1
|
Rozwalak P, Barylski J, Wijesekara Y, Dutilh BE, Zielezinski A. Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces. Nat Commun 2024; 15:495. [PMID: 38263397 PMCID: PMC10805732 DOI: 10.1038/s41467-023-44370-0] [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: 06/13/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.
Collapse
Affiliation(s)
- Piotr Rozwalak
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Yasas Wijesekara
- Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475, Greifswald, Germany
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
| | - Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland.
| |
Collapse
|
2
|
Ghafari M, Sõmera M, Sarmiento C, Niehl A, Hébrard E, Tsoleridis T, Ball J, Moury B, Lemey P, Katzourakis A, Fargette D. Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses. PLoS Pathog 2024; 20:e1011911. [PMID: 38206964 PMCID: PMC10807823 DOI: 10.1371/journal.ppat.1011911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/24/2024] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.
Collapse
Affiliation(s)
- Mahan Ghafari
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annette Niehl
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Theocharis Tsoleridis
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Jonathan Ball
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Denis Fargette
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| |
Collapse
|
3
|
Chacón RD, Sánchez-Llatas CJ, Diaz Forero AJ, Guimarães MB, Pajuelo SL, Astolfi-Ferreira CS, Ferreira AJP. Evolutionary Analysis of a Parrot Bornavirus 2 Detected in a Sulphur-Crested Cockatoo ( Cacatua galerita) Suggests a South American Ancestor. Animals (Basel) 2023; 14:47. [PMID: 38200778 PMCID: PMC10778322 DOI: 10.3390/ani14010047] [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: 10/20/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Parrot bornavirus (PaBV) is an RNA virus that causes Proventricular Dilatation Disease (PDD), neurological disorders, and death in Psittaciformes. Its diversity in South America is poorly known. We examined a Cacatua galerita presenting neuropathies, PDD, and oculopathies as the main signs. We detected PaBV through reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of the nucleoprotein (N) and matrix (M) genes. Maximum likelihood and Bayesian phylogenetic inferences classified it as PaBV-2. The nucleotide identity of the sequenced strain ranged from 88.3% to 90.3% against genotype PaBV-2 and from 80.2% to 84.4% against other genotypes. Selective pressure analysis detected signs of episodic diversifying selection in both the N and M genes. No recombination events were detected. Phylodynamic analysis estimated the time to the most recent common ancestor (TMRCA) as the year 1758 for genotype PaBV-2 and the year 1049 for the Orthobornavirus alphapsittaciforme species. Substitution rates were estimated at 2.73 × 10-4 and 4.08 × 10-4 substitutions per year per site for N and M, respectively. The analysis of population dynamics showed a progressive decline in the effective population size during the last century. Timescale phylogeographic analysis revealed a potential South American ancestor as the origin of genotypes 1, 2, and 8. These results contribute to our knowledge of the evolutionary origin, diversity, and dynamics of PaBVs in South America and the world. Additionally, it highlights the importance of further studies in captive Psittaciformes and the potential impact on endangered wild birds.
Collapse
Affiliation(s)
- Ruy D. Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University of Madrid (UCM), 28040 Madrid, Spain;
| | - Andrea J. Diaz Forero
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Marta B. Guimarães
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Sarah L. Pajuelo
- Faculty of Biological Sciences, National University of Trujillo, Trujillo 13001, La Libertad, Peru;
| | - Claudete S. Astolfi-Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Antonio J. Piantino Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| |
Collapse
|
4
|
Jaya FR, Brito BP, Darling AE. Evaluation of recombination detection methods for viral sequencing. Virus Evol 2023; 9:vead066. [PMID: 38131005 PMCID: PMC10734630 DOI: 10.1093/ve/vead066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/03/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Recombination is a key evolutionary driver in shaping novel viral populations and lineages. When unaccounted for, recombination can impact evolutionary estimations or complicate their interpretation. Therefore, identifying signals for recombination in sequencing data is a key prerequisite to further analyses. A repertoire of recombination detection methods (RDMs) have been developed over the past two decades; however, the prevalence of pandemic-scale viral sequencing data poses a computational challenge for existing methods. Here, we assessed eight RDMs: PhiPack (Profile), 3SEQ, GENECONV, recombination detection program (RDP) (OpenRDP), MaxChi (OpenRDP), Chimaera (OpenRDP), UCHIME (VSEARCH), and gmos; to determine if any are suitable for the analysis of bulk sequencing data. To test the performance and scalability of these methods, we analysed simulated viral sequencing data across a range of sequence diversities, recombination frequencies, and sample sizes. Furthermore, we provide a practical example for the analysis and validation of empirical data. We find that RDMs need to be scalable, use an analytical approach and resolution that is suitable for the intended research application, and are accurate for the properties of a given dataset (e.g. sequence diversity and estimated recombination frequency). Analysis of simulated and empirical data revealed that the assessed methods exhibited considerable trade-offs between these criteria. Overall, we provide general guidelines for the validation of recombination detection results, the benefits and shortcomings of each assessed method, and future considerations for recombination detection methods for the assessment of large-scale viral sequencing data.
Collapse
Affiliation(s)
- Frederick R Jaya
- Australian Institute for Microbiology & Infection, University of Technology Sydney, 15 Broadway, Ultimo, New South Wales 2007, Australia
- Ecology and Evolution, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2600, Australia
| | - Barbara P Brito
- Australian Institute for Microbiology & Infection, University of Technology Sydney, 15 Broadway, Ultimo, New South Wales 2007, Australia
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, New South Wales 2568, Australia
| | - Aaron E Darling
- Australian Institute for Microbiology & Infection, University of Technology Sydney, 15 Broadway, Ultimo, New South Wales 2007, Australia
- Illumina Australia Pty Ltd, Ultimo, New South Wales 2007, Australia
| |
Collapse
|
5
|
Zhang Q, Folk RA, Mo ZQ, Ye H, Zhang ZY, Peng H, Zhao JL, Yang SX, Yu XQ. Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae). Mol Phylogenet Evol 2023; 188:107912. [PMID: 37648181 DOI: 10.1016/j.ympev.2023.107912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/09/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Gene tree discordance is a significant legacy of biological evolution. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss. Resolving the background of gene tree discordance is a critical way to uncover the process of species diversification. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history. We used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests to distinguish hard and soft conflict. A selective pressure analysis was also performed to assess the impact of selection on phylogenetic topology reconstruction. Our results detected different levels of gene tree discordance in the backbone of Camellia, and recovered rapid diversification as one of the possible causes of gene tree discordance. Furthermore, we confirmed that none of the currently proposed sections of Camellia was monophyletic. Comparisons among datasets partitioned under different selective pressure regimes showed that integrating all orthologous genes provided the best phylogenetic resolution of the species tree of Camellia. The findings of this study reveal rapid diversification as a major source of gene tree discordance in Camellia and will facilitate future investigation of reticulate relationships at the species level in this important plant genus.
Collapse
Affiliation(s)
- Qiong Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, MS 39762, United States
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hang Ye
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, Nanning 530002, Guangxi, China
| | - Zhao-Yuan Zhang
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, Nanning 530002, Guangxi, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
| | - Shi-Xiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Xiang-Qin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| |
Collapse
|
6
|
Otomaru H, Nguyen HAT, Vo HM, Toizumi M, Le MN, Mizuta K, Moriuchi H, Bui MX, Dang DA, Yoshida LM. A decade of human metapneumovirus in hospitalized children with acute respiratory infection: molecular epidemiology in central Vietnam, 2007-2017. Sci Rep 2023; 13:15757. [PMID: 37735242 PMCID: PMC10514255 DOI: 10.1038/s41598-023-42692-z] [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: 03/30/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Human metapneumovirus (hMPV) can cause severe acute respiratory infection (ARI). We aimed to clarify the clinical and molecular epidemiological features of hMPV. We conducted an ARI surveillance targeting hospitalized children aged 1 month to 14 years in Nha Trang, Vietnam. Nasopharyngeal swabs were tested for respiratory viruses with PCR. We described the clinical characteristics of hMPV patients in comparison with those with respiratory syncytial virus (RSV) and those with neither RSV nor hMPV, and among different hMPV genotypes. Among 8822 patients, 278 (3.2%) were hMPV positive, with a median age of 21.0 months (interquartile range: 12.7-32.5). Among single virus-positive patients, hMPV cases were older than patients with RSV (p < 0.001) and without RSV (p = 0.003). The proportions of clinical pneumonia and wheezing in hMPV patients resembled those in RSV patients but were higher than in non-RSV non-hMPV patients. Seventy percent (n = 195) were genotyped (A2b: n = 40, 20.5%; A2c: n = 99, 50.8%; B1: n = 37, 19%; and B2: n = 19, 9.7%). The wheezing frequency was higher in A2b patients (76.7%) than in those with other genotypes (p = 0.033). In conclusion, we found a moderate variation in clinical features among hMPV patients with various genotypes. No seasonality was observed, and the multiple genotype co-circulation was evident.
Collapse
Affiliation(s)
- Hirono Otomaru
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hien Anh Thi Nguyen
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Hien Minh Vo
- Department of Pediatrics, Khanh Hoa General Hospital, Nha Trang, Vietnam
| | - Michiko Toizumi
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Minh Nhat Le
- Antimicrobial Resistance Research Centre, National Institute of Infectious Disease (NIID), Sinjuku, Japan
- Tay Nguyen Institute of Science Research, Vietnam Academy of Science and Technology (VAST), Da Lat, Vietnam
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Hiroyuki Moriuchi
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Minh Xuan Bui
- Khanh Hoa Health Service Department, Nha Trang, Vietnam
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Lay-Myint Yoshida
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
| |
Collapse
|
7
|
Burk RD, Mirabello L, DeSalle R. Distinguishing Genetic Drift from Selection in Papillomavirus Evolution. Viruses 2023; 15:1631. [PMID: 37631973 PMCID: PMC10458755 DOI: 10.3390/v15081631] [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: 06/27/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing Alphapapillomavirus types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.
Collapse
Affiliation(s)
- Robert D. Burk
- Departments of Pediatrics, Microbiology & Immunology, Epidemiology & Population Health, Obstetrics, Gynecology and Woman’s Health, and Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Robert DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| |
Collapse
|
8
|
Pekar JE, Lytras S, Ghafari M, Magee AF, Parker E, Havens JL, Katzourakis A, Vasylyeva TI, Suchard MA, Hughes AC, Hughes J, Robertson DL, Dellicour S, Worobey M, Wertheim JO, Lemey P. The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548617. [PMID: 37502985 PMCID: PMC10369958 DOI: 10.1101/2023.07.12.548617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 has led to increased sampling of related sarbecoviruses circulating primarily in horseshoe bats. These viruses undergo frequent recombination and exhibit spatial structuring across Asia. Employing recombination-aware phylogenetic inference on bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed just ~1-3 years prior to their emergence in humans. Phylogeographic analyses examining the movement of related sarbecoviruses demonstrate that they traveled at similar rates to their horseshoe bat hosts and have been circulating for thousands of years in Asia. The closest-inferred bat virus ancestor of SARS-CoV likely circulated in western China, and that of SARS-CoV-2 likely circulated in a region comprising southwest China and northern Laos, both a substantial distance from where they emerged. This distance and recency indicate that the direct ancestors of SARS-CoV and SARS-CoV-2 could not have reached their respective sites of emergence via the bat reservoir alone. Our recombination-aware dating and phylogeographic analyses reveal a more accurate inference of evolutionary history than performing only whole-genome or single gene analyses. These results can guide future sampling efforts and demonstrate that viral genomic fragments extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.
Collapse
Affiliation(s)
- Jonathan E Pekar
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093, USA
- These authors contributed equally
| | - Spyros Lytras
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
- These authors contributed equally
| | - Mahan Ghafari
- Department of Biology, University of Oxford, Oxford, UK
| | - Andrew F Magee
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jennifer L Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Tetyana I Vasylyeva
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alice C Hughes
- School of Biological Sciences, University of Hong Kong, Hong Kong
- China Biodiversity Green Development Foundation, Beijing, China
| | - Joseph Hughes
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - David L Robertson
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
- These authors jointly supervised the work
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, 1050, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
- These authors jointly supervised the work
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- These authors jointly supervised the work
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- These authors jointly supervised the work
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
- These authors jointly supervised the work
| |
Collapse
|
9
|
Molteni C, Forni D, Cagliani R, Arrigoni F, Pozzoli U, De Gioia L, Sironi M. Selective events at individual sites underlie the evolution of monkeypox virus clades. Virus Evol 2023; 9:vead031. [PMID: 37305708 PMCID: PMC10256197 DOI: 10.1093/ve/vead031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/31/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
In endemic regions (West Africa and the Congo Basin), the genetic diversity of monkeypox virus (MPXV) is geographically structured into two major clades (Clades I and II) that differ in virulence and host associations. Clade IIb is closely related to the B.1 lineage, which is dominating a worldwide outbreak initiated in 2022. Lineage B.1 has however accumulated mutations of unknown significance that most likely result from apolipoprotein B mRNA editing catalytic polypeptide-like 3 (APOBEC3) editing. We applied a population genetics-phylogenetics approach to investigate the evolution of MPXV during historical viral spread in Africa and to infer the distribution of fitness effects. We observed a high preponderance of codons evolving under strong purifying selection, particularly in viral genes involved in morphogenesis and replication or transcription. However, signals of positive selection were also detected and were enriched in genes involved in immunomodulation and/or virulence. In particular, several genes showing evidence of positive selection were found to hijack different steps of the cellular pathway that senses cytosolic DNA. Also, a few selected sites in genes that are not directly involved in immunomodulation are suggestive of antibody escape or other immune-mediated pressures. Because orthopoxvirus host range is primarily determined by the interaction with the host immune system, we suggest that the positive selection signals represent signatures of host adaptation and contribute to the different virulence of Clade I and II MPXVs. We also used the calculated selection coefficients to infer the effects of mutations that define the predominant human MPXV1 (hMPXV1) lineage B.1, as well as the changes that have been accumulating during the worldwide outbreak. Results indicated that a proportion of deleterious mutations were purged from the predominant outbreak lineage, whose spread was not driven by the presence of beneficial changes. Polymorphic mutations with a predicted beneficial effect on fitness are few and have a low frequency. It remains to be determined whether they have any significance for ongoing virus evolution.
Collapse
Affiliation(s)
| | | | | | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della scienza, Milan 20126, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Via don Luigi Monza, Bosisio Parini 23842, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della scienza, Milan 20126, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Via don Luigi Monza, Bosisio Parini 23842, Italy
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Molteni C, Forni D, Cagliani R, Mozzi A, Clerici M, Sironi M. Evolution of the orthopoxvirus core genome. Virus Res 2023; 323:198975. [PMID: 36280003 PMCID: PMC9586335 DOI: 10.1016/j.virusres.2022.198975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
Abstract
Orthopoxviruses comprise several relevant pathogens, including the causative agent of smallpox and monkeypox virus. Analysis of orthopoxvirus genome evolution mainly focused on gene gains/losses. We instead analyzed core genes, which are conserved in all orthopoxviruses. We show that, despite their strong constraint, some genes involved in viral morphogenesis and transcription/replication were targets of pervasive positive selection, which was relatively uncommon in immunomodulatory genes. However at least three of the positively selected genes, E3L, A24R, and H3L, might have evolved in response to immune selection. Episodic positive selection was particularly common on the internal branches of the orthopox phylogeny and on the monkeypox virus lineage. The latter showed evidence of episodic positive selection at the D14L gene, which encodes a modulator of complement activation (MOPICE). Notably, two genes (B1R and A33R) targeted by episodic selection on more than one branch are involved in forms of intra-genomic conflict. Finally, we found that, in orthopoxvirus proteomes, intrinsically disordered regions (IDRs) tend to be less constrained and are common targets of positive selection. Extension of our analysis to all poxviruses showed no evidence that the IDR fraction differs with host range. Conversely, we found a strong effect of base composition, which was however not sufficient to explain IDR fraction. We thus suggest that, in poxviruses, the IDR fraction is maintained by modulating GC content to accommodate disorder-promoting codons. Overall, our data provide novel insight in orthopoxvirus evolution and provide a list of genes and sites that are expected to modulate viral phenotypes.
Collapse
Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| |
Collapse
|
12
|
Druelle V, Neher RA. Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates. Virus Evol 2022; 9:veac118. [PMID: 36632482 PMCID: PMC9829961 DOI: 10.1093/ve/veac118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) is a rapidly evolving virus able to evade host immunity through rapid adaptation during chronic infection. The HIV-1 group M has diversified since its zoonosis into several subtypes at a rate of the order of 10-3 changes per site per year. This rate varies between different parts of the genome, and its inference is sensitive to the timescale and diversity spanned by the sequence data used. Higher rates are estimated on short timescales and particularly for within-host evolution, while rate estimates spanning decades or the entire HIV-1 pandemic tend to be lower. The underlying causes of this difference are not well understood. We investigate here the role of rapid reversions toward a preferred evolutionary sequence state on multiple timescales. We show that within-host reversion mutations are under positive selection and contribute substantially to sequence turnover, especially at conserved sites. We then use the rates of reversions and non-reversions estimated from longitudinal within-host data to parameterize a phylogenetic sequence evolution model. Sequence simulation of this model on HIV-1 phylogenies reproduces diversity and apparent evolutionary rates of HIV-1 in gag and pol, suggesting that a tendency to rapidly revert to a consensus-like state can explain much of the time dependence of evolutionary rate estimates in HIV-1.
Collapse
|
13
|
Neher RA. Contributions of adaptation and purifying selection to SARS-CoV-2 evolution. Virus Evol 2022; 8:veac113. [PMID: 37593203 PMCID: PMC10431346 DOI: 10.1093/ve/veac113] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/30/2022] [Accepted: 12/05/2022] [Indexed: 08/19/2023] Open
Abstract
Continued evolution and adaptation of SARS-CoV-2 has led to more transmissible and immune-evasive variants with profound impacts on the course of the pandemic. Here I analyze the evolution of the virus over 2.5 years since its emergence and estimate the rates of evolution for synonymous and non-synonymous changes separately for evolution within clades-well-defined monophyletic groups with gradual evolution-and for the pandemic overall. The rate of synonymous mutation is found to be around 6 changes per year. Synonymous rates within variants vary little from variant to variant and are compatible with the overall rate of 7 changes per year (or [Formula: see text] per year and codon). In contrast, the rate at which variants accumulate amino acid changes (non-synonymous mutations) was initially around 12-16 changes per year, but in 2021 and 2022 it dropped to 6-9 changes per year. The overall rate of non-synonymous evolution, that is across variants, is estimated to be about 26 amino acid changes per year (or [Formula: see text] per year and codon). This strong acceleration of the overall rate compared to within clade evolution indicates that the evolutionary process that gave rise to the different variants is qualitatively different from that in typical transmission chains and likely dominated by adaptive evolution. I further quantify the spectrum of mutations and purifying selection in different SARS-CoV-2 proteins and show that the massive global sampling of SARS-CoV-2 is sufficient to estimate site-specific fitness costs across the entire genome. Many accessory proteins evolve under limited evolutionary constraints with little short-term purifying selection. About half of the mutations in other proteins are strongly deleterious.
Collapse
Affiliation(s)
- Richard A Neher
- Biozentrum, University of Basel, Spitalstrasse 41, Basel
4053, Switzerland
- Swiss Institute of Bioinformatics, Spitalstrasse 41, Basel
4053, Switzerland
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Götting J, Baier C, Panagiota V, Maecker-Kolhoff B, Dhingra A, Heim A. High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years. Virus Evol 2022; 8:veac067. [PMID: 36533152 PMCID: PMC9748976 DOI: 10.1093/ve/veac067] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/29/2022] [Accepted: 08/03/2022] [Indexed: 06/22/2024] Open
Abstract
Type 31 of human adenovirus species A (HAdV-A31) is a significant pathogen primarily associated with diarrhoea in children but also with life-threatening disseminated disease in allogeneic haematopoietic stem cell transplant (HSCT) recipients. Nosocomial outbreaks of HAdV-A31 have been frequently described. However, the evolution of HAdV-A31 has not been studied in detail. The evolution of other HAdV types is driven either by intertypic recombination, where different types exchange genome regions, or by immune escape selection of neutralisation determinants. Complete genomic HAdV-A31 sequences from sixty diagnostic specimens of the past 18 years (2003-21) were generated, including fourteen specimens of a presumed outbreak on two HSCT wards. Additionally, twenty-three complete genomes from GenBank were added to our phylogenetic analysis as well as in silico generated and previously published restriction fragment polymorphism (RFLP) data. Phylogenetic analysis of eighty-three genomes indicated that HAdV-A31 evolved slowly with six lineages co-circulating. The two major lineages were lineage 1, which included the prototype from 1962 and nine recent isolates, and lineage 2, which split into four sublineages and included most isolates from 2003 to 2021. The average nucleotide identity within lineages was high (99.8 per cent) and identity between lineages was 98.7 and 99.2 per cent. RFLP data allowed the construction of a lower-resolution phylogeny with two additional putative lineages. Surprisingly, regions of higher diversity separating lineages were found in gene regions coding for non-structural and minor capsid proteins. Intertypic recombinations were not observed, but the phylogeny of lineage 3 was compatible with an interlineage recombination event in the fibre gene. Applying the phylogenetic analysis to the presumed nosocomial outbreak excluded two suspected transmission events and separated it into two different, simultaneous outbreaks caused by different sublineages of lineage 2. However, due to the high nucleotide identity within HAdV-A31 lineages, the proof of infection chains remains debatable. This in-depth study on the molecular phylogeny of HAdV-A31 highlights the high genetic stability of co-circulating HAdV-A31 lineages over almost six decades. It also supports the epidemiological hypothesis that HAdV-A31 circulates as an etiological agent of a childhood disease infecting immunologically naive patients without strong positive selection of immune escape variants and recombinants.
Collapse
Affiliation(s)
- Jasper Götting
- Institute of Virology, Hannover Medical
School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Claas Baier
- Institute for Medical Microbiology and Hospital
Epidemiology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover
30625, Germany
| | - Victoria Panagiota
- Department of Hematology, Hemostaseology,
Oncology and Stem Cell Transplantation, Hannover Medical School,
Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Britta Maecker-Kolhoff
- Department of Paediatric Haematology and
Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625,
Germany
| | - Akshay Dhingra
- Institute of Virology, Hannover Medical
School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Albert Heim
- Institute of Virology, Hannover Medical
School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| |
Collapse
|
16
|
Rochman ND, Wolf YI, Koonin EV. Molecular adaptations during viral epidemics. EMBO Rep 2022; 23:e55393. [PMID: 35848484 PMCID: PMC9346483 DOI: 10.15252/embr.202255393] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 07/20/2023] Open
Abstract
In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.
Collapse
Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Yuri I Wolf
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Eugene V Koonin
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| |
Collapse
|
17
|
Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
Collapse
Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
| |
Collapse
|
18
|
Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches. Proc Natl Acad Sci U S A 2022; 119:e2121335119. [PMID: 35639694 PMCID: PMC9191635 DOI: 10.1073/pnas.2121335119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Numerous pathogenic viruses are endemic in humans and cause a broad variety of diseases, but what is their potential for causing new pandemics? We show that most human pathogenic RNA viruses form multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and occupy distinct epidemiological niches that are not regionally or seasonally defined, and their persistence appears to stem from limited outbreaks in small communities so that only a small fraction of the global susceptible population is infected at any time. However, due to globalization, interaction and competition between lineages might increase, potentially leading to increased diversification and pathogenicity. Thus, endemic viruses appear to merit global attention with respect to the prevention of future pandemics. Many pathogenic viruses are endemic among human populations and can cause a broad variety of diseases, some potentially leading to devastating pandemics. How virus populations maintain diversity and what selective pressures drive population turnover is not thoroughly understood. We conducted a large-scale phylodynamic analysis of 27 human pathogenic RNA viruses spanning diverse life history traits, in search of unifying trends that shape virus evolution. For most virus species, we identify multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and likely occupy semiindependent epidemiological niches that are not regionally or seasonally defined. Typically, intralineage mutational signatures are similar to interlineage signatures. The principal exception are members of the family Picornaviridae, for which mutations in capsid protein genes are primarily lineage defining. Interlineage turnover is slower than expected under a neutral model, whereas intralineage turnover is faster than the neutral expectation, further supporting the existence of independent niches. The persistence of virus lineages appears to stem from limited outbreaks within small communities, so that only a small fraction of the global susceptible population is infected at any time. As disparate communities become increasingly connected through globalization, interaction and competition between lineages might increase as well, which could result in changing selective pressures and increased diversification and/or pathogenicity. Thus, in addition to zoonotic events, ongoing surveillance of familiar, endemic viruses appears to merit global attention with respect to the prevention or mitigation of future pandemics.
Collapse
|
19
|
Divergent Viruses Discovered in Swine Alter the Understanding of Evolutionary History and Genetic Diversity of the Respirovirus Genus and Related Porcine Parainfluenza Viruses. Microbiol Spectr 2022; 10:e0024222. [PMID: 35647875 PMCID: PMC9241844 DOI: 10.1128/spectrum.00242-22] [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: 01/07/2023] Open
Abstract
Paramyxoviridae is a rapidly growing family of viruses, whose potential for cross-species transmission makes it difficult to predict the harm of newly emerging viruses to humans and animals. To better understand their diversity, evolutionary history, and co-evolution with their hosts, we analyzed a collection of porcine parainfluenza virus (PPIV) genomes to reconstruct the species classification basis and evolutionary history of the Respirovirus genus. We sequenced 17 complete genomes of porcine respirovirus 1 (also known as porcine parainfluenza virus 1; PPIV-1), thereby nearly tripling the number of currently available PPIV-1 genomes. We found that PPIV-1 was widely prevalent in China with two divergent lineages, PPIV-1a and PPIV-1b. We further provided evidence that a new species, porcine parainfluenza virus 2 (PPIV-2), had recently emerged in China. Our results pointed to a need for revising the current species demarcation criteria of the Respirovirus genus. In addition, we used PPIV-1 as an example to explore recombination and diversity of the Respirovirus genus. Interestingly, we only detected heterosubtypic recombination events between PPIV-1a and PPIV-1b with no intrasubtypic recombination events. The recombination hotspots highlighted a diverse geography-dependent genome structure of paramyxovirus infecting swine in China. Furthermore, we found no evidence of co-evolution between respirovirus and its host, indicating frequent cross-species transmission. In summary, our analyses showed that swine can be infected with a broad range of respiroviruses and recombination may serve as an important evolutionary mechanism for the Respirovirus genus’ greater diversity in genome structure than previously anticipated. IMPORTANCE Livestock have emerged as critically underrecognized sources of paramyxovirus diversity, including pigs serving as the source of Nipah virus (NiV) and swine parainfluenza virus type 3, and goats and bovines harboring highly divergent viral lineages. Here, we identified a new species of Respirovirus genus named PPIV-2 in swine and proposed to revise the species demarcation criteria of the Respirovirus genus. We found heterosubtypic recombination events and high genetic diversity in PPIV-1. Further, we showed that genetic recombination may have occurred in the Respirovirus genus which may be associated with host range expansion. The continued expansion of Respirovirus genus diversity in livestock with relatively high human contact rates requires enhanced surveillance and ongoing evaluation of emerging cross-species transmission threats.
Collapse
|
20
|
Abstract
Healthy development and function of essentially all physiological systems and organs, including the brain, require exposure to the microbiota of our mothers and of the natural environment, especially in early life. We also know that some infections, if we survive them, modulate the immune system in relevant ways. If we study the evolution of the immune and metabolic systems, we can understand how these requirements developed and the nature of the organisms that we need to encounter. We can then begin to identify the mechanisms of the beneficial effects of these exposures. Against this evolutionary background, we can analyze the ways in which the modern urban lifestyle, particularly for individuals experiencing low socioeconomic status (SES), results in deficient or distorted microbial exposures and microbiomes. Thus, an evolutionary approach facilitates the identification of practical solutions to the growing scandal of health disparities linked to inequality.
Collapse
|
21
|
Ghafari M, du Plessis L, Raghwani J, Bhatt S, Xu B, Pybus OG, Katzourakis A. Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza. Mol Biol Evol 2022; 39:6509523. [PMID: 35038728 PMCID: PMC8826518 DOI: 10.1093/molbev/msac009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Crucially, there are an increasing number of molecular clock analyses using external evolutionary rate priors to infer evolutionary parameters. However, it is not clear which rate prior is appropriate for a given time window of observation due to the time-dependent nature of evolutionary rate estimates. Here, we characterize the molecular evolutionary dynamics of SARS-CoV-2 and 2009 pandemic H1N1 (pH1N1) influenza during the first 12 months of their respective pandemics. We use Bayesian phylogenetic methods to estimate the dates of emergence, evolutionary rates, and growth rates of SARS-CoV-2 and pH1N1 over time and investigate how varying sampling window and data set sizes affect the accuracy of parameter estimation. We further use a generalized McDonald-Kreitman test to estimate the number of segregating nonneutral sites over time. We find that the inferred evolutionary parameters for both pandemics are time dependent, and that the inferred rates of SARS-CoV-2 and pH1N1 decline by ∼50% and ∼100%, respectively, over the course of 1 year. After at least 4 months since the start of sequence sampling, inferred growth rates and emergence dates remain relatively stable and can be inferred reliably using a logistic growth coalescent model. We show that the time dependency of the mean substitution rate is due to elevated substitution rates at terminal branches which are 2-4 times higher than those of internal branches for both viruses. The elevated rate at terminal branches is strongly correlated with an increasing number of segregating nonneutral sites, demonstrating the role of purifying selection in generating the time dependency of evolutionary parameters during pandemics.
Collapse
Affiliation(s)
- Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, United Kingdom
| | - Bo Xu
- Department of Earth System Science, Tsinghua University, Beijing, China
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
22
|
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.
Collapse
Affiliation(s)
- Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | |
Collapse
|
23
|
Calvignac-Spencer S, Düx A, Gogarten JF, Patrono LV. Molecular archeology of human viruses. Adv Virus Res 2021; 111:31-61. [PMID: 34663498 DOI: 10.1016/bs.aivir.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The evolution of human-virus associations is usually reconstructed from contemporary patterns of genomic diversity. An intriguing, though still rarely implemented, alternative is to search for the genetic material of viruses in archeological and medical archive specimens to document evolution as it happened. In this chapter, we present lessons from ancient DNA research and incorporate insights from virology to explore the potential range of applications and likely limitations of archeovirological approaches. We also highlight the numerous questions archeovirology will hopefully allow us to tackle in the near future, and the main expected roadblocks to these avenues of research.
Collapse
Affiliation(s)
- Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany.
| | - Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany
| | - Jan F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany
| | - Livia V Patrono
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany
| |
Collapse
|
24
|
Morales AC, Rice AM, Ho AT, Mordstein C, Mühlhausen S, Watson S, Cano L, Young B, Kudla G, Hurst LD. Causes and Consequences of Purifying Selection on SARS-CoV-2. Genome Biol Evol 2021; 13:evab196. [PMID: 34427640 PMCID: PMC8504154 DOI: 10.1093/gbe/evab196] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 02/06/2023] Open
Abstract
Owing to a lag between a deleterious mutation's appearance and its selective removal, gold-standard methods for mutation rate estimation assume no meaningful loss of mutations between parents and offspring. Indeed, from analysis of closely related lineages, in SARS-CoV-2, the Ka/Ks ratio was previously estimated as 1.008, suggesting no within-host selection. By contrast, we find a higher number of observed SNPs at 4-fold degenerate sites than elsewhere and, allowing for the virus's complex mutational and compositional biases, estimate that the mutation rate is at least 49-67% higher than would be estimated based on the rate of appearance of variants in sampled genomes. Given the high Ka/Ks one might assume that the majority of such intrahost selection is the purging of nonsense mutations. However, we estimate that selection against nonsense mutations accounts for only ∼10% of all the "missing" mutations. Instead, classical protein-level selective filters (against chemically disparate amino acids and those predicted to disrupt protein functionality) account for many missing mutations. It is less obvious why for an intracellular parasite, amino acid cost parameters, notably amino acid decay rate, is also significant. Perhaps most surprisingly, we also find evidence for real-time selection against synonymous mutations that move codon usage away from that of humans. We conclude that there is common intrahost selection on SARS-CoV-2 that acts on nonsense, missense, and possibly synonymous mutations. This has implications for methods of mutation rate estimation, for determining times to common ancestry and the potential for intrahost evolution including vaccine escape.
Collapse
Affiliation(s)
- Atahualpa Castillo Morales
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Alan M Rice
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Alexander T Ho
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Christine Mordstein
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, United Kingdom
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Stefanie Mühlhausen
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Samir Watson
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Laura Cano
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, United Kingdom
| | - Bethan Young
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, United Kingdom
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| |
Collapse
|
25
|
Hayman DTS, Knox MA. Estimating the age of the subfamily Orthocoronavirinae using host divergence times as calibration ages at two internal nodes. Virology 2021; 563:20-27. [PMID: 34411808 PMCID: PMC8365511 DOI: 10.1016/j.virol.2021.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022]
Abstract
Viruses of the subfamily Orthocoronavirinae can cause mild to severe disease in people, including COVID-19, MERS and SARS. Their most common natural hosts are bat and bird species, which are mostly split across four virus genera. Molecular clock analyses of orthocoronaviruses suggested the most recent common ancestor of these viruses might have emerged either around 10,000 years ago or, using models accounting for selection, many millions of years. Here, we reassess the evolutionary history of these viruses. We present time-aware phylogenetic analyses of a RNA-dependent RNA polymerase locus from 123 orthocoronaviruses isolated from birds and bats, including those in New Zealand, which were geographically isolated from other bats around 35 million years ago. We used this age, as well as the age of the avian-mammals split, to calibrate the molecular clocks, under the assumption that these ages are applicable to the analyzed viruses. We found that the time to the most recent ancestor common for all orthocoronaviruses is likely 150 or more million years, supporting clock analyses that account for selection.
Collapse
Affiliation(s)
- David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand.
| | - Matthew A Knox
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, New Zealand
| |
Collapse
|
26
|
Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing global and regional adaptive evolution of SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2104241118. [PMID: 34292871 PMCID: PMC8307621 DOI: 10.1073/pnas.2104241118] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
Collapse
Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
| |
Collapse
|
27
|
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.
Collapse
|
28
|
Wertheim JO, Hostager R, Ryu D, Merkel K, Angedakin S, Arandjelovic M, Ayimisin EA, Babweteera F, Bessone M, Brun-Jeffery KJ, Dieguez P, Eckardt W, Fruth B, Herbinger I, Jones S, Kuehl H, Langergraber KE, Lee K, Madinda NF, Metzger S, Ormsby LJ, Robbins MM, Sommer V, Stoinski T, Wessling EG, Wittig RM, Yuh YG, Leendertz FH, Calvignac-Spencer S. Discovery of Novel Herpes Simplexviruses in Wild Gorillas, Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2. Mol Biol Evol 2021; 38:2818-2830. [PMID: 33720357 PMCID: PMC8233514 DOI: 10.1093/molbev/msab072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Viruses closely related to human pathogens can reveal the origins of human infectious diseases. Human herpes simplexvirus type 1 (HSV-1) and type 2 (HSV-2) are hypothesized to have arisen via host-virus codivergence and cross-species transmission. We report the discovery of novel herpes simplexviruses during a large-scale screening of fecal samples from wild gorillas, bonobos, and chimpanzees. Phylogenetic analysis indicates that, contrary to expectation, simplexviruses from these African apes are all more closely related to HSV-2 than to HSV-1. Molecular clock-based hypothesis testing suggests the divergence between HSV-1 and the African great ape simplexviruses likely represents a codivergence event between humans and gorillas. The simplexviruses infecting African great apes subsequently experienced multiple cross-species transmission events over the past 3 My, the most recent of which occurred between humans and bonobos around 1 Ma. These findings revise our understanding of the origins of human herpes simplexviruses and suggest that HSV-2 is one of the earliest zoonotic pathogens.
Collapse
Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Reilly Hostager
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Diane Ryu
- Viral Evolution, Robert Koch Institute, Berlin, Germany.,Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Kevin Merkel
- Viral Evolution, Robert Koch Institute, Berlin, Germany.,Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | | | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Winnie Eckardt
- Dian Fossey Gorilla Fund International, Atlanta, GA, USA.,Department of Environmental Sciences and Program in Population Biology, Ecology and Evolution, Emory University, Druid Hills, GA, USA
| | - Barbara Fruth
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom.,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | | | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Royal Society for the Protection of Birds, Centre for Conservation Science, Cambridge, United Kingdom
| | - Hjalmar Kuehl
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Kevin Lee
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Nadege F Madinda
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sonja Metzger
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Volker Sommer
- Department of Anthropology, University College London, London, United Kingdom.,Gashaka Primate Project, Serti/Taraba, Nigeria
| | - Tara Stoinski
- Dian Fossey Gorilla Fund International, Atlanta, GA, USA.,Department of Environmental Sciences and Program in Population Biology, Ecology and Evolution, Emory University, Druid Hills, GA, USA
| | - Erin G Wessling
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Yisa Ginath Yuh
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Viral Evolution, Robert Koch Institute, Berlin, Germany.,Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| |
Collapse
|
29
|
Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.10.12.336644. [PMID: 33083804 PMCID: PMC7574262 DOI: 10.1101/2020.10.12.336644] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the trends in SARS-CoV-2 evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the nuclear localization signal (NLS) associated region of the nucleocapsid protein are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS associated variants across multiple partitions rose to global prominence in March-July, during a period of stasis in terms of inter-regional diversity. Finally, beginning July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
Collapse
Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| |
Collapse
|
30
|
Puller V, Sagulenko P, Neher RA. Efficient inference, potential, and limitations of site-specific substitution models. Virus Evol 2020; 6:veaa066. [PMID: 33343922 PMCID: PMC7733610 DOI: 10.1093/ve/veaa066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Natural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states, or only change in concert with other sites. On one hand, such constraints on sequence evolution can be to infer biological function, one the other hand they need to be accounted for in phylogenetic reconstruction. Phylogenetic models often account for this complexity by partitioning sites into a small number of discrete classes with different rates and/or state preferences. Appropriate model complexity is typically determined by model selection procedures. Here, we present an efficient algorithm to estimate more complex models that allow for different preferences at every site and explore the accuracy at which such models can be estimated from simulated data. Our iterative approximate maximum likelihood scheme uses information in the data efficiently and accurately estimates site-specific preferences from large data sets with moderately diverged sequences and known topology. However, the joint estimation of site-specific rates, and site-specific preferences, and phylogenetic branch length can suffer from identifiability problems, while ignoring variation in preferences across sites results in branch length underestimates. Site-specific preferences estimated from large HIV pol alignments show qualitative concordance with intra-host estimates of fitness costs. Analysis of these substitution models suggests near saturation of divergence after a few hundred years. Such saturation can explain the inability to infer deep divergence times of HIV and SIVs using molecular clock approaches and time-dependent rate estimates.
Collapse
Affiliation(s)
- Vadim Puller
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 61, Basel, Switzerland
| | - Pavel Sagulenko
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Richard A Neher
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 61, Basel, Switzerland
| |
Collapse
|
31
|
Jean Louis F, Domercant JW, Ignacio C, Gianella S, Galbaud G, Leonard M, Smith DM, Chaillon A. High Prevalence of HIV-1 Drug Resistance and Dynamics of Transmission Among High-Risk Populations in Port-au-Prince, Haiti. J Acquir Immune Defic Syndr 2020; 85:416-422. [PMID: 33136738 PMCID: PMC7592887 DOI: 10.1097/qai.0000000000002475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/05/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND In low HIV prevalence settings, understanding the transmission dynamics and the impact of drug resistance is critical to curb down the epidemic. This study aims to explore the prevalence and dynamics of transmission of HIV drug-resistance mutations (DRMs) among key populations in Haiti. SETTINGS Eligible participants (naive, treated) were selected from 7 key population friendly health care centers in Port-au-Prince, Haiti, from September 2018 to July 2019. METHODS A total of 119 HIV-1 pol sequences were analyzed from men having sex with men (MSM), female sex workers (FSWs), and their sexual partners. Screening for HIV DRMs was performed using the Stanford University Drug Resistance Database. Phylogenetic and network analyses using HIV-TRACE software were performed to infer putative relationships and shared DRMs. RESULTS Of the 119 participants, 62.2% were men (74/119), and 75.7% of them (56/74) reported MSM as a main risk factor. The overall DRM prevalence was 58.8% (70/119). A DRM was observed in 37.5% of MSM (21/56), 82.2% of FSWs (37/45), and 66.7% (12/18) among FSWs' clients. In a multivariate model, age and FSWs were significant predictors for DRMs (P = 0.001). Transmission network analysis found 24 of the 119 (20.2%) genetically linked individuals forming 8 clusters. Clustering participants were mostly MSM (15/24; 62.5%). Five clusters (62.5%) had shared DRMs, and K103N and M184V were the main shared mutations. CONCLUSIONS High prevalence of HIV DRMs was observed among MSM, FSWs, and their clients in Port-au-Prince, Haiti. Network analysis revealed frequent DRM transmission among genetically linked individuals, highlighting the need for appropriate interventions to limit HIV transmission in these high-risk populations.
Collapse
Affiliation(s)
| | | | - Caroline Ignacio
- Division of Infectious Diseases, University of California San Diego, San Diego, CA
| | - Sara Gianella
- Division of Infectious Diseases, University of California San Diego, San Diego, CA
| | | | | | | | | |
Collapse
|
32
|
Forni D, Cagliani R, Sironi M. Recombination and Positive Selection Differentially Shaped the Diversity of Betacoronavirus Subgenera. Viruses 2020; 12:E1313. [PMID: 33207802 PMCID: PMC7698105 DOI: 10.3390/v12111313] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022] Open
Abstract
The Betacoronavirus genus of mammal-infecting viruses includes three subgenera (Sarbecovirus, Embecovirus, and Merbecovirus), in which most known human coronaviruses, including SARS-CoV-2, cluster. Coronaviruses are prone to host shifts, with recombination and positive selection possibly contributing to their high zoonotic potential. We analyzed the role of these two forces in the evolution of viruses belonging to the Betacoronavirus genus. The results showed that recombination has been pervasive during sarbecovirus evolution, and it is more widespread in this subgenus compared to the other two. In both sarbecoviruses and merbecoviruses, recombination hotspots are clearly observed. Conversely, positive selection was a less prominent force in sarbecoviruses compared to embecoviruses and merbecoviruses and targeted distinct genomic regions in the three subgenera, with S being the major target in sarbecoviruses alone. Overall, the results herein indicate that Betacoronavirus subgenera evolved along different trajectories, which might recapitulate their host preferences or reflect the origins of the presently available coronavirus sequences.
Collapse
Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy; (R.C.); (M.S.)
| | | | | |
Collapse
|
33
|
Murri S, Madrières S, Tatard C, Piry S, Benoit L, Loiseau A, Pradel J, Artige E, Audiot P, Leménager N, Lacôte S, Vulin J, Charbonnel N, Marianneau P, Castel G. Detection and Genetic Characterization of Puumala Orthohantavirus S-Segment in Areas of France Non-Endemic for Nephropathia Epidemica. Pathogens 2020; 9:pathogens9090721. [PMID: 32882953 PMCID: PMC7559001 DOI: 10.3390/pathogens9090721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/15/2020] [Accepted: 08/22/2020] [Indexed: 12/30/2022] Open
Abstract
Puumala virus (PUUV) in Europe causes nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). The incidence of NE is highly heterogeneous spatially, whereas the geographic distribution of the wild reservoir of PUUV, the bank vole, is essentially homogeneous. Our understanding of the processes driving this heterogeneity remains incomplete due to gaps in knowledge. Little is known about the current distribution and genetic variation of PUUV in the areas outside the well-identified zones of NE endemicity. We trapped bank voles in four forests in French regions in which NE is considered non-endemic, but sporadic NE cases have been reported recently. We tested bank voles for anti-PUUV IgG and characterized the S segment sequences of PUUV from seropositive animals. Phylogenetic analyses revealed specific amino-acid signatures and genetic differences between PUUV circulating in non-endemic and nearby NE-endemic areas. We also showed, in temporal surveys, that the amino-acid sequences of PUUV had undergone fewer recent changes in areas non-endemic for NE than in endemic areas. The evolutionary history of the current French PUUV clusters was investigated by phylogeographic approaches, and the results were considered in the context of the history of French forests. Our findings highlight the need to monitor the circulation and genetics of PUUV in a larger array of bank vole populations, to improve our understanding of the risk of NE.
Collapse
Affiliation(s)
- Séverine Murri
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Sarah Madrières
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Caroline Tatard
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Sylvain Piry
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Laure Benoit
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Anne Loiseau
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Julien Pradel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Emmanuelle Artige
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Philippe Audiot
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Nicolas Leménager
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Sandra Lacôte
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Johann Vulin
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Nathalie Charbonnel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
| | - Philippe Marianneau
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France; (S.M.); (S.M.); (S.L.); (J.V.); (P.M.)
| | - Guillaume Castel
- CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, 34000 Montpellier, France; (C.T.); (S.P.); (L.B.); (A.L.); (J.P.); (E.A.); (P.A.); (N.L.); (N.C.)
- Correspondence:
| |
Collapse
|
34
|
Li N, Li A, Liu Y, Wu W, Li C, Yu D, Zhu Y, Li J, Li D, Wang S, Liang M. Genetic diversity and evolution of Hantaan virus in China and its neighbors. PLoS Negl Trop Dis 2020; 14:e0008090. [PMID: 32817670 PMCID: PMC7462299 DOI: 10.1371/journal.pntd.0008090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/01/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare. METHODOLOGY AND PRINCIPAL FINDINGS To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s. CONCLUSIONS/SIGNIFICANCE These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.
Collapse
Affiliation(s)
- Naizhe Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Aqian Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Liu
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wei Wu
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chuan Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongyang Yu
- Department of Microbiology, Anhui Medical University, Hefei, China
| | - Yu Zhu
- Department of Microbiology, Anhui Medical University, Hefei, China
| | - Jiandong Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dexin Li
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shiwen Wang
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- China CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P. R. China
- * E-mail: (SW); (ML)
| | - Mifang Liang
- Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of People's Republic of China, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- China CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P. R. China
- * E-mail: (SW); (ML)
| |
Collapse
|
35
|
Oliveira RN, Freire CC, Iamarino A, Zanotto PM, Pessoa R, Sanabani SS, Souza SPD, Castilho JG, Batista HBCR, Carnieli P, Macedo CI, Watanabe JT, Brandão PE. Rabies virus diversification in aerial and terrestrial mammals. Genet Mol Biol 2020; 43:e20190370. [PMID: 32745160 PMCID: PMC7416755 DOI: 10.1590/1678-4685-gmb-2019-0370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Rabies is a fatal zoonotic infection of the central nervous system of mammals and has been known to humans for millennia. The etiological agent, is a neurotropic RNA virus in the order Mononegavirales, family Rhabdoviridae, genus Lyssavirus. There are currently accepted to be two cycles for rabies transmission: the urban cycle and the sylvatic cycle. The fact that both cycles originated from a common RABV or lyssavirus ancestor and the adaptive divergence that occurred since then as this ancestor virus adapted to a wide range of fitness landscapes represented by reservoir species in the orders Carnivora and Chiroptera led to the emergence of the diverse RABV lineages currently found in the sylvatic and urban cycles. Here we study full genome phylogenies and the time to the most recent common ancestor (TMRCA) of the RABVs in the sylvatic and urban cycles. Results show that there were differences between the nucleotide substitution rates per site per year for the same RABV genes maintained independently in the urban and sylvatic cycles. The results identify the most suitable gene for phylogenetic analysis, heterotachy among RABV genes and the TMRCA for the two cycles.
Collapse
Affiliation(s)
- Rafael N Oliveira
- Instituto Pasteur, Laboratório de Biologia Molecular, São Paulo, SP, Brazil
| | - Caio C Freire
- Universidade de São Paulo, Instituto de Ciências Biomédicas (ICB-II), Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brazil
| | - Atila Iamarino
- Universidade de São Paulo, Instituto de Ciências Biomédicas (ICB-II), Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brazil
| | - Paolo M Zanotto
- Universidade de São Paulo, Instituto de Ciências Biomédicas (ICB-II), Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática, São Paulo, SP, Brazil
| | - Rodrigo Pessoa
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Departamento de Virologia, São Paulo, SP, Brazil
| | - Sabri S Sanabani
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Departamento de Virologia, São Paulo, SP, Brazil
| | | | - Juliana G Castilho
- Instituto Pasteur, Laboratório de Biologia Molecular, São Paulo, SP, Brazil
| | | | - Pedro Carnieli
- Instituto Pasteur, Laboratório de Biologia Molecular, São Paulo, SP, Brazil
| | - Carla I Macedo
- Instituto Pasteur, Laboratório de Biologia Molecular, São Paulo, SP, Brazil
| | - Jaqueline T Watanabe
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Departamento de Virologia, São Paulo, SP, Brazil
| | - Paulo E Brandão
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnica, Departamento de Medicina Veterinária Preventiva e Saúde Animal, São Paulo, SP, Brazil
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Cagliani R, Forni D, Clerici M, Sironi M. Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2. J Virol 2020; 94:e00411-20. [PMID: 32238584 PMCID: PMC7307108 DOI: 10.1128/jvi.00411-20] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/26/2020] [Indexed: 11/20/2022] Open
Abstract
The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that recently emerged in China is thought to have a bat origin, as its closest known relative (BatCoV RaTG13) was described previously in horseshoe bats. We analyzed the selective events that accompanied the divergence of SARS-CoV-2 from BatCoV RaTG13. To this end, we applied a population genetics-phylogenetics approach, which leverages within-population variation and divergence from an outgroup. Results indicated that most sites in the viral open reading frames (ORFs) evolved under conditions of strong to moderate purifying selection. The most highly constrained sequences corresponded to some nonstructural proteins (nsps) and to the M protein. Conversely, nsp1 and accessory ORFs, particularly ORF8, had a nonnegligible proportion of codons evolving under conditions of very weak purifying selection or close to selective neutrality. Overall, limited evidence of positive selection was detected. The 6 bona fide positively selected sites were located in the N protein, in ORF8, and in nsp1. A signal of positive selection was also detected in the receptor-binding motif (RBM) of the spike protein but most likely resulted from a recombination event that involved the BatCoV RaTG13 sequence. In line with previous data, we suggest that the common ancestor of SARS-CoV-2 and BatCoV RaTG13 encoded/encodes an RBM similar to that observed in SARS-CoV-2 itself and in some pangolin viruses. It is presently unknown whether the common ancestor still exists and, if so, which animals it infects. Our data, however, indicate that divergence of SARS-CoV-2 from BatCoV RaTG13 was accompanied by limited episodes of positive selection, suggesting that the common ancestor of the two viruses was poised for human infection.IMPORTANCE Coronaviruses are dangerous zoonotic pathogens; in the last 2 decades, three coronaviruses have crossed the species barrier and caused human epidemics. One of these is the recently emerged SARS-CoV-2. We investigated how, since its divergence from a closely related bat virus, natural selection shaped the genome of SARS-CoV-2. We found that distinct coding regions in the SARS-CoV-2 genome evolved under conditions of different degrees of constraint and are consequently more or less prone to tolerate amino acid substitutions. In practical terms, the level of constraint provides indications about which proteins/protein regions are better suited as possible targets for the development of antivirals or vaccines. We also detected limited signals of positive selection in three viral ORFs. However, we warn that, in the absence of knowledge about the chain of events that determined the human spillover, these signals should not be necessarily interpreted as evidence of an adaptation to our species.
Collapse
Affiliation(s)
- Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- 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
| |
Collapse
|
38
|
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.
Collapse
|
39
|
Zhang D, Wu J, Zhang Y, Shen Y, Dai S, Wang X, Xing H, Lin J, Han J, Li J, Qin Y, Liu Y, Miao L, Su B, Li H, Li L. Genetic characterization of HIV-1 epidemic in Anhui Province, China. Virol J 2020; 17:17. [PMID: 32014042 PMCID: PMC6998069 DOI: 10.1186/s12985-020-1281-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/13/2020] [Indexed: 11/13/2022] Open
Abstract
Background Anhui Province in China is facing a severe HIV epidemic with an increasing number of newly diagnosed cases. Methods In this study, HIV genetic characteristics in the province were investigated. Newly reported HIV-positive individuals from 15 districts of Anhui Province were enrolled and interviewed. Total viral RNA was extracted from plasma isolated from blood samples. We amplified and sequenced an HIV pol fragment of the 1062 bp. The sequences were used for determination of HIV subtypes and the presence of drug resistance mutations. Transmission networks were constructed to explore possible relationships. And all of assembled partial pol genes were submitted to the Stanford HIV Drug Resistance Database website to find the transmitted drug resistance. Results Partial pol gene sequences were obtained from 486 cases. The results showed that MSM was the most dominant transmission route (253, 52.06%), followed by heterosexual transmission (210, 43.21%) and blood-borne transmission (1, 0.21%). Many subtypes were identified, including CRF01_AE (226, 46.50%), CRF07_BC (151, 31.07%), subtype B (28, 5.76%), CRF08_BC (20, 4.12%), CRF55_01B (15, 3.09%), CRF68_01B (7, 1.44%), CRF67_01B (3, 0.62%), CRF57_BC (2, 0.41%), CRF59_01B (2, 0.41%), CRF79_0107 (2, 0.41%), subtype C (2, 0.41%), CRF64_BC (1, 0.21%), and circulating recombinant forms (URFs) (27, 5.55%). Four transmission subnetworks containing high transmission risk individuals (with degree ≥4) were identified based on CRF01_AE and CRF07_BC sequences, including two CRF01_AE transmission subnetworks constituted by elderly people with average ages of 67.9 and 61.5 years. Infection occurred most likely through heterosexual transmission, while the other two CRF07_BC transmission subnetworks consist mainly of MSMs with average ages of 31.73 and 34.15. The level of HIV-transmitted drug resistance is 3.09%. Conclusions The simultaneous spread of multiple HIV subtypes in Anhui province underscores that close surveillance of the local HIV epidemic is necessary. Furthermore, the elderly people were frequently involved, arguing for behaviour intervention in this specific population besides the MSM risk group.
Collapse
Affiliation(s)
- Dong Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Jianjun Wu
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Yu Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Yuelan Shen
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Sheying Dai
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jin Lin
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Yizu Qin
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Lifeng Miao
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, Hefei, 230601, China.
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dongda Street, Fengtai District, Beijing, 100071, China.
| |
Collapse
|
40
|
Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P. Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates. Mol Biol Evol 2020; 36:1793-1803. [PMID: 31004175 PMCID: PMC6657730 DOI: 10.1093/molbev/msz094] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Many factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.
Collapse
Affiliation(s)
- Jade Vincent Membrebe
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA.,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,Fogarty International Center, National Institutes of Health, Bethesda, MD
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| |
Collapse
|
41
|
Abstract
Recent discoveries of contemporary genotypes of hepatitis B virus and parvovirus B19 in ancient human remains demonstrate that little genetic change has occurred in these viruses over 4,500-6,000 years. Endogenous viral elements in host genomes provide separate evidence that viruses similar to many major contemporary groups circulated 100 million years ago or earlier. In this Opinion article, we argue that the extraordinary conservation of virus genome sequences is best explained by a niche-filling model in which fitness optimization is rapidly achieved in their specific hosts. Whereas short-term substitution rates reflect the accumulation of tolerated sequence changes within adapted genomes, longer-term rates increasingly resemble those of their hosts as the evolving niche moulds and effectively imprisons the virus in co-adapted virus-host relationships. Contrastingly, viruses that jump hosts undergo strong and stringent adaptive selection as they maximize their fit to their new niche. This adaptive capability may paradoxically create evolutionary stasis in long-term host relationships. While viruses can evolve and adapt rapidly, their hosts may ultimately shape their longer-term evolution.
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
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.
Collapse
|
44
|
Minarovits J, Niller HH. Truncated oncoproteins of retroviruses and hepatitis B virus: A lesson in contrasts. INFECTION GENETICS AND EVOLUTION 2019; 73:342-357. [DOI: 10.1016/j.meegid.2019.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/14/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
|
45
|
Phylogeography of Puumala orthohantavirus in Europe. Viruses 2019; 11:v11080679. [PMID: 31344894 PMCID: PMC6723369 DOI: 10.3390/v11080679] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
Puumala virus is an RNA virus hosted by the bank vole (Myodes glareolus) and is today present in most European countries. Whilst it is generally accepted that hantaviruses have been tightly co-evolving with their hosts, Puumala virus (PUUV) evolutionary history is still controversial and so far has not been studied at the whole European level. This study attempts to reconstruct the phylogeographical spread of modern PUUV throughout Europe during the last postglacial period in the light of an upgraded dataset of complete PUUV small (S) segment sequences and by using most recent computational approaches. Taking advantage of the knowledge on the past migrations of its host, we identified at least three potential independent dispersal routes of PUUV during postglacial recolonization of Europe by the bank vole. From the Alpe-Adrian region (Balkan, Austria, and Hungary) to Western European countries (Germany, France, Belgium, and Netherland), and South Scandinavia. From the vicinity of Carpathian Mountains to the Baltic countries and to Poland, Russia, and Finland. The dissemination towards Denmark and North Scandinavia is more hypothetical and probably involved several independent streams from south and north Fennoscandia.
Collapse
|
46
|
Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens. Mol Biol Evol 2019; 35:1812-1819. [PMID: 29401317 DOI: 10.1093/molbev/msy016] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoe-leather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, that is, on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from www.github.com/veg/hivtrace, along with the accompanying result visualization module from www.github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens.
Collapse
Affiliation(s)
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Andrew J Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA
| |
Collapse
|
47
|
Chisholm PJ, Busch JW, Crowder DW. Effects of life history and ecology on virus evolutionary potential. Virus Res 2019; 265:1-9. [PMID: 30831177 DOI: 10.1016/j.virusres.2019.02.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 11/28/2022]
Abstract
The life history traits of viruses pose many consequences for viral population structure. In turn, population structure may influence the evolutionary trajectory of a virus. Here we review factors that affect the evolutionary potential of viruses, including rates of mutation and recombination, bottlenecks, selection pressure, and ecological factors such as the requirement for hosts and vectors. Mutation, while supplying a pool of raw genetic material, also results in the generation of numerous unfit mutants. The infection of multiple host species may expand a virus' ecological niche, although it may come at a cost to genetic diversity. Vector-borne viruses often experience a diminished frequency of positive selection and exhibit little diversity, and resistance against vector-borne viruses may thus be more durable than against non-vectored viruses. Evidence indicates that adaptation to a vector is more evolutionarily difficult than adaptation to a host. Overall, a better understanding of how various factors influence viral dynamics in both plant and animal pathosystems will lead to more effective anti-viral treatments and countermeasures.
Collapse
Affiliation(s)
- Paul J Chisholm
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164, USA.
| | - David W Crowder
- Department of Entomology, Washington State University, 166 FSHN Building, Pullman, WA, 99164, USA.
| |
Collapse
|
48
|
Uhl EW, Kelderhouse C, Buikstra J, Blick JP, Bolon B, Hogan RJ. New world origin of canine distemper: Interdisciplinary insights. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 24:266-278. [PMID: 30743216 DOI: 10.1016/j.ijpp.2018.12.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 11/29/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
OBJECTIVE Canine distemper virus (CDV), human measles virus (HMV), and rinderpest virus (RPV) of cattle are morbilliviruses that have caused devastating outbreaks for centuries. This paper seeks to reconstruct the evolutionary history of CDV. MATERIALS AND METHODS An interdisciplinary approach is adopted, synthesizing paleopathological analysis of 96 Pre-Columbian dogs (750-1470 CE) from the Weyanoke Old Town, Virginia site, with historical reports, molecular analysis and morbilliviral epidemiology. RESULTS Both measles (c.900CE) and rinderpest (c. 376 BCE) were first reported in Eurasia, while canine distemper was initially described in South America much later (1735 CE); there are no paleopathological indications of CDV in Weyanoke Old Town dogs. Molecularly, CDV is closely related to HMV, while viral codon usage indicates CDV may have previously infected humans; South American measles epidemics occurred prior to the emergence of canine distemper and would have facilitated HMV transmission and adaptation to dogs. CONCLUSIONS The measles epidemics that decimated indigenous South American populations in the 1500-1700 s likely facilitated the establishment of CDV as a canine pathogen, which eventually spread to Europe and beyond. SIGNIFICANCE Understanding the historical and environmental conditions that have driven morbilliviral evolution provides important insights into potential future threats of animal/human cross-species infections. LIMITATIONS Interpreting historical disease descriptions is difficult and the archaeological specimens are limited. Molecular sequence data and codon usage analyses rely on modern viruses. SUGGESTIONS FOR FURTHER RESEARCH Interdisciplinary approaches are increasingly needed to understand diseases of the past and present, as critical information and knowledge is scattered in different disciplines.
Collapse
Affiliation(s)
- Elizabeth W Uhl
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602-7388, USA.
| | - Charles Kelderhouse
- Augusta University/University of Georgia Medical Partnership, Athens, GA, 30602-7388, USA.
| | - Jane Buikstra
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287-2402, USA.
| | - Jeffrey P Blick
- Department of Government and Sociology, Georgia College and State University, Milledgeville, GA 31061-0490, USA
| | - Brad Bolon
- Department of Government and Sociology, Georgia College and State University, Milledgeville, GA 31061-0490, USA.
| | - Robert J Hogan
- Department of Veterinary Biosciences and Imaging, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602-7388, USA.
| |
Collapse
|
49
|
Olabode AS, Avino M, Ng GT, Abu-Sardanah F, Dick DW, Poon AFY. Evidence for a recombinant origin of HIV-1 Group M from genomic variation. Virus Evol 2019; 5:vey039. [PMID: 30687518 PMCID: PMC6342232 DOI: 10.1093/ve/vey039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Reconstructing the early dynamics of the HIV-1 pandemic can provide crucial insights into the socioeconomic drivers of emerging infectious diseases in human populations, including the roles of urbanization and transportation networks. Current evidence indicates that the global pandemic comprising almost entirely of HIV-1/M originated around the 1920s in central Africa. However, these estimates are based on molecular clock estimates that are assumed to apply uniformly across the virus genome. There is growing evidence that recombination has played a significant role in the early history of the HIV-1 pandemic, such that different regions of the HIV-1 genome have different evolutionary histories. In this study, we have conducted a dated-tip analysis of all near full-length HIV-1/M genome sequences that were published in the GenBank database. We used a sliding window approach similar to the 'bootscanning' method for detecting breakpoints in inter-subtype recombinant sequences. We found evidence of substantial variation in estimated root dates among windows, with an estimated mean time to the most recent common ancestor of 1922. Estimates were significantly autocorrelated, which was more consistent with an early recombination event than with stochastic error variation in phylogenetic reconstruction and dating analyses. A piecewise regression analysis supported the existence of at least one recombination breakpoint in the HIV-1/M genome with interval-specific means around 1929 and 1913, respectively. This analysis demonstrates that a sliding window approach can accommodate early recombination events outside the established nomenclature of HIV-1/M subtypes, although it is difficult to incorporate the earliest available samples due to their limited genome coverage.
Collapse
Affiliation(s)
- Abayomi S Olabode
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada
| | - Mariano Avino
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada
| | - Garway T Ng
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada
| | - Faisal Abu-Sardanah
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada
| | - David W Dick
- Department of Applied Mathematics, Western University, London, Ontario, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada.,Department of Applied Mathematics, Western University, London, Ontario, Canada.,Department of Microbiology & Immunology, Western University, London, Ontario, Canada
| |
Collapse
|
50
|
Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
Collapse
Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
| |
Collapse
|