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they grouped together in a separate clade also
called “Andean” (PVS
A
) (Cox and Jones, 2010a).
The acronym PVS
O-CS
(CS = “
Chenopodium
sys-
temic”) was therefore suggested for isolates that
invaded
Chenopodium
spp. systemically but be-
haved as PVS
O
on phylogenetic analysis (Ma-
toušek
et al
., 2005). Should any isolates be found
in the future that fit within PVS
O
biologically but
within PVS
A
on phylogenetic analysis, the acro-
nym PVS
A-CL
(CL = “
Chenopodium
localized”) has
been suggested (Cox and Jones, 2010a).
distinguished because PVC caused a hypersen-
sitive phenotype in some potato cultivars
(Bawden, 1936). In 1944, PVC was included
within PVY, becoming strain group Y
C
(Bawden
and Sheffield, 1944), and additional strain group
PVY
N
was recognized (Nobrega and Silber-
schmidt, 1944). Original or “ordinary” PVY
then became strain group PVY
O
(Singh
et al
.,
2008). In the 1980s-1990s, two further PVY
strain groups were identified, PVY
Z
(Jones,
1990), followed by PVY
ZE
(Kerlan
et al
., 1999),
later renamed PVY
E
(Singh
et al
., 2008). These
five strain groups are defined by phenotypes in-
duced by inoculation to potato cultivar differen-
tials with known hypersensitivity genes
Nc
,
Ny
tbr
, and (putative)
Nz
, and to tobacco plants.
PVY
C
elicits
Nc
, PVY
O
elicits
Ny
tbr
, Y
Z
elicits
Nz
,
and PVY
N
elicits necrosis in tobacco. In contrast,
PVY
E
overcomes
Nc
,
Ny
tbr
, and
Nz
, and does not
induce necrosis in tobacco (Jones, 1990; Kerlan
et al
., 1999, 2011; Singh
et al
., 2008). The PVY
gene that elicits host genes
Nc
and
Ny
tbr
is the
helper component proteinase (HC-Pro) (Moury
et al
., 2011). HC-Pro is also involved in eliciting
the veinal necrosis phenotype in tobacco (Hu
et al
., 2009b; Tian and Valkonen, 2013), but the
nuclear inclusion (protease) gene (NIa) is in-
volved in eliciting gene
Ry
(Mestre
et al
., 2000,
2003). The PVY gene that elicits
Nz
remains
unidentified. However, “biologically” defined, so-
called “PVY
O
” isolates, are often just PVY isolates
that produce no necrosis in tobacco, because,
with a few exceptions (e.g. Singh
et al
., 2008;
Dullemans
et al
., 2011; Galvino-Costa
et al
.,
2011; Kehoe and Jones, 2011; Kerlan
et al
.,
2011; Karasev and Gray, 2013a,b; Tian and
Valkonen, 2013), much of the recent PVY litera-
ture ignores strain groups PVY
C
, PVY
Z
, and
PVY
E
. In addition, isolates have often been de-
fined as “PVY
O
” by immunological tests with
strain-specific antibodies without any recourse
to inoculation to potato differentials (e.g. Nie
et al
., 2004; Hu
et al
., 2009a,b). Strain-specific
MAbs do not distinguish between biologically
defined strain groups PVY
O
, PVY
Z
, and PVY
E
,
and Karasev
et al
. (2010) documented PVY
N
misidentification by immunological tests. More-
over, a group of isolates called PVY
O5
(Ellis
et al
.,
1977, 1996; Baldauf
et al
., 2006) was distin-
guished from others only by its reactions with
MAbs. Because, as mentioned above, the pro-
teinase (HC-Pro) rather than the CP gene is
Potato virus X
strains
With PVX, when the CP genes of isolates defined
biologically by the symptoms elicited in the pres-
ence of hypersensitivity genes
Nx
and
Nb
were
sequenced, the two clades found were named
B and X. This was on the assumption that type
B isolates, but not type X isolates, overcame
Nx
(Santa-Cruz and Baulcombe, 1995). Malcuit
et al
. (2000) found strain groups
1
and
3
within
X, and strain groups
2
and
4
within B, which was
still consistent with this suggestion. However,
Cox and Jones (2010b) subsequently found that
isolates belonging to biological strain group
4
(which overcomes
Nx
and
Nb
) could also occur in
clade X, showing that the biologically and phylo-
genetically defined PVX strain groupings did not
necessarily coincide. This finding supported the
change in PVX clade nomenclature from X to I
and from B to II made previously by others (e.g.
Komatsu
et al
., 2005; Yu
et al.
, 2008). Clade I iso-
lates were from six different continents, but clade
II subclades II-
1
and II-
2
were only from Europe
(II-1) or North and South America (II-2) (Cox
and Jones, 2010b). The PVX genes that elicit the
different host PVX resistance genes are known:
the PVX
25-
kDa movement protein gene elicits
hypersensitivity in plants with
Nb
but the CP
gene elicits hypersensitivity in plants with
Nx
,
and extreme resistance in plants with gene
Rx
(Kavanagh
et al
., 1992; Goulden
et al
., 1993;
Bendahmane
et al
., 1995; Malcuit
et al
., 1999).
Potato virus Y
strains
PVY and
Potato virus C
(PVC) were first recog-
nized in 1931 and 1936, respectively, being
