Previous Article | Next Article 
Journal of Virology, October 1999, p. 8741-8749, Vol. 73, No. 10
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Evidence of Recombination among
Enteroviruses
Juhana
Santti,1,*
Timo
Hyypiä,1,2
Leena
Kinnunen,3 and
Mika
Salminen4
MediCity Research Laboratory and Department
of Virology, University of Turku, FIN-20520
Turku,1 Department of Virology, Haartman
Institute, FIN-00014 University of Helsinki,2
and Department of Epidemiology and Health
Promotion3 and HIV Laboratory,
Department of Infectious Disease Epidemiology,4
National Public Health Institute, FIN-00300 Helsinki, Finland
Received 1 February 1999/Accepted 6 July 1999
 |
ABSTRACT |
Human enteroviruses consist of more than 60 serotypes, reflecting a
wide range of evolutionary divergence. They have been genetically
classified into four clusters on the basis of sequence homology in the
coding region of the single-stranded RNA genome. To explore further the
genetic relationships between human enteroviruses and to characterize
the evolutionary mechanisms responsible for variation, previously
sequenced genomes were subjected to detailed comparison. Bootstrap and
genetic similarity analyses were used to systematically scan the
alignments of complete genomic sequences. Bootstrap analysis provided
evidence from an early recombination event at the junction of the 5'
noncoding and coding regions of the progenitors of the current
clusters. Analysis within the genetic clusters indicated that
enterovirus prototype strains include intraspecies recombinants.
Recombination breakpoints were detected in all genomic regions except
the capsid protein coding region. Our results suggest that
recombination is a significant and relatively frequent mechanism in the
evolution of enterovirus genomes.
| |
INTRODUCTION |
Human enteroviruses have been
subgrouped into polioviruses (PVs) (3 serotypes), coxsackie A viruses
(CAVs) (23 serotypes), coxsackie B viruses (CBVs) (6 serotypes),
echoviruses (EVs) (28 serotypes), and enteroviruses 68 to 71, mainly on
the basis of pathogenicity in experimental animals. Recent studies have
indicated that human enterovirus genomes, approximately
7,500-nucleotide (nt) single-stranded RNA molecules of positive
polarity, can be phylogenetically divided into two distinct groups in
the 5' noncoding region (NCR) (nt 1 to 750); PVs, CAV21, CAV24, and
enterovirus 70 belong to group I, while all sequenced EVs, CBVs, CAV9,
CAV16, and enterovirus 71 form group II (13, 28, 29). In the
coding region and the 3' NCR, group I viruses divide further into
clusters C and D and group II viruses divide into clusters A and B. Partial sequence analysis has shown that all enterovirus prototype
strains fall into these clades (12, 27, 30). A proposed new
species classification for human enteroviruses is based on the four
clusters (A to D) (18). PVs, although genetically
representatives of cluster C, have been separated as their own species
on the basis of unique clinical features and receptor usage.
The spectrum of clinical manifestations of enterovirus infection varies
from asymptomatic infections and the common cold to fatal cases of
myocarditis and infections of the central nervous system. The high
degree of enterovirus diversity is also reflected by the number of cell
surface molecules they recognize during entry into the host cell. At
least six different membrane proteins are known to interact with human
enteroviruses (5). These include members of the
immunoglobulin superfamily (poliovirus receptor, intercellular adhesion
molecule 1, and coxsackievirus-adenovirus receptor), integrins, and
decay accelerating factor, the normal function of which is to protect
cells from the action of complement. Expression of virus receptors and
other cellular factors interacting with viral macromolecules are
important determinants in the pathogenesis of infection.
Since different parts of the enterovirus genome have distinct roles
during the replication cycle, they may also evolve differently and
possibly exhibit remarkable independence during evolution. The 5' NCR
has two functions: it contains the initiation site for synthesis of the
genomic RNA strand and the internal ribosome entry site responsible for
initiation of cap-independent translation. The capsid, encoded by the
P1 region of the genome, mediates attachment and entry of the virus
into target cells and is therefore essential for tissue and host
tropism. The capsid is also an important target for host immune
responses. The nonstructural (NS) (P2 and P3) region codes for proteins
which function in RNA replication, and the 3' NCR is involved in
initiation of synthesis of the complementary RNA strand. The interplay
between these elements includes processing of capsid proteins by NS
proteases and recognition of replication initiation sites by the
polymerase complex.
Mutation and recombination are the mechanistic alternatives for
enterovirus evolution. Due to the absence of proofreading activity, the
misinsertion rate of the viral polymerase is high, averaging up to one
mutation per newly synthesized genome (4). Consequently,
enteroviruses, like other RNA viruses, exist as quasispecies, diverse
mixtures of virus mutants differing from each other at one or several
sites (10). Recombination has been shown to occur between
PVs of vaccine and wild-type origin (2, 8). The evidence
supports a model of homologous recombination by strand switching (copy
choice) (14, 19). For many other RNA viruses, recombination
and reassortment have been shown to be important features of viral
evolution. Acquisition of new genome segments by influenza A virus
strains has been correlated with the initiation of new pandemics and
therefore has a profound impact on the biology and evolution of the
virus (16). Recently, evidence of recombination between
hantaviruses has also been reported (39). Among
retroviruses, such as the human immunodeficiency virus (HIV), recombination is a frequent phenomenon and contributes significantly to
viral evolution (3, 9, 32, 36). HIV type 1 (HIV-1) strains
are assigned to genetic subtypes (A to J), which are defined in a way
similar to that of enterovirus clusters (25). It has been
estimated that up to 10% of all characterized HIV-1 strains are
intersubtype recombinants (32).
To obtain a detailed picture of the genetic relationships and molecular
evolution of human enteroviruses, previously sequenced strains were
selected for systematic analysis of all genomic regions.
| |
MATERIALS AND METHODS |
Bootscanning analysis.
Enteroviral sequences were analyzed
systematically for phylogenetic clustering patterns in different genome
regions. Full-length genomic sequences of 27 human enteroviruses, 3 swine vesicular disease viruses (SVDVs), and 4 human rhinoviruses
(HRVs) available in the databases were analyzed (Table
1). SVDV strains were selected for
analysis because of their antigenic and genetic similarity to CBV5
(43), while HRV sequences were included to serve as an
outgroup, since they have previously been shown to represent the
closest genetic relatives of enteroviruses (11, 13).
Sequences were aligned with Clustal W software (41), and the
resulting alignment was further optimized manually with Genetic Data
Environment (GDE), version 2.2 (40). Regions where gaps had
to be introduced in the alignment were deleted from all phylogenetic
analyses by the masking feature of GDE. Bootscanning of the aligned
sequences was performed as previously described (35). The
method makes use of the bootstrapping procedure, which estimates the
support for the clustering pattern of the phylogenetic tree by
resampling the input sequence data (6). Bootstrap scores of
>70% are usually thought to indicate significant support. During the
bootscanning procedure, the alignment was divided into sequential
segments of 300 nt, overlapping every previous segment by 250 nt. A
bootstrapped phylogenetic analysis with 100 replicates was applied to
each segment by using the neighbor-joining algorithm. For each segment, bootstrap values for the studied virus clusters were plotted along the
genome. The PHYLIP package, version 3.572c, was used for phylogenetic analysis (7). PHYLIP outfiles give bootstrap values for all taxon clusters found in the bootstrap replicates, which permits estimation of support for clusters which are not represented in the
consensus tree. The bootscanning package consists of subprograms for
extraction of segments from the full-length alignment (chop) and for extraction of bootstrap values from the PHYLIP outfiles generated from each genome segment (analyse and collect). A
series of shell scripts was used to perform phylogenetic analyses on each segment. The bootscanning package is available in ANSI-C source
code, as well as in Sun and Linux binary formats (36a).
Similarity analysis.
To analyze genetic relationships and
recombination within enterovirus species, similarity analysis was
employed separately for each cluster by using the SimPlot program
(23, 31). A segmented analysis equivalent to the
Bootscanning procedure was performed, but instead of bootstrap values,
pairwise genetic similarities of a query sequence against other
sequences of the alignment were calculated for each segment (a 400-nt
window which was moved 20 nt at a time). Similarity values were then
plotted along the genome.
| |
RESULTS |
Enterovirus clades along the genome.
By bootscanning of the
full-length genome alignment, the occurrence and stability of the
previously described genetic groups, I and II, and clusters A to C were
systematically tested in different parts of the genome. Groups I and II
were highly supported in the 5' NCR (>70%) (Fig.
1). At positions 600 (group I) and 750 (group II) of the alignment, the bootstrap values of the groups fell
sharply and stayed low along the rest of the genome, except for a few
scattered positions (Fig. 1). Separate analysis of the genome areas
corresponding to such peaks in the group II bootscan revealed that they
were due to the relative proximity of the cluster A and B viruses,
which, however, remained clearly separated in the coding region and the
3' NCR (data not shown). Similarly, in some regions, enterovirus 70 appeared momentarily somewhat closer to cluster C viruses but still
remained clearly distinct.
View larger version (27K):
[in this window]
[in a new window]
|
FIG. 1.
(A) Phylogenetic tree illustrating genetic relationships
between enterovirus and rhinovirus genomes in the 5' NCR. Enterovirus
5' NCR groups I and II are indicated. (B) Bootscanning analysis of
groups I (upper panel) and II (lower panel) along the genome was
performed by the neighbor-joining method as implemented in the PHYLIP
package (see text for details). PHYLIP reports bootstrap frequencies
for all clusters found in the bootstrap replicates, which permits
plotting of values for clusters which are not found in the consensus
tree (areas of low bootstrap values). Bootstrap values are shown at the
midpoint of each window.
|
|
High bootstrap values were obtained for enterovirus clusters A to C in
the coding region and in the 3' NCR (Fig.
2). Since
enterovirus 70 is the only
completely sequenced member of proposed
species D, its occurrence as an
independent monophyletic lineage
could not be directly tested by
bootstrap analysis. However, it
always remained as an outlier in trees
derived from the coding
region and the 3' NCR, which supports its
classification as a
separate enteroviral species. Low bootstrap values
for clusters
A, B, and C in the 5' NCR suggest that this clustering
does not
exist as a substructure of groups I and II. Two depressions in
the cluster C bootscan, corresponding to the genome alignment
from
position 601 to 1200 and from position 2400 to 2800, were
found to be
due to separation of two viruses (CAV21 and CAV24)
from the cluster
into independent lineages. Separate phylogenetic
analysis showed that
between positions 601 and 900 of the alignment,
CAV21 appears as a
single outlier equidistant from the other clades
(Fig.
3A). In the adjacent genome region
(position 901 to 1200),
CAV21 is joined by CAV24 (Fig.
3B). Again, in
the VP1 capsid protein
coding region (position 2400 to 2800), these two
viruses separate
from the rest of cluster C to form an independent
clade which
is not directly associated with any of the other clusters
(Fig.
3C).
View larger version (27K):
[in this window]
[in a new window]
|
FIG. 2.
(A) Grouping of enteroviruses and rhinoviruses in the
coding region and the 3' NCR of the genome. The four genetic clusters
(A to D) of enteroviruses are shown. (B) Bootscanning of clusters A, B,
and C (performed as described in the legend to Fig. 1).
|
|
View larger version (18K):
[in this window]
[in a new window]
|
FIG. 3.
Alterations in clustering of enteroviruses and
rhinoviruses in the 5'-terminal region of the genome. Trees correspond
to nt 601 to 900 (A), 901 to 1200 (B), and 2400 to 2800 (C) of the
alignment. Viruses interacting with poliovirus receptor are marked with
shaded circles, and those recognizing intercellular adhesion molecule 1 are marked with open circles (C). Bars indicate 10% divergence.
|
|
Recombination may explain the phylogenetic division of groups I and
II.
Bootscanning analysis extends the previous results by showing
that the abrupt change in phylogenetic grouping which occurs between
the 5' NCR and the coding region-3' NCR (approximately position 700 of
the alignment) is a consistent feature of the enteroviral genome (Fig.
1 and 2). Groups I and II are highly supported only in the region
preceding the initiation codon, and there is no indication of
substructure within the two groups (Fig. 1B and 2B). After position
700, groups I and II split, and high support is seen only for the
species-defining clusters A to C (Fig. 1B and 2B) (except for the
regions where divergence of the CAV21 and CAV24 sequences lowers the
bootstrap values of cluster C). Such a marked difference in clustering
strongly supports the alternative that the mechanism resulting in the
change may be recombination rather than conservation. Indirect evidence
for this possibility could be drawn from the analysis of variation within clusters A to C, which indicates that intraspecies recombination frequently occurs. This was especially evident within cluster B (see below).
Variation within enterovirus clusters.
Sequences within each
cluster were separately subjected to genetic similarity analyses, in
which each strain was compared to all other strains of the cluster. For
cluster A, three complete genome sequences were available (Table 1).
Comparison of CAV16 with the two enteroviruses 71 strains resulted in
similarity curves showing more variation in the P1 region than in the
5' NCR or the NS region (Fig. 4A). The
genetic similarity between the two enterovirus 71 strains in the P1
region (nt 1000 to 3500 in the alignment) was significantly higher than
that observed between enterovirus 71 and CAV16 (Fig. 4B). In contrast,
all three viruses appeared equidistant in the NS region (nt 3500 to
7500).
View larger version (29K):
[in this window]
[in a new window]
|
FIG. 4.
Genetic distances between cluster A enteroviruses along
the genome as determined by similarity analysis (window, 400 nt; step,
20 nt). Query sequences are noted. Phylogenetic trees correspond to the
capsid (P1 [C]) and NS (P2 and P3 [D]) protein coding regions.
|
|
Results of the similarity plots can be explained by the occurrence of
intraspecies recombination. By this interpretation,
the low divergence
between the two enterovirus 71 strains in the
P1 region could represent
a recent recombination event between
equidistantly evolved members of
enterovirus species A which have
recombined at the P1-P2 junction to
form intraspecies chimeras.
Findings of the similarity analysis were
supported by phylogenetic
analysis of the two regions (Fig.
4C and
D).
Seventeen cluster B genomic sequences were available (Table
1). SimPlot
analysis resulted in a pattern of interstrain variation
generally
similar to that seen for cluster A (Fig.
5). High average
sequence similarity was
seen in the 5' NCR (80 to 95%), lower
similarity was seen in the P1
region (60 to 80%), and, again,
higher similarity was seen in the
region coding for NS proteins
and the 3' NCR (80 to 90%). However, in
all viruses examined,
and in all genome areas, regions of
higher-than-average intersequence
similarity were detected, suggesting
a role for intraspecies recombination
in the evolution of cluster B
viruses.
View larger version (61K):
[in this window]
[in a new window]
|
FIG. 5.
Genetic distances between cluster B enteroviruses
(SimPlot analysis) (window, 400 nt; step, 20 nt). Query sequences are
noted.
|
|
As for species A, many examples of higher-than-average similarity in
the P1 region were detected in comparisons between different
strains of
the same serotype. These included the two CBV3 (Fig.
5D and E), CBV4
(Fig.
5F and G), and EV9 strains (Fig.
5K and
L), as well as the three
strains of SVDV and CBV5 (Fig.
5H and
O), which represent the same
serotype despite different hosts.
The three SVDV strains showed high
similarity (>95%) to each other
in all genome regions (Fig.
5O).
However, in contrast to species
A, many regions of higher-than-average
similarity were also seen
in the NS region: CAV9 showed >90%
similarity to EV9H and CBV1
at nt 6210 to 7520 and to CBV3W at nt 5500 to 7520 (Fig.
5A).
CBV1 also showed >90% similarity to EV6 from
position 4470 to
5050 and >95% similarity to the two CBV3 strains in
the 5' NCR
(Fig.
5B). CBV2 showed higher-than-average similarity to two
other
serotypes: CBV3N from position 4500 to 5500 and EV11 from
position
7000 to the end of the genome (Fig.
5C). For the two CBV3
strains,
positions 1 to 4000 showed high similarity (>95%),
indicating
recent divergence between the strains in this region (Fig.
5D
and E). The viruses differed from each other in the NS region,
where
the CBV3N strain showed homology to CBV2 (Fig.
5D) whereas
the CBV3W
strain displayed high similarity to EV9H, CBV1, and
CAV9 (Fig.
5E). For
the CBV3W strain, the longest region of similarity
in the NS region was
to EV9H (Fig.
5E). Clear areas of high similarity
in the NS region were
also detected between CBV6 and EV12 (Fig.
5I and N), as well as between
EV9H and EV11 (Fig.
5L and M). Increased
similarity between EV9B and
SVDVs, which Zhang et al. (
43) detected
in a partial
sequence (615 nt), was seen at nt 5200 to 6500 (Fig.
5K and
O).
The results of intraspecies comparisons for cluster B provide strong
evidence that multiple recombination events, both within
and between
serotypes, have shaped the evolution of this cluster.
It would be
difficult to envision any other evolutionary process
which would lead
to the patterns observed, especially in the case
of the CBV3 strains
included in the analysis. The results for
cluster B also make the
recombination interpretation of the patterns
seen in cluster A more
likely.
Results of similarity analysis for enterovirus cluster C agree with the
findings observed in the bootscanning procedure. However,
the analysis
did not find suggestions of intraspecies recombination
as clear as for
clusters A and B. Comparison of each strain against
the other viruses
of cluster C indicates that CAV21 and CAV24
diverge from the PVs in the
P1 region but also around nt 3000
to 5300 (Fig.
6A and B). In the P1 region, CAV21 and
CAV24 are
more closely related to each other than to PVs. However, in
the
P2 region, the two CAVs are as distant from each other as from
the
PVs, which form a more coherent group. These patterns of similarity
suggest that the viruses have evolved through complex evolutionary
pathways which the methods employed here are not able to resolve.
The
serotype classification seems to follow the degree of similarity
between the strains in the P1 region but is not necessarily reflected
in the NS region. This is illustrated particularly well by the
PV3
isolate from Finland (PV3F), which shows increased homology
to the
other PV3 strains only in the P1 region (Fig.
6C) and actually
seems to
be closest to PV2 in the NS region (data not shown).
View larger version (30K):
[in this window]
[in a new window]
|
FIG. 6.
SimPlot analysis of cluster C enteroviruses (window, 400 nt; step, 20 nt). Query sequences are noted.
|
|
The patterns of similarity between members of enterovirus cluster C are
more difficult to interpret than are those of clusters
A and B. Although some suggestions for possible interstrain recombination
were
seen, especially in comparisons of the CAV21 and CAV24 strains,
we
cannot rule out the possibility that the evolution of cluster
C viruses
follows pathways different from those of clusters A
and B. However, the
number of analyzed full-length sequences that
belong to cluster C is
currently small, representing mostly PV
vaccine and vaccine-related
strains, and may therefore not be
representative of wild-type
viruses.
| |
DISCUSSION |
Enterovirus recombination has previously been demonstrated with
PVs, and artificial chimeras between different enteroviral species have
been produced in vitro. However, direct evidence of recombination
contributing to the evolution of enteroviruses other than PVs has not
been presented. In PVs, it has been estimated that the intratypic
recombination frequency for the entire genome is approximately 15%
(17). Recombination between intertypic PV strains, which
have 85% nucleotide identity, has been observed at a 100-fold-lower
frequency than intratypic recombination between completely homologous
parents (19). Viable recombinants have also been produced
between members of different enterovirus species by exchanging various
genomic regions in vitro with molecular cloning techniques (15,
24, 33, 34, 37, 42). While not all artificially produced
interspecies chimeras were viable, these studies have demonstrated that
some genome regions may be interchangeable between different enteroviruses.
The existence of only two enterovirus clades in the 5' NCR but four
elsewhere in the genome has previously been proposed to be a
consequence of strong evolutionary restrictions in this genomic region
(29) and to reflect conservation of the RNA secondary structures required for efficient replication and translation (34). We were interested in studying this phenomenon further by using novel phylogenetic approaches.
Results of bootscanning analyses of 30 complete enterovirus genomes
were, in general, consistent with previously established clades for the
proposed regions: groups I and II were supported by high bootstrap
values in the 5' NCR, while clusters A, B, and C were supported in the
coding region and the 3' NCR. However, our findings suggest that the
reduction in the number of enterovirus clades observed in the 5' NCR
compared to the coding region and the 3' NCR could be a consequence of
recombination rather than structural conservation. In support of such a
hypothesis, the low bootstrap values for groups I and II in the coding
region and the 3' NCR indicate that groups I and II do not represent earlier states of enterovirus evolution in these genome regions. Similarly, 5' NCR groups I and II do not exhibit signs of separate subclades for cluster A, B, C, or D, which would be expected if the
viruses had evolved only by accumulation of point mutations. Since the
clusters are equidistantly separated in the different regions, a model
in which four clusters have evolved from two is difficult to envisage.
Instead, the different phylogenetic grouping of enteroviruses in the 5'
NCR compared to the rest of the genome could be explained by two
recombination events, in which two of the progenitors of current clades
A to D have replaced their original 5' regions with those of the other
two clades (Fig. 7), perhaps to gain more
efficient translation initiation machinery. Although this model might
be overly simplistic, it provides an approximation for a hypothesis
based on recombination. The alternative possibility is that viruses
originating from common progenitors have evolved to form two extra
clusters in the coding region and the 3' NCR, while in the 5' NCR the
same virus genomes have remained in the two original genetic groups.
This would require strong conservation in the 5' NCR, which is
certainly possible, but also a large number of highly convergent point
mutations in the rest of the genome to form the two additional
clusters, which may be more difficult to generate during evolution.
However, such a possibility cannot be formally excluded.
View larger version (22K):
[in this window]
[in a new window]
|
FIG. 7.
Schematic presentation of proposed recombination events
between the 5' NCR and the rest of the genome during enterovirus
evolution which could explain the existence of currently known
subgroups. First, four genetic lineages evolved from a common
enterovirus progenitor by point mutations. During evolution, the
lineage A virus acquired the lineage B virus 5' NCR by recombination.
Alternatively, the lineage B virus could have acquired the lineage A
virus 5' NCR. A similar recombination event may have occurred between
lineage C and D viruses. Current species classification of human
enteroviruses is based mainly on four genetic lineages (clusters A to
D) observed in the coding region and the 3' NCR. Due to the proposed
recombination, only two genetic groups are seen in the 5' NCR. Viruses
containing the 5' NCR from the other two lineages have disappeared or
have not been sampled to date.
|
|
A highly speculative possibility concerning the origin of the two extra
clades in the coding region-3' NCR is that these genetic lineages
originate from animal viruses which have acquired a more efficient 5'
NCR for human cells by recombination. Recent work on animal models
showing that the 5' NCR can include determinants that affect the host
range supports this hypothesis (38). However, without direct
evidence from animal enteroviruses, such a hypothesis cannot be
verified. An alternative hypothesis is that the original 5' NCRs were
simply lost due to chance or poor fitness compared to the current 5' NCRs.
More direct evidence for the role of recombination in enterovirus
evolution was provided by sequence comparisons within the species-defining clusters. In enteroviruses, variation in the capsid
protein coding sequences is known to be clearly more extensive than
that in the NS regions, and this was also evident in the similarity
analysis. Examination of sequence variation within enterovirus species
revealed a general pattern of high sequence homology in the 5' NCR,
lower homology in the P1 region, and, again, higher homology in the
region coding for the NS proteins and the 3' NCR, resulting in the
characteristic wavelike shape of the curve in similarity plots (Fig. 4
to 6). While the exact degree and localization of similarity was
somewhat different between clusters, the basic shape of the similarity
plot was repeated in the intraspecies comparisons of all clusters.
However, exceptions to the basic shape were also detected within each
cluster. Especially in cluster B, many regions of higher-than-average similarity in pairwise comparisons were seen between individual strains
(Fig. 5). Perhaps the most striking example of this was between the two
CBV3 strains (Nancy and Woodruff 20-22]). From the 5' end of the
genome up to position 4000, similarity values in excess of 95% were
observed. In contrast, similarity in the NS gene region was much lower
and did not correlate with the serotype classification. Instead,
several regions in the 3' half of the genome exhibited
higher-than-average sequence homology to other strains. Versions of
this pattern were also repeated between viruses of different serotypes.
We interpret the patterns of higher-than-average similarity as evidence
of recombination events between viruses of the same species.
In intraspecies comparisons, none of the putative recombination
breakpoints were detected within the P1 region, suggesting that the
virus capsid is a relatively stable unit. In contrast, several
breakpoints occurred within the P2 and P3 regions. The fact that the NS
genes are more homologous than the structural genes between members of
genetic clusters may explain the occurrence of frequent recombination
events in the NS protein coding region. Notably, only a few of the
putative recombination breakpoints observed in the NS region were
situated at the cleavage sites of individual viral proteins. Instead,
most of the regions of higher-than-average sequence homology between
different members of a species either covered only a part of one
individual viral gene or spanned several neighboring genes. In general,
crossover sites in the NS region seemed to be relatively randomly
distributed rather than being concentrated on some specific genome
region. Based on the results obtained by similarity analyses of the
cluster A and B viruses, it seems likely that enterovirus genomes
contain regions that are interchangeable and that viable virus chimeras arise frequently between the members of a species.
Results of the bootstrap as well as the similarity analysis of cluster
C indicated that CAV21 and CAV24 carry sequences in the capsid protein
coding region which clearly separate them from the PVs. However, in
other genomic regions these strains were no more related to each other
than to the PVs. It is known that cluster C coxsackieviruses utilize
intercellular adhesion molecule 1 (1, 30) for cell entry
while polioviruses recognize another member of the immunoglobulin
superfamily, the poliovirus receptor (26). The differences
seen between CAVs and PVs in the capsid protein coding region could be
responsible for the differences seen in receptor utilization and could
therefore affect the clinical outcomes of diseases caused by these
viruses. Based on the results of our analyses, we were not able to
conclude how the regions of the capsid shared by CAV21 and CAV24 and
unrelated to the PVs have evolved.
In conclusion, the complex patterns of regions of higher-than-average
similarity in pairwise comparisons across serotypes, as observed for
enterovirus clusters A, B, and C, are not easily explained with a model
of evolution based only on gradual accumulation of mutations and
subsequent starlike divergence from a common ancestor. Instead, we
propose that they could have been generated through multiple homologous
recombination events, leading to shuffling of gene segments between
various strains. All of the observed relationships of high homology
between different serotypes could be verified with high (>90%)
bootstrap values (data not shown). The results indicate that there may
be several potential recombination hot spots in the enterovirus genome,
including the junction between the 5' NCR and the P1 region and around
the region coding for the C terminus of VP1. The NS region may also
contain locations where recombination events accumulate. Our
observations support the possibility that exchange of different genomic
regions by recombination, in addition to the great adaptability
provided by the high mutation rate, is an important mechanism in
enterovirus evolution. This would allow independent evolution of
elements with different functions needed during the viral replication
cycle and would permit rapid alterations in host and tissue tropism. Our observations also suggest that enterovirus serotypes accurately reflect the capsid type of the virus but not necessarily other parts of
the genome.
| |
ACKNOWLEDGMENTS |
This study was supported by grants from the Turku University
Foundation, the Finnish Cultural Foundation, the Finnish Medical Foundation, the Academy of Finland, and the Sigrid Juselius Foundation.
We thank Tapani Hovi, Alexander Plyusnin, and Glyn Stanway for helpful comments.
| |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Virology, University of Turku, Kiinamyllynkatu 13, FIN-20520 Turku,
Finland. Phone: 358-2-3337461. Fax: 358-2-2513303. E-mail:
juhana.santti{at}utu.fi.
| |
REFERENCES |
| 1.
|
Abraham, G., and R. J. Colonno.
1984.
Many rhinovirus serotypes share the same cellular receptor.
J. Virol.
51:340-345[Abstract/Free Full Text].
|
| 2.
|
Cammack, N.,
A. Phillips,
G. Dunn,
V. Patel, and P. D. Minor.
1988.
Intertypic genomic rearrangements of poliovirus strains in vaccinees.
Virology
167:507-514[Medline].
|
| 3.
|
Carr, J. K.,
M. O. Salminen,
J. Albert,
E. Sanders-Buell,
D. Gotte,
D. L. Birx, and F. E. McCutchan.
1998.
Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants.
Virology
247:22-31[Medline].
|
| 4.
|
Drake, J. W.
1993.
Rates of spontaneous mutation among RNA viruses.
Proc. Natl. Acad. Sci. USA
90:4171-4175[Abstract/Free Full Text].
|
| 5.
|
Evans, D. J., and J. W. Almond.
1998.
Cell receptors for picornaviruses as determinants of cell tropism and pathogenesis.
Trends Microbiol.
6:198-202[Medline].
|
| 6.
|
Felsenstein, J.
1985.
Confidence limits on phylogenies: an approach using the bootstrap.
Evolution
39:783-791.
|
| 7.
|
Felsenstein, J.
1996.
PHYLIP: phylogeny inference package, version 3.572c.
University of Washington, Seattle.
|
| 8.
|
Furione, M.,
S. Guillot,
D. Otelea,
J. Balanant,
A. Candrea, and R. Crainic.
1993.
Polioviruses with natural recombinant genomes isolated from vaccine-associated paralytic poliomyelitis.
Virology
196:199-208[Medline].
|
| 9.
|
Gao, F.,
D. L. Robertson,
S. G. Morrison,
H. Hui,
S. Craig,
J. Decker,
P. N. Fultz,
M. Girard,
G. M. Shaw,
B. H. Hahn, and P. M. Sharp.
1996.
The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin.
J. Virol.
70:7013-7029[Abstract/Free Full Text].
|
| 10.
|
Holland, J., and E. Domingo.
1998.
Origin and evolution of viruses.
Virus Genes
16:13-21[Medline].
|
| 11.
|
Horsnell, C.,
R. E. Gama,
P. J. Hughes, and G. Stanway.
1995.
Molecular relationships between 21 human rhinovirus serotypes.
J. Gen. Virol.
76:2549-2555[Abstract/Free Full Text].
|
| 12.
|
Huttunen, P.,
J. Santti,
T. Pulli, and T. Hyypiä.
1996.
The major echovirus group is genetically coherent and related to coxsackie B viruses.
J. Gen. Virol.
77:715-725[Abstract/Free Full Text].
|
| 13.
|
Hyypiä, T.,
T. Hovi,
N. J. Knowles, and G. Stanway.
1997.
Classification of enteroviruses based on molecular and biological properties.
J. Gen. Virol.
78:1-11[Medline].
|
| 14.
|
Jarvis, T. C., and K. Kirkegaard.
1992.
Poliovirus RNA recombination: mechanistic studies in the absence of selection.
EMBO J.
11:3135-3145[Medline].
|
| 15.
|
Johnson, V. H., and B. L. Semler.
1988.
Defined recombinants of poliovirus and coxsackievirus: sequence-specific deletions and functional substitutions in the 5'-noncoding regions of viral RNAs.
Virology
162:47-57[Medline].
|
| 16.
|
Kendal, A. P.
1987.
Epidemiologic implications of changes in the influenza virus genome.
Am. J. Med.
82:4-14[Medline].
|
| 17.
|
King, A. M. Q.
1988.
Recombination in positive strand RNA viruses, p. 149-165.
In
E. Domingo, J. J. Holland, and P. Ahlquist (ed.), RNA genetics, vol. 2. CRC, Boca Raton, Fla.
|
| 18.
|
King, A. M. Q.,
F. Brown,
P. Christian,
T. Hovi,
T. Hyypiä,
N. J. Knowles,
S. M. Lemon,
P. D. Minor,
A. C. Palmenberg,
T. Skern, and G. Stanway.
1999.
Picornaviridae, p. 996.
In
M. H. V. van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carsten, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle, and R. B. Wickner (ed.), Virus taxonomy. Seventh report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, Calif.
|
| 19.
|
Kirkegaard, K., and D. Baltimore.
1986.
The mechanism of RNA recombination in poliovirus.
Cell
47:433-443[Medline].
|
| 20.
|
Klump, W. M.,
I. Bergmann,
B. C. Müller,
D. Ameis, and R. Kandolf.
1990.
Complete nucleotide sequence of infectious coxsackievirus B3 cDNA: two initial 5' uridine residues are regained during plus-strand RNA synthesis.
J. Virol.
64:1573-1583[Abstract/Free Full Text].
|
| 21.
|
Knowlton, K. U.,
E.-S. Jeon,
N. Berkley,
R. Wessely, and S. Huber.
1996.
A mutation in the puff region of VP2 attenuates the myocarditic phenotype of an infectious cDNA of the Woodruff variant of coxsackievirus B3.
J. Virol.
70:7811-7818[Abstract/Free Full Text].
|
| 22.
|
Lindberg, A. M.,
P. O. K. Stålhandske, and U. Pettersson.
1987.
Genome of coxsackievirus B3.
Virology
156:50-63[Medline].
|
| 23.
|
Lole, K. S.,
R. C. Bollinger,
R. S. Paranjape,
D. Gadkari,
S. S. Kulkarni,
N. G. Novak,
R. Ingersoll,
H. W. Sheppard, and S. C. Ray.
1999.
Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
J. Virol.
73:152-160[Abstract/Free Full Text].
|
| 24.
|
Lu, H.-H.,
X. Li,
A. Cuconati, and E. Wimmer.
1995.
Analysis of picornavirus 2Apro proteins: separation of proteinase from translation and replication functions.
J. Virol.
69:7445-7452[Abstract/Free Full Text].
|
| 25.
|
McCutchan, F. E.,
M. O. Salminen,
J. K. Carr, and D. S. Burke.
1996.
HIV-1 genetic diversity.
AIDS
10:S13-S20.
|
| 26.
|
Mendelsohn, C. L.,
E. Wimmer, and V. R. Racaniello.
1989.
Cellular receptor for poliovirus: molecular cloning, nucleotide sequence, and expression of a new member of the immunoglobulin superfamily.
Cell
56:855-865[Medline].
|
| 27.
|
Oberste, M. S.,
K. Maher, and M. A. Pallansch.
1998.
Molecular phylogeny of all human enterovirus serotypes based on comparison of sequences at the 5' end of the region encoding VP2.
Virus Res.
58:35-43[Medline].
|
| 28.
|
Pöyry, T.,
T. Hyypiä,
C. Horsnell,
L. Kinnunen,
T. Hovi, and G. Stanway.
1994.
Molecular analysis of coxsackievirus A16 reveals a new genetic group of enteroviruses.
Virology
202:982-987[Medline].
|
| 29.
|
Pöyry, T.,
L. Kinnunen,
T. Hyypiä,
B. Brown,
C. Horsnell,
T. Hovi, and G. Stanway.
1996.
Genetic and phylogenetic clustering of enteroviruses.
J. Gen. Virol.
77:1699-1717[Abstract/Free Full Text].
|
| 30.
|
Pulli, T.,
P. Koskimies, and T. Hyypiä.
1995.
Molecular comparison of coxsackie A virus serotypes.
Virology
212:30-38[Medline].
|
| 31.
| Ray, S. C. 1997. SimPlot for Windows 95/NT,
version 1.2.2. [Online.] Baltimore, Md. (Distributed by author.)
http://www.welch.jhu.edu/~sray/download.
|
| 32.
|
Robertson, D. L.,
P. M. Sharp,
F. E. McCutchan, and B. H. Hahn.
1995.
Recombination in HIV-1.
Nature
374:124-126[Medline].
|
| 33.
|
Rohll, J. B.,
D. H. Moon,
D. J. Evans, and J. W. Almond.
1995.
The 3' untranslated region of picornavirus RNA: features required for efficient genome replication.
J. Virol.
69:7835-7844[Abstract/Free Full Text].
|
| 34.
|
Rohll, J. B.,
N. Percy,
R. Ley,
D. J. Evans,
J. W. Almond, and W. S. Barclay.
1994.
The 5'-untranslated regions of picornavirus RNAs contain independent functional domains essential for RNA replication and translation.
J. Virol.
68:4384-4391[Abstract/Free Full Text].
|
| 35.
|
Salminen, M. O.,
J. K. Carr,
D. S. Burke, and F. E. McCutchan.
1995.
Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning.
AIDS Res. Hum. Retroviruses
11:1423-1425[Medline].
|
| 36.
|
Salminen, M. O.,
J. K. Carr,
D. L. Robertson,
P. Hegerich,
D. Gotte,
C. Koch,
E. Sanders-Buell,
F. Gao,
P. M. Sharp,
B. H. Hahn,
D. S. Burke, and F. E. McCutchan.
1997.
Evolution and probable transmission of intersubtype recombinant human immunodeficiency virus type 1 in a Zambian couple.
J. Virol.
71:2647-2655[Abstract/Free Full Text].
|
| 36a.
| Salminen, M. O., and W. Cobb. 11 September 1998, revision date. [Online.] Bootscanning package for Unix/Linux, version
1. National Public Health Institute, Helsinki, Finland.
http://www.ktl.fi/hiv.
|
| 37.
|
Semler, B. L.,
V. H. Johnson, and S. Tracy.
1986.
A chimeric plasmid from cDNA clones of poliovirus and coxsackievirus produces a recombinant virus that is temperature-sensitive.
Proc. Natl. Acad. Sci. USA
83:1777-1781[Abstract/Free Full Text].
|
| 38.
|
Shiroki, K.,
T. Ishii,
T. Aoki,
Y. Ota,
W. X. Yang,
T. Komatsu,
Y. Ami,
M. Arita,
S. Abe,
S. Hashizume, and A. Nomoto.
1997.
Host range phenotype induced by mutations in the internal ribosomal entry site of poliovirus RNA.
J. Virol.
71:1-8[Abstract/Free Full Text].
|
| 39.
|
Sibold, C.,
H. Meisel,
D. H. Krüger,
M. Labuda,
J. Lysy,
O. Kozuch,
M. Pejcoch,
A. Vaheri, and A. Pluysnin.
1999.
Recombination in Tula hantavirus evolution: analysis of genetic lineages from Slovakia.
J. Virol.
73:667-675[Abstract/Free Full Text].
|
| 40.
|
Smith, S. W.,
R. Overbeek,
C. R. Woese,
W. Gilbert, and P. M. Gillevet.
1994.
The Genetic Data Environment: an expandable GUI for multiple sequence analysis.
Comput. Appl. Biosci.
10:671-675[Abstract/Free Full Text].
|
| 41.
|
Thompson, J. D.,
D. G. Higgins, and T. J. Gibson.
1994.
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acids Res.
22:4673-4680[Abstract/Free Full Text].
|
| 42.
|
van Kuppeveld, F. J.,
P. J. van den Hurk,
W. van der Vliet,
J. M. Galama, and W. J. Melchers.
1997.
Chimeric coxsackie B3 virus genomes that express hybrid coxsackievirus-poliovirus 2B proteins: functional dissection of structural domains involved in RNA replication.
J. Gen. Virol.
78:1833-1840[Abstract].
|
| 43.
|
Zhang, G.,
G. Wilsden,
N. J. Knowles, and J. W. McCauley.
1993.
Complete nucleotide sequence of a coxsackie B5 virus and its relationship to swine vesicular disease virus.
J. Gen. Virol.
74:845-853[Abstract/Free Full Text].
|
Journal of Virology, October 1999, p. 8741-8749, Vol. 73, No. 10
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
This article has been cited by other articles:
-
Benschop, K. S. M., de Vries, M., Minnaar, R. P., Stanway, G., van der Hoek, L., Wolthers, K. C., Simmonds, P.
(2010). Comprehensive full-length sequence analyses of human parechoviruses: diversity and recombination. J. Gen. Virol.
91: 145-154
[Abstract]
[Full Text]
-
Williams, C. H., Panayiotou, M., Girling, G. D., Peard, C. I., Oikarinen, S., Hyoty, H., Stanway, G.
(2009). Evolution and conservation in human parechovirus genomes. J. Gen. Virol.
90: 1702-1712
[Abstract]
[Full Text]
-
Blomqvist, S., Savolainen-Kopra, C., Paananen, A., Hovi, T., Roivainen, M.
(2009). Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses. J. Gen. Virol.
90: 1371-1381
[Abstract]
[Full Text]
-
Leitch, E. C. M., Bendig, J., Cabrerizo, M., Cardosa, J., Hyypia, T., Ivanova, O. E., Kelly, A., Kroes, A. C. M., Lukashev, A., MacAdam, A., McMinn, P., Roivainen, M., Trallero, G., Evans, D. J., Simmonds, P.
(2009). Transmission Networks and Population Turnover of Echovirus 30. J. Virol.
83: 2109-2118
[Abstract]
[Full Text]
-
Benschop, K. S. M., Williams, C. H., Wolthers, K. C., Stanway, G., Simmonds, P.
(2008). Widespread recombination within human parechoviruses: analysis of temporal dynamics and constraints. J. Gen. Virol.
89: 1030-1035
[Abstract]
[Full Text]
-
Lukashev, A. N., Ivanova, O. E., Eremeeva, T. P., Gmyl, L. V.
(2008). Analysis of Echovirus 30 Isolates from Russia and New Independent States Revealing Frequent Recombination and Reemergence of Ancient Lineages. J. Clin. Microbiol.
46: 665-670
[Abstract]
[Full Text]
-
Mirand, A., Henquell, C., Archimbaud, C., Chambon, M., Charbonne, F., Peigue-Lafeuille, H., Bailly, J.-L.
(2008). Prospective Identification of Enteroviruses Involved in Meningitis in 2006 through Direct Genotyping in Cerebrospinal Fluid. J. Clin. Microbiol.
46: 87-96
[Abstract]
[Full Text]
-
Smura, T., Blomqvist, S., Paananen, A., Vuorinen, T., Sobotova, Z., Bubovica, V., Ivanova, O., Hovi, T., Roivainen, M.
(2007). Enterovirus surveillance reveals proposed new serotypes and provides new insight into enterovirus 5'-untranslated region evolution. J. Gen. Virol.
88: 2520-2526
[Abstract]
[Full Text]
-
Bouslama, L., Nasri, D., Chollet, L., Belguith, K., Bourlet, T., Aouni, M., Pozzetto, B., Pillet, S.
(2007). Natural Recombination Event within the Capsid Genomic Region Leading to a Chimeric Strain of Human Enterovirus B. J. Virol.
81: 8944-8952
[Abstract]
[Full Text]
-
Hellen, C. U. T., de Breyne, S.
(2007). A Distinct Group of Hepacivirus/Pestivirus-Like Internal Ribosomal Entry Sites in Members of Diverse Picornavirus Genera: Evidence for Modular Exchange of Functional Noncoding RNA Elements by Recombination. J. Virol.
81: 5850-5863
[Abstract]
[Full Text]
-
Legrand-Abravanel, F., Claudinon, J., Nicot, F., Dubois, M., Chapuy-Regaud, S., Sandres-Saune, K., Pasquier, C., Izopet, J.
(2007). New Natural Intergenotypic (2/5) Recombinant of Hepatitis C Virus. J. Virol.
81: 4357-4362
[Abstract]
[Full Text]
-
Smura, T. P., Junttila, N., Blomqvist, S., Norder, H., Kaijalainen, S., Paananen, A., Magnius, L. O., Hovi, T., Roivainen, M.
(2007). Enterovirus 94, a proposed new serotype in human enterovirus species D. J. Gen. Virol.
88: 849-858
[Abstract]
[Full Text]
-
Al-Sunaidi, M., Williams, C. H., Hughes, P. J., Schnurr, D. P., Stanway, G.
(2007). Analysis of a New Human Parechovirus Allows the Definition of Parechovirus Types and the Identification of RNA Structural Domains. J. Virol.
81: 1013-1021
[Abstract]
[Full Text]
-
Mirand, A., Henquell, C., Archimbaud, C., Peigue-Lafeuille, H., Bailly, J.-L.
(2007). Emergence of recent echovirus 30 lineages is marked by serial genetic recombination events. J. Gen. Virol.
88: 166-176
[Abstract]
[Full Text]
-
Simmonds, P.
(2006). Recombination and Selection in the Evolution of Picornaviruses and Other Mammalian Positive-Stranded RNA Viruses. J. Virol.
80: 11124-11140
[Abstract]
[Full Text]
-
Zhao, Y. N., Perlin, D. S., Park, S., Jiang, R. J., Chen, L., Chen, Y., Gardiner, R., Jiang, Q. W.
(2006). FDJS03 Isolates Causing an Outbreak of Aseptic Meningitis in China That Evolved from a Distinct Echovirus 30 Lineage Imported from Countries of the Commonwealth of Independent States. J. Clin. Microbiol.
44: 4142-4148
[Abstract]
[Full Text]
-
Richter, J., Koptides, D., Tryfonos, C., Christodoulou, C.
(2006). Molecular typing of enteroviruses associated with viral meningitis in Cyprus, 2000-2002.. J Med Microbiol
55: 1035-1041
[Abstract]
[Full Text]
-
Williams, C. H., Oikarinen, S., Tauriainen, S., Salminen, K., Hyoty, H., Stanway, G.
(2006). Molecular Analysis of an Echovirus 3 Strain Isolated from an Individual Concurrently with Appearance of Islet Cell and IA-2 Autoantibodies. J. Clin. Microbiol.
44: 441-448
[Abstract]
[Full Text]
-
Zell, R., Krumbholz, A., Dauber, M., Hoey, E., Wutzler, P.
(2006). Molecular-based reclassification of the bovine enteroviruses. J. Gen. Virol.
87: 375-385
[Abstract]
[Full Text]
-
Tsugawa, T., Numata-Kinoshita, K., Honma, S., Nakata, S., Tatsumi, M., Sakai, Y., Natori, K., Takeda, N., Kobayashi, S., Tsutsumi, H.
(2006). Virological, Serological, and Clinical Features of an Outbreak of Acute Gastroenteritis Due to Recombinant Genogroup II Norovirus in an Infant Home. J. Clin. Microbiol.
44: 177-182
[Abstract]
[Full Text]
-
Simmonds, P., Welch, J.
(2006). Frequency and Dynamics of Recombination within Different Species of Human Enteroviruses. J. Virol.
80: 483-493
[Abstract]
[Full Text]
-
Lukashev, A. N., Lashkevich, V. A., Ivanova, O. E., Koroleva, G. A., Hinkkanen, A. E., Ilonen, J.
(2005). Recombination in circulating Human enterovirus B: independent evolution of structural and non-structural genome regions. J. Gen. Virol.
86: 3281-3290
[Abstract]
[Full Text]
-
Rohayem, J., Munch, J., Rethwilm, A.
(2005). Evidence of Recombination in the Norovirus Capsid Gene. J. Virol.
79: 4977-4990
[Abstract]
[Full Text]
-
Oberste, M. S., Maher, K., Michele, S. M., Belliot, G., Uddin, M., Pallansch, M. A.
(2005). Enteroviruses 76, 89, 90 and 91 represent a novel group within the species Human enterovirus A. J. Gen. Virol.
86: 445-451
[Abstract]
[Full Text]
-
Shimizu, H., Thorley, B., Paladin, F. J., Brussen, K. A., Stambos, V., Yuen, L., Utama, A., Tano, Y., Arita, M., Yoshida, H., Yoneyama, T., Benegas, A., Roesel, S., Pallansch, M., Kew, O., Miyamura, T.
(2004). Circulation of Type 1 Vaccine-Derived Poliovirus in the Philippines in 2001. J. Virol.
78: 13512-13521
[Abstract]
[Full Text]
-
Simmonds, P.
(2004). Genetic diversity and evolution of hepatitis C virus - 15 years on. J. Gen. Virol.
85: 3173-3188
[Abstract]
[Full Text]
-
Oberste, M. S., Maher, K., Schnurr, D., Flemister, M. R., Lovchik, J. C., Peters, H., Sessions, W., Kirk, C., Chatterjee, N., Fuller, S., Hanauer, J. M., Pallansch, M. A.
(2004). Enterovirus 68 is associated with respiratory illness and shares biological features with both the enteroviruses and the rhinoviruses. J. Gen. Virol.
85: 2577-2584
[Abstract]
[Full Text]
-
Savolainen, C., Laine, P., Mulders, M. N., Hovi, T.
(2004). Sequence analysis of human rhinoviruses in the RNA-dependent RNA polymerase coding region reveals large within-species variation. J. Gen. Virol.
85: 2271-2277
[Abstract]
[Full Text]
-
Oberste, M. S., Penaranda, S., Maher, K., Pallansch, M. A.
(2004). Complete genome sequences of all members of the species Human enterovirus A. J. Gen. Virol.
85: 1597-1607
[Abstract]
[Full Text]
-
Oberste, M. S., Penaranda, S., Pallansch, M. A.
(2004). RNA Recombination Plays a Major Role in Genomic Change during Circulation of Coxsackie B Viruses. J. Virol.
78: 2948-2955
[Abstract]
[Full Text]
-
Thoelen, I., Moes, E., Lemey, P., Mostmans, S., Wollants, E., Lindberg, A. M., Vandamme, A.-M., Van Ranst, M.
(2004). Analysis of the Serotype and Genotype Correlation of VP1 and the 5' Noncoding Region in an Epidemiological Survey of the Human Enterovirus B Species. J. Clin. Microbiol.
42: 963-971
[Abstract]
[Full Text]
-
Lukashev, A. N., Lashkevich, V. A., Koroleva, G. A., Ilonen, J., Hinkkanen, A. E.
(2004). Recombination in uveitis-causing enterovirus strains. J. Gen. Virol.
85: 463-470
[Abstract]
[Full Text]
-
Oberste, M. S., Maher, K., Pallansch, M. A.
(2004). Evidence for Frequent Recombination within Species Human Enterovirus B Based on Complete Genomic Sequences of All Thirty-Seven Serotypes. J. Virol.
78: 855-867
[Abstract]
[Full Text]
-
Colina, R., Casane, D., Vasquez, S., Garcia-Aguirre, L., Chunga, A., Romero, H., Khan, B., Cristina, J.
(2004). Evidence of intratypic recombination in natural populations of hepatitis C virus. J. Gen. Virol.
85: 31-37
[Abstract]
[Full Text]
-
Costa-Mattioli, M., Napoli, A. D., Ferre, V., Billaudel, S., Perez-Bercoff, R., Cristina, J.
(2003). Genetic variability of hepatitis A virus. J. Gen. Virol.
84: 3191-3201
[Abstract]
[Full Text]
-
Lukashev, A. N., Lashkevich, V. A., Ivanova, O. E., Koroleva, G. A., Hinkkanen, A. E., Ilonen, J.
(2003). Recombination in Circulating Enteroviruses. J. Virol.
77: 10423-10431
[Abstract]
[Full Text]
-
Lindberg, A. M., Andersson, P., Savolainen, C., Mulders, M. N., Hovi, T.
(2003). Evolution of the genome of Human enterovirus B: incongruence between phylogenies of the VP1 and 3CD regions indicates frequent recombination within the species. J. Gen. Virol.
84: 1223-1235
[Abstract]
[Full Text]
-
Tosh, C., Hemadri, D., Sanyal, A.
(2002). Evidence of recombination in the capsid-coding region of type A foot-and-mouth disease virus. J. Gen. Virol.
83: 2455-2460
[Abstract]
[Full Text]
-
Oprisan, G., Combiescu, M., Guillot, S., Caro, V., Combiescu, A., Delpeyroux, F., Crainic, R.
(2002). Natural genetic recombination between co-circulating heterotypic enteroviruses. J. Gen. Virol.
83: 2193-2200
[Abstract]
[Full Text]
-
Harvala, H., Kalimo, H., Dahllund, L., Santti, J., Hughes, P., Hyypia, T., Stanway, G.
(2002). Mapping of tissue tropism determinants in coxsackievirus genomes. J. Gen. Virol.
83: 1697-1706
[Abstract]
[Full Text]
-
Norder, H., Bjerregaard, L., Magnius, L. O.
(2002). Open reading frame sequence of an Asian enterovirus 73 strain reveals that the prototype from California is recombinant. J. Gen. Virol.
83: 1721-1728
[Abstract]
[Full Text]
-
Oberste, M. S., Maher, K., Pallansch, M. A.
(2002). Molecular Phylogeny and Proposed Classification of the Simian Picornaviruses. J. Virol.
76: 1244-1251
[Abstract]
[Full Text]
-
Sironen, T., Vaheri, A., Plyusnin, A.
(2001). Molecular Evolution of Puumala Hantavirus. J. Virol.
75: 11803-11810
[Abstract]
[Full Text]
-
Tolou, H. J. G., Couissinier-Paris, P., Durand, J.-P., Mercier, V., de Pina, J.-J., de Micco, P., Billoir, F., Charrel, R. N., de Lamballerie, X.
(2001). Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome sequences. J. Gen. Virol.
82: 1283-1290
[Abstract]
[Full Text]
-
Kilpatrick, D. R., Quay, J., Pallansch, M. A., Oberste, M. S.
(2001). Type-Specific Detection of Echovirus 30 Isolates Using Degenerate Reverse Transcriptase PCR Primers. J. Clin. Microbiol.
39: 1299-1302
[Abstract]
[Full Text]
-
Oberste, M. S., Schnurr, D., Maher, K., al-Busaidy, S., Pallansch, M. A.
(2001). Molecular identification of new picornaviruses and characterization of a proposed enterovirus 73 serotype. J. Gen. Virol.
82: 409-416
[Abstract]
[Full Text]
-
Georgopoulou, A., Markoulatos, P., Spyrou, N., Vamvakopoulos, N. C.
(2000). Improved Genotyping Vaccine and Wild-Type Poliovirus Strains by Restriction Fragment Length Polymorphism Analysis: Clinical Diagnostic Implications. J. Clin. Microbiol.
38: 4337-4342
[Abstract]
[Full Text]
-
Liu, H.-M., Zheng, D.-P., Zhang, L.-B., Oberste, M. S., Pallansch, M. A., Kew, O. M.
(2000). Molecular Evolution of a Type 1 Wild-Vaccine Poliovirus Recombinant during Widespread Circulation in China. J. Virol.
74: 11153-11161
[Abstract]
[Full Text]
-
Schierup, M. H., Hein, J.
(2000). Consequences of Recombination on Traditional Phylogenetic Analysis. Genetics
156: 879-891
[Abstract]
[Full Text]
-
Schierup, M. H., Hein, J.
(2000). Recombination and the Molecular Clock. Mol Biol Evol
17: 1578-1579
[Full Text]
-
Santti, J., Harvala, H., Kinnunen, L., Hyypiä, T.
(2000). Molecular epidemiology and evolution of coxsackievirus A9. J. Gen. Virol.
81: 1361-1372
[Abstract]
[Full Text]
Top
Abstract
Introduction
