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Zamorano A, Carevic P, Gamboa C, Cui W, Curkovic T, Córdova P, Higuera G, Ramos-Castillo L, Quiroga N, Fiore N. Old and New Aphid-Borne Viruses in Coriander in Chile: An Epidemiological Approach. Viruses 2024; 16:226. [PMID: 38400002 PMCID: PMC10893044 DOI: 10.3390/v16020226] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
In Chile, edible herbs are mainly grown by small farmers. This type of horticultural crop typically requires intensive management because it is highly susceptible to insects, some of which transmit viruses that severely affect crop yield and quality. In 2019, in coriander plants tested negative for all previously reported viruses, RNA-Seq analysis of one symptomatic plant revealed a plethora of viruses, including one virus known to infect coriander, five viruses never reported in coriander, and a new cytorhabdovirus with a 14,180 nucleotide RNA genome for which the species name Cytorhabdovirus coriandrum was proposed. Since all the detected viruses were aphid-borne, aphids and weeds commonly growing around the coriander field were screened for viruses. The results showed the occurrence of the same seven viruses and the alfalfa mosaic virus, another aphid-borne virus, in aphids and weeds. Together, our findings document the presence of multiple viruses in coriander and the potential role of weeds as virus reservoirs for aphid acquisition.
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Affiliation(s)
- Alan Zamorano
- Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (A.Z.); (P.C.); (C.G.); (W.C.); (T.C.); (L.R.-C.)
| | - Paulina Carevic
- Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (A.Z.); (P.C.); (C.G.); (W.C.); (T.C.); (L.R.-C.)
| | - Camila Gamboa
- Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (A.Z.); (P.C.); (C.G.); (W.C.); (T.C.); (L.R.-C.)
| | - Weier Cui
- Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (A.Z.); (P.C.); (C.G.); (W.C.); (T.C.); (L.R.-C.)
| | - Tomislav Curkovic
- Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (A.Z.); (P.C.); (C.G.); (W.C.); (T.C.); (L.R.-C.)
| | - Pamela Córdova
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Avenida El Líbano 5524, Santiago 7830490, Chile; (P.C.); (G.H.)
| | - Gastón Higuera
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Avenida El Líbano 5524, Santiago 7830490, Chile; (P.C.); (G.H.)
| | - Luz Ramos-Castillo
- Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (A.Z.); (P.C.); (C.G.); (W.C.); (T.C.); (L.R.-C.)
| | - Nicolás Quiroga
- Institute of Agri-Food, Animal and Environmental Sciences (ICA3), Universidad de O’Higgins, Campus Colchagua, San Fernando 3070000, Chile;
| | - Nicola Fiore
- Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (A.Z.); (P.C.); (C.G.); (W.C.); (T.C.); (L.R.-C.)
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Litov AG, Belova OA, Kholodilov IS, Kalyanova AS, Gadzhikurbanov MN, Rogova AA, Gmyl LV, Karganova GG. Viromes of Tabanids from Russia. Viruses 2023; 15:2368. [PMID: 38140608 PMCID: PMC10748123 DOI: 10.3390/v15122368] [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: 10/30/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Advances in sequencing technologies and bioinformatics have greatly enhanced our knowledge of virus biodiversity. Currently, the viromes of hematophagous invertebrates, such as mosquitoes and ixodid ticks, are being actively studied. Tabanidae (Diptera) are a widespread family, with members mostly known for their persistent hematophagous behavior. They transmit viral, bacterial, and other pathogens, both biologically and mechanically. However, tabanid viromes remain severely understudied. In this study, we used high-throughput sequencing to describe the viromes of several species in the Hybomitra, Tabanus, Chrysops, and Haematopota genera, which were collected in two distant parts of Russia: the Primorye Territory and Ryazan Region. We assembled fourteen full coding genomes of novel viruses, four partial coding genomes, as well as several fragmented viral sequences, which presumably belong to another twelve new viruses. All the discovered viruses were tested for their ability to replicate in mammalian porcine embryo kidney (PEK), tick HAE/CTVM8, and mosquito C6/36 cell lines. In total, 16 viruses were detected in at least one cell culture after three passages (for PEK and C6/36) or 3 weeks of persistence in HAE/CTVM8. However, in the majority of cases, qPCR showed a decline in virus load over time.
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Affiliation(s)
- Alexander G. Litov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Oxana A. Belova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Anna S. Kalyanova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Magomed N. Gadzhikurbanov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anastasia A. Rogova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Larissa V. Gmyl
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
- Institute for Translational Medicine and Biotechnology, Sechenov University, 119991 Moscow, Russia
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3
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Ramathani I, Sserumaga JP, Nanyiti S, Mukasa SB, Alicai T. Molecular Diversity of Rice Yellow Mottle Virus in Uganda and Relationships with Other Strains from Africa. Plant Dis 2023; 107:3475-3486. [PMID: 37133339 DOI: 10.1094/pdis-08-22-1989-re] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Rice yellow mottle virus disease, caused by Rice yellow mottle virus (RYMV), is the most important disease of lowland rice in Uganda. However, little is known about its genetic diversity in Uganda and relationships with other strains elsewhere across Africa. A new degenerate primer pair that targets amplification of the entire RYMV coat protein gene (circa 738 bp) was designed to aid virus variability analysis using RT-PCR and Sanger sequencing. A total of 112 rice leaf samples from plants with RYMV mottling symptoms were collected during the year 2022 in 35 lowland rice fields within Uganda. The RYMV RT-PCR results were 100% positive, and all 112 PCR products were sequenced. BLASTn analysis revealed that all isolates were closely related (93 to 98%) to those previously studied originating from Kenya, Tanzania, and Madagascar. Despite high purifying selection pressure, diversity analysis on 81 out of 112 RYMV CP sequences revealed a very low diversity index of 3 and 1.0% at the nucleotide and amino acid levels, respectively. Except for glutamine, amino acid profile analysis revealed that all 81 Ugandan isolates shared the primary 19 amino acids based on the RYMV coat protein region examined. Except for one isolate (UG68) from eastern Uganda that clustered alone, phylogeny analysis revealed two major clades. The Ugandan RYMV isolates were phylogenetically related to those from the Democratic Republic of Congo, Madagascar, and Malawi but not to RYMV isolates in West Africa. Thus, the RYMV isolates in this study are related to serotype 4, a strain common in eastern and southern Africa. RYMV serotype 4 originated in Tanzania, where evolutionary forces of mutation have resulted in the emergence and spread of new variants. Furthermore, mutations are evident within the coat protein gene of the Ugandan isolates, which may be attributed to changing RYMV pathosystems as a result of rice production intensification in Uganda. Overall, the diversity of RYMV was limited and most noticeably in eastern Uganda.
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Affiliation(s)
- Idd Ramathani
- National Crops Resources Research Institute (NaCRRI), National Agricultural Research Organisation, Kampala, Uganda
| | - Julius P Sserumaga
- National Livestock Resources Research Institute (NaLIRRI), National Agricultural Research Organisation, Kampala, Uganda
| | - Sarah Nanyiti
- National Crops Resources Research Institute (NaCRRI), National Agricultural Research Organisation, Kampala, Uganda
| | - Settumba B Mukasa
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Titus Alicai
- National Crops Resources Research Institute (NaCRRI), National Agricultural Research Organisation, Kampala, Uganda
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Puthanveed V, Singh K, Poimenopoulou E, Pettersson J, Siddique AB, Kvarnheden A. Milder Autumns May Increase Risk for Infection of Crops with Turnip Yellows Virus. Phytopathology 2023; 113:1788-1798. [PMID: 36802872 DOI: 10.1094/phyto-11-22-0446-v] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Climate change has increased the risk for infection of crops with insect-transmitted viruses. Mild autumns provide prolonged active periods to insects, which may spread viruses to winter crops. In autumn 2018, green peach aphids (Myzus persicae) were found in suction traps in southern Sweden that presented infection risk for winter oilseed rape (OSR; Brassica napus) with turnip yellows virus (TuYV). A survey was carried out in spring 2019 with random leaf samples from 46 OSR fields in southern and central Sweden using DAS-ELISA, and TuYV was detected in all fields except one. In the counties of Skåne, Kalmar, and Östergötland, the average incidence of TuYV-infected plants was 75%, and the incidence reached 100% for nine fields. Sequence analyses of the coat protein gene revealed a close relationship between TuYV isolates from Sweden and other parts of the world. High-throughput sequencing for one of the OSR samples confirmed the presence of TuYV and revealed coinfection with TuYV-associated RNA. Molecular analyses of seven sugar beet (Beta vulgaris) plants with yellowing, collected in 2019, revealed that two of them were infected by TuYV, together with two other poleroviruses: beet mild yellowing virus and beet chlorosis virus. The presence of TuYV in sugar beet suggests a spillover from other hosts. Poleroviruses are prone to recombination, and mixed infection with three poleroviruses in the same plant poses a risk for the emergence of new polerovirus genotypes. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Vinitha Puthanveed
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Khushwant Singh
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Division of Crop Protection and Plant Health, Crop Research Institute, Prague 161 06, Czech Republic
| | - Efstratia Poimenopoulou
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Josefin Pettersson
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Abu Bakar Siddique
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Anders Kvarnheden
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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Mahas JW, Mahas JB, Ray C, Kesheimer A, Steury TD, Conzemius SR, Crow W, Gore J, Greene JK, Kennedy GG, Kerns D, Malone S, Paula-Moraes S, Roberts P, Stewart SD, Taylor S, Toews M, Jacobson AL. The Spatiotemporal Distribution, Abundance, and Seasonal Dynamics of Cotton-Infesting Aphids in the Southern U.S. Insects 2023; 14:639. [PMID: 37504645 PMCID: PMC10380445 DOI: 10.3390/insects14070639] [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] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
Cotton leafroll dwarf virus (CLRDV) is an emerging aphid-borne pathogen infecting cotton, Gossypium hirsutum L., in the southern United States (U.S.). The cotton aphid, Aphis gossypii Glover, infests cotton annually and is the only known vector to transmit CLRDV to cotton. Seven other species have been reported to feed on, but not often infest, cotton: Protaphis middletonii Thomas, Aphis craccivora Koch, Aphis fabae Scopoli, Macrosiphum euphorbiae Thomas, Myzus persicae Sulzer, Rhopalosiphum rufiabdominale Sasaki, and Smynthurodes betae Westwood. These seven have not been studied in cotton, but due to their potential epidemiological importance, an understanding of the intra- and inter-annual variations of these species is needed. In 2020 and 2021, aphids were monitored from North Carolina to Texas using pan traps around cotton fields. All of the species known to infest cotton, excluding A. fabae, were detected in this study. Protaphis middletonii and A. gossypii were the most abundant species identified. The five other species of aphids captured were consistently low throughout the study and, with the exception of R. rufiabdominale, were not detected at all locations. The abundance, distribution, and seasonal dynamics of cotton-infesting aphids across the southern U.S. are discussed.
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Affiliation(s)
- John W Mahas
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Jessica B Mahas
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Charles Ray
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Adam Kesheimer
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Todd D Steury
- College of Forestry, Wildlife and Environment, Auburn University, 602 Duncan Drive, Auburn, AL 36849, USA
| | - Sophia R Conzemius
- Edisto Research and Education Center, Department of Plant and Environmental Sciences, Clemson University, Blackville, SC 29817, USA
| | - Whitney Crow
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS 39762, USA
| | - Jeffrey Gore
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS 39762, USA
| | - Jeremy K Greene
- Edisto Research and Education Center, Department of Plant and Environmental Sciences, Clemson University, Blackville, SC 29817, USA
| | - George G Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, 3210 Ligon St., Raleigh, NC 27695, USA
| | - David Kerns
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Sean Malone
- Virginia Tech, Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437, USA
| | - Silvana Paula-Moraes
- West Florida Research and Education Center, Department of Entomology and Nematology, University of Florida, Jay, FL 32565, USA
| | - Phillip Roberts
- Department of Entomology, University of Georgia, 2360 Rainwater Rd., Tifton, GA 31793, USA
| | - Scott D Stewart
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sally Taylor
- Virginia Tech, Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437, USA
| | - Michael Toews
- Department of Entomology, University of Georgia, 2360 Rainwater Rd., Tifton, GA 31793, USA
| | - Alana L Jacobson
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
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Omiat EG, Asante MD, Traoré VSE, Oppong A, Ifie BE, Ofosu KA, Aribi J, Pinel-Galzi A, Comte A, Fargette D, Hébrard E, Traoré O, Offei SK, Danquah EY, Poulicard N. Genetic diversity and epidemic histories of rice yellow mottle virus in Ghana. Virus Res 2023; 329:199106. [PMID: 36990396 DOI: 10.1016/j.virusres.2023.199106] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
Rice yellow mottle virus (RYMV) has persisted as a major biotic constraint to rice production in Africa. However, no data on RYMV epidemics were available in Ghana, although it is an intensive rice-producing country. Surveys were performed from 2010 to 2020 in eleven rice-growing regions of Ghana. Symptom observations and serological detections confirmed that RYMV is circulating in most of these regions. Coat protein gene and complete genome sequencings revealed that RYMV in Ghana almost exclusively belongs to the strain S2, one of the strains covering the largest area in West Africa. We also detected the presence of the S1ca strain which is being reported for the first time outside its area of origin. These results suggested a complex epidemiological history of RYMV in Ghana and a recent expansion of S1ca to West Africa. Phylogeographic analyses reconstructed at least five independent RYMV introductions in Ghana for the last 40 years, probably due to rice cultivation intensification in West Africa leading to a better circulation of RYMV. In addition to identifying some routes of RYMV dispersion in Ghana, this study contributes to the epidemiological surveillance of RYMV and helps to design disease management strategies, especially through breeding for rice disease resistance.
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Affiliation(s)
- Emmanuel Gilbert Omiat
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, PMB 30, Legon, Accra, Ghana; National Agricultural Research Organisation (NARO), Buginyanya Zonal Agricultural Research and Development Institute, P. O. Box 1356, Mbale, Uganda
| | - Maxwell Darko Asante
- Council for Scientific and Industrial Research - Crops Research Institute (CSIR- CRI), Fumesua, P. O. Box 3785, Kumasi, Ghana; Department of Plant Resources Development, CSIR College of Science and Technology, Fumesua, Kumasi, Ghana
| | | | - Allen Oppong
- Council for Scientific and Industrial Research - Crops Research Institute (CSIR- CRI), Fumesua, P. O. Box 3785, Kumasi, Ghana
| | - Beatrice Elohor Ifie
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, PMB 30, Legon, Accra, Ghana
| | - Kirpal Agyemang Ofosu
- Council for Scientific and Industrial Research - Crops Research Institute (CSIR- CRI), Fumesua, P. O. Box 3785, Kumasi, Ghana
| | - Jamel Aribi
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | - Agnès Pinel-Galzi
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | - Aurore Comte
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | - Denis Fargette
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | - Eugénie Hébrard
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | | | - Samuel Kwame Offei
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, PMB 30, Legon, Accra, Ghana
| | - Eric Yirenkyi Danquah
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, PMB 30, Legon, Accra, Ghana
| | - Nils Poulicard
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France.
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Tarazi R, Vaslin MFS. The Viral Threat in Cotton: How New and Emerging Technologies Accelerate Virus Identification and Virus Resistance Breeding. Front Plant Sci 2022; 13:851939. [PMID: 35449884 PMCID: PMC9016188 DOI: 10.3389/fpls.2022.851939] [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] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/07/2022] [Indexed: 05/12/2023]
Abstract
Cotton (Gossypium spp. L., Malvaceae) is the world's largest source of natural fibers. Virus outbreaks are fast and economically devasting regarding cotton. Identifying new viruses is challenging as virus symptoms usually mimic nutrient deficiency, insect damage, and auxin herbicide injury. Traditional viral identification methods are costly and time-consuming. Developing new resistant cotton lines to face viral threats has been slow until the recent use of molecular virology, genomics, new breeding techniques (NBT), remote sensing, and artificial intelligence (AI). This perspective article demonstrates rapid, sensitive, and cheap technologies to identify viral diseases and propose their use for virus resistance breeding.
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Affiliation(s)
- Roberto Tarazi
- Plant Molecular Virology Laboratory, Department of Virology, Microbiology Institute, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biotecnologia e Bioprocessos da UFRJ, Rio de Janeiro, Brazil
| | - Maite F. S. Vaslin
- Plant Molecular Virology Laboratory, Department of Virology, Microbiology Institute, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biotecnologia e Bioprocessos da UFRJ, Rio de Janeiro, Brazil
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8
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Kavalappara SR, Milner H, Riley DG, Bag S. First report of turnip yellows virus infecting cabbage (Brassica oleracea var. capitata) in the USA. Plant Dis 2022; 106:2273. [PMID: 35084946 DOI: 10.1094/pdis-10-21-2174-pdn] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
During the spring of 2021, cabbage (Brassica oleracea var. capitata) planted in the research farm at the University of Georgia, Tifton, exhibited leaf distortion, yellow and purple discoloration at the leaf margin of older leaves, and severe stunting. Symptoms were present on nearly 30% of the plants in the field. To identify the potential agents associated, leaf tissues from two symptomatic plants were sent for high throughput sequencing (HTS) of small RNA (sRNA; DNB sequencing, SE read 1x75bp) to Beijing Genomics Institute, China. From each sample, ~ 18 million raw reads were generated. The reads with poor quality and adapter sequences were removed using CLC Genomics Workbench 21.2 (Qiagen, Germantown, MD). Of the total reads, 2,093 and 3,889 reads aligned to the genome of turnip yellows virus (TuYV) in samples one and two, respectively. Reads of turnip mosaic virus (TuMV) were also detected (data not shown). Partial sequences of TuYV assembled from samples one and two showed 89.5% and 89.9% match and 86% and 93% coverage, respectively, with the genome of the type isolate of TuYV (NC_003743) from the United Kingdom. To confirm the presence of TuYV in the samples collected from the same location, specific primers were designed targeting the P0 region (FP- 5'ACAAAAGAAACCAG- GAGGGAATCC3'; RP-5'GCCTTTTCATACAAACATTTCGGTG3') and coat protein (CP) region (FP-5'GTTAATGAATACGGTCGTGGGTAG3'; RP-5'ATTCTGAAAGAACCAGCT- ATCGATG3') of the virus. Eight of 20 (40%) symptomatic samples were determined to be infected with TuYV based on the amplification of expected size products of the P0 (786 nt) and the CP gene (581 nt) in reverse transcription-PCR (RT-PCR). All samples were also tested for the presence of TuMV by RT-PCR as in Sanchez et al. (2003), but none tested positive despite being identified in HTS. Symptoms on samples from which eithervirus could not be detected indicates the involvement of other factors and would require further studies. The partial P0 and CP gene amplicons of TuYV from two samples each were Sanger sequenced bi-directionally at Genewiz (South Plainfield, NJ) and confirmed as TuYV using BLASTn. The partial CP gene sequences from two samples shared 98.7% nucleotide sequence identity with each other and 88.0% (OK349421) and 87.1% (OK349422) identity with the type isolate. The partial P0 gene sequences (OK349423 and OK349424) shared 99.6% nucleotide sequence identity with each other and 92.2% identity with the type isolate. TuYV, formerly known as beet western yellows virus (BWYV) (Mayo, 2002), genus Palerovirus, family Solemoviridae (Walker et al., 2021), is transmitted persistently by aphids (Stevens et al., 2008), and is distributed throughout temperate regions of the world (Kawakubo et al., 2021). TuYV has a wide host range, including brassica, vegetables and weeds (Stevens et al., 2008). However, losses have been reported primarily on canola (B. napus) in Australia (Jones, 2007) and Europe (Stevens et al., 2008). On cabbage, TuYV infections have been reported from China (Zhang et al., 2016), Serbia (Milošević et al., 2020) and the Philippines (Buxton-Kirk et al, 2020). TuYV (BWYV) has been found infecting shepherd's purse (Capsella bursa-pastoris) in California (Falk and Duffus, 1984), but there are no reports of the virus from any cultivated crops in the USA. To our knowledge, this is the first report of TuYV in cabbage in the USA. More studies are needed to understand its occurrence and impact on cabbage crops in Georgia as well as other regions in the USA.
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Affiliation(s)
- Saritha Raman Kavalappara
- University of Georgia College of Agricultural and Environmental Sciences, 96665, Department of Plant Pathology, Tifton, Georgia, United States;
| | - Hayley Milner
- University of Georgia College of Agricultural and Environmental Sciences, 96665, Department of Plant Pathology, Tifton, Georgia, United States;
| | - David G Riley
- University of Georgia College of Agricultural and Environmental Sciences - Tifton Campus, 117299, Department of Entomology, Tifton, Georgia, United States;
| | - Sudeep Bag
- University of Georgia College of Agricultural and Environmental Sciences - Tifton Campus, 117299, Department of Plant Pathology, Tifton, Georgia, United States;
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Abstract
The family Solemoviridae includes viruses with icosahedral particles (26–34 nm in diameter) assembled on T=3 symmetry with a 4–6 kb positive-sense, monopartite, polycistronic RNA genome. Transmission of members of the genera Sobemovirus and Polemovirus occurs via mechanical wounding, vegetative propagation, insect vectors or abiotically through soil; members of the genera Polerovirus and Enamovirus are transmitted by specific aphids. Most solemoviruses have a narrow host range. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Solemoviridae, which is available at ictv.global/report/solemoviridae.
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Affiliation(s)
- Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
| | - Denis Fargette
- IRD, Cirad, Université Montpellier, IPME, Montpellier 34394, France
| | - Eugénie Hébrard
- IRD, Cirad, Université Montpellier, IPME, Montpellier 34394, France
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
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Litov AG, Belova OA, Kholodilov IS, Gadzhikurbanov MN, Gmyl LV, Oorzhak ND, Saryglar AA, Ishmukhametov AA, Karganova GG. Possible Arbovirus Found in Virome of Melophagus ovinus. Viruses 2021; 13:2375. [PMID: 34960644 DOI: 10.3390/v13122375] [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: 11/10/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/22/2022] Open
Abstract
Members of the Lipopteninae subfamily are blood-sucking ectoparasites of mammals. The sheep ked (Melophagus ovinus) is a widely distributed ectoparasite of sheep. It can be found in most sheep-rearing areas and can cause skin irritation, restlessness, anemia, weight loss and skin injuries. Various bacteria and some viruses have been detected in M. ovinus; however, the virome of this ked has never been studied using modern approaches. Here, we study the virome of M. ovinus collected in the Republic of Tuva, Russia. In our research, we were able to assemble full genomes for five novel viruses, related to the Rhabdoviridae (Sigmavirus), Iflaviridae, Reoviridae and Solemoviridae families. Four viruses were found in all five of the studied pools, while one virus was found in two pools. Phylogenetically, all of the novel viruses clustered together with various recently described arthropod viruses. All the discovered viruses were tested on their ability to replicate in the mammalian porcine embryo kidney (PEK) cell line. Aksy-Durug Melophagus sigmavirus RNA was detected in the PEK cell line cultural supernate after the first, second and third passages. Such data imply that this virus might be able to replicate in mammalian cells, and thus, can be considered as a possible arbovirus.
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Ramos-Sobrinho R, Adegbola RO, Lawrence K, Schrimsher DW, Isakeit T, Alabi OJ, Brown JK. Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability. Viruses 2021; 13:2230. [PMID: 34835036 DOI: 10.3390/v13112230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 09/28/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022] Open
Abstract
Cotton leafroll dwarf virus (CLRDV) was first reported in the United States (US) in 2017 from cotton plants in Alabama (AL) and has become widespread in cotton-growing states of the southern US. To investigate the genomic variability among CLRDV isolates in the US, complete genomes of the virus were obtained from infected cotton plants displaying mild to severe symptoms from AL, Florida, and Texas. Eight CLRDV genomes were determined, ranging in size from 5865 to 5867 bp, and shared highest nucleotide identity with other CLRDV isolates in the US, at 95.9–98.7%. Open reading frame (ORF) 0, encoding the P0 silencing suppressor, was the most variable gene, sharing 88.5–99.6% and 81.2–89.3% amino acid similarity with CLRDV isolates reported in cotton growing states in the US and in Argentina and Brazil in South America, respectively. Based on Bayesian analysis, the complete CLRDV genomes from cotton in the US formed a monophyletic group comprising three relatively divergent sister clades, whereas CLRDV genotypes from South America clustered as closely related sister-groups, separate from US isolates, patterns reminiscent of phylogeographical structuring. The CLRDV isolates exhibited a complex pattern of recombination, with most breakpoints evident in ORFs 2 and 3, and ORF5. Despite extensive nucleotide diversity among all available CLRDV genomes, purifying selection (dN/dS < 1) was implicated as the primary selective force acting on viral protein evolution.
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