Page 7 - Volume 2,Issue 2, July 2009

© Benaki Phytopathological Institute
Pepino mosaic virus 51
no. AM109896). Full length sequence data
were also obtained from an isolate collected
from a wild L. peruvianum during a survey in
Peru (LP2001; Soler et al. , 2002).
The EU-tomato isolate of PepMV, first de-
scribed in 1999, clearly differs in a number of
characteristics from the original pepino iso-
late from Peru. The differences are most pro-
nounced in the reactions of both isolates on
tomato (S. lycopersicum) in which the pepi-
no isolate does not cause symptoms, where-
as the tomato isolate causes more distinct
symptoms. The two isolates could be also
distinguished on a number of test plants,
most clearly on N. glutinosa and D. stramoni-
um (Verhoeven et al., 2003).
Since 1999, a large number of differ-
ent PepMV isolates were described in com-
mercial tomato crops in different countries.
Many partial sequences and a number of full
length sequences of tomato isolates have
been obtained. Comparisons show that iso-
lates of the Peruvian and the EU-tomato
strains are closely related and share approxi-
mately 95% overall nucleotide sequence ho-
mology between their genomes. Compari-
son of full length nucleotide sequences and
deduced amino acid sequences of a number
of tomato isolates from different countries
(Aguilar et al., 2002; Cotillon et al., 2002; Ló-
pez et al., 2005) confirmed the very high lev-
els of sequence identity (over 99%) within
the tomato isolates. Table 1 lists the current-
ly available full length sequences of PepMV.
In 2005, Maroon-Lango et al. (2005) pub-
lished the full sequences of two isolates (US1
and US2) collected in 2000 in the USA. These
sequences were obtained directly from total
RNA isolated fromamix of dried symptomat-
ic tomato leaves collected in Arizona. Direct
nucleotide sequence comparisons showed
only 79-82% overall identity between Euro-
pean tomato isolates from France and Spain
and US1 and US2 and 86% overall nucleotide
identity between the RNA genomes of both
US isolates. Pairwise comparisons of each of
the ORFs of US1 and US2 with European to-
mato isolates showed similar levels of iden-
tity. Based on the overall levels of homology
between them, US1 and US2 were consid-
ered as new PepMV strains distinct from the
Peruvian and EU-tomato strains.
Two additional full length sequences,
namely Chile-1 (Ch1) and Chile-2 (Ch2), were
obtained from tomato seed batches import-
ed from Chile into the US (Ling, 2007). Both
showed the highest nucleotide similarity
with the previously described US1 and US2
isolates; 98.7% between Ch1 and US1 and
90.7% between Ch2 and US2. Ch1 and Ch2
shared only 78% nucleotide identity and be-
tween 78 and 86% identity to five isolates of
the EU-tomato strain.
At that point the Ch1 isolate was con-
sidered to belong to the US1 group and the
Ch2 isolate to the US2 group. However, de-
tailed sequence alignments of the various
ORFs between Ch2 and US2 (Van der Vlugt,
unpublished) showed a possible recom-
bination point in the ORF1 nt sequence of
US2. Up to nt 2305 the US2 sequence clearly
resembles the Ch2 sequence. However, be-
tween nt 2306 and 4742 the US2 sequence is
nearly identical to the US1 sequence. From
Table 1. Full genome sequences of Pepino
mosaic virus isolates.
Acc no Host Isolate Strain
FJ212288 Tomato ?
EF408821 Tomato PK Ch2
DQ000984 Tomato
seed US1
DQ000985 Tomato
seed Ch2
AY509926 Tomato US1
AY559927 Tomato US2
AM491606 Tomato Hungary EU-tomato
AM109896 Pepino BBA1137 (SM74)1 Peruvian
AJ606359 Tomato LE2000 EU-tomato
AJ606360 Tomato LE2002 EU-tomato
AJ606361 Tomato LP2001 Peruvian
AJ438767 Tomato Fr EU-tomato
AF484251 Tomato Sp13 EU-tomato
FJ940223 Tomato PD99901066 EU-tomato
FJ940224 Tomato DB1 EU-tomato
FJ940225 Tomato US1 US1
FJ612601 Tomato PA
1 Original PepMV isolate, as described by Jones et al.
(1980).