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Jain H, Kaur R, Sain SK, Siwach P. Development, Design, and Application of Efficient siRNAs Against Cotton Leaf Curl Virus-Betasatellite Complex to Mediate Resistance Against Cotton Leaf Curl Disease. Indian J Microbiol 2024; 64:558-571. [PMID: 39011016 PMCID: PMC11246389 DOI: 10.1007/s12088-024-01191-z] [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: 11/18/2023] [Accepted: 01/01/2024] [Indexed: 07/17/2024] Open
Abstract
Cotton leaf curl disease (CLCuD), caused by the Cotton leaf curl virus, is one of the most irrepressible diseases in cotton due to high recombination in the virus. RNA interference (RNAi) is widely used as a biotechnological approach for sequence-specific gene silencing guided by small interfering RNAs (siRNAs) to generate resistance against viruses. The success of RNAi depends upon the fact that the target site of the designed siRNA must be conserved even if the genome undergoes recombination. Thus, the present study designs the most efficient siRNA against the conserved sites of the Cotton leaf curl Multan virus (CLCuMuV) and the Cotton leaf curl Multan betasatellite (CLCuMB). From an initial prediction of 9 and 7 siRNAs against CLCuMuV and CLCuMB, respectively, the final selection was made for 2 and 1 siRNA based on parameters such as no off-targets, good GC content, high validity score, and targeting coding region. The target sites of siRNA were observed to lie in the AC3 and an overlapping region of AC2-AC1 of CLCuMuV and βC1 of CLCuMB; all target sites showed a highly conserved nature in recombination analysis. Docking the designed siRNAs with the Argonaute-2 protein of Gossypium hirsutum showed stable binding. Finally, BLASTn of siRNA-target positions in genomes of other BGVs indicated the suitability of designed siRNAs against a broad range of BGVs. The designed siRNAs of the present study could help gain complete control over the virus, though experimental validation is highly required to suggest predicted siRNAs for CLCuD resistance. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-024-01191-z.
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Affiliation(s)
- Heena Jain
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana 125055 India
| | - Ramandeep Kaur
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana 125055 India
| | - Satish Kumar Sain
- Central Institute of Cotton Research, Regional Station, Sirsa, Haryana 125055 India
| | - Priyanka Siwach
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana 125055 India
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Jain H, Singh I, Chahal S, Kaur R, Siwach P. Phylogenetic and recombination analysis of Begomoviruses associated with Cotton leaf curl disease and in silico analysis of viral-host protein interactions. Microb Pathog 2024; 186:106504. [PMID: 38122873 DOI: 10.1016/j.micpath.2023.106504] [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: 09/21/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Cotton leaf curl disease (CLCuD), caused by numerous begomoviruses (BGVs), is a highly disastrous disease in cotton crops worldwide. To date, several efforts have shown limited success in controlling this disease. CLCuD-associated BGVs (CABs) are known for their high rate of intra and interspecific recombinations, which raises an urgent need to find an efficient and conserved target region to combat disease. In the present study, phylogenetic analysis of selected 11 CABs, along with associated alphasatellites, and betasatellites revealed a close evolutionary relationship among them. Recombination analysis of 1374 isolates of CABs revealed 54 recombination events for the major players of CLCuD in cotton and the Cotton leaf curl Multan virus (CLCuMuV) as the most recombinant CAB. Recombination breakpoints were frequent in all regions except C2 and C3. C3-encoded protein, known as viral replication enhancer (REn), promotes viral replication by enhancing the activity of replicase (Rep) protein. Both proteins were found to contain significantly conserved domains and motifs. The identified motifs were found crucial for their interaction with host protein PCNA (Proliferating cell nuclear antigen), facilitating viral replication. Interruption at the REn-PCNA and Rep-PCNA interactions by targeting the identified conserved motifs is proposed as a prospect to halt viral replication, after suitable experimental validation.
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Affiliation(s)
- Heena Jain
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, 125055, Haryana, India
| | - Inderjeet Singh
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, 125055, Haryana, India
| | - Shiwani Chahal
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, 125055, Haryana, India
| | - Ramandeep Kaur
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, 125055, Haryana, India
| | - Priyanka Siwach
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, 125055, Haryana, India.
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Fox A, Gibbs AJ, Fowkes AR, Pufal H, McGreig S, Jones RAC, Boonham N, Adams IP. Enhanced Apiaceous Potyvirus Phylogeny, Novel Viruses, and New Country and Host Records from Sequencing Apiaceae Samples. PLANTS 2022; 11:plants11151951. [PMID: 35956429 PMCID: PMC9370115 DOI: 10.3390/plants11151951] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022]
Abstract
The family Apiaceae comprises approximately 3700 species of herbaceous plants, including important crops, aromatic herbs and field weeds. Here we report a study of 10 preserved historical or recent virus samples of apiaceous plants collected in the United Kingdom (UK) import interceptions from the Mediterranean region (Egypt, Israel and Cyprus) or during surveys of Australian apiaceous crops. Seven complete new genomic sequences and one partial sequence, of the apiaceous potyviruses apium virus Y (ApVY), carrot thin leaf virus (CaTLV), carrot virus Y (CarVY) and celery mosaic virus (CeMV) were obtained. When these 7 and 16 earlier complete non-recombinant apiaceous potyvirus sequences were subjected to phylogenetic analyses, they split into 2 separate lineages: 1 containing ApVY, CeMV, CarVY and panax virus Y and the other CaTLV, ashitabi mosaic virus and konjac virus Y. Preliminary dating analysis suggested the CarVY population first diverged from CeMV and ApVY in the 17th century and CeMV from ApVY in the 18th century. They also showed the “time to most recent common ancestor” of the sampled populations to be more recent: 1997 CE, 1983 CE and 1958 CE for CarVY, CeMV and ApVY, respectively. In addition, we found a new family record for beet western yellows virus in coriander from Cyprus; a new country record for carrot torradovirus-1 and a tentative novel member of genus Ophiovirus as a co-infection in a carrot sample from Australia; and a novel member of the genus Umbravirus recovered from a sample of herb parsley from Israel.
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Affiliation(s)
- Adrian Fox
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
- Correspondence:
| | - Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia;
| | - Aimee R. Fowkes
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
| | - Hollie Pufal
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, King’s Road, Newcastle upon Tyne NE1 7RU, UK; (H.P.); (N.B.)
| | - Sam McGreig
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
| | - Roger A. C. Jones
- UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia;
| | - Neil Boonham
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, King’s Road, Newcastle upon Tyne NE1 7RU, UK; (H.P.); (N.B.)
| | - Ian P. Adams
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
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Rueca M, Lanini S, Giombini E, Messina F, Castilletti C, Ippolito G, Capobianchi MR, Valli MB. Detection of recombinant breakpoint in the genome of human enterovirus E11 strain associated with a fatal nosocomial outbreak. Virol J 2022; 19:97. [PMID: 35659257 PMCID: PMC9166486 DOI: 10.1186/s12985-022-01821-2] [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: 10/04/2021] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aim of this study was to characterize the genome of a recombinant Enterovirus associated with severe and fatal nosocomial infection; it was typed as Echovirus 11 (E-11) according to the VP1 gene. Enterovirus infection is generally asymptomatic and self-limited, but occasionally it may progress to a more severe clinical manifestation, as in the case described here. Recombination plays a crucial role in the evolution of Enteroviruses (EVs) and has been recognized as the main driving force behind the emergence of epidemic strains associated with severe infection. Therefore, it is of utmost importance to monitor the circulation of recombinant strains for surveillance purposes. METHODS Enterovirus-RNA was detected in the serum and liver biopsy of patients involved in the nosocomial cluster by commercial One-Step qRT-PCR method and the Enterovirus strains were isolated in vitro. The EVs typing was determined by analyzing the partial-length of the 5'UTR and VP1 sequences with the web-based open-access Enterovirus Genotyping Tool Version 0.1. The amplicons targeting 5'UTR, VP1 and overlapping fragments of the entire genome were sequenced with the Sanger method. Phylogenetic analysis was performed comparing the VP1 and the full-genome sequences of our strains against an appropriate reference set of Enterovirus prototypes of the Picornaviridae genera and species retrieved from the Enterovirus Genotyping Tool. Recombination analysis was performed using RDP4 software. RESULTS The Neighbor-Joining tree of the VP1 gene revealed that the 4 patients were infected with an identical molecular variant of Echovirus 11 (E-11). While the phylogenetic and the RDP4 analysis of the full-genome sequences provided evidence that it was a chimeric strain between an E-11 and a Coxsackievirus B (CV-B). CONCLUSIONS The chimeric structure of the E-11 genome might have contributed to the severe infection and epidemic feature of the strain, but further biological characterizations are needed. The evidence reported in this study, highlights the limit of typing techniques based on the VP1 gene, as they fail to identify the emergence of recombinant strains with potentially more pathogenic or epidemic properties, thus providing only partial information on the epidemiology and pathogenesis of Enteroviruses.
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Affiliation(s)
- Martina Rueca
- National Institute for Infectious Diseases L. Spallanzani IRCCS, Rome, Italy
| | - Simone Lanini
- National Institute for Infectious Diseases L. Spallanzani IRCCS, Rome, Italy
| | - Emanuela Giombini
- National Institute for Infectious Diseases L. Spallanzani IRCCS, Rome, Italy.
| | - Francesco Messina
- National Institute for Infectious Diseases L. Spallanzani IRCCS, Rome, Italy
| | | | - Giuseppe Ippolito
- National Institute for Infectious Diseases L. Spallanzani IRCCS, Rome, Italy
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Revisiting the recombinant history of HIV-1 group M with dynamic network community detection. Proc Natl Acad Sci U S A 2022; 119:e2108815119. [PMID: 35500121 PMCID: PMC9171507 DOI: 10.1073/pnas.2108815119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recombination is a major mechanism through which HIV type 1 (HIV-1) maintains genetic diversity and interferes with viral eradication efforts. There is growing evidence demonstrating a recombinant origin of primate lentiviruses including HIV-1 group M (HIV-1/M). Inferring the extent of recombination across the entire HIV-1/M genome is of great importance as it provides deeper insights into the origin, dynamics, and evolution of the global pandemic. Here we propose an alternative method that can reconstruct the extent of genome-wide recombination in HIV-1, uncover reticulate patterns, and serve as a framework for HIV-1 classification. Our method provides an alternative approach for understanding the roles of virus recombination in the early evolutionary history of zoonosis for other emerging viruses. The prevailing abundance of full-length HIV type 1 (HIV-1) genome sequences provides an opportunity to revisit the standard model of HIV-1 group M (HIV-1/M) diversity that clusters genomes into largely nonrecombinant subtypes, which is not consistent with recent evidence of deep recombinant histories for simian immunodeficiency virus (SIV) and other HIV-1 groups. Here we develop an unsupervised nonparametric clustering approach, which does not rely on predefined nonrecombinant genomes, by adapting a community detection method developed for dynamic social network analysis. We show that this method (dynamic stochastic block model [DSBM]) attains a significantly lower mean error rate in detecting recombinant breakpoints in simulated data (quasibinomial generalized linear model (GLM), P<8×10−8), compared to other reference-free recombination detection programs (genetic algorithm for recombination detection [GARD], recombination detection program 4 [RDP4], and RDP5). When this method was applied to a representative sample of n = 525 actual HIV-1 genomes, we determined k = 29 as the optimal number of DSBM clusters and used change-point detection to estimate that at least 95% of these genomes are recombinant. Further, we identified both known and undocumented recombination hotspots in the HIV-1 genome and evidence of intersubtype recombination in HIV-1 subtype reference genomes. We propose that clusters generated by DSBM can provide an informative framework for HIV-1 classification.
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Gaunt MW, Pettersson JHO, Kuno G, Gaunt B, de Lamballerie X, Gould EA. Widespread Interspecific Phylogenetic Tree Incongruence Between Mosquito-Borne and Insect-Specific Flaviviruses at Hotspots Originally Identified in Zika Virus. Virus Evol 2022; 8:veac027. [PMID: 35591877 PMCID: PMC9113262 DOI: 10.1093/ve/veac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 10/22/2021] [Accepted: 04/17/2022] [Indexed: 11/16/2022] Open
Abstract
Intraspecies (homologous) phylogenetic incongruence, or ‘tree conflict’ between different loci within the same genome of mosquito-borne flaviviruses (MBFV), was first identified in dengue virus (DENV) and subsequently in Japanese encephalitis virus (JEV), St Louis encephalitis virus, and Zika virus (ZIKV). Recently, the first evidence of phylogenetic incongruence between interspecific members of the MBFV was reported in ZIKV and its close relative, Spondweni virus. Uniquely, these hybrid proteomes were derived from four incongruent trees involving an Aedes-associated DENV node (1 tree) and three different Culex-associated flavivirus nodes (3 trees). This analysis has now been extended across a wider spectrum of viruses within the MBFV lineage targeting the breakpoints between phylogenetic incongruent loci originally identified in ZIKV. Interspecies phylogenetic incongruence at these breakpoints was identified in 10 of 50 viruses within the MBFV lineage, representing emergent Aedes and Culex-associated viruses including JEV, West Nile virus, yellow fever virus, and insect-specific viruses. Thus, interspecies phylogenetic incongruence is widespread amongst the flaviviruses and is robustly associated with the specific breakpoints that coincide with the interspecific phylogenetic incongruence previously identified, inferring they are ‘hotspots’. The incongruence amongst the emergent MBFV group was restricted to viruses within their respective associated epidemiological boundaries. This MBFV group was RY-coded at the third codon position (‘wobble codon’) to remove transition saturation. The resulting ‘wobble codon’ trees presented a single topology for the entire genome that lacked any robust evidence of phylogenetic incongruence between loci. Phylogenetic interspecific incongruence was therefore observed for exactly the same loci between amino acid and the RY-coded ‘wobble codon’ alignments and this incongruence represented either a major part, or the entire genomes. Maximum likelihood codon analysis revealed positive selection for the incongruent lineages. Positive selection could result in the same locus producing two opposing trees. These analyses for the clinically important MBFV suggest that robust interspecific phylogenetic incongruence resulted from amino acid selection. Convergent or parallel evolutions are evolutionary processes that would explain the observation, whilst interspecific recombination is unlikely.
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Affiliation(s)
- Michael W Gaunt
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - John H-O Pettersson
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - Goro Kuno
- Formerly, Centers for Disease Control, Fort Collins, CO 80521, USA
| | - Bill Gaunt
- Aeon-sys, MBCS Kensington Road, Barnsley S75 2TU, UK
| | - Xavier de Lamballerie
- UMR “Unité des Virus Emergents”, Aix-Marseille Université-IRD 190-Inserm 1207-IHU Méditerranée Infection, Marseille, France
- APHM Public Hospitals of Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Ernest A Gould
- UMR “Unité des Virus Emergents”, Aix-Marseille Université-IRD 190-Inserm 1207-IHU Méditerranée Infection, Marseille, France
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Fuentes S, Gibbs AJ, Adams IP, Hajizadeh M, Kreuze J, Fox A, Blouin AG, Jones RAC. Phylogenetics and Evolution of Potato Virus V: Another Potyvirus that Originated in the Andes. PLANT DISEASE 2022; 106:691-700. [PMID: 34633236 DOI: 10.1094/pdis-09-21-1897-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Potato virus V (PVV) causes a disease of potato (Solanum tubersosum) in South and Central America, Europe, and the Middle East. We report here the complete genomic sequences of 42 new PVV isolates from the potato's Andean domestication center in Peru and of eight historical or recent isolates from Europe. When the principal open reading frames of these genomic sequences together with those of nine previously published genomic sequences were analyzed, only two from Peru and one from Iran were found to be recombinant. The phylogeny of the 56 nonrecombinant open reading frame sequences showed that the PVV population had two major phylogroups, one of which formed three minor phylogroups (A1 to A3) of isolates, all of which are found only in the Andean region of South America (Peru and Colombia), and the other formed two minor phylogroups, a basal one of Andean isolates (A4) that is paraphyletic to a crown cluster containing all the isolates found outside South America (World). This suggests that PVV originated in the Andean region, with only one minor phylogroup spreading elsewhere in the world. In minor phylogroups A1 and A3, there were two subclades on long branches containing isolates from S. phureja evolving more rapidly than the others, and these interfered with dating calculations. Although no temporal signal was directly detected among the dated nonrecombinant sequences, PVV and potato virus Y (PVY) are from the same potyvirus lineage and are ecologically similar, so "subtree dating" was done via a single maximum likelihood phylogeny of PVV and PVY sequences, and PVY's well-supported 157 ce "time to most common recent ancestor" was extrapolated to date that of PVV as 29 bce. Thus the independent historical coincidences supporting the datings of the PVV and PVY phylogenies are the same; PVV arose ≥2,000 years ago in the Andes and was taken to Europe during the Columbian Exchange, where it diversified around 1853 ce, soon after the European potato late blight pandemic. PVV is likely to be more widespread than currently realized and is of biosecurity relevance for world regions that have not yet recorded its presence.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Segundo Fuentes
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Adrian J Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2600, Australia
| | - Ian P Adams
- Fera Science Ltd, Sand Hutton, York YO41 1LZ, UK
| | - Mohammad Hajizadeh
- Plant Protection Department, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Adrian Fox
- Fera Science Ltd, Sand Hutton, York YO41 1LZ, UK
| | - Arnaud G Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux 5031, Belgium
| | - Roger A C Jones
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia
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Çelik A, Santosa AI, Gibbs AJ, Ertunç F. Prunus necrotic ringspot virus in Turkey: an immigrant population. Arch Virol 2022; 167:553-562. [DOI: 10.1007/s00705-022-05374-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
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Pollett S, Conte MA, Sanborn M, Jarman RG, Lidl GM, Modjarrad K, Maljkovic Berry I. A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic. Sci Rep 2021; 11:17365. [PMID: 34462471 PMCID: PMC8405798 DOI: 10.1038/s41598-021-96626-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/09/2021] [Indexed: 11/11/2022] Open
Abstract
The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in the non-ORF1 region of the genome containing structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.
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Affiliation(s)
- Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mark Sanborn
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Grace M Lidl
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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Koç BT, Akkutay-Yoldar Z, Oğuzoğlu TÇ. New members to Arctic-like lineage of canine distemper virus from Turkey. Comp Immunol Microbiol Infect Dis 2021; 78:101678. [PMID: 34147825 DOI: 10.1016/j.cimid.2021.101678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/26/2022]
Abstract
Canine distemper virus (CDV) causes a multisystemic fatal disease, briefly named as distemper, in domestic and wild animals. Molecular characterization studies serve to identify local strains, accordingly, helps to determine the scope of vaccination in prevention of distemper. We aimed with this study to update the molecular status of CDV in domestic dogs in Turkey. Sequence analysis of the H gene revealed that novel Turkish sequences formed a separated clade in Arctic-like lineage. Italian clade which mainly included strains originated from wild canid or non-canid localized nearly to novel Turkish clade. Codons 530th and 549th determining the affinity of domestic or wild animals to distemper were Asparagine and Tyrosine, respectively. This report presented the presence of CDV strains belonging to Arctic-like lineage for the first time in domestic dogs in Turkey. The findings pave the way for the reassessment of the circulation and geographical shifting of Arctic-like lineages of CDV.
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Affiliation(s)
- B Taylan Koç
- Department of Virology, Faculty of Veterinary Medicine, Aydin Adnan Menderes University, Efeler, Aydin, 09016 Turkey.
| | - Zeynep Akkutay-Yoldar
- Department of Virology, Faculty of Veterinary Medicine, Ankara University, Diskapi, Ankara, 06110, Turkey
| | - T Çiğdem Oğuzoğlu
- Department of Virology, Faculty of Veterinary Medicine, Ankara University, Diskapi, Ankara, 06110, Turkey
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Fuentes S, Gibbs AJ, Hajizadeh M, Perez A, Adams IP, Fribourg CE, Kreuze J, Fox A, Boonham N, Jones RAC. The Phylogeography of Potato Virus X Shows the Fingerprints of Its Human Vector. Viruses 2021; 13:644. [PMID: 33918611 PMCID: PMC8070401 DOI: 10.3390/v13040644] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/23/2022] Open
Abstract
Potato virus X (PVX) occurs worldwide and causes an important potato disease. Complete PVX genomes were obtained from 326 new isolates from Peru, which is within the potato crop's main domestication center, 10 from historical PVX isolates from the Andes (Bolivia, Peru) or Europe (UK), and three from Africa (Burundi). Concatenated open reading frames (ORFs) from these genomes plus 49 published genomic sequences were analyzed. Only 18 of them were recombinants, 17 of them Peruvian. A phylogeny of the non-recombinant sequences found two major (I, II) and five minor (I-1, I-2, II-1, II-2, II-3) phylogroups, which included 12 statistically supported clusters. Analysis of 488 coat protein (CP) gene sequences, including 128 published previously, gave a completely congruent phylogeny. Among the minor phylogroups, I-2 and II-3 only contained Andean isolates, I-1 and II-2 were of both Andean and other isolates, but all of the three II-1 isolates were European. I-1, I-2, II-1 and II-2 all contained biologically typed isolates. Population genetic and dating analyses indicated that PVX emerged after potato's domestication 9000 years ago and was transported to Europe after the 15th century. Major clusters A-D probably resulted from expansions that occurred soon after the potato late-blight pandemic of the mid-19th century. Genetic comparisons of the PVX populations of different Peruvian Departments found similarities between those linked by local transport of seed potato tubers for summer rain-watered highland crops, and those linked to winter-irrigated crops in nearby coastal Departments. Comparisons also showed that, although the Andean PVX population was diverse and evolving neutrally, its spread to Europe and then elsewhere involved population expansion. PVX forms a basal Potexvirus genus lineage but its immediate progenitor is unknown. Establishing whether PVX's entirely Andean phylogroups I-2 and II-3 and its Andean recombinants threaten potato production elsewhere requires future biological studies.
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Affiliation(s)
- Segundo Fuentes
- Crop and System Sciences Division, International Potato Center, La Molina Lima 15023, Peru; (S.F.); (A.P.); (J.K.)
| | - Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2600, Australia;
| | - Mohammad Hajizadeh
- Plant Protection Department, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran;
| | - Ana Perez
- Crop and System Sciences Division, International Potato Center, La Molina Lima 15023, Peru; (S.F.); (A.P.); (J.K.)
| | - Ian P. Adams
- Fera Science Ltd., Sand Hutton York YO41 1LZ, UK; (I.P.A.); (A.F.)
| | - Cesar E. Fribourg
- Departamento de Fitopatologia, Universidad Nacional Agraria, La Molina Lima 12056, Peru;
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center, La Molina Lima 15023, Peru; (S.F.); (A.P.); (J.K.)
| | - Adrian Fox
- Fera Science Ltd., Sand Hutton York YO41 1LZ, UK; (I.P.A.); (A.F.)
| | - Neil Boonham
- Institute for Agrifood Research Innovations, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
| | - Roger A. C. Jones
- UWA Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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12
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Ahmed N, Amin I, Zaidi SSEA, Rahman SU, Farooq M, Fauquet CM, Mansoor S. Circular DNA enrichment sequencing reveals the viral/satellites genetic diversity associated with the third epidemic of cotton leaf curl disease. Biol Methods Protoc 2021; 6:bpab005. [PMID: 33884305 PMCID: PMC8046901 DOI: 10.1093/biomethods/bpab005] [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: 02/10/2021] [Revised: 03/16/2021] [Accepted: 03/24/2021] [Indexed: 11/13/2022] Open
Abstract
Cotton leaf curl disease (CLCuD) is the most important limiting factor for cotton production in Pakistan. The CLCuD passed through two major epidemics in this region with distinct begomoviruses/satellites complexes. Since 2015 the disease has again started to appear in epidemic form, causing heavy losses to cotton crop, which we termed as the “third epidemic”. We applied CIDER-seq (Circular DNA Enrichment Sequencing), a recently developed sequencing method for PCR-free virus enrichment to produce a full length read of a single circular viral genome coupled with Sanger sequencing to explore the genetic diversity of the disease complex. We identified a highly recombinant strain of Cotton leaf curl Multan virus and a recently evolved strain of Cotton leaf curl Multan betasatellite that are dominant in all major cotton growing regions in the country. Moreover, we also identified multiple species of alphasatellites with one distinct species, Mesta yellow vein mosaic alphasatellite (MeYVMA) for the first time in cotton. Relative abundance of virus and associated satellites was also determined by real-time quantitative PCR. To the best of our knowledge, this is the first study that determined the CLCuD complex associated with its third epidemic.
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Affiliation(s)
- Nasim Ahmed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | - Syed Shan-E-Ali Zaidi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | - Saleem Ur Rahman
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | - Muhammad Farooq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
| | | | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad 38000, Pakistan
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13
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Sircar S, Malik YS, Kumar P, Ansari MI, Bhat S, Shanmuganathan S, Kattoor JJ, Vinodhkumar O, Rishi N, Touil N, Ghosh S, Bányai K, Dhama K. Genomic Analysis of an Indian G8P[1] Caprine Rotavirus-A Strain Revealing Artiodactyl and DS-1-Like Human Multispecies Reassortment. Front Vet Sci 2021; 7:606661. [PMID: 33585597 PMCID: PMC7873603 DOI: 10.3389/fvets.2020.606661] [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] [Received: 09/15/2020] [Accepted: 12/14/2020] [Indexed: 12/03/2022] Open
Abstract
The surveillance studies for the presence of caprine rotavirus A (RVA) are limited in India, and the data for the whole-genome analysis of the caprine RVA is not available. This study describes the whole-genome-based analysis of a caprine rotavirus A strain, RVA/Goat-wt/IND/K-98/2015, from a goat kid in India. The genomic analysis revealed that the caprine RVA strain K-98, possess artiodactyl-like and DS-1 human-like genome constellation G8P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The three structural genes (VP2, VP4, and VP7) were close to caprine host having nucleotide-based identity range between 97.5 and 98.9%. Apart from them, other gene segments showed similarity with either bovine or human like genes, ultimately pointing toward a common evolutionary origin having an artiodactyl-type backbone of strain K-98. Phylogenetically, the various genes of the current study isolate also clustered inside clades comprising Human-Bovine-Caprine isolates from worldwide. The current findings add to the knowledge on caprine rotaviruses and might play a substantial role in designing future vaccines or different alternative strategies combating such infections having public health significance. To the best of our knowledge, this is the first report on the whole-genome characterization of a caprine RVA G8P[1] strain from India. Concerning the complex nature of the K-98 genome, whole-genome analyses of more numbers of RVA strains from different parts of the country are needed to comprehend the genomic nature and genetic diversity among caprine RVA.
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Affiliation(s)
- Shubhankar Sircar
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
- Amity Institute of Virology and Immunology, J-3 Block, Amity University, Noida, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Prashant Kumar
- Amity Institute of Virology and Immunology, J-3 Block, Amity University, Noida, India
| | - Mohd Ikram Ansari
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - Sudipta Bhat
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - S. Shanmuganathan
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - Jobin Jose Kattoor
- Animal Disease Diagnsotic Laboratory, Purdue University, West Lafayette, IN, United States
| | - O.R. Vinodhkumar
- Division of Epidemiology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - Narayan Rishi
- Amity Institute of Virology and Immunology, J-3 Block, Amity University, Noida, India
| | - Nadia Touil
- Laboratoire de Recherche et de Biosécurité, Hôpital Militaire d'instruction Med V de Rabat, Rabat, Morocco
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Krisztián Bányai
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
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14
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Fuentes S, Gibbs AJ, Adams IP, Wilson C, Botermans M, Fox A, Kreuze J, Boonham N, Kehoe MA, Jones RAC. Potato Virus A Isolates from Three Continents: Their Biological Properties, Phylogenetics, and Prehistory. PHYTOPATHOLOGY 2021; 111:217-226. [PMID: 33174824 DOI: 10.1094/phyto-08-20-0354-fi] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Forty-seven potato virus A (PVA) isolates from Europe, Australia, and South America's Andean region were subjected to high-throughput sequencing, and 46 complete genomes from Europe (n = 9), Australia (n = 2), and the Andes (n = 35) obtained. These and 17 other genomes gave alignments of 63 open reading frames 9,180 nucleotides long; 9 were recombinants. The nonrecombinants formed three tightly clustered, almost equidistant phylogroups; A comprised 14 Peruvian potato isolates; W comprised 37 from potato in Peru, Argentina, and elsewhere in the world; and T contained three from tamarillo in New Zealand. When five isolates were inoculated to a potato cultivar differential, three strain groups (= pathotypes) unrelated to phylogenetic groupings were recognized. No temporal signal was detected among the dated nonrecombinant sequences, but PVA and potato virus Y (PVY) are from related lineages and ecologically similar; therefore, "relative dating" was obtained using a single maximum-likelihood phylogeny of PVA and PVY sequences and PVY's well-supported 157 CE "time to most common recent ancestor". The PVA datings obtained were supported by several independent historical coincidences. The PVA and PVY populations apparently arose in the Andes approximately 18 centuries ago, and were taken to Europe during the Columbian Exchange, radiating there after the mid-19th century potato late blight pandemic. PVA's phylogroup A population diverged more recently in the Andean region, probably after new cultivars were bred locally using newly introduced Solanum tuberosum subsp. tuberosum as a parent. Such cultivars became widely grown, and apparently generated the A × W phylogroup recombinants. Phylogroup A, and its interphylogroup recombinants, might pose a biosecurity risk.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Segundo Fuentes
- Crop and System Sciences Division, International Potato Center (CIP), La Molina, Lima, Peru
| | - Adrian J Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT, Australia
| | | | - Calum Wilson
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, Tasmania, Australia
| | - Marleen Botermans
- National Reference Centre of Plant Health, Dutch National Plant Protection Organization Service, Wageningen, The Netherlands
| | - Adrian Fox
- Fera Science Ltd., Sand Hutton, York, U.K
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center (CIP), La Molina, Lima, Peru
| | - Neil Boonham
- Institute for Agrifood Research Innovations, Newcastle University, Newcastle upon Tyne, U.K
| | - Monica A Kehoe
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Roger A C Jones
- Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
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15
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Sorokin DY, Mosier D, Zorz JK, Dong X, Strous M. Wenzhouxiangella Strain AB-CW3, a Proteolytic Bacterium From Hypersaline Soda Lakes That Preys on Cells of Gram-Positive Bacteria. Front Microbiol 2020; 11:597686. [PMID: 33281797 PMCID: PMC7691419 DOI: 10.3389/fmicb.2020.597686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
A new haloalkaliphilic species of Wenzhouxiangella, strain AB-CW3, was isolated from a system of hypersaline alkaline soda lakes in the Kulunda Steppe using cells of Staphylococcus aureus as growth substrate. AB-CW3's complete, circular genome was assembled from combined nanopore and Illumina sequencing and its proteome was determined for three different experimental conditions. AB-CW3 is an aerobic gammaproteobacterium feeding mainly on proteins and peptides. Unique among Wenzhouxiangella, it uses a flagellum for motility, fimbria for cell attachment and is capable of complete denitrification. AB-CW3 can use proteins derived from living or dead cells of Staphylococcus and other Gram-positive bacteria as the carbon and energy source. It encodes and expresses production of a novel Lantibiotic, a class of antimicrobial peptides which have so far only been found to be produced by Gram-positive bacteria. AB-CW3 likely excretes this peptide via a type I secretion system encoded upstream of the genes for production of the Lanthipeptide. Comparison of AB-CW3's genome to 18 other Wenzhouxiangella genomes from marine, hypersaline, and soda lake habitats indicated one or two transitions from marine to soda lake environments followed by a transition of W. marina back to the oceans. Only 19 genes appear to set haloalkaliphilic Wenzhouxiangella apart from their neutrophilic relatives. As strain AB-CW3 is only distantly related to other members of the genus, we propose to provisionally name it "Wenzhouxiangella alkaliphila".
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Federal Research Centre for Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Damon Mosier
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jackie K Zorz
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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16
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Mwatuni FM, Nyende AB, Njuguna J, Xiong Z, Machuka E, Stomeo F. Occurrence, genetic diversity, and recombination of maize lethal necrosis disease-causing viruses in Kenya. Virus Res 2020; 286:198081. [PMID: 32663481 PMCID: PMC7450272 DOI: 10.1016/j.virusres.2020.198081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 06/20/2020] [Accepted: 06/27/2020] [Indexed: 11/22/2022]
Abstract
Maize is the most important food crop in Kenya accounting for more than 51 % of all staples grown in the country. Out of Kenya's 5.3 million ha total crops area, more than 2.1 million ha is occupied by maize which translates to 40 % of all crops area. However, with the emergence of maize lethal necrosis (MLN) disease in 2011, the average yields plummeted to all-time lows with severely affected counties recording 90-100% yield loss in 2013 and 2014. The disease is mainly caused by Maize chlorotic mottle virus (MCMV) in combination with Sugarcane mosaic virus (SCMV) or other potyviruses. In this study, a country-wide survey was carried out to assess the MLN causing viruses in Kenya, their distribution, genetic diversity, and recombination. The causative viruses of MLN were determined by RT-PCR using virus-specific primers and DAS-ELISA. Next-generation sequencing (NGS) data was generated, viral sequences identified, genetic diversity of MLN viruses was determined, and recombination was evaluated. MCMV and SCMV were detected in all the maize growing regions at varying levels of incidence, and severity while MaYMV, a polerovirus was detected in some samples through NGS. However, there were some samples in this study where only MCMV was detected with severe MLN symptoms. SCMV Sequences were highly diverse while MCMV sequences exhibited low variability. Potential recombination events were detected only in SCMV explaining the elevated level of diversity and associated risk of this virus in Kenya and the eastern Africa region.
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Affiliation(s)
- Francis M Mwatuni
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041 - 00621, Nairobi, Kenya; Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00100, Nairobi, Kenya; Kenya Plant Health Inspectorate Service(KEPHIS), P.O. Box 49592-00100, Nairobi, Kenya.
| | - Aggrey Bernard Nyende
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00100, Nairobi, Kenya
| | - Joyce Njuguna
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA - ILRI) Hub, P.O. Box 30709-00100, Nairobi, Kenya
| | | | - Eunice Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA - ILRI) Hub, P.O. Box 30709-00100, Nairobi, Kenya
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA - ILRI) Hub, P.O. Box 30709-00100, Nairobi, Kenya
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17
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Gaunt MW, Gubler DJ, Pettersson JHO, Kuno G, Wilder-Smith A, de Lamballerie X, Gould EA, Falconar AK. Recombination of B- and T-cell epitope-rich loci from Aedes- and Culex-borne flaviviruses shapes Zika virus epidemiology. Antiviral Res 2019; 174:104676. [PMID: 31837392 DOI: 10.1016/j.antiviral.2019.104676] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 12/06/2019] [Accepted: 12/08/2019] [Indexed: 02/07/2023]
Abstract
Sporadic human Zika virus (ZIKV) infections have been recorded in Africa and Asia since the 1950s. Major epidemics occurred only after ZIKV emerged in the Pacific islands and spread to the Americas. Specific biological determinants of the explosive epidemic nature of ZIKV have not been identified. Phylogenetic studies revealed incongruence in ZIKV placement in relation to Aedes-borne dengue viruses (DENV) and Culex-borne flaviviruses. We hypothesized that this incongruence reflects interspecies recombination resulting in ZIKV evasion of cross-protective T-cell immunity. We investigated ZIKV phylogenetic incongruence in relation to: DENV T-cell epitope maps experimentally identified ex vivo, published B-cell epitope loci, and CD8+ T-cell epitopes predicted in silico for mosquito-borne flaviviruses. Our findings demonstrate that the ZIKV proteome is a hybrid of Aedes-borne DENV proteins interspersed amongst Culex-borne flavivirus proteins derived through independent interspecies recombination events. These analyses infer that DENV-associated proteins in the ZIKV hybrid proteome generated immunodominant human B-cell responses, whereas ZIKV recombinant derived Culex-borne flavivirus-associated proteins generated immunodominant CD8+ and/or CD4+ T-cell responses. In silico CD8+ T-cell epitope ZIKV cross-reactive prediction analyses verified this observation. We propose that by acquiring cytotoxic T-cell epitope-rich regions from Culex-borne flaviviruses, ZIKV evaded DENV-generated T-cell immune cross-protection. Thus, Culex-borne flaviviruses, including West Nile virus and Japanese encephalitis virus, might induce cross-protective T-cell responses against ZIKV. This would explain why explosive ZIKV epidemics occurred in DENV-endemic regions of Micronesia, Polynesia and the Americas where Culex-borne flavivirus outbreaks are infrequent and why ZIKV did not cause major epidemics in Asia where Culex-borne flaviviruses are widespread.
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Affiliation(s)
- Michael W Gaunt
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Duane J Gubler
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, 169857, Singapore
| | - John H-O Pettersson
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Goro Kuno
- 1648 Collindale Dr, Fort Collins, CO, 80525, USA
| | - Annelies Wilder-Smith
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Department of Public Health and Clinical Medicine, Epidemiology and Public Health, Umeå University, Umeå, Sweden; Heidelberg Institute of Global Health, University of Heidelberg, Germany
| | - Xavier de Lamballerie
- UMR "Unité des Virus Emergents", Aix-Marseille Université-IRD 190, Inserm, 1207-IHU Méditerranée Infection, Marseille, France
| | - Ernest A Gould
- UMR "Unité des Virus Emergents", Aix-Marseille Université-IRD 190, Inserm, 1207-IHU Méditerranée Infection, Marseille, France
| | - Andrew K Falconar
- Departmento de Medicina, Universidad del Norte, Barranquilla, Colombia
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18
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Hajizadeh M, Gibbs AJ, Amirnia F, Glasa M. The global phylogeny o f Plum pox virus is emerging. J Gen Virol 2019; 100:1457-1468. [PMID: 31418674 DOI: 10.1099/jgv.0.001308] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The 206 complete genomic sequences of Plum pox virus in GenBank (January 2019) were downloaded. Their main open reading frames (ORF)s were compared by phylogenetic and population genetic methods. All fell into the nine previously recognized strain clusters; the PPV-Rec and PPV-T strain ORFs were all recombinants, whereas most of those in the PPV-C, PPV-CR, PPV-CV, PPV-D, PPV-EA, PPV-M and PPV-W strain clusters were not. The strain clusters ranged in size from 2 (PPV-CV and PPV-EA) to 74 (PPV-D). The isolates of eight of the nine strains came solely from Europe and the Levant (with an exception resulting from a quarantine breach), but many PPV-D strain isolates also came from east and south Asia and the Americas. The estimated time to the most recent common ancestor (TMRCA) of all 134 non-recombinant ORFs was 820 (865-775) BCE. Most strain populations were only a few decades old, and had small intra-strain, but large inter-strain, differences; strain PPV-W was the oldest. Eurasia is clearly the 'centre of emergence' of PPV and the several PPV-D strain populations found elsewhere only show evidence of gene flow with Europe, so have come from separate introductions from Europe. All ORFs and their individual genes show evidence of strong negative selection, except the positively selected pipo gene of the recently migrant populations. The possible ancient origins of PPV are discussed.
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Affiliation(s)
- Mohammad Hajizadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Adrian J Gibbs
- Emeritus Faculty Australian National University, Canberra, Australia
| | - Fahimeh Amirnia
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia
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19
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Fuentes S, Jones RAC, Matsuoka H, Ohshima K, Kreuze J, Gibbs AJ. Potato virus Y; the Andean connection. Virus Evol 2019; 5:vez037. [PMID: 31559020 PMCID: PMC6755682 DOI: 10.1093/ve/vez037] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Potato virus Y (PVY) causes disease in potatoes and other solanaceous crops. The appearance of its necrogenic strains in the 1980s made it the most economically important virus of potatoes. We report the isolation and genomic sequences of 32 Peruvian isolates of PVY which, together with 428 published PVY genomic sequences, gave an alignment of 460 sequences. Of these 190 (41%) were non-recombinant, and 162 of these provided a dated phylogeny, that corresponds well with the likely history of PVY, and show that PVY originated in South America which is where potatoes were first domesticated. The most basal divergences of the PVY population produced the N and C: O phylogroups; the origin of the N phylogroup is clearly Andean, but that of the O and C phylogroups is unknown, although they may have been first to establish in European crops. The current PVY population originated around 156 CE. PVY was probably first taken from South America to Europe in the 16th century in tubers. Most of the present PVY diversity emerged in the second half of the 19th century, after the Phytophthora infestans epidemics of the mid-19th century destroyed the European crop and stimulated potato breeding. Imported breeding lines were shared, and there was no quarantine. The early O population was joined later by N phylogroup isolates and their recombinants generated the R1 and R2 populations of damaging necrogenic strains. Our dating study has confirmed that human activity has dominated the phylodynamics of PVY for the last two millennia.
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Affiliation(s)
- Segundo Fuentes
- Crop and System Sciences Division, International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Roger A C Jones
- Crop and System Sciences Division, International Potato Center (CIP), Apartado 1558, Lima 12, Peru
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA
| | - Hiroki Matsuoka
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, Australia
| | - Kazusato Ohshima
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, Australia
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Adrian J Gibbs
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, Japan
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20
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Bletsa M, Suchard MA, Ji X, Gryseels S, Vrancken B, Baele G, Worobey M, Lemey P. Divergence dating using mixed effects clock modelling: An application to HIV-1. Virus Evol 2019; 5:vez036. [PMID: 31720009 PMCID: PMC6830409 DOI: 10.1093/ve/vez036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The need to estimate divergence times in evolutionary histories in the presence of various sources of substitution rate variation has stimulated a rich development of relaxed molecular clock models. Viral evolutionary studies frequently adopt an uncorrelated clock model as a generic relaxed molecular clock process, but this may impose considerable estimation bias if discrete rate variation exists among clades or lineages. For HIV-1 group M, rate variation among subtypes has been shown to result in inconsistencies in time to the most recent common ancestor estimation. Although this calls into question the adequacy of available molecular dating methods, no solution to this problem has been offered so far. Here, we investigate the use of mixed effects molecular clock models, which combine both fixed and random effects in the evolutionary rate, to estimate divergence times. Using simulation, we demonstrate that this model outperforms existing molecular clock models in a Bayesian framework for estimating time-measured phylogenies in the presence of mixed sources of rate variation, while also maintaining good performance in simpler scenarios. By analysing a comprehensive HIV-1 group M complete genome data set we confirm considerable rate variation among subtypes that is not adequately modelled by uncorrelated relaxed clock models. The mixed effects clock model can accommodate this rate variation and results in a time to the most recent common ancestor of HIV-1 group M of 1920 (1915-25), which is only slightly earlier than the uncorrelated relaxed clock estimate for the same data set. The use of complete genome data appears to have a more profound impact than the molecular clock model because it reduces the credible intervals by 50 per cent relative to similar estimates based on short envelope gene sequences.
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Affiliation(s)
- Magda Bletsa
- 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 at UCLA, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
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Fribourg CE, Gibbs AJ, Adams IP, Boonham N, Jones RAC. Biological and Molecular Properties of Wild potato mosaic virus Isolates from Pepino ( Solanum muricatum). PLANT DISEASE 2019; 103:1746-1756. [PMID: 31082318 DOI: 10.1094/pdis-12-18-2164-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In 1976, a virus with flexuous, filamentous virions typical of the family Potyviridae was isolated from symptomatic pepino (Solanum muricatum) plants growing in two valleys in Peru's coastal desert region. In 2014, a virus with similar-shaped virions was isolated from asymptomatic fruits obtained from pepino plants growing in six coastal valleys and a valley in Peru's Andean highlands. Both were identified subsequently as Wild potato mosaic virus (WPMV) by serology or high-throughput sequencing (HTS). The symptoms caused by two old and seven new isolates from pepino were examined in indicator plants. Infected solanaceous hosts varied considerably in their sensitivities to infection and individual isolates varied greatly in virulence. All seven new isolates caused quick death of infected Nicotiana benthamiana plants and more than half of them killed infected plants of Physalis floridana and S. chancayense. These three species were the most sensitive to infection. The most virulent isolate was found to be BA because it killed five of eight solanaceous host species whereas CA was the least severe because it only killed N. benthamiana. Using HTS, complete genomic sequences of six isolates were obtained, with one isolate (FE) showing evidence of recombination. The distances between individual WPMV isolates in phylogenetic trees and the geographical distances between their collection sites were found to be unrelated. The individual WPMV isolates displayed nucleotide sequence identities of 80.9-99.8%, whereas the most closely related virus, Potato virus V (PVV), was around 75% identical to WPMV. WPMV, PVV, and Peru tomato virus formed clusters of similar phylogenetic diversity, and were found to be distinct but related viruses within the overall Potato virus Y lineage. WPMV infection seems widespread and of likely economic significance to pepino producers in Peru's coastal valleys. Because it constitutes the fifth virus found infecting pepino and this crop is entirely vegetatively propagated, development of healthy pepino stock programs is advocated.
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Affiliation(s)
- Cesar E Fribourg
- 1 Departamento de Fitopatologia, Universidad Nacional Agraria, La Molina, Lima, Peru
| | - Adrian J Gibbs
- 2 Emeritus Faculty, Australian National University, Canberra, ACT, Australia
| | | | - Neil Boonham
- 4 Institute for Agrifood Research Innovations, Newcastle University, Newcastle upon Tyne, U.K
| | - Roger A C Jones
- 5 Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA, Australia, and Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, Australia
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22
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Santillan FW, Fribourg CE, Adams IP, Gibbs AJ, Boonham N, Kehoe MA, Maina S, Jones RAC. The Biology and Phylogenetics of Potato virus S Isolates from the Andean Region of South America. PLANT DISEASE 2018; 102:869-885. [PMID: 30673374 DOI: 10.1094/pdis-09-17-1414-re] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biological characteristics of 11 Potato virus S (PVS) isolates from three cultivated potato species (Solanum spp.) growing in five Andean countries and 1 from Scotland differed in virulence depending on isolate and host species. Nine isolates infected Chenopodium quinoa systemically but two others and the Scottish isolate remained restricted to inoculated leaves; therefore, they belonged to biologically defined strains PVSA and PVSO, respectively. When nine wild potato species were inoculated, most developed symptomless systemic infection but Solanum megistacrolobum developed systemic hypersensitive resistance (SHR) with one PVSO and two PVSA isolates. Andean potato cultivars developed mostly asymptomatic primary infection but predominantly symptomatic secondary infection. In both wild and cultivated potato plants, PVSA and PVSO elicited similar foliage symptoms. Following graft inoculation, all except two PVSO isolates were detected in partially PVS-resistant cultivar Saco, while clone Snec 66/139-19 developed SHR with two isolates each of PVSA and PVSO. Myzus persicae transmitted all nine PVSA isolates but none of the three PVSO isolates. All 12 isolates were transmitted by plant-to-plant contact. In infective sap, all isolates had thermal inactivation points of 55 to 60°C. Longevities in vitro were 25 to 40 days with six PVSA isolates but less than 21 days for the three PVSO isolates. Dilution end points were 10-3 for two PVSO isolates but 10-4 to 10-6 with the other isolates. Complete new genome sequences were obtained from seven Andean PVS isolates; seven isolates from Africa, Australia, or Europe; and single isolates from S. muricatum and Arracacia xanthorhiza. These 17 new genomes and 23 from GenBank provided 40 unique sequences; however, 5 from Eurasia were recombinants. Phylogenetic analysis of the 35 nonrecombinants revealed three major lineages, two predominantly South American (SA) and evenly branched and one non-SA with a single long basal branch and many distal subdivisions. Using least squares dating and nucleotide sequences, the two nodes of the basal PVS trifurcation were dated at 1079 and 1055 Common Era (CE), the three midphylogeny nodes of the SA lineages at 1352, 1487, and 1537 CE, and the basal node to the non-SA lineage at 1837 CE. The Potato rough dwarf virus/Potato virus P (PVS/PRDV/PVP) cluster was sister to PVS and diverged 5,000 to 7,000 years ago. The non-SA PVS lineage contained 18 of 19 isolates from S. tuberosum subsp. tuberosum but the two SA lineages contained 6 from S. tuberosum subsp. andigena, 4 from S. phureja, 3 from S. tuberosum subsp. tuberosum, and 1 each from S. muricatum, S. curtilobum, and A. xanthorrhiza. This suggests that a potato-infecting proto-PVS/PRDV/PVP emerged in South America at least 5,000 years ago, became endemic, and diverged into a range of local Solanum spp. and other species, and one early lineage spread worldwide in potato. Preventing establishment of the SA lineages is advised for all countries still without them.
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Affiliation(s)
- Franklin W Santillan
- Departamento de Fitopatologia, Universidad Nacional Agraria, La Molina, Lima, Peru; and Universidad de Cuenca, Cuenca, Azuay, Ecuador
| | - Cesar E Fribourg
- Departamento de Fitopatologia, Universidad Nacional Agraria, Peru
| | | | - Adrian J Gibbs
- Emeritus Faculty, Australian National University, ACT, Australia
| | - Neil Boonham
- Fera Ltd.; and Institute for Agrifood Research Innovations, Newcastle University, Newcastle upon Tyne, UK
| | - Monica A Kehoe
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Solomon Maina
- Department of Agriculture and Environment and Institute of Agriculture, University of Western Australia, Crawley, Perth, WA, Australia
| | - Roger A C Jones
- Institute of Agriculture, University of Western Australia; and Crop Protection Branch, Department of Primary Industries and Regional Development, South Perth, WA, Australia
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23
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Sullivan AR, Schiffthaler B, Thompson SL, Street NR, Wang XR. Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae). Mol Biol Evol 2017; 34:1689-1701. [PMID: 28383641 PMCID: PMC5455968 DOI: 10.1093/molbev/msx111] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of ∼35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.
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Affiliation(s)
- Alexis R Sullivan
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Bastian Schiffthaler
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Stacey Lee Thompson
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden.,Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Nathaniel R Street
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, Sweden
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24
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Zubair M, Zaidi SSEA, Shakir S, Farooq M, Amin I, Scheffler JA, Scheffler BE, Mansoor S. Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton. Sci Rep 2017; 7:680. [PMID: 28386113 PMCID: PMC5429635 DOI: 10.1038/s41598-017-00727-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/10/2017] [Indexed: 11/09/2022] Open
Abstract
The first epidemic of cotton leaf curl disease (CLCuD) in early 1990's in the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in late 1990's but soon resistance was broken and was associated with a single recombinant begomovirus named Burewala strain of Cotton leaf curl Kokhran virus that lacks a full complement of a gene encoding a transcription activator protein (TrAP). In order to understand the ongoing changes in CLCuD complex in Pakistan, CLCuD affected plants from cotton fields at Vehari were collected. Illumina sequencing was used to assess the diversity of CLCuD complex. At least three distinct begomoviruses characterized from the first epidemic; Cotton leaf curl Multan virus, Cotton leaf curl Kokhran virus and Cotton leaf curl Alabad virus, several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD. These viruses were also cloned and sequenced through Sanger sequencing to confirm the identity of the begomoviruses and that all clones possessed a full complement of the TrAP gene. A new strain of betasatellite was identified here and named CLCuMuBVeh. The implications of these findings in efforts to control CLCuD are discussed.
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Affiliation(s)
- Muhammad Zubair
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Syed Shan-E-Ali Zaidi
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Sara Shakir
- Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jodi A Scheffler
- USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA
| | - Brian E Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
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25
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Tsimpidis M, Bachoumis G, Mimouli K, Kyriakopoulou Z, Robertson DL, Markoulatos P, Amoutzias GD. T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. BMC Bioinformatics 2017; 18:13. [PMID: 28056784 PMCID: PMC5216575 DOI: 10.1186/s12859-016-1420-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/10/2016] [Indexed: 12/22/2022] Open
Abstract
Background Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods. Results T-RECs, a Windows based graphical tool, employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions. Conclusions T-RECs is very effective, as demonstrated by an analysis of 555 Norovirus complete genomes and 2500 sequence fragments, where a recombination hotspot was identified at the ORF1-ORF2 junction.
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Affiliation(s)
- Michail Tsimpidis
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Georgios Bachoumis
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Kalliopi Mimouli
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Zaharoula Kyriakopoulou
- Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece
| | | | - Panayotis Markoulatos
- Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece
| | - Grigoris D Amoutzias
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
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26
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Gibbs AJ, Ohshima K, Yasaka R, Mohammadi M, Gibbs MJ, Jones RAC. The phylogenetics of the global population of potato virus Y and its necrogenic recombinants. Virus Evol 2017; 3:vex002. [PMID: 28458913 PMCID: PMC5399925 DOI: 10.1093/ve/vex002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Potato virus Y (PVY) is a major pathogen of potatoes and other solanaceous crops worldwide. It is most closely related to potyviruses first or only found in the Americas, and it almost certainly originated in the Andes, where its hosts were domesticated. We have inferred the phylogeny of the published genomic sequences of 240 PVY isolates collected since 1938 worldwide, but not the Andes. All fall into five groupings, which mostly, but not exclusively, correspond with groupings already devised using biological and taxonomic data. Only 42 percent of the sequences are not recombinant, and all these fall into one or other of three phylogroups; the previously named C (common), O (ordinary), and N (necrotic) groups. There are also two other distinct groups of isolates all of which are recombinant; the R-1 isolates have N (5' terminal minor) and O (major) parents, and the R-2 isolates have R-1 (major) and N (3' terminal minor) parents. Many isolates also have additional minor intra- and inter-group recombinant genomic regions. The complex interrelationships between the genomes were resolved by progressively identifying and removing recombinants using partitioned sequences of synonymous codons. Least squared dating and BEAST analyses of two datasets of gene sequences from non-recombinant heterochronously-sampled isolates (seventy-three non-recombinant major ORFs and 166 partial ORFs) found the 95% confidence intervals of the TMRCA estimates overlap around 1,000 CE (Common Era; AD). We attempted to identify the most accurate datings by comparing the estimated phylogenetic dates with historical events in the worldwide adoption of potato and other PVY hosts as crops, but found that more evidence from gene sequences of non-potato isolates, especially from South America, was required.
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Affiliation(s)
- Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Ryosuke Yasaka
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Musa Mohammadi
- Department of Plant Protection, Vali-e-asr University of Rafsanjan, Rafsanjan, Iran
| | | | - Roger A. C. Jones
- Department of Agriculture and Food Western Australia, Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- 3 Baron-Hay Court, South Perth, WA 6151, Australia
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27
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Aiewsakun P, Katzourakis A. Time dependency of foamy virus evolutionary rate estimates. BMC Evol Biol 2015; 15:119. [PMID: 26111824 PMCID: PMC4480597 DOI: 10.1186/s12862-015-0408-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/02/2015] [Indexed: 12/19/2022] Open
Abstract
Background It appears that substitution rate estimates co-vary very strongly with their timescale of measurement; the shorter the timescale, the higher the estimated value. Foamy viruses have a long history of co-speciation with their hosts, and one of the lowest estimated rates of evolution among viruses. However, when their rate of evolution is estimated over short timescales, it is more reminiscent of the rapid rates seen in other RNA viruses. This discrepancy between their short-term and long-term rates could be explained by the time-dependency of substitution rate estimates. Several empirical models have been proposed and used to correct for the time-dependent rate phenomenon (TDRP), such as a vertically-translated exponential rate decay model and a power-law rate decay model. Nevertheless, at present, it is still unclear which model best describes the rate dynamics. Here, we use foamy viruses as a case study to empirically describe the phenomenon and to determine how to correct rate estimates for its effects. Four empirical models were investigated: (i) a vertically-translated exponential rate decay model, (ii) a simple exponential rate decay model, (iii) a vertically-translated power-law rate decay model, and (iv) a simple power-law rate decay model. Results Our results suggest that the TDRP is likely responsible for the large discrepancy observed in foamy virus short-term and long-term rate estimates, and the simple power-law rate decay model is the best model for inferring evolutionary timescales. Furthermore, we demonstrated that, within the Bayesian phylogenetic framework, currently available molecular clocks can severely bias evolutionary date estimates, indicating that they are inadequate for correcting for the TDRP. Our analyses also suggest that different viral lineages may have different TDRP dynamics, and this may bias date estimates if it is unaccounted for. Conclusions As evolutionary rate estimates are dependent on their measurement timescales, their values must be used and interpreted under the context of the timescale of rate estimation. Extrapolating rate estimates across large timescales for evolutionary inferences can severely bias the outcomes. Given that the TDRP is widespread in nature but has been noted only recently the estimated timescales of many viruses may need to be reconsidered and re-estimated. Our models could be used as a guideline to further improve current phylogenetic inference tools. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0408-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
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28
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Martin DP, Murrell B, Golden M, Khoosal A, Muhire B. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol 2015; 1:vev003. [PMID: 27774277 PMCID: PMC5014473 DOI: 10.1093/ve/vev003] [Citation(s) in RCA: 2106] [Impact Index Per Article: 234.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RDP4 is the latest version of recombination detection program (RDP), a Windows computer program that implements an extensive array of methods for detecting and visualising recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP4 is capable of analysing twice as many sequences (up to 2,500) that are up to three times longer (up to 10 Mb) than those that could be analysed by older versions of the program. RDP4 is therefore also applicable to the analysis of bacterial full-genome sequence datasets. Other novelties in RDP4 include (1) the capacity to differentiate between recombination and genome segment reassortment, (2) the estimation of recombination breakpoint confidence intervals, (3) a variety of ‘recombination aware’ phylogenetic tree construction and comparison tools, (4) new matrix-based visualisation tools for examining both individual recombination events and the overall phylogenetic impacts of multiple recombination events and (5) new tests to detect the influences of gene arrangements, encoded protein structure, nucleic acid secondary structure, nucleotide composition, and nucleotide diversity on recombination breakpoint patterns. The key feature of RDP4 that differentiates it from other recombination detection tools is its flexibility. It can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.
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Affiliation(s)
- Darren P. Martin
- Department of Integrative Biomedical Sciences, Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road Observatory 7549, Cape Town, South Africa
- *Corresponding author: E-mail:
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Michael Golden
- Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG, Oxford, UK
| | - Arjun Khoosal
- Department of Integrative Biomedical Sciences, Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road Observatory 7549, Cape Town, South Africa
| | - Brejnev Muhire
- Department of Integrative Biomedical Sciences, Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road Observatory 7549, Cape Town, South Africa
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29
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Park ES, Suzuki M, Kimura M, Maruyama K, Mizutani H, Saito R, Kubota N, Furuya T, Mizutani T, Imaoka K, Morikawa S. Identification of a natural recombination in the F and H genes of feline morbillivirus. Virology 2014; 468-470:524-531. [PMID: 25262470 DOI: 10.1016/j.virol.2014.09.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 07/31/2014] [Accepted: 09/04/2014] [Indexed: 01/11/2023]
Abstract
Feline morbillivirus (FmoPV) has recently been identified in Hong Kong and Japan. FmoPV is considered to belong to the genus Morbillivirus, in the family Paramyxoviridae. In this study, the complete nucleotide sequences of three strains of FmoPV detected in cats in Japan were determined. Among the six genes in FmoPV; N, P/V/C, M, F, H and L, the P gene showed the highest polymorphism in the nucleotide and putative amino acid sequences among the FmoPV strains. There was no geographical association in terms of the FmoPV phylogeny; however, from extensive phylogenetic and recombination analyses, we found that one Japanese FmoPV strain, MiJP003, was a probable recombinant between two virus strains in the independent lineages found in Japan and Hong Kong, respectively. The recombination was considered to have occurred within the F and H genes. Such recombination is thought to be involved in the evolution of FmoPV.
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Affiliation(s)
- Eun-Sil Park
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Michio Suzuki
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masanobu Kimura
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Keiji Maruyama
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Hiroshi Mizutani
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Ryuichi Saito
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Nami Kubota
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Tetsuya Furuya
- Research and education center for prevention of global infectious diseases of animals, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Tetsuya Mizutani
- Research and education center for prevention of global infectious diseases of animals, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Koichi Imaoka
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
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30
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Katzourakis A, Aiewsakun P, Jia H, Wolfe ND, LeBreton M, Yoder AD, Switzer WM. Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution. Retrovirology 2014; 11:61. [PMID: 25091111 PMCID: PMC4261875 DOI: 10.1186/1742-4690-11-61] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/02/2014] [Indexed: 02/06/2023] Open
Abstract
Background Foamy viruses (FVs) are a unique subfamily of retroviruses that are widely distributed in mammals. Owing to the availability of sequences from diverse mammals coupled with their pattern of codivergence with their hosts, FVs have one of the best-understood viral evolutionary histories ever documented, estimated to have an ancient origin. Nonetheless, our knowledge of some parts of FV evolution, notably that of prosimian and afrotherian FVs, is far from complete due to the lack of sequence data. Results Here, we report the complete genome of the first extant prosimian FV (PSFV) isolated from a lorisiforme galago (PSFVgal), and a novel partial endogenous viral element with high sequence similarity to FVs, present in the afrotherian Cape golden mole genome (ChrEFV). We also further characterize a previously discovered endogenous PSFV present in the aye-aye genome (PSFVaye). Using phylogenetic methods and available FV sequence data, we show a deep divergence and stable co-evolution of FVs in eutherian mammals over 100 million years. Nonetheless, we found that the evolutionary histories of bat, aye-aye, and New World monkey FVs conflict with the evolutionary histories of their hosts. By combining sequence analysis and biogeographical knowledge, we propose explanations for these mismatches in FV-host evolutionary history. Conclusion Our discovery of ChrEFV has expanded the FV host range to cover the whole eutherian clade, and our evolutionary analyses suggest a stable mammalian FV-host co-speciation pattern which extends as deep as the exafroplacentalian basal diversification. Nonetheless, two possible cases of host switching were observed. One was among New World monkey FVs, and the other involves PSFVaye and a bat FV which may involve cross-species transmission at the level of mammalian orders. Our results highlight the value of integrating multiple sources of information to elucidate the evolutionary history of viruses, including continental and geographical histories, ancestral host locations, in addition to the natural history of host and virus. Electronic supplementary material The online version of this article (doi:10.1186/1742-4690-11-61) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, South Parks Road, Oxford OX1 3PS, UK.
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31
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Bulla I, Schultz AK, Chesneau C, Mark T, Serea F. A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection. BMC Bioinformatics 2014; 15:205. [PMID: 24946781 PMCID: PMC4230192 DOI: 10.1186/1471-2105-15-205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfamily separately by one pHMM. However, a major drawback of this approach is the difficulty of dealing with subfamilies composed of very few sequences. One of the most crucial bioinformatical tasks affected by the problem of small-size subfamilies is the subtyping of human immunodeficiency virus type 1 (HIV-1) sequences, i.e., HIV-1 subtypes for which only a small number of sequences is known. RESULTS To deal with small samples for particular subfamilies of HIV-1, we introduce a novel model-based information sharing protocol. It estimates the emission probabilities of the pHMM modeling a particular subfamily not only based on the nucleotide frequencies of the respective subfamily but also incorporating the nucleotide frequencies of all available subfamilies. To this end, the underlying probabilistic model mimics the pattern of commonality and variation between the subtypes with regards to the biological characteristics of HI viruses. In order to implement the proposed protocol, we make use of an existing HMM architecture and its associated inference engine. CONCLUSIONS We apply the modified algorithm to classify HIV-1 sequence data in the form of partial HIV-1 sequences and semi-artificial recombinants. Thereby, we demonstrate that the performance of pHMMs can be significantly improved by the proposed technique. Moreover, we show that our algorithm performs significantly better than Simplot and Bootscanning.
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Affiliation(s)
- Ingo Bulla
- Institut für Mathematik und Informatik, Universität Greifswald, Walther-Rathenau-Straße 47, 17487 Greifswald, Germany.
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Restrepo S, Tabima JF, Mideros MF, Grünwald NJ, Matute DR. Speciation in fungal and oomycete plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:289-316. [PMID: 24906125 DOI: 10.1146/annurev-phyto-102313-050056] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The process of speciation, by definition, involves evolution of one or more reproductive isolating mechanisms that split a single species into two that can no longer interbreed. Determination of which processes are responsible for speciation is important yet challenging. Several studies have proposed that speciation in pathogens is heavily influenced by host-pathogen dynamics and that traits that mediate such interactions (e.g., host mobility, reproductive mode of the pathogen, complexity of the life cycle, and host specificity) must lead to reproductive isolation and ultimately affect speciation rates. In this review, we summarize the main evolutionary processes that lead to speciation of fungal and oomycete plant pathogens and provide an outline of how speciation can be studied rigorously, including novel genetic/genomic developments.
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Affiliation(s)
- Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
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Balakirev ES, Romanov NS, Mikheev PB, Ayala FJ. Mitochondrial DNA variation and introgression in Siberian taimen Hucho taimen. PLoS One 2013; 8:e71147. [PMID: 23951096 PMCID: PMC3741329 DOI: 10.1371/journal.pone.0071147] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/22/2013] [Indexed: 11/18/2022] Open
Abstract
Siberian taimen Hucho taimen is the largest representative of the family Salmonidae inhabiting rivers of northern Eurasia. The species is under intensive aquaculture activity. To monitor natural taimen populations we have sequenced a portion (8,141 bp) of the mitochondrial (mt) genome in 28 specimens of H. taimen from six localities in the Amur River basin. Nucleotide variability is low (π = 0.0010), but structured in two divergent haplotype groups. A comparison of the data with the GenBank H. taimen mt genome (HQ897271) reveals significant differences between them in spite of the fact that the fish specimens come from neighboring geographical areas. The distribution of divergence is non-uniform with two highly pronounced divergent regions centered on two genes, ND3 and ND6. To clarify the pattern of divergence we sequenced the corresponding portion of the mt genome of lenok Brachymystax tumensis and analyzed the GenBank complete mt genomes of related species. We have found that the first and second divergent regions are identical between the GenBank H. taimen and two lenok subspecies, B. lenok and B. lenok tsinlingensis, respectively. Consequently, both divergent regions represent introgressed mtDNA resulting from intergeneric hybridization between the two lenok subspecies and H. taimen. Introgression is, however, not detected in our specimens. This plus the precise identity of the introgressed fragments between the donor and the recipient GenBank sequence suggests that the introgression is local and very recent, probably due to artificial manipulations involving taimen – lenok intergeneric hybridization. Human-mediated hybridization may become a major threat to aquatic biodiversity. Consequently we suggest that due attention needs to be given to this threat by means of responsible breeding program management, so as to prevent a potential spread of hybrid fishes that could jeopardize the resilience of locally adapted gene pools of the native H. taimen populations.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA.
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Abstract
One of the major characteristics of HIV-1 is its high genetic variability and extensive heterogeneity. This characteristic is due to its molecular traits, which in turn allows it to vary, recombine, and diversify at a high frequency. As such, it generates complex molecular forms, termed recombinants, which evade the human immune system and so survive. There is no sequence constraint to the recombination pattern as it appears to occur at inter-group (between groups M and O), as well as interand intra-subtype within group M. Rapid emergence and active global transmission of HIV-1 recombinants, known as circulating recombinant forms (CRFs) and unique recombinant forms (URFs), requires urgent attention. To date, 55 CRFs have been reported around the world. The first CRF01_AE originated from Central Africa but spread widely in Asia. The most recent CRF; CRF55_01B is a recombinant form of CRF01_AE and subtype B, although its origin is yet to be publicly disclosed. HIV-1 recombination is an ongoing event and plays an indispensable role in HIV epidemics in different regions. Africa, Asia and South America are identified as recombination hot-spots. They are affected by continual emergence and cocirculation of newly emerging CRFs and URFs, which are now responsible for almost 20% of HIV-1 infections worldwide. Better understanding of recombinants is necessary to determine their biological and molecular attributes.
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Affiliation(s)
- Katherine A Lau
- Retroviral Genetics Division, Centre for Virus Research, Westmead Millennium Institute , Westmead Hospital, The University of Sydney
| | - Justin J L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute , Royal Prince Alfred Hospital, The University of Sydney, Sydney, Australia
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Yang J, Grünewald S, Wan XF. Quartet-net: a quartet-based method to reconstruct phylogenetic networks. Mol Biol Evol 2013; 30:1206-17. [PMID: 23493256 DOI: 10.1093/molbev/mst040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic networks can model reticulate evolutionary events such as hybridization, recombination, and horizontal gene transfer. However, reconstructing such networks is not trivial. Popular character-based methods are computationally inefficient, whereas distance-based methods cannot guarantee reconstruction accuracy because pairwise genetic distances only reflect partial information about a reticulate phylogeny. To balance accuracy and computational efficiency, here we introduce a quartet-based method to construct a phylogenetic network from a multiple sequence alignment. Unlike distances that only reflect the relationship between a pair of taxa, quartets contain information on the relationships among four taxa; these quartets provide adequate capacity to infer a more accurate phylogenetic network. In applications to simulated and biological data sets, we demonstrate that this novel method is robust and effective in reconstructing reticulate evolutionary events and it has the potential to infer more accurate phylogenetic distances than other conventional phylogenetic network construction methods such as Neighbor-Joining, Neighbor-Net, and Split Decomposition. This method can be used in constructing phylogenetic networks from simple evolutionary events involving a few reticulate events to complex evolutionary histories involving a large number of reticulate events. A software called "Quartet-Net" is implemented and available at http://sysbio.cvm.msstate.edu/QuartetNet/.
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Affiliation(s)
- Jialiang Yang
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, USA
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Urbino C, Gutiérrez S, Antolik A, Bouazza N, Doumayrou J, Granier M, Martin DP, Peterschmitt M. Within-host dynamics of the emergence of Tomato yellow leaf curl virus recombinants. PLoS One 2013; 8:e58375. [PMID: 23472190 PMCID: PMC3589402 DOI: 10.1371/journal.pone.0058375] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 02/04/2013] [Indexed: 11/18/2022] Open
Abstract
Tomato yellow leaf curl virus (TYLCV) is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV) has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi), and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci. We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection–a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our results anticipate the outcomes of natural encounters between TYLCV and ToLCKMV.
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Smith SE, Showers-Corneli P, Dardenne CN, Harpending HH, Martin DP, Beiko RG. Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. PLoS One 2012; 7:e50070. [PMID: 23189179 PMCID: PMC3506542 DOI: 10.1371/journal.pone.0050070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 10/19/2012] [Indexed: 02/01/2023] Open
Abstract
The genus Mycobacterium encompasses over one hundred named species of environmental and pathogenic organisms, including the causative agents of devastating human diseases such as tuberculosis and leprosy. The success of these human pathogens is due in part to their ability to rapidly adapt to their changing environment and host. Recombination is the fastest way for bacterial genomes to acquire genetic material, but conflicting results about the extent of recombination in the genus Mycobacterium have been reported. We examined a data set comprising 18 distinct strains from 13 named species for evidence of recombination. Genomic regions common to all strains (accounting for 10% to 22% of the full genomes of all examined species) were aligned and concatenated in the chromosomal order of one mycobacterial reference species. The concatenated sequence was screened for evidence of recombination using a variety of statistical methods, with each proposed event evaluated by comparing maximum-likelihood phylogenies of the recombinant section with the non-recombinant portion of the dataset. Incongruent phylogenies were identified by comparing the site-wise log-likelihoods of each tree using multiple tests. We also used a phylogenomic approach to identify genes that may have been acquired through horizontal transfer from non-mycobacterial sources. The most frequent associated lineages (and potential gene transfer partners) in the Mycobacterium lineage-restricted gene trees are other members of suborder Corynebacterinae, but more-distant partners were identified as well. In two examined cases of potentially frequent and habitat-directed transfer (M. abscessus to Segniliparus and M. smegmatis to Streptomyces), observed sequence distances were small and consistent with a hypothesis of transfer, while in a third case (M. vanbaalenii to Streptomyces) distances were larger. The analyses described here indicate that whereas evidence of recombination in core regions within the genus is relatively sparse, the acquisition of genes from non-mycobacterial lineages is a significant feature of mycobacterial evolution.
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Affiliation(s)
- Silvia E. Smith
- School of Medicine, Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, United States of America
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | | | - Caitlin N. Dardenne
- School of Medicine, Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, United States of America
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Henry H. Harpending
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
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Balakirev ES, Krupnova TN, Ayala FJ. DNA variation in the phenotypically-diverse brown alga Saccharina japonica. BMC PLANT BIOLOGY 2012; 12:108. [PMID: 22784095 PMCID: PMC3490969 DOI: 10.1186/1471-2229-12-108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 06/21/2012] [Indexed: 05/17/2023]
Abstract
BACKGROUND Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the "longipes" (LON) and "shallow-water" (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica. RESULTS The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI "barcoding" region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events. CONCLUSION Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA
- A. V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch of the Russian Academy of Science, Vladivostok, 690059, Russia
| | - Tatiana N Krupnova
- Pacific Research Fisheries Centre (TINRO-Centre), Vladivostok, 690600, Russia
| | - Francisco J Ayala
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA
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Affiliation(s)
- Miguel Arenas
- Computational and Molecular Population Genetics Lab-CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
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40
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Hemelaar J. The origin and diversity of the HIV-1 pandemic. Trends Mol Med 2012; 18:182-92. [PMID: 22240486 DOI: 10.1016/j.molmed.2011.12.001] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/24/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
Abstract
This review examines the enormous progress that has been made in the past decade in understanding the origin of HIV, HIV genetic variability, and the impact of global HIV diversity on the pandemic. Multiple zoonotic transmissions of simian immunodeficiency virus (SIV) have resulted in different HIV lineages in humans. In addition, the high mutation and recombination rates during viral replication result in a great genetic variability of HIV within individuals, as well as within populations, upon which evolutionary selection pressures act. The global HIV pandemic is examined in the context of HIV evolution, and the global diversity of HIV subtypes and recombinants is discussed in detail. Finally, the impact of HIV diversity on pathogenesis, transmission, diagnosis, treatment, the immune response, and vaccine development is reviewed.
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Affiliation(s)
- Joris Hemelaar
- Nuffield Department of Obstetrics and Gynaecology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
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van der Sanden S, van Eek J, Martin DP, van der Avoort H, Vennema H, Koopmans M. Detection of recombination breakpoints in the genomes of human enterovirus 71 strains isolated in the Netherlands in epidemic and non-epidemic years, 1963–2010. INFECTION GENETICS AND EVOLUTION 2011; 11:886-94. [DOI: 10.1016/j.meegid.2011.02.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 02/10/2011] [Accepted: 02/14/2011] [Indexed: 11/25/2022]
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Abstract
Throughout the living world, genetic recombination and nucleotide substitution are the primary processes that create the genetic variation upon which natural selection acts. Just as analyses of substitution patterns can reveal a great deal about evolution, so too can analyses of recombination. Evidence of genetic recombination within the genomes of apparently asexual species can equate with evidence of cryptic sexuality. In sexually reproducing species, nonrandom patterns of sequence exchange can provide direct evidence of population subdivisions that prevent certain individuals from mating. Although an interesting topic in its own right, an important reason for analysing recombination is to account for its potentially disruptive influences on various phylogenetic-based molecular evolution analyses. Specifically, the evolutionary histories of recombinant sequences cannot be accurately described by standard bifurcating phylogenetic trees. Taking recombination into account can therefore be pivotal to the success of selection, molecular clock and various other analyses that require adequate modelling of shared ancestry and draw increased power from accurately inferred phylogenetic trees. Here, we review various computational approaches to studying recombination and provide guidelines both on how to gain insights into this important evolutionary process and on how it can be properly accounted for during molecular evolution studies.
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Affiliation(s)
- Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Martin DP, Briddon RW, Varsani A. Recombination patterns in dicot-infecting mastreviruses mirror those found in monocot-infecting mastreviruses. Arch Virol 2011; 156:1463-9. [PMID: 21484422 DOI: 10.1007/s00705-011-0994-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 03/28/2011] [Indexed: 11/28/2022]
Abstract
Recombination has profoundly shaped the evolution of viruses in the family Geminiviridae and has been studied extensively in the two best characterised geminivirus lineages: the dicotyledonous plant infecting begomoviruses and the monocotyledonous plant infecting mastreviruses. Here, we demonstrate that the sizes and distributions of recombination events detectable within the members of a third major geminivirus lineage--the dicotyledonous plant infecting mastreviruses--are very similar to those of the monocot-infecting mastreviruses. This suggests that, despite host range differences, very similar biochemical, ecological and evolutionary factors must underlie recombination patterns in the dicot- and monocot-infecting mastreviruses.
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Affiliation(s)
- Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
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Novitsky V, Wang R, Margolin L, Baca J, Rossenkhan R, Moyo S, van Widenfelt E, Essex M. Transmission of single and multiple viral variants in primary HIV-1 subtype C infection. PLoS One 2011; 6:e16714. [PMID: 21415914 PMCID: PMC3048432 DOI: 10.1371/journal.pone.0016714] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 12/23/2010] [Indexed: 01/11/2023] Open
Abstract
To address whether sequences of viral gag and env quasispecies collected during the early post-acute period can be utilized to determine multiplicity of transmitted HIV's, recently developed approaches for analysis of viral evolution in acute HIV-1 infection [1], [2] were applied. Specifically, phylogenetic reconstruction, inter- and intra-patient distribution of maximum and mean genetic distances, analysis of Poisson fitness, shape of highlighter plots, recombination analysis, and estimation of time to the most recent common ancestor (tMRCA) were utilized for resolving multiplicity of HIV-1 transmission in a set of viral quasispecies collected within 50 days post-seroconversion (p/s) in 25 HIV-infected individuals with estimated time of seroconversion. The decision on multiplicity of HIV infection was made based on the model's fit with, or failure to explain, the observed extent of viral sequence heterogeneity. The initial analysis was based on phylogeny, inter-patient distribution of maximum and mean distances, and Poisson fitness, and was able to resolve multiplicity of HIV transmission in 20 of 25 (80%) cases. Additional analysis involved distribution of individual viral distances, highlighter plots, recombination analysis, and estimation of tMRCA, and resolved 4 of the 5 remaining cases. Overall, transmission of a single viral variant was identified in 16 of 25 (64%) cases, and transmission of multiple variants was evident in 8 of 25 (32%) cases. In one case multiplicity of HIV-1 transmission could not be determined. In primary HIV-1 subtype C infection, samples collected within 50 days p/s and analyzed by a single-genome amplification/sequencing technique can provide reliable identification of transmission multiplicity in 24 of 25 (96%) cases. Observed transmission frequency of a single viral variant and multiple viral variants were within the ranges of 64% to 68%, and 32% to 36%, respectively.
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Affiliation(s)
- Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health AIDS Initiative, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Botswana–Harvard AIDS Institute, Gaborone, Botswana
| | - Rui Wang
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Lauren Margolin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health AIDS Initiative, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Jeannie Baca
- Department of Immunology and Infectious Diseases, Harvard School of Public Health AIDS Initiative, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | | | | | | | - M. Essex
- Department of Immunology and Infectious Diseases, Harvard School of Public Health AIDS Initiative, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Botswana–Harvard AIDS Institute, Gaborone, Botswana
- * E-mail:
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Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010; 26:2462-3. [PMID: 20798170 PMCID: PMC2944210 DOI: 10.1093/bioinformatics/btq467] [Citation(s) in RCA: 1283] [Impact Index Per Article: 91.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Summary: RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments. Among other novelties, this version includes four new recombination analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), new tests for recombination hot-spots, a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction. Complementary to a high degree of analysis flow automation, RDP3 also has a highly interactive and detailed graphical user interface that enables more focused hands-on cross-checking of results with a wide variety of newly implemented phylogenetic tree construction and matrix-based recombination signal visualization methods. The new RDP3 can accommodate large datasets and is capable of analyzing alignments ranging in size from 1000×10 kilobase sequences to 20×2 megabase sequences within 48 h on a desktop PC. Availability: RDP3 is available for free from its web site http://darwin.uvigo.es/rdp/rdp.html Contact:darrenpatrickmartin@gmail.com Supplementary information: The RDP3 program manual contains detailed descriptions of the various methods it implements and a step-by-step guide describing how best to use these.
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Affiliation(s)
- Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Centre for High Performance Computing, Rosebank, Cape Town, South Africa.
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Siebenga JJ, Lemey P, Kosakovsky Pond SL, Rambaut A, Vennema H, Koopmans M. Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. PLoS Pathog 2010; 6:e1000884. [PMID: 20463813 PMCID: PMC2865530 DOI: 10.1371/journal.ppat.1000884] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 03/30/2010] [Indexed: 12/16/2022] Open
Abstract
Noroviruses are the most common cause of viral gastroenteritis. An increase in the number of globally reported norovirus outbreaks was seen the past decade, especially for outbreaks caused by successive genogroup II genotype 4 (GII.4) variants. Whether this observed increase was due to an upswing in the number of infections, or to a surveillance artifact caused by heightened awareness and concomitant improved reporting, remained unclear. Therefore, we set out to study the population structure and changes thereof of GII.4 strains detected through systematic outbreak surveillance since the early 1990s. We collected 1383 partial polymerase and 194 full capsid GII.4 sequences. A Bayesian MCMC coalescent analysis revealed an increase in the number of GII.4 infections during the last decade. The GII.4 strains included in our analyses evolved at a rate of 4.3-9.0x10(-3) mutations per site per year, and share a most recent common ancestor in the early 1980s. Determinants of adaptation in the capsid protein were studied using different maximum likelihood approaches to identify sites subject to diversifying or directional selection and sites that co-evolved. While a number of the computationally determined adaptively evolving sites were on the surface of the capsid and possible subject to immune selection, we also detected sites that were subject to constrained or compensatory evolution due to secondary RNA structures, relevant in virus-replication. We highlight codons that may prove useful in identifying emerging novel variants, and, using these, indicate that the novel 2008 variant is more likely to cause a future epidemic than the 2007 variant. While norovirus infections are generally mild and self-limiting, more severe outcomes of infection frequently occur in elderly and immunocompromized people, and no treatment is available. The observed pattern of continually emerging novel variants of GII.4, causing elevated numbers of infections, is therefore a cause for concern.
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Affiliation(s)
- J Joukje Siebenga
- National Institute for Public Health and the Environment, RIVM, Bilthoven, The Netherlands.
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Bulla I, Schultz AK, Schreiber F, Zhang M, Leitner T, Korber B, Morgenstern B, Stanke M. HIV classification using the coalescent theory. ACTA ACUST UNITED AC 2010; 26:1409-15. [PMID: 20400454 DOI: 10.1093/bioinformatics/btq159] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those of HIV, since in HIV recombinants with multiple cross-over points between the parental strains frequently arise. Hence, ambiguous cases in the classification of HIV sequences into subtypes and circulating recombinant forms (CRFs) have been treated with ad hoc methods in lack of tools based on a comprehensive coalescent model accounting for complex recombination patterns. RESULTS We developed the program ARGUS that scores classifications of sequences into subtypes and recombinant forms. It reconstructs ancestral recombination graphs (ARGs) that reflect the genealogy of the input sequences given a classification hypothesis. An ARG with maximal probability is approximated using a Markov chain Monte Carlo approach. ARGUS was able to distinguish the correct classification with a low error rate from plausible alternative classifications in simulation studies with realistic parameters. We applied our algorithm to decide between two recently debated alternatives in the classification of CRF02 of HIV-1 and find that CRF02 is indeed a recombinant of Subtypes A and G. AVAILABILITY ARGUS is implemented in C++ and the source code is available at http://gobics.de/software.
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Affiliation(s)
- Ingo Bulla
- Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
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Varsani A, Monjane AL, Donaldson L, Oluwafemi S, Zinga I, Komba EK, Plakoutene D, Mandakombo N, Mboukoulida J, Semballa S, Briddon RW, Markham PG, Lett JM, Lefeuvre P, Rybicki EP, Martin DP. Comparative analysis of Panicum streak virus and Maize streak virus diversity, recombination patterns and phylogeography. Virol J 2009; 6:194. [PMID: 19903330 PMCID: PMC2777162 DOI: 10.1186/1743-422x-6-194] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 11/10/2009] [Indexed: 11/10/2022] Open
Abstract
Background Panicum streak virus (PanSV; Family Geminiviridae; Genus Mastrevirus) is a close relative of Maize streak virus (MSV), the most serious viral threat to maize production in Africa. PanSV and MSV have the same leafhopper vector species, largely overlapping natural host ranges and similar geographical distributions across Africa and its associated Indian Ocean Islands. Unlike MSV, however, PanSV has no known economic relevance. Results Here we report on 16 new PanSV full genome sequences sampled throughout Africa and use these together with others in public databases to reveal that PanSV and MSV populations in general share very similar patterns of genetic exchange and geographically structured diversity. A potentially important difference between the species, however, is that the movement of MSV strains throughout Africa is apparently less constrained than that of PanSV strains. Interestingly the MSV-A strain which causes maize streak disease is apparently the most mobile of all the PanSV and MSV strains investigated. Conclusion We therefore hypothesize that the generally increased mobility of MSV relative to other closely related species such as PanSV, may have been an important evolutionary step in the eventual emergence of MSV-A as a serious agricultural pathogen. The GenBank accession numbers for the sequences reported in this paper are GQ415386-GQ415401
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Affiliation(s)
- Arvind Varsani
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa
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Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W. Prokaryotic evolution and the tree of life are two different things. Biol Direct 2009; 4:34. [PMID: 19788731 PMCID: PMC2761302 DOI: 10.1186/1745-6150-4-34] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 09/29/2009] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution. RESULTS It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes. CONCLUSION Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution. REVIEWERS This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier.
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