany. .,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
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25
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Mojsiejczuk L, Torres C, Flichman D, Campos RH. Long-term evolution of hepatitis B virus genotype F: Strong association between viral diversification and the prehistoric settlement of Central and South America. J Viral Hepat 2020; 27:620-630. [PMID: 32052519 DOI: 10.1111/jvh.13273] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 12/13/2022]
Abstract
The genotype F (HBV-F) is an autochthonous Native American strain of the hepatitis B virus. In this study, we reconstruct the HBV-F long-term evolution under a hypothesis of co-divergence with humans in Central and South America, since their entry into the region 14.5-16 thousand years ago. The Bayesian phylogeographic reconstruction supported a virus-host co-expansion; however, two evolutionary scenarios would have been present. Whereas subgenotype F1 spreads along a Pacific coastal route and would have evolved associated with Central American and Andean cultures from the west of the continent, subgenotypes F2-F6 spread along the Atlantic coastline and inner pathways associated with communities inhabiting the tropical forest lowlands. Then, we propose a model for HBV-F evolution in which the selection of differential biological characteristics in these two main groups would be related to their evolution in host populations with different genetic backgrounds and dissimilar demographic conditions.
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Affiliation(s)
- Laura Mojsiejczuk
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carolina Torres
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Flichman
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina
| | - Rodolfo Héctor Campos
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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26
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A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue. Proc Natl Acad Sci U S A 2020; 117:12222-12229. [PMID: 32430331 DOI: 10.1073/pnas.1913682117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long prediscovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,645 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Central Africa between 1958 and 1966. We report the near-complete viral genome in one HIV-1 positive specimen from Kinshasa, Democratic Republic of Congo (DRC), from 1966 ("DRC66")-a nonrecombinant sister lineage to subtype C that constitutes the oldest HIV-1 near full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of the DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978 to 2014, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to a time period around the turn of the 20th century (1881 to 1918). In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.
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27
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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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28
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The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses 2019; 11:v11111032. [PMID: 31698764 PMCID: PMC6893659 DOI: 10.3390/v11111032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 12/05/2022] Open
Abstract
Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.
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29
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Cagliani R, Forni D, Sironi M. Mode and tempo of human hepatitis virus evolution. Comput Struct Biotechnol J 2019; 17:1384-1395. [PMID: 31768229 PMCID: PMC6872792 DOI: 10.1016/j.csbj.2019.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 02/07/2023] Open
Abstract
Human viral hepatitis, a major cause of morbidity and mortality worldwide, is caused by highly diverse viruses with different genetic, ecological, and pathogenetic features. Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. Thus, with the exclusion of hepatitis D virus, close or distant relatives of these human pathogens were identified in a number of domestic and wild mammals. Also, sequences of human viral strains isolated from different geographic locations and over different time-spans have allowed the application of phylogeographic and molecular dating approaches to large viral phylogenies. In this review, we summarize the most recent insights into our understanding of the evolutionary events and ecological contexts that determined the origin and spread of human hepatitis viruses.
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Affiliation(s)
- Rachele Cagliani
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
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30
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Novel Polyomaviruses in Mammals from Multiple Orders and Reassessment of Polyomavirus Evolution and Taxonomy. Viruses 2019; 11:v11100930. [PMID: 31658738 PMCID: PMC6833039 DOI: 10.3390/v11100930] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 12/14/2022] Open
Abstract
As the phylogenetic organization of mammalian polyomaviruses is complex and currently incompletely resolved, we aimed at a deeper insight into their evolution by identifying polyomaviruses in host orders and families that have either rarely or not been studied. Sixteen unknown and two known polyomaviruses were identified in animals that belong to 5 orders, 16 genera, and 16 species. From 11 novel polyomaviruses, full genomes could be determined. Splice sites were predicted for large and small T antigen (LTAg, STAg) coding sequences (CDS) and examined experimentally in transfected cell culture. In addition, splice sites of seven published polyomaviruses were analyzed. Based on these data, LTAg and STAg annotations were corrected for 10/86 and 74/86 published polyomaviruses, respectively. For 25 polyomaviruses, a spliced middle T CDS was observed or predicted. Splice sites that likely indicate expression of additional, alternative T antigens, were experimentally detected for six polyomaviruses. In contrast to all other mammalian polyomaviruses, three closely related cetartiodactyl polyomaviruses display two introns within their LTAg CDS. In addition, the VP2 of Glis glis (edible dormouse) polyomavirus 1 was observed to be encoded by a spliced transcript, a unique experimental finding within the Polyomaviridae family. Co-phylogenetic analyses based on LTAg CDS revealed a measurable signal of codivergence when considering all mammalian polyomaviruses, most likely driven by relatively recent codivergence events. Lineage duplication was the only other process whose influence on polyomavirus evolution was unambiguous. Finally, our analyses suggest that an update of the taxonomy of the family is required, including the creation of novel genera of mammalian and non-mammalian polyomaviruses.
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