1
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Christensen KT, Pierard F, Bonsall D, Bowden R, Barnes E, Florence E, Ansari MA, Nguyen D, de Cesare M, Nevens F, Robaeys G, Schrooten Y, Busschots D, Simmonds P, Vandamme AM, Van Wijngaerden E, Dierckx T, Cuypers L, Van Laethem K. Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes. Viruses 2023; 15:2391. [PMID: 38140632 PMCID: PMC10747466 DOI: 10.3390/v15122391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 12/24/2023] Open
Abstract
The hepatitis C virus (HCV) epidemic in Western countries is primarily perpetuated by the sub-populations of men who have sex with men (MSM) and people who inject drugs (PWID). Understanding the dynamics of transmission in these communities is crucial for removing the remaining hurdles towards HCV elimination. We sequenced 269 annotated HCV plasma samples using probe enrichment and next-generation sequencing, obtaining 224 open reading frames of HCV (OR497849-OR498072). Maximum likelihood phylogenies were generated on the four most prevalent subtypes in this study (HCV1a, 1b, 3a, 4d) with a subsequent transmission cluster analysis. The highest rate of clustering was observed for HCV4d samples (13/17 (76.47%)). The second highest rate of clustering was observed in HCV1a samples (42/78 (53.85%)) with significant association with HIV-positive MSM. HCV1b and HCV3a had very low rates of clustering (2/83 (2.41%) and (0/29)). The spread of the prevalent subtype HCV1b appears to have been largely curtailed, and we demonstrate the onwards transmission of HCV1a and HCV4d in the HIV-positive MSM population across municipal borders. More systematic data collection and sequencing is needed to allow a better understanding of the HCV transmission among the community of PWID and overcome the remaining barriers for HCV elimination in Belgium.
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Affiliation(s)
- Kasper T. Christensen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
| | - Florian Pierard
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK;
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (R.B.); (D.N.); (M.d.C.)
| | - Rory Bowden
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (R.B.); (D.N.); (M.d.C.)
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK;
- Translational Gastroenterology Unit, University of Oxford, Oxford OX3 9DU, UK
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Eric Florence
- Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, 2650 Edegem, Belgium;
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - M. Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK;
| | - Dung Nguyen
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (R.B.); (D.N.); (M.d.C.)
| | - Mariateresa de Cesare
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (R.B.); (D.N.); (M.d.C.)
| | - Frederik Nevens
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium; (F.N.); (G.R.)
| | - Geert Robaeys
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium; (F.N.); (G.R.)
- Faculty of Medicine and Life Sciences—LCRC, UHasselt, Agoralaan, 3590 Diepenbeek, Belgium;
- Department of Gastroenterology and Hepatology, Ziekenhuis Oost-Limburg, 3600 Genk, Belgium
| | - Yoeri Schrooten
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
- Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Dana Busschots
- Faculty of Medicine and Life Sciences—LCRC, UHasselt, Agoralaan, 3590 Diepenbeek, Belgium;
- Department of Gastroenterology and Hepatology, Ziekenhuis Oost-Limburg, 3600 Genk, Belgium
| | - Peter Simmonds
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK;
| | - Anne-Mieke Vandamme
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Eric Van Wijngaerden
- Department of General Internal Medicine, University Hospitals Leuven, 3000 Leuven, Belgium;
| | - Tim Dierckx
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
| | - Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
- Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Kristel Van Laethem
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
- Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
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2
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King S, Baron MD, Kidane M, Aklilu F, Kapur V, Herzog CM, Batten C. Complete genome of a 2014 isolate of peste des petits ruminants virus from Ethiopia. Microbiol Resour Announc 2023; 12:e0024223. [PMID: 37462384 PMCID: PMC10508127 DOI: 10.1128/mra.00242-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/01/2023] [Indexed: 09/20/2023] Open
Abstract
This report describes the complete genome sequence of a peste des petits ruminants virus (PPRV) isolate from Ethiopia in 2014. The strain (PPRV/Ethiopia/Habru/2014), which showed a normal virulence and relatively low morbidity in the field, belongs to the North African subclade of Lineage IV.
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Affiliation(s)
- Simon King
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | | | | | | | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Catherine M. Herzog
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carrie Batten
- The Pirbright Institute, Woking, Surrey, United Kingdom
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3
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Calvelage S, Freuling CM, Fooks AR, Höper D, Marston DA, McElhinney L, Rasmussen TB, Finke S, Beer M, Müller T. Full-Genome Sequences and Phylogenetic Analysis of Archived Danish European Bat Lyssavirus 1 (EBLV-1) Emphasize a Higher Genetic Resolution and Spatial Segregation for Sublineage 1a. Viruses 2021; 13:634. [PMID: 33917139 DOI: 10.3390/v13040634] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/25/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
European bat lyssavirus type 1 (EBLV-1) is the causative agent for almost all reported rabies cases found in European bats. In recent years, increasing numbers of available EBLV-1 full genomes and their phylogenetic analyses helped to further elucidate the distribution and genetic characteristics of EBLV-1 and its two subtypes, namely EBLV-1a and EBLV-1b. Nonetheless, the absence of full-genome sequences from regions with known detections of EBLV-1 still limit the understanding of the phylogeographic relations between viruses from different European regions. In this study, a set of 21 archived Danish EBLV-1 samples from the years 1985 to 2009 was processed for the acquisition of full-genome sequences using a high-throughput sequencing approach. Subsequent phylogenetic analysis encompassing all available EBLV-1 full genomes from databases revealed the Danish sequences belong to the EBLV-1a subtype and further highlighted the distinct, close phylogenetic relationship of Danish, Dutch and German isolates in this region. In addition, the formation of five putative groups nearly exclusively formed by Danish isolates and the overall increased resolution of the EBLV-1a branch indicate a higher genetic diversity and spatial segregation for this sublineage than was previously known. These results emphasize the importance of phylogenetic analyses of full-genome sequences of lyssaviruses for genetic geography.
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4
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Abd El Rahman S, Hoffmann B, Karam R, El-Beskawy M, Hamed MF, Forth LF, Höper D, Eschbaumer M. Sequence Analysis of Egyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus. Viruses 2020; 12:E990. [PMID: 32899903 DOI: 10.3390/v12090990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/29/2020] [Accepted: 09/02/2020] [Indexed: 01/24/2023] Open
Abstract
In spite of annual mass vaccination programs with polyvalent inactivated vaccines, the incidence and economic impact of foot-and-mouth disease (FMD) in Egypt is high. Viruses of the A, O and SAT 2 serotypes are endemic and repeated incursions of new lineages from other countries lead to an unstable situation that makes the selection of appropriate vaccine antigens very difficult. In this study, whole genome sequencing of a 2016 serotype A isolate from Egypt revealed a recombination event with an African serotype O virus. Based on available vaccine matching data, none of the vaccines currently used in Egypt are expected to sufficiently protect against this virus or other viruses of this lineage (A/AFRICA/G-IV) circulating there since 2012. In addition to the risk of vaccine failure caused by strain mismatch, the production of inactivated FMD vaccines is dangerous if adequate biosafety cannot be maintained. Using a high-throughput sequencing protocol optimized for short nucleic acid fragments, the composition of a local inactivated vaccine was analyzed in depth. The serotype O strain identified in the vaccine was genetically identical to viruses found in recent FMD outbreaks in Egypt.
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5
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Magiorkinis G, Matthews PC, Wallace SE, Jeffery K, Dunbar K, Tedder R, Mbisa JL, Hannigan B, Vayena E, Simmonds P, Brewer DS, Gihawi A, Rallapalli G, Lahnstein L, Fowler T, Patch C, Maleady-Crowe F, Lucassen A, Cooper C. Potential for diagnosis of infectious disease from the 100,000 Genomes Project Metagenomic Dataset: Recommendations for reporting results. Wellcome Open Res 2019; 4:155. [PMID: 32055707 PMCID: PMC6993825 DOI: 10.12688/wellcomeopenres.15499.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/30/2022] Open
Abstract
The identification of microbiological infection is usually a diagnostic investigation, a complex process that is firstly initiated by clinical suspicion. With the emergence of high-throughput sequencing (HTS) technologies, metagenomic analysis has unveiled the power to identify microbial DNA/RNA from a diverse range of clinical samples (1). Metagenomic analysis of whole human genomes at the clinical/research interface bypasses the steps of clinical scrutiny and targeted testing and has the potential to generate unexpected findings relating to infectious and sometimes transmissible disease. There is no doubt that microbial findings that may have a significant impact on a patient’s treatment and their close contacts should be reported to those with clinical responsibility for the sample-donating patient. There are no clear recommendations on how such findings that are incidental, or outside the original investigation, should be handled. Here we aim to provide an informed protocol for the management of incidental microbial findings as part of the 100,000 Genomes Project
which may have broader application in this emerging field. As with any other clinical information, we aim to prioritise the reporting of data that are most likely to be of benefit to the patient and their close contacts. We also set out to minimize risks, costs and potential anxiety associated with the reporting of results that are unlikely to be of clinical significance. Our recommendations aim to support the practice of microbial metagenomics by providing a simplified pathway that can be applied to reporting the identification of potential pathogens from metagenomic datasets. Given that the ambition for UK sequenced human genomes over the next 5 years has been set to reach 5 million and the field of metagenomics is rapidly evolving, the guidance will be regularly reviewed and will likely adapt over time as experience develops.
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Affiliation(s)
- Gkikas Magiorkinis
- Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - Philippa C Matthews
- University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | | | - Katie Jeffery
- University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | | | | | | | - Effy Vayena
- Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | | | - Daniel S Brewer
- University of East Anglia, Norwich, UK.,Earlham Institute, Norwich, UK
| | | | | | | | | | | | | | - Anneke Lucassen
- Faculty of Medicine, University of Southampton, Southampton, UK
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6
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Lasecka-Dykes L, Wright CF, Di Nardo A, Logan G, Mioulet V, Jackson T, Tuthill TJ, Knowles NJ, King DP. Full Genome Sequencing Reveals New Southern African Territories Genotypes Bringing Us Closer to Understanding True Variability of Foot-and-Mouth Disease Virus in Africa. Viruses 2018; 10:E192. [PMID: 29652800 PMCID: PMC5923486 DOI: 10.3390/v10040192] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/06/2018] [Accepted: 04/08/2018] [Indexed: 01/09/2023] Open
Abstract
Foot-and-mouth disease virus (FMDV) causes a highly contagious disease of cloven-hooved animals that poses a constant burden on farmers in endemic regions and threatens the livestock industries in disease-free countries. Despite the increased number of publicly available whole genome sequences, FMDV data are biased by the opportunistic nature of sampling. Since whole genomic sequences of Southern African Territories (SAT) are particularly underrepresented, this study sequenced 34 isolates from eastern and southern Africa. Phylogenetic analyses revealed two novel genotypes (that comprised 8/34 of these SAT isolates) which contained unusual 5′ untranslated and non-structural encoding regions. While recombination has occurred between these sequences, phylogeny violation analyses indicated that the high degree of sequence diversity for the novel SAT genotypes has not solely arisen from recombination events. Based on estimates of the timing of ancestral divergence, these data are interpreted as being representative of un-sampled FMDV isolates that have been subjected to geographical isolation within Africa by the effects of the Great African Rinderpest Pandemic (1887–1897), which caused a mass die-out of FMDV-susceptible hosts. These findings demonstrate that further sequencing of African FMDV isolates is likely to reveal more unusual genotypes and will allow for better understanding of natural variability and evolution of FMDV.
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Affiliation(s)
| | - Caroline F Wright
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| | - Antonello Di Nardo
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| | - Grace Logan
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| | - Valerie Mioulet
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| | - Terry Jackson
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| | - Tobias J Tuthill
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
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7
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Agoti CN, Munywoki PK, Phan MVT, Otieno JR, Kamau E, Bett A, Kombe I, Githinji G, Medley GF, Cane PA, Kellam P, Cotten M, Nokes DJ. Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis. Virus Evol 2017; 3:vex006. [PMID: 28458916 PMCID: PMC5399923 DOI: 10.1093/ve/vex006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Detailed information on the source, spread and evolution of respiratory syncytial virus (RSV) during seasonal community outbreaks remains sparse. Molecular analyses of attachment (G) gene sequences from hospitalized cases suggest that multiple genotypes and variants co-circulate during epidemics and that RSV persistence over successive seasons is characterized by replacement and multiple new introductions of variants. No studies have defined the patterns of introduction, spread and evolution of RSV at the local community and household level. We present a whole genome sequence analysis of 131 RSV group A viruses collected during 6-month household-based RSV infection surveillance in Coastal Kenya, 2010 within an area of 12 km2. RSV infections were identified by regular symptom-independent screening of all household members twice weekly. Phylogenetic analysis revealed that the RSV A viruses in nine households were closely related to genotype GA2 and fell within a single branch of the global phylogeny. Genomic analysis allowed the detection of household-specific variation in seven households. For comparison, using only G gene analysis, household-specific variation was found only in one of the nine households. Nucleotide changes were observed both intra-host (viruses identified from same individual in follow-up sampling) and inter-host (viruses identified from different household members) and these coupled with sampling dates enabled a partial reconstruction of the within household transmission chains. The genomic evolutionary rate for the household dataset was estimated as 2.307 × 10 − 3 (95% highest posterior density: 0.935–4.165× 10 − 3) substitutions/site/year. We conclude that (i) at the household level, most RSV infections arise from the introduction of a single virus variant followed by accumulation of household specific variation and (ii) analysis of complete virus genomes is crucial to better understand viral transmission in the community. A key question arising is whether prevention of RSV introduction or spread within the household by vaccinating key transmitting household members would lead to a reduced onward community-wide transmission.
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Affiliation(s)
- Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Collaborative Programme, Kilifi, Kenya.,School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Collaborative Programme, Kilifi, Kenya.,School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - My V T Phan
- The Wellcome Trust Sanger Institute, Cambridge, UK.,Virosciences Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - James R Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Collaborative Programme, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Collaborative Programme, Kilifi, Kenya
| | - Anne Bett
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Collaborative Programme, Kilifi, Kenya
| | - Ivy Kombe
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Collaborative Programme, Kilifi, Kenya
| | - George Githinji
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Collaborative Programme, Kilifi, Kenya
| | - Graham F Medley
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, UK
| | - Patricia A Cane
- Virus Reference Department, Public Health England, London, UK
| | - Paul Kellam
- The Wellcome Trust Sanger Institute, Cambridge, UK.,Department of Infectious Diseases and Immunity, Imperial College London, London, UK
| | - Matthew Cotten
- The Wellcome Trust Sanger Institute, Cambridge, UK.,Virosciences Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Collaborative Programme, Kilifi, Kenya.,School of Life Sciences and WIDER, University of Warwick, Coventry, UK
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8
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Pavey SA, Laporte M, Normandeau E, Gaudin J, Letourneau L, Boisvert S, Corbeil J, Audet C, Bernatchez L. Draft genome of the American Eel (Anguilla rostrata). Mol Ecol Resour 2016; 17:806-811. [PMID: 27754597 DOI: 10.1111/1755-0998.12608] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 11/28/2022]
Abstract
Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American eel. This genome contained 305 043 contigs (N50 = 7397) and 79 209 scaffolds (N50 = 86 641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein-coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly and a total of 26 564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exhibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of freshwater eels.
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Affiliation(s)
- Scott A Pavey
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada.,Department of Biological Sciences and Canadian Rivers Institute, University of New Brunswick, Saint-John, NB, E2L 4L5, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
| | - Jérémy Gaudin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
| | - Louis Letourneau
- McGill University and Génome Québec Innovation Centre, Montréal, QC, H3A0G1, Canada
| | - Sébastien Boisvert
- Faculty of Medicine, CHUL Research Center, Université Laval, Québec, QC, G1V4G2, Canada
| | - Jacques Corbeil
- Faculty of Medicine, CHUL Research Center, Université Laval, Québec, QC, G1V4G2, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, Rimouski, Québec, G5L 3A1, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
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9
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Zhang QJ, Zhu T, Xia EH, Shi C, Liu YL, Zhang Y, Liu Y, Jiang WK, Zhao YJ, Mao SY, Zhang LP, Huang H, Jiao JY, Xu PZ, Yao QY, Zeng FC, Yang LL, Gao J, Tao DY, Wang YJ, Bennetzen JL, Gao LZ. Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc Natl Acad Sci U S A 2014; 111:E4954-62. [PMID: 25368197 DOI: 10.1073/pnas.1418307111] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.
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10
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Vandenbussche F, Sailleau C, Rosseel T, Desprat A, Viarouge C, Richardson J, Eschbaumer M, Hoffmann B, De Clercq K, Bréard E, Zientara S. Full-Genome Sequencing of Four Bluetongue Virus Serotype 11 Viruses. Transbound Emerg Dis 2013; 62:565-71. [PMID: 24750582 DOI: 10.1111/tbed.12178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Indexed: 11/29/2022]
Abstract
Recently, a contamination incident was described in which the challenge inoculum used in a bluetongue virus serotype 8 (BTV-8) vaccination trial was contaminated with a BTV-11 virus that was closely related to the Belgian BTV-11 virus from 2008. This study reports the first complete genome sequences of four BTV-11 viruses: the BTV-11 contaminant, BTV-11 reference strain, BTV-11 vaccine strain and a recently isolated BTV-11 field strain from Martinique. Full-genome analysis showed that these viruses belong to serotype 11/nucleotype A and cluster together with other western topotype bluetongue viruses. Detailed comparisons of the genomes further indicated that the contaminant was derived from the BTV-11 reference strain, as they were distinguished by a single synonymous nucleotide substitution. The previously reported partial sequence of genome segment 2 of the Belgian BTV-11 was found to be identical to that of the BTV-11 vaccine strain, indicating that it most likely was the BTV-11 vaccine strain. These findings also suggest that the BTV-11 contaminant and the Belgian BTV-11 are not the same viruses. Finally, comparison of the reference and vaccine strain did not allow determining the amino acid substitutions that contribute to the attenuated phenotype.
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Affiliation(s)
- F Vandenbussche
- Operational Directorate of Viral Diseases, Molecular Platform, Veterinary and Agrochemical Research Centre, Ukkel, Belgium
| | - C Sailleau
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - T Rosseel
- Operational Directorate of Viral Diseases, Molecular Platform, Veterinary and Agrochemical Research Centre, Ukkel, Belgium
| | - A Desprat
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - C Viarouge
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - J Richardson
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - M Eschbaumer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - B Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - K De Clercq
- Operational Directorate of Viral Diseases, Vesicular and Exotic Diseases, Veterinary and Agrochemical Research Centre, Ukkel, Belgium
| | - E Bréard
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
| | - S Zientara
- ANSES, LSA (Animal Health Laboratory) UMR 1161 ANSES/INRA/ENVA, Maisons-Alfort, France
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