Differentiation Study between Alfalfa Mosaic Virus and Red Clover Mottle Virus Affecting Broad Bean by Biological and Molecular Characterization
Sabry Y.M. Mahmoud,
Abdel-Sabour G.A. Khaled
This study aimed to identifying the causal virus (es) inducing wilting and necrotic symptoms on broad bean plants. Amplification of total RNA extracted from infected broad bean yielded 200-550 bp using Comovirus-specific primers. The amplified cDNAs was cloned, sequenced and analyzed. Nucleic acid sequence analysis of smallest and biggest bands revealed of 100 and 95% sequence identity with other Red Clover Mottle Virus (RCMV) and Alfalfa Mosaic Virus (AMV) isolates, respectively. Two viruses were isolated and biologically purified by single local lesion method on Phaseolus vulgaris plants. The obtained isolates were mechanically transmitted and has narrow host range included most plants belonging to Fabaceae and Solanaceae. The AMV was aphid transmitted in a non-persistent manner through Myzus persicae and Aphis craccifora. In contrast, RCMV don't transmit. Electron microscopy has revealed presence of AMV particles within the cytoplasm; also, non-aggregated particles packed side by side in the vacuoles of Nicotiana tabaccum var. White Burley cells was showed. On the other hand, spherical particles, about 30 nm in diameter were shown on partially purified RCMV preparations. Biological and molecular properties of the Egyptian isolates from broad bean established its identity as an AMV and RCMV, respectively.
to cite this article:
Sabry Y.M. Mahmoud, Abdel-Sabour G.A. Khaled and Karel Petrzik, 2010. Differentiation Study between Alfalfa Mosaic Virus and Red Clover Mottle Virus Affecting Broad Bean by Biological and Molecular Characterization. International Journal of Virology, 6: 224-239.
June 22, 2010; Accepted: September 09, 2010;
Published: November 01, 2010
Faba bean (Vicia faba L.) is an economically important legume crop in
many countries. In Egypt, it is considered the most popular food legume crop.
Worldwide, this crop is known to be naturally infected by about 44 viruses (Cockbain,
1983), which cause considerable yield losses.
In Egypt, many viruses have been identified including AMV. However, until now
no trails to study status of that virus or other unidentified viruses on faba
bean have been done. Since, its first report by Weimer in 1931 (Jung
et al., 2000), AMV has been found in most countries infecting many
plants. The virus is easily transmitted by sap inoculation and by several aphid
species in a non-persistent manner to some of 430 plant species in 51 dicotyledonous
families (Jung et al., 2000; Rivas
et al., 2005; Gillaspie et al., 2006;
Nair et al., 2009). It can cause extensive yield
losses and economic damage (Van Regenmortel and Pinck, 1981).
The AMV is one of the most biologically variable plant viruses and numerous
natural variants having different pathogenicity (Hajimorad
and Francki, 1991). The AMV is the type species of the genus Alfamovirus
and belongs to the family Bromoviridae. It has a tripartite single-stranded
genome. RNAs 1, 2, 3 and subgenomic RNA4 are separately encapsidated into bacilliform
particles which are 18 nm wide and have lengths characteristic of the RNA encapsided
(about 56, 43, 35 and 30 nm, respectively) (Sehnke and Johnson,
1994; Thole et al., 1998). The three genomic
RNAs are not infective. Infection can start only in the presence of RNA4 or
its translation product of Coat Protein (CP). Strains that have been studied
in most detail are the Leiden and Madison isolates of strain 425 (425L and 425
M) (Hagedorn and Hanson, 1963), the Strasbourg isolate
(S) (Walter et al., 1985), the 15/64 and VRU
strains (Crill et al., 1970) and Korean isolates
of strain KR (KR1 and KR2) (Jung et al., 2000).
The complete nucleotide sequence of the AMV RNAs has been determined (Cornelissen
et al., 1983a, b). RNA1 and RNA2 contain single open reading frame
(ORF) encoding the viral replicas subunits (P1 and P2, respectively). RNA3 contains
two ORFs encoding the movement protein and CP (Taschner
et al., 1991). The CP is expressed from a fourth subgenomic RNA (sgRNA).
The RCMV is a member of the genus Comovirus, family Secoviridae, which
represents nonenveloped plant viruses with icosahedral capsids and bipartite,
single-stranded, positive-sense RNA genomes. As in other comoviruses,
the two RNA molecules are encapsidated separately in isometric particles composed
each of a large (L) and a small (S) coat proteins (Lomonossoff
and Johnson, 1991). Two strains (O and S) of RCMV have been characterized
(Lapchic et al., 1998; Lin
et al., 2000) and the complete nucleotide sequence of the genome
of strain S has been determined (Shanks et al., 1986).
The RCMV has a mode of gene expression similar to Cowpea mosaic virus
(CPMV), the type member of the group (Shanks et al.,
During a survey in kafr El-Sheikh governorate, for virus infection in faba bean fields (2006-2008), viral symptoms such as severe chlorosis, necrosis, rolling, ring spots on leaves and generally plant stunting were observed. They were spread during the growing season causing considerable quantitative deleterious effect on plant yield. Therefore, the objective of this investigation was to isolate and identify the causal virus(es) by biological and molecular methods.
MATERIALS AND METHODS
This study was carried out in cooperation between Agricultural Microbiology Department, Faculty of Agriculture, Sohag University, Egypt and Plant Virology Department, Institute of Plant Molecular Biology, Academy of Sciences, Czech Republic in the framework of personal scientific cooperation since 2006.
The incidence of virus-like symptoms including chlorosis, necrosis, rolling,
ring spots on leaves, stunting and plant death (Fig. 1) was
about 60% in broad bean plants at Kafr El-Sheikh Governorate. The infection
agent(s) were mechanically transmitted by macerating in 0.01 M phosphate buffer
and (pH 7.0) to leaves of Ph. vulgaris, V. faba, Chenopodium amaranticolor
and C. quinoa and Nicotiana tabacum.
||Leaf rolling, stunting, necrosis and plant death showing on
naturally infected faba bean
A preliminary study by DAS-ELISA using polyclonal antibodies of Cucumber mosaic
virus (CMV), Bean yellow mosaic virus (BYMV), Broad bean stain virus (BbSV)
and Faba bean necrotic yellow vein virus (FBNYVV) was done.
Extraction of RNA and RT-PCR Procedures
The RNA for reverse transcription and real time-PCR was isolated from about
0.1 g of infected leaves of faba bean sample with Nucleospin RNA plant kit (Macherey
Nagel, Germany) according to the manufacturers recommendations and eluted
with 30 μL of water. Complementary DNA (cDNA) was synthesized from 7 μL
of RNA with iScript synthesis kit (Bio-Rad) in 10 μL reaction volume. Comovirus-specific
primers 5'-AANCCRGANGGDATNC-CRCAYTC-3' and 5'-GGATTGATACCTACCTGGCA-3' were used
for amplification of 181 bp long segment of the RNA polymerase gene.
The 20 μL PCR reaction mixture contains 10 mM Tris-HCl, pH 8.8, 50 mM KCl, 0.1% Triton X-100, 1.5 mM MgCl2, 200 μM each of dNTPs, 1 U Dream Taq DNA polymerase (Fermentas, Lithuania), 2 μL of cDNA and 20 pmol of primers. The amplifications were performed in an amplification program of 35 cycles with 30 sec denaturation at 95°C, 1 min annealing at 45°C and 1 min synthesis at 72°C. All samples were analyzed on 1.5% agarose gel electrophoresis.
Cloning and Sequences Analysis
Three fragments of about (200, 380 and 500 bp) were individually cloned
to pre-cleaved blunt-ended vector plasmid pJET1.2/blunt (2974 bp, Fermentas)
and sequenced using the BigDye sequencing terminator kit, version 3.1 (PE Biosystems,
UK) then analyses on ABI PRISM 310 sequencer (PE Applied Biosystems, USA).
Multiple alignments of amino acid sequences were obtained using the default
options of the AligX, Vector NTI Advance 9.1 program (Invitrogen). Search homologies
with proteins from the BLAST basic local alignment search tool of National Center
of Biotechnology Institute (NCBI) was done with the FASTA (Pearson
and Lipman, 1988) and TBLASTN program 2.2.22+ (Altschul
et al., 1990).
Red Clover Mottle Virus
The amino acid sequence corresponding to 200 bp fragment was compared with
most corresponding known other viruses belonging to Comovirus genus of
Phylogenetic tree was constructed with deduced amino acid sequences of Red
clover mottle virus-Egyptian isolate (RCMV-Eg, GQ923687), Red clover mottle
virus (RCMV, CAA46104), Squash mosaic virus (SqMV-R, BAB62139), Squash mosaic
virus isolate CH 99/211 (SqMV-P1, ABZ89551), Squash mosaic virus of RdRp (SqMV-RdRp,
CAG27555), Bean pod mottle virus (BPMV-R, ABP96717), Bean pod mottle virus (BPMV-P,
AAD09629), Bean pod mottle virus of K-Hancock1 strain (BPMV-Ha, AAM73715), Bean
pod mottle virus of K-Hopkins1 strain (BPMV-Ho, AAM73718), Bean pod mottle virus
of subgroup I (BPMV-I, AAW69768), Bean pod mottle virus of subgroup II (BPMV-II,
AAW69769), Radish mosaic virus isolate 1 (RaMV1, ACE06773), Radish mosaic virus
(RaMV-P, BAF75830), Radish mosaic virus of California strain (RaMV-Ca, BAG84602),
Radish mosaic virus (RaMV-R, AAY32935), Cowpea mosaic virus (CPMV-R, ABP96716),
Cowpea mosaic virus (CPMV, CAA25029) and Andean potato mottle virus (APMV, AAA42422).
Alfalfa Mosaic Virus
The amino acid sequence corresponding to 550 bp fragment was compared with
Alfalfa mosaic virus, the sole member of Alfamovirus genus and some other
corresponding known viruses belonging to Ilarvirus genus of Bromoviridae
family. Phylogenetic tree was constructed with predicted amino acid sequences
of Alfalfa mosaic virus Egyptian isolate (AMV-Eg, GQ923686), Alfalfa mosaic
virus of Leiden strain 425 (AMVTc-2, AAA46289), Prune dwarf virus (PDV, AAB39537),
Fragaria chiloensis latent virus (FCILV, AAV68306), Humulus japonicus latent
virus (HjLV, AAS86438), Prunus necrotic ringspot virus (PNRSV, AAK69474), American
plum line pattern virus (APLPV, AAK15026) and Apple mosaic virus (ApMV, AAD55722).
The phylogenetic trees were constructed using the ClustalX2 Multiple Sequence
Alignment Program (Thompson et al., 1997) with
1000 bootstrap replicates. Protein function analysis was performed using the
fowling software (http://www.ebi.ac.uk/
The viruses from naturally infected broad beans were mechanically transmitted
by macerating in 0.01 M phosphate buffer (pH 7.0) to leaves of Ph. vulgaris
and single local lesions were taken for biological purification. Two isolates
from differed single local lesions were then propagated in Nicotiana tabacum
var. White Burley or Ph. vulgaris and three cycles of purification were
repeated. Purified virus isolates were confirmed by study on the basis of host
range, symptomatology, mode of transmission and stability in the infectious
sap. Also, viruses were insured by electron microscopy.
Host Range and Symptomatology
Host range study was performed using the symptomatic leaf extracts of N.
tabacum and Ph. vulgaris. Each leaf extract grounded in extraction
buffer (0.01 M Na2HPO4, pH 7.2; 0.01 M sodium sulfite;
1 mM EDTA) and then inoculated onto V. faba, Vigna radiata,
V. unguiculata, Ph. vulgaris, Cicer arietinum, Lens
esculenta, Lupinus termis, Pisum sativum, C. amaranticolor, C.
quinoa, Beta vulgaris, Capsicum annuum, Datura metal, D. stramonium, Solanum
nigrum, N. tabacum var White Burley, N. glutinosa, Sonchus oleraceus,
Gomphrena globosa, Ocimum basilicum and Rumex acetosa. Ten seedlings
of each host plant were inoculated and each inoculation was repeated three times.
All tested plants were kept in a greenhouse (20-25°C) and observed daily
for symptoms development.
Two aphid species Myzus persicae and Aphis craccifora (provided
from Plant protection department, Faculty of Agriculture, Sohag University)
were used for transmission test. The aphids were raised on healthy cabbage (for
M. persicae) or wheat plants (for A. crassifora) free of viruses.
The aphids were placed onto N. tabacum or Ph. vulgaris systemically
infected leaf pieces for acquisition feeding for 1 h in a Petri dish after 2
h fasting. Aphids were moved onto healthy three-leaf seedlings overnight (5
insects per plant) for inoculation feeding before being killed. A total of 10
plants were inoculated for each species of aphids. Mosaic symptoms on plants
were observed 20 days post-inoculation. The virus-free insects were maintained
on five healthy N. tabacum or P. vulgaris plants as control.
Assay of in vitro Stability
Dilution End Point (DEP), Thermal Inactivation Point (TIP) and longevity
in vitro (LIV) of the virus isolates were determined according to Noordam
(1973) by using C. amaranticolor and C. quinoa as indicator
Electron Microscopy (EM)
Partial Purification of the Virus Isolates
According to Hajimorad and Francki (1991), Systemically
infected N. tabacum leaves were homogenized in 2 volumes (w/v) of extraction
buffer (0.2 M Na2HPO4; 0.3% 2-mercaptoethanol; 0.01 M
EDTA, pH 7.6) and clarified by 0.5% cold mercaptoethanol; 0.01 M EDTA, pH 7.6)
then clarified again by 5% cold chloroform and butanol (1: 1= v/v). After polyethylene-glycol
(PEG, MW 6000, 8% w/v) precipitation, the sediments were resuspended in a buffer
containing 0.02 M Na2HPO4, pH 7.6 and 1 mM EDTA followed
by centrifugation through a 30% sucrose cushion for 2 h at 30.000 rpm at 4°C.
The virus pellet was then resuspended in 0.5 mL TE buffer (10 mM Tris-HCl, 1
mM EDTA; pH 8.0). Virus concentration was estimated using an assumed extinction
coefficient of 4.9 (Vloten-Doting and Jaspars, 1973).
According to Shanks et al. (1986), systemically
infected Ph. vulgaris leaves were grind in 0.1 M phosphate buffer, pH
8; containing 0.02 M 2-mercaptoethanol and 10% (w/v) sucrose. The extract was
filtered through cheesecloth and clarified by low speed centrifugation. Supernatant
was mixed with equal volume of chilled 1, 1, 2-trichloro- 1, 2, 2-trifluoro-ethane
9 freon (113) and emulsified briefly. Aqueous phase was polyethylene-glycol
(PEG, MW 6000, 8% w/v) precipitated and then the sediment was treated as mentioned
Electron Microscopic Examination
Electron microscopic examination of the partially purified suspension of
tow isolates were negatively stained with 2% phosphotungstic acid (PTA). A small
droplet of purified virus preparations was placed on a carbon-coated Formvar
grid for 1 min and excess was removed. Another drop of 2% PTA, pH 6.0 was placed
on the same grid for 1 min. Excess stain was removed by touching the edge of
grid with a filter paper. After air drying the grids were examined by electron
Fresh leaf samples collected from N. tabacum or Ph. vulgaris
systemically infected plants were fixed in 3% glutaraldehyde, in 0.05 M phosphate
buffer (pH 7), for 3 h. Samples were rinsed several times in 0.05 M phosphate
buffer and then were post fixed with 1% OsO4 in 0.05 M phosphate
buffer for 2 h. Samples were rinsed several times with 0.05 phosphate buffer
and taken to the laboratory. Samples were then dehydrated in a gradient acetone
series and embedded in Spurr's medium (Spurr, 1969).
Ultrathin sections (60 nm thick) were stained with uranyl acetate and lead citrate.
Specimens were viewed with a Jeol-1010 transmission electron microscope at 100
kV (Unit of Electron Microscopy at Sohag University, Egypt).
RESULTS AND DISCUSSION
Preliminary biological indication and serological analysis by DAS-ELISA indicated probably presence of Comovirus-isolate. Hence, RT-PCR was directly used to ensure this hypothesis.
RT-PCR and Nucleotide Sequences
RT-PCR assays performed with two Comovirus-specific primers for
amplification of 181 bp long segment of the RNA polymerase gene. The results
of RT-PCR showed three different bands (about 200, 380 and 550 bp) (Fig.
2). Once the sequences were determined, two fragments, 163 nucleotide (nt)
and 569 nt were obtained from smallest and biggest bands, respectively. These
sequences were disposed in the GenBank under accession numbers (GQ923686) and
(GQ923687) for RCMV-Eg and AMV-Eg, respectively.
Analysis of Viral Sequences
From in silico comparison of alignment of the amino acid sequences
corresponding to 163 nt fragments, with most other corresponding known viruses
revealed identical percentages 70, 72, 75, 79, 81 and 100% for SqMV-R, (SqMV-RdRp
and RaMV), (APMV and SqMV), CPMV, BPMV and RCMV isolates, respectively. The
Phylogenetic tree showed that the Egyptian isolate clustered along with RCMV
at 1000 bootstrap value (Fig. 3) and the same clustering of
isolate was observed with the multiple alignment (Fig. 4).
|| RT-PCR products amplified from total RNA of infected leaves
of faba bean sample
||Phylogenetic tree constructed with deduced amino acid sequences
of RCMV-Eg with most Comovirus genus of Comoviridae family
||Alignment of the amino acid sequences of RCMV-Eg with most
Comovirus genus of Comoviridae family viruses. Regions with identical
sequences are highlighted in gray. Amino acid residues that are conserved
sequences in the majority of the amino acid sequences of proteins of viruses
are highlighted in black
The RCMV-Eg amplified sequence encodes a polypeptide of 44 amino acid (aa)
with a predicted molecular weight of 5.567 kDa, identified as the RNA binding
and RNA-directed RNA polymerase (RdRp-1) due to the presence of conserved stretches
common to the corresponding protein of Comoviruses, three longer amino
acid stretches [I:(EKLP), II:(KPKTR) and III:(FVRFIM)] were identical in all
figured sequences (Fig. 4).
||Alignment of the amino acid sequences of AMV-Eg with AMV Tc-2
of Alfamovirus genus and some viruses of the Ilarvirus genus.
Regions with identical sequences are highlighted in gray. Amino acid residues
that are conserved sequences in the majority of the amino acid sequences
of proteins of viruses are highlighted in black
On the other hand, computer-assisted analysis of the assembled amino acid sequences corresponding to 569 nt fragments with AMV Tc-2 and some other corresponding known viruses revealed identical percentages of 38, 39, 47, 52 and 95% for APLPV, (FCILV and ApMV), (HjLV and PNRSV), PDV and AMV Tc-2 isolates, respectively (Fig. 5). The phylogenetic tree relationships deduced from multiple alignments of Egyptian isolate with others showed two major clades that clustered at 404 bootstrap values (Fig. 5). The first clade contained AMV-Eg that clustered along with AMV Tc-2 of the same Genus at 1000 bootstrap value, whereas the second clade comprised the other ilarvirus. This is consistent with the clustering based on the sequence alignments (Fig. 6).
The obtained sequence of AMV-E g (569 nt in size) contains a short Single Open Reading Frame (ORF) that initiates with a start codon (AUG) at nt position 1-3 from 5' end and terminates with an amber stop codon (UAG) at nt position 59-61. The result of multiple alignments of AMV-E g with others showed that this short ORF is conserved between AMV-Eg and AMV Tc-2 isolates (Fig. 5).
The AMV-E g amplified sequence encodes a polypeptide of 190 aa with a predicted
molecular weight of 21.049 kDa, identified as the RNA binding and mRNA methyltransferase
due to the presence of conserved stretches common to the corresponding protein
of the Bromoviridae family.
||Phylogenetic tree constructed with deduced amino acid sequences
of AMV-Eg with AMV Tc-2 of Alfamovirus genus and some viruses of
the Ilarvirus genus
The multiple alignments of AMV-Eg with others showed identical amino acid stretches,
two amino acid blocks [I: (RSCAW) and II: (LSS)] were identical in all deduced
amino acid sequences (Fig. 5).
At the end of the molecular study, the authors were sure to have a mixed
infection of two viruses (RCMV and AMV), but they need to separate them and
confirm it via biological definition and EM.
Host Range Studies
Characteristic development symptoms of AMV and RCMV isolates observed on
Fabaceae, Solanaceae and on other indicator plants are summarized in Table
1, Fig. 7a-i and 8a-f.
In general, more sever symptoms were induced by AMV than that of RCMV. So that,
clear differences in symptoms between two isolates were obtained. Symptoms induced
by AMV isolate were greatly influenced by environmental conditions. RCMV induced
only necrotic local symptoms on C. amaranticolor and Lupinus termis,
also induced necrotic ring spots on S. nigrum. In contrast, RCMV
isolate induced necrotic ring lesions and local lesions in inoculated V.
faba and Ph. vulgaris leaves followed by stem necrosis and sever
mosaic, respectively, but induced mild mosaic directly on Pisum sativum
without local infection. On the other hand, necrotic local lesions followed
by a mild mottle, stem necrosis and plant death were noticed on V.
faba after AMV inoculation. Also, local infections induced on C. amaranticolor
and Phaseolus vulgaris turned to mosaic and chlorotic flecking as systemic
infections, respectively. Mild mosaic was observed on N. tabacum
var. White Burley, bright yellow mosaic induced on Ocimum basilicum and
Capsicum annuum var. California but vein clearing and mosaic symptoms
were induced on Sonchus oleraceus after inoculation with AMV isolate.
The same isolate induced yellowing, shoot tip necrosis and stunting in Cicer
arietinum, Lens esculenta and Pisum sativum, whereas induced chlorotic
flecking and mottling on V. radiate. This isolate induced necrotic
local lesions only on Rumex acetosa V. unguiculata, Lupinus termis,
C. quinoa and G. globosa.
Three and five out 10 N. tabacum seedlings developed mosaic symptom
12 days after AMV transmission inoculation by each of the two aphid species
Myzus persica and Aphis cracciforae, respectively.
||Differentiation between RCMV and AMV isolates via host range
and symptoms after mechanical inoculation
|NLL: Necrotic local lesions, NRL: Necrotic ring lesions, BNLL:
Black necrotic local lesions, CLL: Chlorotic local lesions, NRS: Necrotic
ring spots, MM: Mild mosaic, SM: Severe mosaic, CF: Chlorotic flecking,
SN: Systemic necrosis, D: Death, Y: Yellow; STN: Shoot tip necrosis, S:
Stunting, BYM: Bright yellow mosaic, VC: Vein clearing, Mot, Mottling, -:
On the other hand, no symptoms were detected on Ph. vulgaris
plants after RCMV transmission inoculation by aphid species. Results confirming
the transmissibility of AMV by these two aphid species, in contrast was noticed
when RCMV isolate was used.
Stability in vitro
The infectivity test of AMV inoculum after various treatments showed
that the Eg isolate had a TIP of 64°C and DEP of 10-3 and its
infectivity was retained in vitro for up to 3 days. These values were
70°C, 10-6 and 14 days, respectively when RCMV isolate was tested.
AMV and RCMV Characteristics
The purified viruses had an absorption spectrum typical of viral nucleoprotein.
The A260/280 values for AMV and RCMV were 1.6 and 1.5, respectively.
The yield of the viruses was approximately 2 and 3 mg per 100 g of fresh leaves.
Purified preparations appeared to be not free from contamination as evidenced
by EM observations. Bacilliform virus-like particles not showed on AMV-Eg preparations
from N. tabacum. EM observation of RCMV-Eg infected Ph. vulgaris
leaves revealed spherical particles in the sap, about 30 nm in diameter (Fig.
||Symptoms on test plants inoculated with Egyptian isolate of
AMV from broad bean. a) necrotic local lesions on inoculated broad bean,
b) systemic necrosis and death on broad bean, c) mild mosaic on broad bean,
d) mosaic on C. amaranticolor, e) necrotic local lesions on bean,
f) chlorotic flecking on uninoculated bean leaves, g) black necrotic local
lesions on Lupinus termis leaves, h) necrotic local lesions on Rumex
acetosa leaves and i) necrotic local lesions on C. quinoa leaves
Ultrathin Sections and Relation with Cells
Amorphous inclusion bodies have been seen as a raft containing particles
packed side by side occur in the vacuoles of N. tabacum-AMV infected
cells (Fig. 10a). On the other hand, inclusion bodies were
not shown on Ph. vulgaris-RCMV infected cells, but many small vacuoles
were distributed within these cells (Fig. 10b).
In the present study, the AMV and RCMV characteristics were studied using infected
plant materials and compared the strain identity using sequence similarities
of the Comovirus-specific primers. Leaves with chlorosis, necrosis, rolling,
ring spots and plant stunting were collected from different broad bean growing
areas in Kafr El-Sheikh Governorate and tested by DAS-ELISA against most viruses
infect broad bean (data not shown). Due to negative ELISA reactions and their
characteristic symptoms the samples were submitted to RT-PCR by using Comovirus-specific
||Symptoms on test plants inoculated with Egyptian isolate of
RCMV from broad bean. (a) necrotic ring spots on inoculated broad bean,
(b) systemic necrosis on broad bean, (c) necrotic local lesions on bean,
(d) severe mosaic on uninoculated bean leaves, (e) necrotic local lesions
on Lupinus termis leaves and (f) necrotic ring spots on S.
||Electron micrograph of partial purified particles of RCMV-Eg
isolate. Bar indicates approximately 30 nm
Altogether, these results indicated that native field broad bean is infected
by mixed infection with AMV and RCMV. Last evidence derived from only a partial
nucleotide sequences, shown that comparison of some gene sequence give good
picture of relationship with the genus Alfamovirus or Comovirus as
do comparisons of longer sequences (Pietersen et al.,
1985; Neeleman et al., 1991).
||Electron micrograph of thin section of (a) N. tabacum and
(b) P. vulgaris AMV and RCMV-infected leaf cells, respectively.
Amorphous inclusion bodies seen as a raft containing particles packed side
by side in the vacuoles of AMV-infected tobacco cells (a). Small vacuoles
were distributed within P. vulgaris cells infected with RCMV
Previously, it has been difficult to classify AMV or RCMV strains, but now
they can be differentiated more accurately based upon molecular properties (Kudela
and Gallo, 1995; Lin et al., 2000). The PCR
primers for Comoviruses were selected to amplification RNA-directed
RNA polymerase (RdRp-1) and RNA binding and mRNA methyltransferase. RNA-directed
RNA polymerase is an essential protein encoded in the genomes of all RNA containing
viruses with no DNA stage (Koonin et al., 1989;
Zanotto et al., 1996). Universal oligonucleotide primers complementary
to conserved shard by all known members of a virus group have been shown to
enable the identification of a new member of the different virus groups, geminiviruses
(Rybicki and Hughes, 1990) and potyviruses (Langeveld
et al., 1991). The obtained sequence of AMV-Eg (569 nt in size) contains
a single short ORF that initiates with a start codon (AUG) at nt position 1-3
from 5' -end and terminates with an amber stop codon (UAG) at nt position 59-61.
The position and sequence of RCMV-Eg corresponds well with supposed length of
the amplification product of primers used, but the amplification of AMV-Eg was
accidental, probably due to misspriming of the second primer. In AMV, RNA 2
contains several ORFs of 100 to 150 nt (Brederode et
al., 1980). An ORF contains 663 nt concluding with a UGA stop coding
in AMV RNA-3 (Barker et al., 1983). In AMV-RNAs
1 and 3 of strain 425, the 5' -proximal AUG codon is closely followed by a termination
codon, whereas, in AMV-RNAs 2 and 4, the first AUG codon from terminal 5' -end
is the beginning of long ORF (Koper-Zwarthoff et al.,
1980; Cornelissen et al., 1983b). Both isolates
supported amplification of the expected fragments, which was also found in AMV
and RCMV strains. The amplified DNA fragments were subjected to sequence analysis.
Results showed that the level of amino acid sequence identity in the RNA binding
and mRNA methyltransferase and RdRp-1 compared with the nucleotide sequence
identity of isolated AMV and RCMV strains were 95 and 100% with AMV-Tc2 and
RCMV, respectively. Present results are agreement with findings of Jung
et al. (2000) and Lapchic et al. (1998)
for AMV and RCMV, respectively and El-Araby et al.
2009 when studied some potato viruses.
Isolation and host range studies showed that broad bean plants infected by
two viruses, one of the Alfamovirus and the other of the Comovirus,
this result agreement with previously reported on several crops (Paliwal,
1982; Valkonen et al., 1992; Lapchic
et al., 1998). The symptoms on some test plants including Rumex
acetosa and S. nigrum inoculated with AMV-Eg and RCMV-Eg, respectively
showed some differences as compared to that of previously described AMV isolated
in Korea (Kudela and Gallo, 1995) and RCMV isolated
in Sweden (Abdelmoeti, 1979). In general, AMV-Eg and RCMV-Eg
could be clearly differentiated by host reactions in some indicator plants such
as C. amaranticolor, L. termis, C. arietinum and Ph.
vulgaris. AMV appears to be common in legume crops such as Lablab niger,
V. faba and Medicago sativa in Sudan and Tanzania (Nour
and Nour, 1962; Kaiser and Robertson, 1976). The
combination of seed-infected plants and spreading by aphids may be resulted
high levels of infection by AMV in broad bean fields in Egypt. Bacilliform virus
particles of AMV-Eg not showed. This is in agreement with the previous report
showing that structural integrity of AMV particles is not stable (Hajimorad
and Francki, 1991). Keeping the virions structurally stable is extremely
important because the low yield of particles often necessitates the bulking
of virus preparations that may involve combining purified materials over several
weeks to months (Pietersen et al., 1985; Valkonen
et al., 1992). In general loss of infectivity of AMV started at a
relatively low temperature and extended over a range of 20°C or more. The
actual inactivation point depends on the concentration of the virus. Although,
El-Attar et al. (1971) mentioned the detection
of AMV from broad bean; this is the first report to fully describe the isolation
and characterization of AMV and RCMV particles associated with broad bean in
The AMV and RCMV were isolated from mixed infection of V. faba plants. Symptoms induced on different hosts are reported. The isolates described in this work showed symptoms, transmission, virus particles and RNA structure analogue to those of strains AMV Tc-2 and RCMV. Further details of molecular characteristics such as full-length genomic RNA sequences and other genes (like coat protein) will be required in order to reveal more knowledge's about the molecular characterization of these strains and relationship with other known AMV and RCMV strains.
Abdelmoeti, M.A.H., 1979. Red clover mottle virus (RCMV)-purification, stability, separation of components and genetic studies. Ph.D. Thesis, Swedish University of Agricultural Sciences, Uppsala, Sweden
Altschul, S.F., W. Gish, W. Miller, E.W. Myers and D.J. Lipman, 1990. Basic local alignment search tool. J. Mol. Biol., 215: 403-410.
CrossRef | PubMed | Direct Link |
Barker, R.F., N.P. Jarvis, D.V. Thompson, L.S. Loesch-Fries and T.C. Hall, 1983. Complete nucleotide sequence of alfalfa mosaic virus RNA3. Nucleic Acids Res., 11: 2881-2891.
Brederode, F.T.H., E.C. Koper-Zwarthoff and J.F. Bolb, 1980. Complete nucleotide sequence of alfalfa mosaic virus RNA 4. Nucleic Acids Res., 8: 2213-2223.
Cockbain, A.J., 1983. Viruses and Virus like Diseases of Vicia Faba L. In: The Faba bean (Vicia faba L.) a Basis for Improvement, Hebblethwaite, P.D. (Ed.). Butterworths, London, pp: 421-426.
Cornelissen, B.J., F.T. Brederode, G.H. Veeneman, J.H. van Boom and J.F. Bol, 1983. Complete nucleotide sequence of alfalfa mosaic virus RNA 2. Nucleic Acids Res., 11: 3019-3025.
Cornelissen, B.J., F.T. Brederode, R.J. Moormann and J.F. Bol, 1983. Complete nucleotide sequence of alfalfa mosaic virus RNA 1. Nucleic Acids Res., 11: 1253-1265.
Crill, P., D.J. Hagedorn and E.W. Hanson, 1970. Alfalfa mosaic, the disease and its virus incitant. Univ. Wisconsin Agric. Sci. Res. Bull., 39: 7-7.
El-Araby, W.S., I.A. Ibrahim, A.A. Hemeida, A. Mahmoud, A.M. Soliman, A.K. El-Attar and H.M. Mazyad, 2009. Biological, serological and molecular diagnosis of three major potato viruses in Egypt. Int. J. Virol., 5: 77-88.
CrossRef | Direct Link |
El-Attar, S., F. Nour El-Din and S.A. Chobrial, 1971. A strain of alfalfa mosaic virus naturally occurring on broad bean in the Arab Republic of Egypt. Agric. Res. Rev. Cairo, 3: 49-52.
Gillaspie, Jr. A.G., N.A. Barkley and J.B. Morris, 2006. An unusual strain of alfalfa mosaic virus detected in Crotalaria L. Germplasm. Plant Pathol. J., 5: 397-400.
CrossRef | Direct Link |
Hagedorn, D.J. and E.W. Hanson, 1963. A strain of alfalfa mosaic virus severe on Trifolium pretense and Melilotus alba. Phytopathology, 53: 188-192.
Hajimorad, M.R. and R.I.B. Francki, 1991. Effect of glutaraldehyde-fixation on the immunogenicity, particle stability and antigenic reactivity of alfalfa mosaic virus and the specificity of elicited antibodies. J. Virol. Methods, 33: 13-25.
Jung, H.W., H.J. Jung, W.S. Yun, H.J. Kim, Y.I. Hahm, K. Kim and J.K. Choi, 2000. Characterization and partial nucleotide sequence analysis of alfalfa mosaic Alfamoviruses isolated from potato and azuki bean in Korea. Plant Pathol. J., 16: 269-279.
Kaiser, W.J. and D.G. Robertson, 1976. Notes on East African virus diseases II Alfalfa mosaic virus. East Afr. Agric. Fores. J., 42: 47-54.
Koonin, E.V., A.E. Gorbalenya and K.M. Chumakov, 1989. Tentative identification of RNA-dependent RNA polymerases of dsRNA viruses and their relationship to positive strand RNA viral polymerases. FEBS Lett., 252: 42-46.
Koper-Zwarthoff, E.C., F.T. Brederode, G. Veeneman, J.H. Van Boom and J.F. Bol, 1980. Nucleotide sequences at the 5'-termini of the alfalfa mosaic virus RNAs and the intercistronic function in RNA3. Nucleic Acids Res., 8: 5635-5647.
Direct Link |
Kudela, O. and J. Gallo, 1995. Characterization of the alfalfa mosaic virus strain T6. Acta Virologica, 39: 131-135.
Langeveld, S.A., J.M. Dore, J. Memelink, A.F.L.M. Derks, C.I.M. Vander Vlught, C.T. Asjes and J.F. Bol, 1991. Identification of potyvirus using the polymerase chain reaction with degenerate primers. J. Genet. Virol., 72: 1531-1541.
Lapchic, L.G., A.J. Clark, G.P. Lomonossoff and M. Shanks, 1998. Red clover mottle virus from Ukraine is an isolate of RCMV strain S. Eur. J. Plant Pathol., 104: 409-412.
Lin, T., A.J. Clark, Z. Chen, M. Shanks and J.B. Daiet al., 2000. Structural fingerprinting: Subgrouping of comoviruses by structural studies of red clover mottle virus to 2.4-Å resolution and comparisons with other comoviruses. J. Virol., 74: 493-504.
Direct Link |
Lomonossoff, G.P. and J.E. Johnson, 1991. The synthesis and structure of comovirus capsids. Prog. Biophys. Mol. Biol., 55: 107-137.
Nair, R.M., N. Habili and J.W. Randles, 2009. Infection of Cullen australasicum (syn. Psoralea australasica) with alfalfa mosaic virus. Aust. Plant Dis. Notes, 4: 46-48.
Direct Link |
Neeleman, L., A.C. van Der Kuyl and J.F. Bol, 1991. Role of alfalfa mosaic virus coat protein gene in symptom formation. Virology, 181: 687-693.
Noordam, D.D., 1973. Identification of Plant Viruses: Methods and Experiments. Center for Agricultural Publishing and Documentation, Netherlands, ISBN-13: 9789022004647, Pages: 207.
Nour, M.A. and J.J. Nour, 1962. A mosaic of Dolichos lablab and diseases of other crops caused by alfalfa mosaic virus in the Sudan. Phytopathology, 52: 427-432.
Paliwal, Y.C., 1982. Virus diseases of alfalfa and biology of alfalfa mosaic virus in Ontario and western Quebec. Canadian J. Plant Pathol., 4: 175-179.
Pearson, W.R. and D.J. Lipman, 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA., 85: 2444-2448.
Pietersen, G., D.J. Engelbrecht and J.M. Kolze, 1985. Characterization of isolates of alfalfa mosaic virus in South Africa. Phytophylactica, 17: 61-65.
Rivas, E.B., L.M.L. Duarte, M.A.V. Alexandre, F.M.C. Fernandes, R. Harakava and C.M. Chagas, 2005. A new Badnavirus species detected in Bougainvillea in Brazil. J. Genet. Plant Pathol., 71: 438-440.
Rybicki, E.P. and F.L. Hughes, 1990. Detection and typing of maize streak virus and other distantly related geminiviruses of grasses by polymerase chain reaction amplification of a conserved viral sequence. J. Gen. Virol., 71: 2519-2526.
CrossRef | Direct Link |
Sehnke, P.C. and J.E. Johnson, 1994. A chromatographic analysis of capsid protein isolated from alfalfa mosaic virus: zinc binding and proteolysis cause distinct charge heterogenecity. Virology, 204: 843-846.
Shanks, M., J. Stanley and G.P. Lomonossoff, 1986. The primary structure of red clover mottle virus middle component RNA. Virology, 155: 697-706.
Spurr, A.R., 1969. A low-viscosity epoxy resin embedding medium for electron microscopy. J. Ultrastruct. Res., 26: 31-43.
Taschner, P.E.M., A.C. van der Kuyl, L. Neeleman and J.F. Bol, 1991. Replication of an incomplete alfalfa mosaic virus genome in plants transformed with viral replicase genes. Virology, 181: 445-450.
Thole, V., R. Miglino and J.F. Bol, 1998. Amino acids of alfalfa mosaic virus coat protein that direct formation of unusually long virus particles. J. Genet. Virol., 79: 3139-3143.
Direct Link |
Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin and D.G. Higgins, 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25: 4876-4882.
CrossRef | PubMed | Direct Link |
Valkonen, J.P.T., E. Pehu and K. Watanabe, 1992. Symptom expression and seed transmission of alfalfa mosaic virus and potato yellowing virus and potato yellowing virus (SB-22) in Solanum brevidens and S. etuberosum. Potato Res., 35: 403-410.
Van Regenmortel, D. and L. Pinck, 1981. Alfalfa Mosaic Virus. In: Handbook of Plant Virus Infections, Kurstak, E. (Ed.). Elsevier, Biomedical Press, Amsterdam, pp: 415-421.
Vloten-Doting, L.V. and E.M.J. Jaspars, 1973. The uncoating of alfalfa mosaic virus by its own RNA. Virology, 48: 699-708.
Walter, B., J. Kuszala, M. Ravelonandro and L. Pinck, 1985. Alfalfa mosaic virus isolated from Buddleia davidii compared with other strains. Plant Dis., 69: 266-267.
Zanotto, P.M., M.J. Gibbs, E.A. Gould and E.C. Holmes, 1996. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J. Virol., 70: 6083-6096.