1
|
Verchot J, Herath V, Jordan R, Hammond J. Genetic Diversity among Rose Rosette Virus Isolates: A Roadmap towards Studies of Gene Function and Pathogenicity. Pathogens 2023; 12:pathogens12050707. [PMID: 37242377 DOI: 10.3390/pathogens12050707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/11/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The phylogenetic relationships of ninety-five rose rosette virus (RRV) isolates with full-length genomic sequences were analyzed. These isolates were recovered mostly from commercial roses that are vegetatively propagated rather than grown from seed. First, the genome segments were concatenated, and the maximum likelihood (ML) tree shows that the branches arrange independent of their geographic origination. There were six major groups of isolates, with 54 isolates in group 6 and distributed in two subgroups. An analysis of nucleotide diversity across the concatenated isolates showed lower genetic differences among RNAs encoding the core proteins required for encapsidation than the latter genome segments. Recombination breakpoints were identified near the junctions of several genome segments, suggesting that the genetic exchange of segments contributes to differences among isolates. The ML analysis of individual RNA segments revealed different relationship patterns among isolates, which supports the notion of genome reassortment. We tracked the branch positions of two newly sequenced isolates to highlight how genome segments relate to segments of other isolates. RNA6 has an interesting pattern of single-nucleotide mutations that appear to influence amino acid changes in the protein products derived from ORF6a and ORF6b. The P6a proteins were typically 61 residues, although three isolates encoded P6a proteins truncated to 29 residues, and four proteins extended 76-94 residues. Homologous P5 and P7 proteins appear to be evolving independently. These results suggest greater diversity among RRV isolates than previously recognized.
Collapse
Affiliation(s)
- Jeanmarie Verchot
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77845, USA
| | - Venura Herath
- Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Ramon Jordan
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - John Hammond
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| |
Collapse
|
2
|
Benfield CTO, Hill S, Shatar M, Shiilegdamba E, Damdinjav B, Fine A, Willett B, Kock R, Bataille A. Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates. Virus Evol 2021; 7:veab062. [PMID: 34754511 PMCID: PMC8570150 DOI: 10.1093/ve/veab062] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 01/06/2023] Open
Abstract
Peste des petits ruminants virus (PPRV) causes disease in domestic and wild ungulates, is the target of a Global Eradication Programme, and threatens biodiversity. Understanding the epidemiology and evolution of PPRV in wildlife is important but hampered by the paucity of wildlife-origin PPRV genomes. In this study, full PPRV genomes were generated from three Mongolian saiga antelope, one Siberian ibex, and one goitered gazelle from the 2016-2017 PPRV outbreak. Phylogenetic analysis showed that for Mongolian and Chinese PPRV since 2013, the wildlife and livestock-origin genomes were closely related and interspersed. There was strong phylogenetic support for a monophyletic group of PPRV from Mongolian wildlife and livestock, belonging to a clade of lineage IV PPRV from livestock and wildlife from China since 2013. Discrete diffusion analysis found strong support for PPRV spread into Mongolia from China, and phylogeographic analysis indicated Xinjiang Province as the most likely origin, although genomic surveillance for PPRV is poor and lack of sampling from other regions could bias this result. Times of most recent common ancestor (TMRCA) were June 2015 (95 per cent highest posterior density (HPD): August 2014 to March 2016) for all Mongolian PPRV genomes and May 2016 (95 per cent HPD: October 2015 to October 2016) for Mongolian wildlife-origin PPRV. This suggests that PPRV was circulating undetected in Mongolia for at least 6 months before the first reported outbreak in August 2016 and that wildlife were likely infected before livestock vaccination began in October 2016. Finally, genetic variation and positively selected sites were identified that might be related to PPRV emergence in Mongolian wildlife. This study is the first to sequence multiple PPRV genomes from a wildlife outbreak, across several host species. Additional full PPRV genomes and associated metadata from the livestock-wildlife interface are needed to enhance the power of molecular epidemiology, support PPRV eradication, and safeguard the health of the whole ungulate community.
Collapse
Affiliation(s)
- Camilla T O Benfield
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, AL9 7TA UK
| | - Sarah Hill
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, AL9 7TA UK
| | - Munkduuren Shatar
- Department of Veterinary Services of Dundgobi province, General Authority for Veterinary Services of Mongolia (GAVS), Mandalgobi, Dundgobi Province 4800 Mongolia
| | - Enkhtuvshin Shiilegdamba
- Wildlife Conservation Society, Mongolia Program, Post Office 20A, PO Box 21 Ulaanbaatar 14200, Mongolia
| | | | - Amanda Fine
- Health Program, Wildlife Conservation Society, Bronx, New York 10460, USA
| | - Brian Willett
- MRC-University of Glasgow Centre for Virus Research, Henry Wellcome Building, Garscube Glasgow, G61 1QH UK
| | - Richard Kock
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, AL9 7TA UK
| | | |
Collapse
|
3
|
King S, Rajko-Nenow P, Ropiak HM, Ribeca P, Batten C, Baron MD. Full genome sequencing of archived wild type and vaccine rinderpest virus isolates prior to their destruction. Sci Rep 2020; 10:6563. [PMID: 32300201 PMCID: PMC7162898 DOI: 10.1038/s41598-020-63707-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/11/2020] [Indexed: 02/06/2023] Open
Abstract
When rinderpest virus (RPV) was declared eradicated in 2011, the only remaining samples of this once much-feared livestock virus were those held in various laboratories. In order to allow the destruction of our institute's stocks of RPV while maintaining the ability to recover the various viruses if ever required, we have determined the full genome sequence of all our distinct samples of RPV, including 51 wild type viruses and examples of three different types of vaccine strain. Examination of the sequences of these virus isolates has shown that the African isolates form a single disparate clade, rather than two separate clades, which is more in accord with the known history of the virus in Africa. We have also identified two groups of goat-passaged viruses which have acquired an extra 6 bases in the long untranslated region between the M and F protein coding sequences, and shown that, for more than half the genomes sequenced, translation of the F protein requires translational frameshift or non-standard translation initiation. Curiously, the clade containing the lapinised vaccine viruses that were developed originally in Korea appears to be more similar to the known African viruses than to any other Asian viruses.
Collapse
Affiliation(s)
- Simon King
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | | | | | - Paolo Ribeca
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
- Biomathematics and Statistics Scotland, JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK
| | - Carrie Batten
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | - Michael D Baron
- The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK.
| |
Collapse
|
4
|
Gil H, Fernández-García A, Mosquera MM, Hübschen JM, Castellanos AM, de Ory F, Masa-Calles J, Echevarría JE. Measles virus genotype D4 strains with non-standard length M-F non-coding region circulated during the major outbreaks of 2011-2012 in Spain. PLoS One 2018; 13:e0199975. [PMID: 30011283 PMCID: PMC6047782 DOI: 10.1371/journal.pone.0199975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/18/2018] [Indexed: 11/19/2022] Open
Abstract
In recent decades, vaccination has substantially reduced the number of measles cases to levels close to the elimination stage. However, major measles outbreaks occurred in Europe during 2010-2012, after the introduction of the D4-Enfield lineage. We have performed a molecular characterization of 75 measles virus genotype D4 strains from patients infected in Spain between 2004 and 2012 by sequencing the N-450 region and the M-F non-coding region (M-F NCR) in order to identify genetic features of these viruses. The analysis of the N-450 region confirmed that all samples obtained since 2008 belonged to variants or sets of identical sequences of the D4-Enfield lineage, including a new one named MVs/Madrid.ESP/46.10/. Analysis of the M-F NCR showed insertions and deletions associated with previously described, uncommon non-standard genome length measles viruses. This genetic feature was identified in the D4-Enfield lineage viruses, but not in the other D4 viruses that were circulating in Spain before 2008, suggesting that these non-standard length M-F NCR sequences are characteristic of the D4-Enfield lineage. The results of the phylogenetic analysis of Spanish M-F NCRs suggest higher resolution in discriminating strains than did the N-450 analysis. In addition, the results of the analysis of the M-F NCR on the MVs/Madrid.ESP/46.10/ sub-lineage seem to support the potential utility of this region as a tool for epidemiological surveillance complementary to the N-450 region, as previously suggested. Further investigation on this question, as well as the surveillance of new potentially emerging strains with non-standard length M-F NCR are strongly recommended as part of future strategies for measles elimination.
Collapse
Affiliation(s)
- Horacio Gil
- National Reference Laboratory for Measles and Rubella, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Aurora Fernández-García
- National Reference Laboratory for Measles and Rubella, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail:
| | - María Mar Mosquera
- National Reference Laboratory for Measles and Rubella, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Judith M. Hübschen
- WHO European Regional Reference Laboratory for Measles and Rubella, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Ana M. Castellanos
- National Reference Laboratory for Measles and Rubella, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando de Ory
- National Reference Laboratory for Measles and Rubella, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Josefa Masa-Calles
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan E. Echevarría
- National Reference Laboratory for Measles and Rubella, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| |
Collapse
|