Biodiversity and full genome sequence of potato viruses Alfalfa mosaic virus and potato leaf roll virus in Egypt

Abstract Solanum tuberosum (potato) is the second most important vegetable crop in Egypt. It is locally consumed, manufactured or supplied for export to Europe and other Arab countries. Potato is subject to infection by a number of plant viruses, which affect its yield and quality. Potato virus Y (PVY), potato leaf roll virus (PLRV), and Alfalfa mosaic virus (AMV) were detected in major potato-growing areas surveyed. Multiplex-RT-PCR assay was used for the detection of these three viruses in one reaction using three specific primer pairs designed to amplify genomic parts of each virus (1594 bp for PLRV, 795 bp for AMV, 801 bp for PVY). All three viruses were detected in a single reaction mixture in naturally infected field-grown potatoes. Multiplex RT-PCR improved sensitivity necessary for the early detection of infection. Incidence of single, double, or triple infection has been recorded in some locations. Full-length sequencing has been performed for an Egyptian FER isolate of PLRV. Through phylogenetic analysis, it was shown to occupy the same clade with isolate JokerMV10 from Germany. Complete nucleotide sequence of an Egyptian FER isolate of AMV and phylogenetic analysis was also performed; we propose that it is a new distinct strain of AMV belonging to a new subgroup IIC. This is the first complete nucleotide sequence of an Egyptian isolate of AMV. Genetic biodiversity of devastating potato viruses necessitates continuous monitoring of new genetic variants of such viruses.

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RT-PCR Based Cloning and Sequencing of Potato Leaf Roll Virus-Coat Protein (PLRV-CP) Gene for Characterization as a Bangladeshi PLRV Isolate and Its Phylogenetic Analysis

European Journal of Agriculture and Food Sciences ◽

10.24018/ejfood.2020.2.3.56 ◽

2020 ◽

Vol 2 (3) ◽

Author(s):

Md. Belal Hossain ◽

Tanjila Hasan ◽

Ibne Siam Joy ◽

Ratna Akter ◽

Saleh Ahmed Shahriar

Keyword(s):

Phylogenetic Analysis ◽

Coat Protein ◽

Leaf Roll ◽

Protein Modeling ◽

Potato Leaf Roll Virus ◽

Rt Pcr ◽

Potato Leaf ◽

Parsimony Method ◽

Total Rna ◽

Cp Gene

An experiment was conducted in Molecular Biology and Plant Virology Laboratory under the Department of Plant Pathology, Sher-e-Bangla Agricultural University, Dhaka-1207, Bangladesh. Total RNA was extracted from Potato leaf roll virus (PLRV) positive leaves and complementary DNA (cDNA) were synthesized from total RNA. Reverse transcriptase polymerase chain reaction (RT-PCR) based detection conditions were optimized by using coat protein (CP) gene specific primers. In PCR amplification cDNA and in nucleotide sequencing PCR product was used as a template. A 346 bp amplicon of PLRV- CP gene was amplified and amplified gene region was sequenced. The expected nucleotide sequence of amplified PLRV-CP gene showed 95 to 98% homology when compared with the isolates sequences reported in Gene Bank database. This explored novel PLRV-CP gene was characterized as a PLRV Bangladeshi isolate (Accession number, Bankit 2274496, MN605963). PLRV-CP gene protein modeling was carried out using Expert Protein Analysis System (ExPaSy), DNASTAR’s protein tools server used for 3D protein modeling. Phylogenetic analysis was also carried out, the tree was made by using MEGA 4.0 software and maximum parsimony method was selected to construct phylogenetic tree. The RT-PCR based molecular technique optimized in this study, would be a useful for early detection, epidemiological studies of PLRV as well as in seed tubers certification program and the novel hyper variable sequenced region of PLRV-CP gene will be useful in pathogen derived resistance breeding program against the PLRV local strain.

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Reducing the spread of potato leaf roll virus, alfalfa mosaic virus and potato virus Y in seed potatoes by trapping aphids on sticky yellow polyethylene sheets

Potato Research ◽

10.1007/bf02366942 ◽

1979 ◽

Vol 22 (2) ◽

pp. 123-131 ◽

Cited By ~ 11

Author(s):

Sara Zimmerman-Gries

Keyword(s):

Mosaic Virus ◽

Potato Virus ◽

Potato Virus Y ◽

Leaf Roll ◽

Alfalfa Mosaic Virus ◽

Potato Leaf Roll Virus ◽

Potato Leaf ◽

Seed Potatoes

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Identification, Characterization, and Molecular Detection of Alfalfa mosaic virus in Potato

Phytopathology ◽

10.1094/phyto-96-1237 ◽

2006 ◽

Vol 96 (11) ◽

pp. 1237-1242 ◽

Cited By ~ 34

Author(s):

H. Xu ◽

J. Nie

Keyword(s):

Mosaic Virus ◽

Gene Sequence ◽

Alfalfa Mosaic Virus ◽

Enzyme Linked Immunosorbent Assay ◽

Polymorphism Analysis ◽

Rt Pcr ◽

Potato Leaf ◽

Simple Method ◽

Cp Gene ◽

Nucleotide Sequence Alignment

Alfalfa mosaic virus (AMV) was detected in potato fields in several provinces in Canada and characterized by bioassay, enzyme-linked immunosorbent assay, and reverse-transcription polymerase chain reaction (RT-PCR). The identity of eight Canadian potato AMV isolates was confirmed by sequence analysis of their coat protein (CP) gene. Sequence and phylogenetic analysis indicated that these eight AMV potato isolates fell into one strain group, whereas a slight difference between Ca175 and the other Canadian AMV isolates was revealed. The Canadian AMV isolates, except Ca175, clustered together among other strains based on alignment of the CP gene sequence. To detect the virus, a pair of primers, AMV-F and AMV-R, specific to the AMV CP gene, was designed based on the nucleotide sequence alignment of known AMV strains. Evaluations showed that RT-PCR using this primer set was specific and sensitive for detecting AMV in potato leaf and tuber samples. AMV RNAs were easily detected in composite samples of 400 to 800 potato leaves or 200 to 400 tubers. Restriction analysis of PCR amplicons with SacI was a simple method for the confirmation of PCR tests. Thus, RT-PCR followed by restriction fragment length polymorphism analysis may be a useful approach for screening potato samples on a large scale for the presence of AMV.

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Preliminarly Survey Results and Phylogenetic Analysis for Tomato Yellow Leaf Curl Virus and Potato Leaf Roll Virus on Tomato Grown in Adana

International Journal of Agriculture Environment and Food Sciences ◽

10.31015/jaefs.2020.2.12 ◽

2020 ◽

Vol 4 (2) ◽

pp. 216-223

Author(s):

Gökmen KOÇ

Keyword(s):

Phylogenetic Analysis ◽

Leaf Roll ◽

Tomato Yellow Leaf ◽

Potato Leaf Roll Virus ◽

Yellow Leaf ◽

Potato Leaf ◽

Survey Results ◽

Leaf Curl Virus ◽

Leaf Curl

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Complete nucleotide sequence of RNA 3 from Alfalfa mosaic virus, strain S.

Biochimie ◽

10.1016/0300-9084(84)90023-3 ◽

1984 ◽

Vol 66 (5) ◽

pp. 395-402 ◽

Cited By ~ 13

Author(s):

Michel Ravelonandro ◽

Monique Pinck ◽

Lothaire Pinck

Keyword(s):

Nucleotide Sequence ◽

Mosaic Virus ◽

Virus Strain ◽

Complete Nucleotide Sequence ◽

Alfalfa Mosaic Virus

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Complete nucleotide sequence of a Spanish isolate of alfalfa mosaic virus: evidence for additional genetic variability

Archives of Virology ◽

10.1007/s00705-011-0941-z ◽

2011 ◽

Vol 156 (6) ◽

pp. 1049-1052 ◽

Cited By ~ 14

Author(s):

Giuseppe Parrella ◽

Nadia Acanfora ◽

Anelise F. Orílio ◽

Jesús Navas-Castillo

Keyword(s):

Nucleotide Sequence ◽

Genetic Variability ◽

Mosaic Virus ◽

Complete Nucleotide Sequence ◽

Alfalfa Mosaic Virus ◽

Spanish Isolate

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Complete nucleotide sequence of alfalfa mosaic virus RNA 4

Nucleic Acids Research ◽

10.1093/nar/8.10.2213 ◽

1980 ◽

Vol 8 (10) ◽

pp. 2213-2224 ◽

Cited By ~ 62

Author(s):

Frans Th. Brederode ◽

Ellen C. Koper-Zwarthoff ◽

John F. Bol

Keyword(s):

Nucleotide Sequence ◽

Mosaic Virus ◽

Complete Nucleotide Sequence ◽

Alfalfa Mosaic Virus ◽

Virus Rna

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Detection of potato leaf roll virus and potato viruses M, S, X and Y by dot immunobinding on plain paper

Potato Research ◽

10.1007/bf02357870 ◽

1988 ◽

Vol 31 (3) ◽

pp. 367-373 ◽

Cited By ~ 10

Author(s):

Morten Heide ◽

Lene Lange

Keyword(s):

Leaf Roll ◽

Potato Leaf Roll Virus ◽

Potato Leaf ◽

Potato Viruses ◽

Plain Paper

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First Report of Potato leaf roll virus (PLRV) Naturally Occurring on Jute (Corchorus olitorius) in India

Plant Disease ◽

10.1094/pdis-07-14-0668-pdn ◽

2014 ◽

Vol 98 (11) ◽

pp. 1592-1592 ◽

Cited By ~ 5

Author(s):

C. Biswas ◽

P. Dey ◽

S. Mitra ◽

A. Bera ◽

S. Satpathy ◽

...

Keyword(s):

Coat Protein ◽

Mosaic Virus ◽

Leaf Roll ◽

Potato Leaf Roll Virus ◽

Corchorus Olitorius ◽

Specific Primer ◽

Potato Leaf ◽

First Report ◽

Stunted Growth ◽

Naturally Occurring

Jute (Corchorus olitorius L.) is an important bast fiber crop that is mainly grown in the Southeast Asian countries like India, Bangladesh, Nepal, China, Indonesia, Thailand, Myanmar, and a few South American countries. In June 2013, symptoms suggestive of a viral disease were noticed on jute (cv. JRO524) in an experimental field of the CRIJAF research farm, Barrackpore, India, and the incidence of the disease was less than 2%. The infected plants showed stunted growth and short height. Mostly the upper leaves elongated with curling and coiling of lamina. Puckering and shoe string effect were also noticed. Petioles and stipules of the affected leaves were exceptionally longer. Although initially the incidence was low, it may spread to larger areas in subsequent years. Because the jute fiber is extracted from the stem, stunted growth and short height would badly affect the fiber yield and quality. Ten symptomatic and ten asymptomatic healthy looking samples were collected from the field. Corchorus golden mosaic begomovirus is common in jute; therefore, all the samples were tested by PCR using JMFL-AF/JMFL-AR, DNA-A component specific primer pair and JMFL-BF/JMFL-BR, DNA-B component specific primer pairs (1). However, there was no amplification. Because the aphid Aphis gossypii was often noticed in the jute field, all the samples were tested by double-antibody sandwich (DAS)-ELISA for common aphid transmitted viruses, e.g., Cucumber mosaic virus, Bean common mosaic virus, Cowpea mosaic virus, Papaya ring spot virus, Potato leaf roll virus (PLRV), Potato virus Y, and Watermelon mosaic virus using commercial diagnostic kits (Agdia). The symptomatic samples showed positive reaction only for PLRV. Five ELISA-positive samples and five asymptomatic healthy samples were used for RNA extraction. Total RNA was extracted by using QIAGEN RNeasy mini kit. RT-PCR was carried out with PLRV CP gene specific primer pair (3) which generated a cDNA amplicon of 627 bp in all ELISA-positive symptomatic samples. PLRV was not detected in symptomless samples. The five purified cDNA products were cloned in a pGEM-T Easy vector (Promega) and were sequenced. One of the five identical sequences was deposited in GenBank (Accession No. KF233880). The consensus sequence was analyzed by NCBI BLAST and found to share 99% similarity with the coat protein sequence of PLRV reference strain (S77421). Nucleotide span and ORF finder (NCBI) analysis indicated the 627-bp PCR amplicon coded part of a coat protein gene that had 100% identity with translated gene product (Protein ID AAB33483). PLRV is a small isometric RNA virus with worldwide distribution belonging to the family Luteoviridae whose natural host range is mainly restricted to solanaceous plants and few plants of other families (2,4). To the best of our knowledge, this is the first report of PLRV naturally occurring on jute (C. olitorius). References: (1) R. Ghosh et al. J. Virol. Methods 159:34, 2009. (2) S. Guyader and D. G. Ducray. J. Gen. Virol. 83:1799, 2002. (3) M. A. Mayo et al. J. Gen. Virol. 70:1037, 1989. (4) K. Mukherjee et al. Virus Genes 26:247, 2003.

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