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Journal of Virology, April 2000, p. 3001-3010, Vol. 74, No. 7
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Evolution of the Sabin Strain of Type 3 Poliovirus
in an Immunodeficient Patient during the Entire 637-Day Period of
Virus Excretion
Javier
Martín,*
Glynis
Dunn,
Robin
Hull,
Varsha
Patel, and
Philip D.
Minor
Division of Virology, National Institute for
Biological Standards and Control, Potters Bar, Hertfordshire,
United Kingdom
Received 4 October 1999/Accepted 21 December 1999
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ABSTRACT |
A 20-year-old female hypogammaglobulinemic patient received
monotypic Sabin 3 vaccine in 1962. The patient excreted type 3 poliovirus for a period of 637 days without developing any symptoms of
poliomyelitis, after which excretion appeared to have ceased spontaneously. The evolution of Sabin 3 throughout the entire period of
virus excretion was studied by characterization of seven sequential
isolates from the patient. The isolates were analyzed in terms of their
antigenic properties, virulence, sensitivity for growth at high
temperatures, and differences in nucleotide sequence from the Sabin
type 3 vaccine. The isolates followed a main lineage of evolution with
a rate of nucleotide substitution that was very similar to that
estimated for wild-type poliovirus during person-to-person
transmission. There was a delay in the appearance of antigenic variants
compared to sequential type 3 isolates from healthy vaccines, which
could be one of the possible explanations for the long-term excretion
of virus from the patient. The distribution of mutations in the
isolates identified regions of the virus possibly involved in
adaptation for growth in the human gut and virus persistence. None of
the isolates showed a full reversion of the attenuated and
temperature-sensitive phenotypes of Sabin 3. Information of this sort
will help in the assessment of the risk of spread of virulent
polioviruses from long-term excretors and in the design of therapies to
stop long-term excretion. This will make an important
contribution to the decision-making process on when to stop
vaccination once wild poliovirus has been eradicated.
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INTRODUCTION |
Poliovirus, the agent responsible
for paralytic poliomyelitis, is a member of the
Picornaviridae family, a group of nonenveloped positive-strand RNA viruses. The coding region of the genome is translated as a single polyprotein and is then processed to generate the viral capsid and nonstructural proteins (Fig.
1). The coding region is preceded by a
long 5' noncoding region (NCR) of approximately 740 nucleotides that
contains important determinants of virulence (32, 46).

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FIG. 1.
Organization of the genome of poliovirus. The protease
(P3C) and polymerase (P3D) can undergo an alternative cleavage within
3D mediated by P2A to give P3C' and P3C'. Reprinted from the
Journal of General Microbiology (32) with
permission of the publisher.
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The Sabin oral poliovirus vaccine, composed of live-attenuated strains
of the three poliovirus serotypes (38), has been used to
control and reduce greatly the incidence of poliomyelitis around the
world during the last 30 years. Sabin strains replicate in the guts of
immunocompetent persons for a limited period after vaccination
(2). During this period, which ranges between several days
and 3 months, vaccinees excrete viruses in which mutations and genetic
rearrangements are selected very rapidly (32). These changes
occur in a sequential manner, probably as a response to different
selective pressures in the gut (29).
In the case of Sabin 3-derived viruses, the changes always involve a
reversion at nucleotide 472 of the 5' NCR (U to C) (9) and
one or several coding mutations in the capsid proteins that restore a
defect in virus assembly caused by a mutation at capsid residue VP3-91
(22). These mutations result in partial or total reversion
of the attenuation phenotype of Sabin 3 (22). More strikingly, virtually all type 3 isolates excreted by healthy vaccinees
(given Sabin trivalent vaccine) more than 11 days after vaccination
display major genetic rearrangements as a consequence of genetic
recombination events (3; A. J. Macadam,
personal communication). These recombination events generate type 3 viruses containing the 5' region of the genome, including the capsid
coding region, from type 3 vaccine virus and large portions of the 3' half of the genome, which involves the nonstructural coding region, from either type 1, type 2, or both viral genomes. Molecular analysis of these viruses has revealed that type 3 recombinant isolates excreted
from healthy vaccinees share common genetic features (3,
18; A. J. Macadam, personal communication). The results indicate that viruses containing the carboxyl-terminal region of the
nonstructural protein 2C and the amino-terminal region of polymerase 3D
from Sabin 3 are selected against in the gut. One of the possible
explanations for this is that Sabin 3 lacks a proteolytic cleavage site
located in the amino-terminal region of 3D which is present in most
poliovirus strains and therefore might confer a selective advantage for
virus replication in vivo (32). This site is incorporated
into the genome of type 3 recombinant viruses from type 1 or type 2 sequences. Cleavage at this site results in an alternative processing
of the protease-polymerase 3CD polypeptide. The biological significance
of this alternative processing of 3CD has not yet been determined
(21).
Although poliovirus strains excreted by vaccines often show an increase
in virulence with respect to the vaccine strains, the rate of
vaccine-associated poliomyelitis (VAP) among healthy vaccinees is very
low and the vaccine is considered to be very safe (34).
However, the situation is different in persons with defects in their
immune systems. Immunodeficient people, particularly those with
antibody deficiencies, have a much higher risk of VAP (iVAP) than do
immunocompetent individuals (an estimated 3,000-fold excess)
(41). Sabin viruses can replicate for very long periods in
these patients, and in some cases, this leads to the fatal disease
(13, 17, 26, 39; G. Dunn, unpublished results). Recent genetic analysis of virus isolates from an asymptomatic immunodeficient person (Dunn, unpublished) or from an immunodeficient person with iVAP (17) have allowed us and others to estimate that excretion of poliovirus can continue for as long as 10 years after
vaccination of immunocompromised persons.
Early studies proposed that reversion of some vaccine phenotypes might
be slower in chronically infected antibody-deficient patients
(27). However, there is very little information about the
molecular properties of polioviruses excreted by immunodeficient patients from the time of vaccination. Patients with diagnosed immunological anomalies are generally not vaccinated with the live-attenuated strains, and only virus isolates recovered after the onset of iVAP are regularly available.
In this paper we describe the genetic and phenotypic properties of
isolates from a hypogammaglobulinemic patient, who was fed monotypic
Sabin 3 vaccine as part of a Medical Research Council study in the late
1950s and early 1960s (26). Seven sequential isolates were
studied to monitor the evolution of the virus during the entire period
of excretion. The isolates extend from day 36 until day 637 after
vaccination, when excretion appeared to have ceased spontaneously.
The results are discussed in terms of evolution of the Sabin 3 poliovirus strain in the human gut and the possible implications of
chronic virus excretion for the strategy of global eradication of polio.
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MATERIALS AND METHODS |
Clinical history of the patient.
The patient (26)
was a 20-year-old woman (222f), who had begun intermittent replacement
therapy in April 1957 at the age of 15 (at which time her
immunoglobulin G [IgG] level was 400 mg/ml) because she was suffering
from recurrent infections. Her IgG level fell during the next year to
200 mg/ml in November 1958 and 120 mg/ml in March 1959. When her serum
was examined before any injections of immunoglobulin, the titer of
neutralizing antibodies for all three polioviruses was 1:16. In
November 1958, the titers were about 1:4. At the time when she was
given monovalent type 1 virus orally in December 1961, her IgG level
was about 500 mg/ml and the titers of poliovirus neutralizing
antibodies were 1:8, 1:8, and 1:32 for types 1, 2, and 3, respectively.
No type 1 virus was recovered, and monovalent type 3 was given on 20 January 1962. Type 3 virus was recovered at regular intervals from then
until December 1962, when virus excretion became intermittent; it
continued so until 30 October 1963. A stool sample collected on 27 November 1963 was negative, as were six consecutive stool samples
collected at weekly intervals until the end of January 1964. Thus
excretion occurred for about 21 months. The number of excreted virus
was never greater than 102 tissue culture infective doses
per g of stool. An attempt to interfere with the excretion of type 3 virus by giving type 2 virus after excretion had been occurring for 3 months was unsuccessful, and no type 2 virus was recovered.
Viruses.
Virus samples taken from days 36, 136, 307, 391, 442, 480, and 637 (isolates H36 to H637) after patient 222f was fed
with monotypic Sabin 3 vaccine were analyzed in this study. Isolation of viruses was performed as previously described (27). The
rest of the type 3 polioviruses examined were obtained from laboratory stocks. Working virus preparations were collected by growth of the
viruses in HEp-2C cells in minimal essential medium without fetal calf
serum at 35°C. The virus stocks were stored at
70°C.
Cells.
HEp-2C cells were used in the different assays
described in this paper and were grown in culture as described
previously (22).
Nucleotide sequencing.
Viral cDNA was synthesized by reverse
transcription of purified viral RNA followed by amplification by PCR,
and the products were sequenced by the use of an ABI Prism 310 Genetic
Analyzer as specified by the manufacturer.
Neutralization of virus isolates with monoclonal antibodies.
Neutralization of virus infectivity with monoclonal antibodies specific
for the four different antigenic sites identified in Sabin 3 was
performed as described elsewhere (29).
Temperature sensitivity.
Temperature sensitivity was assayed
by observation of plaque formation on HEp-2C cells at 39.5 and 40.0°C
as described previously (28).
Neurovirulence.
Viruses were assayed by the standard World
Health Organization-approved test for vaccine safety (44),
except that fewer animals were used per virus.
In vivo labelling of viral proteins.
Viral polypeptides were
labelled with 35S essentially as described previously
(23), except that Tran35S-label and methionine-
and cysteine-free medium (ICN) were used. Infected HEp-2C cell lysates
were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
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RESULTS |
Genomic analysis of the type 3 strains isolated from the
immunodeficient patient.
To study the sequence evolution undergone
by Sabin 3 during long-term replication in the immunodeficient patient,
the genomes of seven sequential strains (H36 to H637) isolated from the
patient were analyzed by nucleotide sequencing (nucleotide 55 to the 3' end). The isolates corresponded to days 36, 136, 307, 391, 442, 480, and 637 after patient 222f was fed with monotypic Sabin 3 vaccine, so
that intertypic recombination was unlikely.
Table 1 shows the differences in the
sequences of the strains in the 5'-end NCR with respect to Sabin 3. All
isolates had a reversion (U to C) at position 472 of the 5' NCR.
Nucleotide 472 is located in domain V of the internal ribosome entry
site (IRES), where mutations play a very important role in the
attenuation phenotype of all three Sabin strains (15, 25, 36,
43). This change restores a G · C base pair in domain V,
and it is known to occur very rapidly upon replication of the virus in
the human gut (8). Viral isolates contained other changes in
the 5' NCR including mutations in other domains of the IRES from day 391 (Table 1 and Fig. 2). Some of the
changes had a potential effect on the secondary-structure stability of
the IRES by strengthening or weakening the predicted base-paired
composition of the stems in domains II, III, and IV (Fig. 2)
(40). All isolates except H480 showed a reversion (G to A)
at position 7432 of the 3' NCR just prior to the poly(A) tract. This
change has been observed in some isolates from healthy vaccinees and
patients with VAP but does not seem to play a significant role in
attenuation (43).
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TABLE 1.
Nucleotide differences between isolates from the
immunodeficient patient and Sabin 3 in the different domains of the
5' NCR of the genome
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FIG. 2.
Predicted secondary structure of the first 620 bases of
the 5' NCR of poliovirus type 3. The locations of mutations with a
potential effect on the secondary-structure stability of the region
found in isolates from patient 222f are indicated.
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Amino acid substitutions.
Amino acid changes in the region of
the genome coding for the structural (capsid) proteins of the different
strains with respect to Sabin 3 are shown in Table
2. Several coding mutations arose and
persisted in the capsid proteins of the sequential isolates. As
represented in Fig. 3, these included
mutations at different locations in the virion. All strains showed a
reversion to wild-type sequence at amino acid VP3-91, which is located
at the interface between protomers and is involved in capsid assembly
and the attenuation phenotype of the vaccine strain (10,
23). Reversion of this phenotype occurs in isolates from
vaccinees and patients with VAP either by direct back mutation at
position VP3-91 or by secondary changes in other capsid residues that
suppress the effect of VP3-91 Phe (22). Residues VP2-139 and
VP2-140, which had changed on days 391 and 136, respectively, are
located in the south rim of the surface depression ("canyon") that
surrounds the fivefold axis of symmetry and form part of the putative
receptor footprint (4, 35). Amino acid VP1-34, mutated from
day 136, maps to the amino-terminal loop of VP1, which makes contact
with VP4 and forms part of the complex internal network of the virion
essential for capsid stability (5). VP2-14 also changed from
day 136 and is situated on the border of a seven-stranded
-sheet
structure that is responsible for the stable interactions between
pentameric subunits (5, 10). Mutations at VP1-275 and
VP2-186 were acquired early in the infection (before day 36); they are
located relatively close to each other in the proximity of antigenic
site 3a (30), where a change was also detected from day 136 (residue VP1-288). A mutation in antigenic site 4, at amino acid 79 of
VP3, and another at internal residue 116 of VP3 were detected on day
391 and persisted until the end of the infection.

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FIG. 3.
Ribbon diagram of the -carbon trace of the Sabin 3 promoter (10), viewed from the front (A) and side (B) of the
virion (in panel B, the outside is toward the top left of the image and
the inside is toward the bottom right). The virus particle consists of
60 protomers, each containing a single copy of VP1, VP2, VP3, and VP4,
arranged in icosahedral symmetry. The fivefold and threefold axes of
symmetry and the canyon are labelled. Amino acid substitutions selected
and maintained in sequential isolates from patient 222f are
highlighted. The location of sphingosine (SPH) in the
hydrocarbon-binding pocket is also indicated.
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Other mutations were located in regions of possible biological
importance but were not maintained during the infection course (Table
2). Amino acids VP1-105, VP1-166, and VP1-256, for example, are
situated in or close to the north rim of the canyon on the roof of the
conserved hydrophobic pocket, which is normally occupied by an
endogenous lipid and where drugs that prevent virus uncoating are
inserted (10, 33).
Coding mutations were also present in nonstructural proteins and
involved protease 2A; proteins 2B, 2C, and 3A; VPg; protease 3C; and
the viral polymerase 3D (Table 3). Less
is known of the structural and functional significance of these
changes, but some mutations appeared at different stages of the
infection and were maintained from then on, presumably because they
conferred some biological advantage. Remarkably, several mutations were
found in the carboxyl-terminal region of protein 2C from isolate H307 onwards (Table 3). The changes map in a cysteine-rich domain (2C-269-302) that is conserved in enteroviruses and rhinoviruses and
in the proximity of an arginine-rich region that constitutes a putative
RNA binding motif (2C-312-317) (37, 42). Mutation at
residue 3D-147 (Ala to Thr), also present from day 307, generates a
recognition site (TY/G) for cleavage by the viral protease 2A.
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TABLE 3.
Amino acid changes between isolates from the
immunodeficient patient and Sabin 3 in the nonstructural region
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Significance of the mutations in the carboxyl-terminal region of
protein 2C and at amino acid 3D-147 (alternative cleavage site).
Both the carboxyl-terminal region of protein 2C and amino acid 3D-147
are found within the region of the genome of type 3 recombinant
viruses, isolated from healthy vaccinees or patients with VAP, that is
exchanged by recombination with either Sabin 1 or Sabin 2 genomes
(3, 22; Macadam, unpublished). Interestingly, Sabin
1 and Sabin 2 strains also contain differences in sequence in those
regions with respect to Sabin 3. To evaluate the relevance of these
mutations, the sequences in the carboxyl-terminal region of protein 2C
and at amino acid 3D-147 of the isolates from patient 222f were
compared to those of four distantly related wild type 3 viruses, two
Sabin 3-derived VAP strains, and Sabin 1 and 2 strains. As shown in
Table 4, all the viruses except the two first isolates from the immunodeficient patient showed changes with
respect to Sabin 3. Amino acid 2C-268 changed in patient 222f from day
307, from a threonine to a methionine, and was found to be a methionine
in all the rest of the viruses except for Sabin 3 and one VAP isolate.
Sabin 1 and 2 strains, the four wild type 3 poliovirus strains, and the
two Sabin 3-derived VAP isolates contain a change at residue 2C-270
with respect to Sabin 3, from an aspartic acid to an asparagine,
whereas amino acid 2C-271 changed from day 391, from a lysine to a
glutamic acid, in isolates from patient 222f. Isolates from the
immunodeficient patient also incorporated changes from day 391 at
residue 2C-295, from a lysine to an arginine, and at amino acid 2C-310,
from an isoleucine to a valine, which is also a valine in Sabin 2, two
of the wild type 3 polioviruses, and one VAP isolate. Sabin 1 and Sabin
2 strains and the four wild type 3 viruses have a threonine at position
3D-147, which changed in the immunodeficient patient from day 307 from
an alanine to a threonine, generating the alternative proteolytic
cleavage site in the 3CD polypeptide.
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TABLE 4.
Sequence differences between isolates from the
immunodeficient patient, wild type 3 polioviruses, Sabin 3-derived
viruses from VAP patients, and Sabin strains in the carboxyl-terminal
region of protein 2C and at amino acid 3D-147
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Genetic evolution of the strains.
Figure
4 shows the accumulation of changes in
the genome of the type 3 strains excreted by the immunodeficient
patient during the 637 days that virus excretion lasted. Incorporation
of nucleotide changes over the whole genome, expressed as a percentage
of changes with respect to the Sabin 3 genome at the different
excretion points, is shown in Fig. 4A. The data could be adjusted to a
linear function (y = 0.0035x; R2 = 0.9971) which gave a rate of evolution of 1.28% of nucleotide changes over the entire genome. This rate corresponds to 1.83 nucleotide changes per week over the entire genome, which is in the
range of the rate of between 1 and 2 changes per week that has been
estimated for wild-type poliovirus evolution during person-to-person transmission (16).

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FIG. 4.
Accumulation of changes in the genome of type 3 isolates
from the immunodeficient patient with respect to the Sabin 3 genome
during the period of excretion. (A) Percentage of nucleotide changes
with respect to Sabin 3 over the whole genome. (B) Percentage of
changes in synonymous third-base codon positions. (C) Percentage of
amino acid substitutions. (D) Rate of sequence evolution at synonymous
third-base codon positions calculated at each excretion point
independently and extrapolated as percentage of changes per year.
Symbols: , capsid region; , nonstructural region. ×, whole
coding region.
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To obtain a better estimate of the rate of sequence evolution,
synonymous changes at third-base codon positions in the coding regions
of the genome were analyzed alone. Changes at those positions are
assumed to have a neutral effect on virus fitness and have been shown
to more accurately reflect the genetic relationships between poliovirus
strains (17, 19). The values were represented together or
separately for the capsid and nonstructural regions and are displayed
in Fig. 4B. The data adjusted to linear functions in the entire coding
region (y = 0.0076x; R2 = 0.9954), the
capsid region (y = 0.0093x; R2 = 0.9973), and the nonstructural region (y = 0.0065x;
R2 = 0.9873). These data produced estimated rates
of evolution of 2.78, 3.40, and 2.37% of nucleotide
substitutions at synonymous third-base codon positions/year over the
entire coding region, the capsid region, and the nonstructural regions, respectively.
To evaluate if the rate of sequence evolution had varied during the
excretion period, the rate of change in synonymous third-base codon
positions was calculated by considering each excretion point independently. As shown in Fig. 4D, the rate of evolution was rather
constant during the excretion period. However, isolates from days 36 and 136 showed values in the nonstructural region that were
significantly lower than those for the rest of the isolates.
The data from these analyses were used to elaborate a phylogenetic tree
representing the genetic relationships between the strains. As shown in
Fig. 5, the phylogenetic tree revealed a branched structure where a main genotypic lineage and various minor
branches could be distinguished. The branches extended for different
lengths of time from the main lineage, presumably reflecting times
during the infection when viruses coreplicated independently in
different sites of the intestinal tract. Viruses from genotypic branches that led to isolates H307 and H442, for example, seem to have
coexisted separately with strains from the main lineage for
approximately 150 and 70 days, respectively (Fig. 5). Analysis of the
accumulation of amino acid changes within each branch strongly supports
this idea (Tables 2 and 3). Viruses from minor lineages seemed to have
subsequently disappeared or been outcompeted by strains from the main
genotypic lineage.

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FIG. 5.
Phylogenetic tree showing the genetic relationships
between the isolates excreted by the immunodeficient patient. The tree
is a mere representation of the differences at synonymous third-base
codon positions between sequential isolates over the entire coding
region. The number in each isolate represents the date of isolation
(days after vaccination). The number of changes accumulated in each
segment is shown.
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The selection of changes in the IRES in the 5' NCR seemed to have
varied during the infection. Isolate H307 contained only two changes in
this region, while strain H391 and the strains thereafter had eight or
more (Table 1).
Changes in amino acid in the capsid and nonstructural regions followed
different patterns. Viruses acquired changes in capsid residues more
rapidly during the initial stages of infection, whereas mutations in
nonstructural proteins seemed to have accumulated in a more uniform
manner (Fig. 4C).
Antigenic structure.
The antigenic structure of the strains
excreted by the immunodeficient patient was determined by studying the
reactivity of the viruses with a panel of monoclonal antibodies of
known specificity (30). The results are presented in Table
5. Antibodies specific for the
immunodominant site 1 neutralized all strains. Isolates H136 and H637
failed to react with three or two antigenic site 2 antibodies,
respectively. All isolates except H36 were resistant to neutralization
by antibodies specific for site 3. Finally, strains H391, H442, H480,
and H637 lost reactivity with monoclonal antibody 1281, which is
specific for antigenic site 4. The results were consistent with the
observed amino acid changes at the predefined antigenic sites (Table
2).
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TABLE 5.
Reactivity of isolates from the immunodeficient patient
with monoclonal antibodies specific for different antigenic sites of
Sabin 3
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Temperature sensitivity and neurovirulence.
The results for
the temperature sensitivity and neurovirulence of the strains are shown
in Table 6. All strains exhibited some
degree of temperature sensitivity for growth in HEp-2C cells compared
to the wild strain Leon. Isolates H136, H307, H442, and H637 showed a
similar or greater reduction in virus titer with respect to Sabin 3 at
39.5 and 40.0°C. Only strains H36 and H391 exhibited a partial loss
of the temperature-sensitive phenotype of Sabin 3. Comparison of the
sequences of the strains suggests that several mutations could be
responsible for the differences in the temperature-sensitive phenotype
between the strains. As suggested previously, the observed phenotypes
could be the result of the combination of the effect of different
mutations that affect different steps of virus replication
(32).
Strains H36, H391, and H637 were examined for neurovirulence. As shown
in Table 6, all three strains exhibited an increase in neurovirulence
compared to Sabin 3. However, all three isolates showed a significantly
lower mean lesion score with respect to the Sabin 3 wild parent virus,
the Leon strain.
Alternative cleavage of 3CD polyprotein.
To confirm that
mutation at 3D-147 (Ala
Thr) introduced a new proteolytic site in the
3CD polypeptide, the protein synthesis of these viruses in tissue
culture was studied. Figure 6 shows the
results of the sodium dodecyl sulfate-polyacrylamide gel
electrophoresis analysis of 35S-labelled HEp-2C cell
extracts infected with the different viruses. As predicted from the
nucleotide sequence, strains from day 307 showed a protein band with an
electrophoretic mobility compatible with that of protein 3D'; a product
of the alternative cleavage of 3CD by the viral protease 2A. A
difference in the electrophoretic mobility of VP2 in isolates from day
136 could clearly be observed in the gel. The difference is very likely
to be the consequence of changes in the amino acid sequence of VP2 in
which several mutations were incorporated from day 136 (Table
2).

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FIG. 6.
Autorradiography of sodium dodecyl
sulfate-polyacrylamide protein gel of 35S-labelled HEp-2C
cell extracts infected with the isolates excreted from the
immunodeficient patient or Sabin 3. The arrow indicates the position of
3D'. 3C' comigrated with other viral proteins and could not be
distinguished from them.
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DISCUSSION |
The study of the evolution of vaccine-derived polioviruses
in humans has been limited to the few weeks that virus excretion after
vaccination normally lasts (2, 32). Here we report a
detailed study of the genetic and phenotypic characteristics of seven
sequential type 3 poliovirus isolates from an immunodeficient patient
(patient 222f) who excreted type 3 poliovirus for 637 days after being
fed with monovalent Sabin 3 vaccine (26).
Analysis of nucleotide changes at synonymous third-base codon positions
in the coding region indicated that sequence evolution was fairly
constant throughout the period of virus excretion. The estimated rate
of sequence evolution over the entire coding region (2.78% of
nucleotide changes at synonymous third-base codon positions/year) is
similar to the rate (3.07% of nucleotide substitutions at synonymous
third-base codon positions/year) calculated for wild-type poliovirus
during person-to-person transmission (16). The rate of
sequence evolution in the capsid region (3.40% of nucleotide
substitutions at synonymous third-base codon positions/year) was
remarkably similar to that in the capsid VP1 recently estimated from a
series of type 1 poliovirus isolates over a period of 200 days from an
iVAP case (3.30% of nucleotide changes at synonymous third-base codon
positions/year) (17). These observations indicate that
poliovirus follows similar patterns of molecular evolution under
different conditions of infection. Differences in selection pressures,
particularly in humoral immune responses, do not seem to affect the
evolution of these presumably neutral positions. Sequence evolution in
isolates from patient 222f appeared to be slower in the region of the
genome coding for nonstructural proteins (2.37% of nucleotide
substitutions at synonymous third-base positions/year), particularly
during the first 136 days of virus excretion. One of the possible
explanations is the presence of RNA secondary-structure motifs that may
function as cis-acting signals for virus replication and
might have limited the incorporation of viable nucleotide mutations in
this region.
The viral isolates displayed a branched phylogenetic tree in which a
major genotypic lineage could be distinguished (Fig. 5). Identification
of minor branches that diverted from the main lineage and seemed to
have survived for considerable lengths of time suggests that viruses
from different lineages coreplicated in the gut as the virus was
presumably colonizing different sites in the gastrointestinal tract.
Generation of virus genetic lineages within individual patients was
observed during the Finnish outbreak of poliomyelitis caused by a wild
type 3 virus (19).
Characteristic mutations were selected in viruses replicating in the
immunodeficient patient at different times during the infection,
suggesting that particular selection pressures may have operated in the
gut at different times. Figure 7 shows
some of the mutations observed in the immunodeficient patient,
displayed in a chronological order and compared to those found in a
healthy vaccinee (29) during their respective entire period
of virus excretion. By day 36, both of the major determinants of
attenuation of Sabin 3 (43), nucleotide 472 in the 5' NCR at
domain V of the IRES and capsid residue VP3-91 (which is also
responsible for temperature sensitivity in Sabin 3), had reverted,
confirming the importance of these two positions for virus fitness in
the gut. Both changes were maintained during the entire period of infection. However, none of the isolates tested showed a full reversion
to the neurovirulent phenotype of the P3/Leon strain, the Sabin 3 wild
parent virus. Moreover, all the strains exhibited some degree of
inhibition of growth at high temperatures compared to the P3/Leon
virus. As described for type 3 isolates from healthy vaccinees or
patients with VAP (22), the isolates from the
immunodeficient patient appeared to show a correlation between loss of
temperature sensitivity and neurovirulence, suggesting that at least
some mutations were responsible for both phenomena. Contrary to the common perception, long-term replication of vaccine-derived type 3 poliovirus in the human gut does not necessarily lead to strains insensitive for growth at high temperatures and highly neurovirulent. From day 391, viruses incorporated further changes in the 5' NCR at
domains II, III, and IV of the IRES. Domains II and IV, together with
domain V, are thought to contain the most important
cis-acting signals in the 5' NCR, which are essential for
the unusual cap-independent initiation of translation of picornaviruses
(25). Notably, none of the changes resulted in the
disruption of the predicted base-paired structure (40),
although some resulted in the weakening of a predicted base pair (Fig.
2). These observations emphasize the biological significance of
maintaining a particular RNA secondary structure in this region.

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|
FIG. 7.
Antigenic and molecular evolution of type 3 poliovirus
in healthy baby DM (29) and in the immunodeficient patient
222f. Ag, antigenic variant; 2A, protease 2A; 2C-COOH,
carboxyl-terminal region of protein 2C; ts, temperature sensitive.
|
|
Capsid mutations involved amino acids in the canyon, the drug-lipid
binding pocket, antigenic sites, internal sequences, monomeric and
pentameric interfaces, and other surface residues of unknown phenotype
(Fig. 3). Several changes were located at positions known to affect
receptor binding or the subsequent receptor-mediated conformational
changes that lead to virus cell entry, including mutations in putative
receptor contact residues. Interestingly, type 3 mutant viruses
generated from the Leon strain that exhibited persistence in HEp-2C
cells possess altered receptor binding properties (7). The
authors proposed that in this manner the mutant strains reduced their
lytic capacity that allowed persistence in tissue culture.
A progressive antigenic drift is normally observed in sequential
isolates from the same individual in healthy vaccines
(29; A. J. Macadam, personal communication). Changes
in antigenic sites can be detected only a few days after vaccination
and, for type 3 viruses, usually involve antigenic sites 2 and 4 and
occasionally site 3 (29; A. J. Macadam, personal
communication). Changes in antigenic site 2 were detected in isolates
from the immunodeficient patient only on days 136 and 637 (the last
isolate), a mutation in antigenic site 3 was found on day 136 and
thereafter, and antigenic site 4 changed from day 391. The delay in the
appearance of antigenic variants could be associated with the deficient
immune pressure exerted against the virus in the patient and,
consequently, with the long-term excretion of virus. Human
antipoliovirus antibodies provided by immunotherapy were insufficient
to eliminate the virus but were probably responsible for the observed
antigenic variation. As reported for type 3 isolates from healthy
vaccinees, no changes were detected in antigenic site 1, which
reinforces the hypothesis of a lack of immune pressure against site 1 in humans (31).
Isolates obtained from day 307 onward incorporated several changes in
the carboxyl-terminal region of protein 2C, important for RNA
replication (37, 42), and a mutation at residue 3D-147 (Ala
Thr), which generated a recognition site (TY/G) for cleavage by
the viral protease 2A that is conserved among most poliovirus strains.
Remarkably, four distantly related wild type 3 polioviruses and two
different Sabin 3-derived VAP isolates that were also analyzed in this
study contained similar amino acid changes with respect to the Sabin 3 strain (Table 4). These results indicate that the changes may provide
the viruses with some selective advantage for growth in the gut. This
suggestion is in agreement with the common observation that type 3 isolates from healthy vaccinees given Sabin trivalent vaccine show a
recombinant genome in which both the carboxyl-terminal region of 2C and
the amino-terminal region of 3D are derived from Sabin 1 or Sabin 2 genomes, which also contain similar changes in these regions with
respect to Sabin 3 (Table 4). These results support the idea that
genetic recombination is a common and efficient mechanism of poliovirus evolution, in that several changes could be acquired at once while stepwise mutation might be less easy although clearly not impossible.
Other changes in nonstructural proteins included two mutations in
protease 2A in strains collected from day 391. Curiously, the
appearance of mutations in protease 2A coincides in time with changes
in the IRES region in the 5' NCR. Sequence changes in both 5' NCR and
protease 2A are known to influence protein synthesis, and in some
cases, mutations in 2A compensate for defects caused by mutations in
the 5' NCR (24).
The reason why patient 222f stopped excreting poliovirus is unclear.
Only 2 of 30 patients who formed part of the same study excreted virus
for prolonged periods after being fed with Sabin vaccine
(26). The second patient excreted type 1 poliovirus for 32 months. At this point, a rapid disappearance of virus was observed,
associated with the shedding of the intestinal mucosa as a result of
infection with Shigella sonnei (26). In another case, an immunodeficient patient who excreted poliovirus type 2 for 3.5 years stopped excreting the virus 2 months after he started receiving
treatment with secretory IgA (13).
Long-term excretion of poliovirus by immunodeficient patients has
important implications for the program for global eradication of polio
(6). The fact that some immunodeficiencies are often acquired late in life and/or not diagnosed before polio immunization is
carried out makes the prevention and control of poliomyelitis in the
immunodeficient population a difficult task. Patients with primary
immunodeficiencies are therefore a potential reservoir of persistent
poliovirus excretion. The World Health Organization considers this
circumstance to be one of the priorities for the establishment of
strategies for stopping immunization once wild poliomyelitis has been
eradicated (45). It is therefore crucial to evaluate and
control the prevalence of persistent poliovirus infection among
immunodeficient individuals. Identification of molecular markers
associated with long-term replication of vaccine-derived viruses in
humans from studies such as the one presented here could be essential
for assessing these issues. Development of efficient treatments that
complement immunoglobulin therapy to eliminate poliovirus from these
patients is under active investigation (11). The use of more
genetically stable live-attenuated poliovirus vaccines (1, 12,
20; A. J. Macadam, personal communication) could help to
reduce the incidence of VAP in nondiagnosed immunodeficient patients
and may contribute to reduce the risk of virulent virus spreading into
the population in the postvaccination era.
 |
ACKNOWLEDGMENTS |
We thank Andrew Macadam and David Wood for fruitful discussions
and Andrew Davies for the artwork. Claire Shorrock was extremely helpful with the automatic sequencing. We are also indebted to Sue
Marsden, Sophie Reid, and Gary Beaven for important contributions.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Division of
Virology, National Institute for Biological Standards and Control,
Blanche Lane, Potters Bar, Hertfordshire EN6 3QG, United Kingdom.
Phone: (44) 1707 654753. Fax: (44) 1707 646 730. E-mail:
jmartin{at}nibsc.ac.uk.
 |
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