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Journal of Clinical Microbiology, October 1998, p. 2893-2899, Vol. 36, No. 10
0095-1137/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Prolonged Replication of a Type 1 Vaccine-Derived
Poliovirus in an Immunodeficient Patient
Olen M.
Kew,1,*
Roland W.
Sutter,2
Baldev K.
Nottay,1
Michael J.
McDonough,1
D. Rebecca
Prevots,3
Linda
Quick,2 and
Mark A.
Pallansch1
Division of Viral and Rickettsial Diseases,
National Center for Infectious Diseases,1 and
Divisions of Eradication of Vaccine-Preventable
Diseases2 and
Epidemiology and
Surveillance,3 National Immunization
Program, Centers for Disease Control and Prevention, Atlanta,
Georgia 30333
Received 11 March 1998/Returned for modification 5 June
1998/Accepted 26 June 1998
 |
ABSTRACT |
VP1 sequences were determined for poliovirus type 1 isolates
obtained over a 189-day period from a poliomyelitis patient with common
variable immunodeficiency syndrome (a defect in antibody formation).
The isolate from the first sample, taken 11 days after onset of
paralysis, contained two poliovirus populations, differing from the
Sabin 1 vaccine strain by ~10%, differing from diverse type 1 wild
polioviruses by 19 to 24%, and differing from each other by 5.5% of
nucleotides. Specimens taken after day 11 appeared to contain only one
major poliovirus population. Evolution of VP1 sequences at synonymous
third-codon positions occurred at an overall rate of ~3.4% per year
over the 189-day period. Assuming this rate to be constant throughout
the period of infection, the infection was calculated to have started
~9.3 years earlier. This estimate is about the time (6.9 years
earlier) the patient received his last oral poliovirus vaccine dose,
approximately 2 years before the diagnosis of immunodeficiency. These
findings may have important implications for the strategy to eliminate
poliovirus immunization after global polio eradication.
 |
INTRODUCTION |
Immunity to infections by
polioviruses and other human enteroviruses is mediated primarily by
neutralizing antibody (24, 31). In immunocompetent persons,
the duration of intestinal infection by polioviruses is typically
limited to 4 to 8 weeks, as indicated by the period of excretion of
poliovirus in the stool (2). In contrast, in immunodeficient
persons, particularly those with B-cell deficiencies associated with
hypogammaglobulinemia (31), poliovirus excretion times as
long as 3.5 years have been reported (10, 38). Prolonged
enteric infections with nonpolio enteroviruses of up to 6.5 years have
been described for persons with hypogammaglobulinemia (24).
Immunodeficient persons are at far higher risk (>3,000-fold) than
immunocompetent persons for vaccine-associated paralytic poliomyelitis
(VAPP) (33). For this reason, exposure of immunocompromised
persons to oral poliovirus vaccine (OPV), either by receipt of the
vaccine or by contact with vaccine recipients, should be avoided
(4). However, because the diagnosis of immunodeficiency is
often not established in the first year of life (22) and
immunization with OPV may begin as early as 2 months of age, some
children receive OPV before their immunodeficiency condition is
recognized (33).
In this report, we describe genetic analyses of type 1 vaccine-derived
polioviruses isolated from a patient with VAPP in whom common variable
immunodeficiency syndrome (CVID) (31) had been diagnosed
nearly 5 years earlier. The extent and rate of nucleotide divergence of
the isolate sequences from the Sabin type 1 vaccine strain sequence
were consistent with prolonged replication of the vaccine-derived
polioviruses in the patient. The combined clinical and genetic data
suggested that the infection was probably initiated by receipt of an
OPV dose given at least 6.9 years before onset of paralysis and at
least 2 years before diagnosis of CVID.
 |
MATERIALS AND METHODS |
Patient.
The case patient, a man born in 1964, had a history
of repeated upper respiratory infections, otitis media, recurrent
fever, chronic cough, sinusitis, and skin infections. At age 9 years, he was diagnosed with allergies to dogs, cats, food items, grass, and
trees. At age 12 years, he was hospitalized with lung infiltrates and
maxillary sinusitis and diagnosed with CVID on the basis of quantitative serum immunoglobulin (Ig) readings of 42 mg/dl for IgG
(normal values, 639 to 1,349 mg/dl), 4.5 mg/dl for IgM (normal values,
56 to 352 mg/dl), and 3.8 mg/dl for IgA (normal values, 70 to 132 mg/dl). He was placed on monthly fresh frozen plasma therapy and
maintained IgG levels of between 62 and 330 mg/dl from 1976 until 1981. In July 1981, at age 16 years, he developed fever and generalized
weakness after a diarrheal illness. Over a period of 4 days, he
developed quadriparesis requiring mechanical ventilation. Paralytic
poliomyelitis was diagnosed. His subsequent clinical course included
multiple hospital admissions for pneumonia and urinary tract
infections. He remained ventilator dependent from 1981 until his death
in October 1990. The patient had no known contact with a polio patient
or vaccine recipient and had not traveled from his state of residence
(Missouri) to an area where polio is endemic. He had received three
doses (at ages 3, 4, and 5 months) of inactivated poliovirus vaccine,
followed by four doses (at ages 3 years, 3 years 2 months, 5 years, and
10 years) of trivalent OPV (5).
Virus isolation and typing.
Serial stool specimens were
obtained from the patient at 11, 23, 48, 126, 158, and 200 days after
onset of paralysis. Stools were processed for virus isolation by
standard methods (35) and passaged twice on monolayers of
primary rhesus monkey kidney cells or RD cells (human rhabdomyosarcoma
cell line; ATCC CCL136). Isolates were typed in neutralization tests
with pooled hyperimmune equine sera. Isolates were passaged a third
time in MA104 cells (African green monkey kidney cell line) for
oligonucleotide fingerprinting and in RD cells to produce poliovirus
RNA templates for nucleic acid sequencing.
Antigenic characterization of poliovirus isolates.
Poliovirus type 1 isolates were analyzed for their antigenic properties
in neutralization tests with cross-absorbed antisera by the method of
van Wezel and Hazendonk (34).
Oligonucleotide fingerprinting.
Viral RNAs were analyzed by
the RNase T1 oligonucleotide fingerprinting method
described earlier (29), as modified for smaller (16 by 16 by
0.15 cm) gels.
Dot blot hybridization.
Preparation of digoxigenin-labeled
RNA transcripts, conditions for dot blot hybridization, and
detection of hybrids by enzyme-linked immunosorbent assay were as
described previously (8), except that the chemiluminescent
substrate disodium
3-(4-methoxyspiro{1,2-dioxetane-3,2'-(5'-chloro)tricyclo[3.3.1.13,7]decan}4-yl)phenyl
phosphate (CSPD) (Boehringer Mannheim Biochemicals, Indianapolis, Ind.)
was used in the assays.
Sequencing of poliovirus RNAs.
Complete VP1 (nucleotides
2480 to 3385) and partial VP1/2A (nucleotides 3296 to 3445) sequences
of the serial poliovirus isolates from the immunodeficient patient were
determined in cycle sequencing reaction mixtures (20)
containing fluorescent dye-labeled dideoxynucleotides (Applied
Biosystems, Foster City, Calif.). The templates were 1,014-bp PCR
products amplified from poliovirus RNAs by using the primer pair
3038/PCR2 (antisense [A] polarity, positions 3431 to 3452, 5'-GGGTGGCCAAGTGATAGTTGCAAAT-3') and seroPV1,2S (sense [S]
polarity, positions 2439 to 2457, 5'-TGCGIGA[C/T]ACIACICA[C/T]AT-3') (19);
deoxyinosine residues are indicated by the letter I, and primer
positions having equimolar amounts of two different nucleotides are
enclosed in brackets. Nucleotide sequences were determined with the aid
of an automated Sequenator (Applied Biosystems). VP1/2A sequences of
other poliovirus isolates were determined either by automated cycle
sequencing or by manual techniques (30). RNA extracted from
purified virions served as templates for extension of a synthetic DNA
primer (A, 3508 to 3527, 5'-AAGAGGTCTCTATTCCACAT-3') by
avian myeloblastosis reverse transcriptase in the presence of
dideoxynucleotide chain terminators (30). All primers for PCR and sequencing reactions (also including VP1/245A, A, 3212 to 3231, 5'-GTIGG[A/G]TT[A/G]TGITC[A/G]TTIAC-3'; panPV/PCR-1, A, 2915 to 2934, 5'-TTIAIIGC[A/G]TGICC[A/G]TT[A/G]TT-3'
[22]; 3038/PCR4, S, 2699 to 2719, 5'-GAGTCTAGTATAGAGTCCTTC-3'; and 3038/PCR3, S, 2927 to 2951, 5'-GCCTTAAATCAAGTATACCAAATTA-3') were prepared and purified
as described previously (36).
Separation of poliovirus populations by plaque purification and
sequence analysis.
Two sequence variants (major [M] and minor
[m]) in the day 11 isolate were separated by plaque purification of
HEp-2 (human larynx epidermoid carcinoma cell line; ATCC CCL23) cell
monolayers (27). The virus of 10 well-separated plaques was
grown on RD monolayers in tubes. RNA was extracted directly from cell
culture lysates for amplification of poliovirus sequences by PCR
(36). Amplicons were sequenced over the interval 2954 to
3385 by automated cycle sequencing methods.
Selective amplification of m variant poliovirus sequences by
PCR.
A nested, two-step PCR assay was developed for selective
amplification of m variant sequences. In the first step, nonselective primers VP1/245A and 3038/PCR4, equivalently matching M and m templates, were used in limiting quantities (2 pmol each) in 50-µl amplification reaction mixtures (denaturation, 94°C, 45 s;
annealing, 42°C, 45 s; extension, 60°C, 90 s; 30 cycles)
otherwise performed as previously described (36), producing
a 533-bp amplicon. Ten microliters of the first-step reaction mixture
was used as template in the second-step reaction mixture containing 10 pmol each of selective primers 2677/m
(A, 3127 to 3144, 5'-GCCGACTGGTCTTTCAGC-3') and 2677/m+ (S, 2759 to 2776, 5'-AACTCAGTTTCCACCGGG-3') designed to perfectly match VP1
sequences of the m variant but to mismatch the M variant in the two
terminal nucleotide positions at the 3'-donor ends of each primer.
Conditions for programmed amplification (25 cycles) were as described
above, except that extensions were performed at 62°C. Identifications
of the 386-bp amplicons were confirmed by digestion with the
restriction endonucleases XbaI (recognition site at position
2861 [m variant only], yielding fragments of 281 and 105 bp) and
EcoRI (recognition sites at position 2846 [m variant only]
and 2876 [both variants], yielding fragments of 266 and 120 bp [M
variant] or 266, 90, and 30 bp [m variant]) and electrophoretic
separation of the digestion products in 12.5% polyacrylamide gels
(36).
Analysis of VP1/2A nucleotide sequences.
Evolutionary
distances between poliovirus genomes were estimated from VP1/2A
sequences (all codon positions), using the two-parameter method of
Kimura (21) to correct for multiple substitutions at a site.
Calculations were performed by the program DNADIST of the PHYLIP 3.5c
program package (11), with a value of 10 used for the
transition/transversion ratio. VP1/2A evolutionary distances among
poliovirus isolates were summarized in a tree constructed by the
neighbor-joining method with the program NEIGHBOR (11).
Estimation of the time of initial infection from the VP1
evolution rate.
The evolution rate of VP1 at third codon positions
was estimated for the M lineage from day 11 to day 200. For each time
point, all positions with a new substitution were given a score of 1; all others were scored as 0 (no change from preceding sequence). At
ambiguous sites, only the base found in a higher molar proportion was
scored. The two-parameter correction method (21) was used to
convert base substitution differences to evolutionary distances (expressed as VP1 third-position substitutions/100 nucleotides). The
rate of evolution over the 189-day period was estimated by drawing a
linear regression line through the evolutionary distance points. The
age of initial poliovirus infection was estimated by increasing all
evolutionary distances by 31.2 (the evolutionary distance between the
Sabin 1 VP1 and the day 11 M variant VP1) and plotting the data points
on rescaled axes (abscissa, patient age in years; ordinate,
evolutionary distance from the Sabin 1 sequence). The estimated age of
initial poliovirus infection was the intercept obtained by
extrapolating the evolution rate line back to zero substitutions in the
Sabin 1 VP1.
Estimation of time of divergence of the M and m lineages.
The estimated time of divergence (timediv M,m) of the M and
m lineages was calculated from the following relationship:
where ageday 11 is the patient age at day 11, ageinit is the patient age at the time of initiation of
infection (estimated as described above), evoldistday 11 M,m is the evolutionary distance (calculated from VP1
third-position substitutions) between the M and m variants, and
evoldistSab1, day 11 M is the evolutionary distance between
Sabin 1 and the M variant.
Nucleotide sequence accession number.
VP1 sequences of
poliovirus isolates from the immunodeficient patient described in this
article have been deposited in the GenBank data library and assigned
accession no. AF083931 to AF083944.
 |
RESULTS |
Initial characterization of isolates.
Clinical specimens from
the patient were obtained as part of the routine surveillance of
poliomyelitis cases in the United States. Poliovirus type 1 was
isolated from each specimen. The initial (day 11) isolate was
characterized in neutralization assays by using cross-absorbed antisera
(34) and was found to have "non-vaccine-like" antigenic
properties (13). However, it is known that the Sabin vaccine
strains, especially the type 1 strain, frequently revert to
non-vaccine-like antigenicities upon replication in the human intestine
(3, 27). Therefore, the isolates were further tested by the
independent method of RNase T1 oligonucleotide fingerprinting.
The fingerprint of the day 11 isolate (not shown) had a high background
of secondary oligonucleotide spots. The fingerprint of a later (day
158) isolate had a low background and a complexity typical of a
poliovirus genome (Fig. 1) (18,
29). The fingerprint of the day 158 isolate was similar to the
primary spots in the fingerprint of the day 11 isolate. However, the
pattern was very different from that of the Sabin type 1 vaccine
strain, LSc 2ab (Fig. 1). Sabin 1 vaccine-related isolates generally
have fingerprints that are very similar (>75% comigrating
oligonucleotides) to that of the reference vaccine strain (18,
29). The fingerprint of the day 158 isolate also differed from
those of the last wild type 1 isolates from the United States, from
cases that occurred in 1979 in the states of Missouri (the last case of
the Turkey
Netherlands
Canada
USA epidemic)
(29) and Illinois (importation from Mexico) (18). Moreover, no other wild poliovirus isolate was found to have a fingerprint similar to that of the day 158 isolate (18, 29). Thus, the initial characterizations did not identify the isolates from
the immunodeficient patient as vaccine derived.

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FIG. 1.
RNase T1 oligonucleotide fingerprints of the
Sabin type 1 OPV reference strain (LSc 2ab) (left) and the day 158 isolate from the immunodeficient patient (right). Electrophoretic
separation of oligonucleotides in the first dimension (separation by
base composition) is from left to right and in the second dimension
(separation by chain length) is from bottom to top. The longer
oligonucleotides (chain lengths of 12 nucleotides) (18),
which having unique sequences representing ~15% of the genome, are
resolved into patterns (fingerprints) that are highly characteristic of
the RNA sequence.
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Sequence properties of the day 11 isolate.
At the time the
case of infection was identified, oligonucleotide fingerprinting was
the most accurate routine method for characterizing poliovirus
isolates. However, fingerprinting is highly sensitive to changes in RNA
sequence, such that quantitative estimates of relatedness are most
reliable when RNA molecules share >95% base sequence similarity
(1). Therefore, if a vaccine-derived poliovirus had evolved
extensively, it might not be correctly identified by fingerprinting.
The most definitive method for characterizing poliovirus isolates is by
nucleotide sequencing. When we determined the VP1
sequences of the day
11 isolate, they differed from the Sabin
1 sequence at >100 sites.
However, 50 of the 906 codon positions
were ambiguous, usually
containing either A+G or C+T. The sequence
ambiguity suggested that the
day 11 isolate contained a mixture
of related type 1 polioviruses. To
resolve the mixture, the day
11 isolate was plaque purified, and the
progeny of 10 plaques
were sequenced over a 432-base VP1 interval (2954 to 3385) having
24 ambiguous sites. Seven of the plaque isolates had
one unambiguous
sequence; the other three plaque isolates had another
unambiguous
sequence that differed from the first only at the ambiguous
sites.
The sequence variant represented by the seven plaques did indeed
appear to correspond to the major population in the original day
11 isolate, because its nucleotides had the stronger bands in
the
sequencing gels at the positions of ambiguity. The day 11
isolate
apparently contained only two principal populations, because
the
combination of the M and m variant sequences fully accounted
for the
observed sequence ambiguity. The presence of two distinct
sequence
variants probably also accounted for the high background
in the
oligonucleotide fingerprint of the day 11 isolate.
The complete VP1 nucleotide sequences were determined for a plaque
isolate of each variant. The M and m variants were related
to, but
nearly equally divergent from, Sabin 1, differing at 9.6%
(87 of 906 [M variant]) and 10.0% (91 of 906 [m variant]) of the
VP1
nucleotide positions (Fig.
2). They were
most closely related
to each other, differing at 5.5% (50 of 906) of
the bases. The
M and m variants probably diverged from a single lineage
derived
from Sabin 1, because they shared ~72% of their VP1 base
differences
from the vaccine strain sequence. Most (85% [151 of
178]) of the
base substitutions occurred in the third codon position,
97% (147
of 151) of which generated synonymous codons.

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FIG. 2.
VP1 nucleotide sequence alignment of the Sabin 1 reference strain (line 1), the day 11 isolate m variant (line 2), and
the day 11 isolate M variant (line 3). Sabin 1 nucleotide positions are
numbered according to the system of Nomoto et al. (28);
those of the day 11 isolates are numbered similarly for comparability.
Boldface letters identify codons of amino acid residues that form NAg I
(2750 to 2785), NAg II (3140 to 3157), and NAg III (3338 to 3355)
(25).
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A small proportion (18% [16 of 91], M variant; 16% [14 of 87], m
variant) of base changes encoded amino acid substitutions
(Fig.
2 and
3). In both variants, five amino acid
substitutions
clustered in the interval 1090 to 1106, spanning
neutralizing
antigenic site I (NAg I) (Fig.
3). Two of these mutations
(I1090M
and T1106A) were reversions to the parental Mahoney sequence,
two others (K1099E [M variant] and K1099G [m variant]) eliminated
a
trypsin cleavage site characteristic of Sabin 1 (
12), and
another (N1100S) restored the consensus residue for type 1 polioviruses
(
26,
37). Another substitution (A1222V) mapped to NAg II of
the M variant (Fig.
3). The remaining substitutions were conservative
(
16) and occurred in domains internalized in the intact
virion
(
14).

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FIG. 3.
VP1 amino acid sequence alignment of the Sabin 1 reference strain (line 1), the day 11 isolate m variant (line 2), and
the day 11 isolate M variant (line 3). Capsid amino acid positions are
indicated by a four-digit number: the first digit identifies the virion
protein, and the next three digits specify the residue position (e.g.,
1001 indicates residue 1 of VP1). Boldface letters identify virion
surface residues that form NAg I (1101 to 1112), NAg II (1221 to 1226),
and NAg III (1287 to 1292) (25).
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Relationships of case isolates to other type 1 polioviruses.
Nucleotide sequencing can detect much more distant genetic
relationships than can oligonucleotide fingerprinting (1,
30). To survey the genetic relationships among poliovirus
isolates, we compared sequences in the VP1/2A junction (nucleotides
3296 to 3445) (17, 30). VP1/2A sequences were determined for
the M and m variants from the day 11 isolate, the day 200 isolate, the
Sabin 1 vaccine strain, 5 Sabin 1 vaccine-derived isolates from
immunodeficient VAPP patients in the United States, and 25 type 1 wild
polioviruses from cases that occurred in different parts of the world
during 1977 to 1986. The sequence relationships, summarized in a tree
(Fig. 4), confirmed that the isolates
from the immunodeficient patient were most closely related to
vaccine-derived polioviruses (~8% VP1/2A sequence difference). In
contrast, wild poliovirus isolates from the same period were more
divergent (19 to 24% sequence differences) (Fig. 4). For example, the
day 11 isolates differed from the last wild isolates from the United States at ~23% (1979 Missouri case) and ~18% (1979 Illinois case) of nucleotide positions.

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FIG. 4.
Tree summarizing sequence relatedness across the
interval of nucleotides 3296 to 3445 (VP1/2A region) among the Sabin 1 vaccine strain, 3 isolates from the immunodeficient patient, 5 type 1 vaccine-related isolates from other immunodeficient VAPP patients in
the United States, and 25 type 1 wild-type polioviruses isolated in
different regions of the world from cases occurring within 5 years of
onset of paralysis in the immunodeficient patient. BRA, Brazil; CHN,
China (FJ, Fujian; GX, Guangxi); DOR, Dominican Republic; ELS, El
Salvador; GEO, Georgia; GRE, Greece; IND, India; INO, Indonesia; MEX,
Mexico; MOG, Mongolia; MOR, Morocco; PER, Peru; SEN, Senegal; SOA,
South Africa; TAI, Taiwan; TUN, Tunisia; TUR, Turkey; USA, United
States; VEN, Venezuela; and ZIM, Zimbabwe (35).
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The M and m variants were also recognized as Sabin 1 related in
hybridization reactions (not shown) with the specific RNA
probe
Sab1/VP1, currently used for routine identification of type
1 poliovirus isolates (
8). Hybridization signal intensities
were reduced relative to that of the control Sabin 1 RNA, probably
because mismatches with the probe (5.3%, M variant; 7.5%, m variant)
reduced the stabilities of the hybrids.
Disappearance of the m variant after day 11.
The sequences of
all isolates from specimens taken after day 11 had very low ambiguity,
and all appeared to be derived from the M variant. However, if the m
variant was present in proportions of <5%, the resulting sequence
ambiguity would be difficult to detect in sequencing gels. To test for
the presence of m variant sequences in the later isolates, we performed
PCR assays using primers that can selectively amplify m variant
sequences present in trace amounts (as low as 0.01%) in preparations
of M variant RNA templates. Using this sensitive PCR assay, we detected
m variant sequences only in the day 11 isolate (data not shown),
suggesting that the m variant lineage had died out between days 11 and
23.
Continued evolution of the M variant lineage.
Additional
nucleotide substitutions accumulated in the VP1 of the M variant
lineage from day 11 to day 200 (Table 1).
Most (10 of 13) of the observed substitutions generated synonymous codons, and 80% (8 of 10) of these occurred in the third codon position. Of the three observed amino acid substitutions, one (A1223V)
occurred within NAg II, another (L1104I) mapped near NAg I, and the
third (I1056V) restored the residue found in the Sabin 1 VP1 (Table 1
and Fig. 3). The overall direction of genetic change during the 189-day
period was further divergence away from the day 11 isolate (by 0.8%,
uncorrected) and from the Sabin 1 vaccine strain (from 9.6% [day 11]
to 9.9% [day 200], uncorrected). However, the pattern of VP1
variability was much more dynamic than could be seen from the net
genetic change alone. For example, nearly half (6 of 13) of the
observed substitutions (at positions 2659, 2693, and 2878) were paired,
such that a substitution found in an isolate from one time point
appeared to have reverted by the time of the next isolate. Five of the
13 substitutions (A2645G, G2659A, C2693A, G2878A, and G3124A) restored
the Sabin 1 base. At least one isolate (day 158) contained two
significant populations, indicated by sequence ambiguity at position
3316 (Table 1). The dynamics of variability within the virus
quasispecies population was probably far higher than what was actually
observed (9).
Estimation of the duration of the chronic infection from the
evolution rate of the M variant lineage.
We estimated the rate of
fixation of third-codon-position substitutions into the VP1 of the main
M variant lineage from day 11 to day 200. Third-position substitutions
were used in the analysis because all were associated with synonymous
mutations, which are most likely to arise through genetic drift rather
than by positive selection, and thus would be expected to accumulate at
a fairly uniform rate. Evolutionary distances were calculated from the observed VP1 third-position substitutions by the two-parameter method
of Kimura (21) to correct for multiple substitutions at a
site. When the evolutionary distances were plotted from day 11 to day
200, the rate of change was estimated to be 0.0092% third-position
substitutions/day, or 3.36% third-position substitutions/year (Fig.
5A). The evolutionary distance data were
replotted on rescaled axes (Fig. 5B), with all points shown in Fig. 5A
increased by 31.2 third-position substitutions/100 nucleotides (the
evolutionary distance between Sabin 1 and the day 11 M variant) and the
time coordinate expressed as the patient age in years. When the line for the evolution rate of 3.36%/year was extrapolated back to zero
substitutions in the Sabin 1 VP1, the intercept was at the patient age
of ~7.7 years, about 2 years prior to receipt of his last OPV dose
(Fig. 5B). The time from the initial infection to the onset of
paralysis was estimated to be 9.3 years.

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FIG. 5.
Estimation of the duration of chronic type 1 poliovirus
vaccine infection from the rate of evolution of VP1 nucleotide
sequences. (A) Rate of fixation of third-codon-position substitutions
into VP1 from day 11 (M variant) to day 200, estimated from
evolutionary distance calculations. On the abscissa, time zero is the
date of onset of paralysis. The ordinate shows evolutionary distances
from the sequence of the day 11 M variant. (B) Evolution rate
calculated in panel A extrapolated back (dashed line) to zero
substitutions in the Sabin 1 VP1. On the abscissa, time zero is the
patient's date of birth. The ordinate shows evolutionary distances
from the Sabin 1 sequence (value for day 11 M variant = 31.2 VP1
third-position substitutions/100 nucleotides [Nts]).
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Approximate time of divergence of the M and m lineages.
The
nearly equivalent evolutionary distances of the M and m variants from
Sabin 1 suggested that the two lineages had diverged from a single
Sabin 1-derived lineage. We assumed that the evolutionary distance of
each variant to the point of divergence was equal to half the total
evolutionary distance separating the two (16.6/2 = 8.3). This
represented 27% (8.3/31.2 = 0.27) of the total distance from
Sabin 1 to the M variant. By further assuming that the rate of
evolution was constant over the period of the infection, the time of
divergence was calculated from the estimated duration of infection (9.3 years × 0.27) to be 2.5 years (Fig.
6).

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FIG. 6.
Time course of chronic type 1 poliovirus vaccine
infection estimated from the VP1 evolution rate shown in Fig. 5. If the
infection was initiated by the last OPV dose received by the
immunodeficient patient, then the actual duration of infection to day
200 would be reduced by 24%, from 9.8 years to 7.4 years.
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DISCUSSION |
The type 1 polioviruses isolated from the immunodeficient patient
described here are, to our knowledge, the most extensively evolved
derivatives of the Sabin 1 vaccine strain reported so far. The
estimated duration of the prolonged poliovirus infection of ~9.8
years, calculated from the rate of VP1 sequence evolution, is over
twice as long as has been described in any previous report (10,
38). Furthermore, we do not know whether poliovirus excretion continued beyond the period of sampling.
Because stool specimens were obtained only after onset of paralysis, we
could not determine from direct measurement precisely when the patient
was first infected with the vaccine-derived polioviruses. Nonetheless,
the estimate obtained from the indirect genetic data fits reasonably
well with the clinical history of the patient. The finding that the
patient was infected with two virus populations that were nearly
equally divergent from the Sabin 1 vaccine strain strongly suggests
that the infection started with a single OPV dose. Although this dose
could have been administered to another person and transmitted by
contact to the immunodeficient child at any time before the divergence
of the two lineages, it seems more likely that the exposure was by
direct immunization. The patient received his last OPV dose at 10 years
of age, 2 years before diagnosis of CVID and 6.9 years before onset of
paralysis. We suggest that this last OPV dose was the initiating dose
and that the patient's still undiagnosed CVID condition had prevented clearance of infection with the Sabin 1 component of the vaccine. Although the interval between infection and onset of paralysis estimated from the evolution rate data (~9.3 years) does not preclude that the infection may have started with an earlier OPV dose, it
appears unlikely that the infection began much later than the time of
the last OPV dose.
The evolution rate measurements used to estimate the duration of
infection have several limitations to their precision. First, the
number of specimens available for analysis was small (six stools), and
the time interval for monitoring the sequence evolution of the
vaccine-derived virus was short (189 days) relative to the estimated
duration of the infection. Second, only a portion of the sequence
information potentially available was used for our evolution rate
estimates. Beyond limiting the sequence comparisons to VP1, we analyzed
only synonymous third-position substitutions in order to minimize the
effects of positive selection on the evolution rates. Finally, the
underlying assumption that the rate of VP1 sequence evolution in
immunodeficient persons is effectively constant over several years is
unproven. Despite these limitations, the estimated rate of VP1
evolution (~3.36% third-position substitutions/year) is close to the
rate (~3.07% third-position substitutions/year) obtained for a wild
poliovirus lineage circulating over 10-year period (7, 17).
The apparent similarities in the evolution rates of synonymous
nucleotide sites during replication in immunodeficient and normal
persons may indicate that the frequencies of genetic bottleneck events
driving the evolution of these presumably neutral sites are similar
under both conditions of infection.
Two aspects of the chronic infection of the immunodeficient patient
were difficult to explain. The first surprising observation was that
two variant populations had apparently coevolved (and therefore
coreplicated) in the patient for years. Replication of the two variants
may have been localized to different sites in the gastrointestinal
tract, and extensive colonization of each site by virus from the other
site may have been blocked by intracellular interference. The second
observation was the apparent disappearance of the m variant soon after
onset of paralysis. The appearance of paralysis was probably an
indication that circulating antibodies could no longer suppress
dissemination of virus to other cells and tissues. Under these new
physiologic conditions, the M variant may have had a higher fitness for
replication and spread (9).
The case described in this report is exceptional because it is the only
known VAPP case in an immunodeficient person in which immunodeficiency
had been diagnosed before onset of paralysis. In all other cases of
VAPP among immunodeficient persons, the appearance of the paralysis was
the event that prompted consideration of the diagnosis of
immunodeficiency. While there is no evidence that this vaccine-derived
poliovirus caused other cases of VAPP, we do not know whether the virus
caused any subclinical infections of contacts.
Apart from hypogammaglobulinemic persons, poliovirus infections of
other immunodeficient persons do not appear to be prolonged (32). However, we currently do not know the prevalence or
typical duration of chronic poliovirus excretion among
hypogammaglobulinemic persons. Stool specimens from immunodeficient
vaccine recipients or contacts are normally taken only after appearance
of paralysis. If poliovirus infection is confirmed from the initial
specimens, subsequent specimens are not routinely taken for virologic
monitoring.
The findings reported here may have implications for the global polio
eradication initiative of the World Health Organization (15), in particular how and when to discontinue immunization after wild polioviruses have been eradicated (6). The
strategy of displacing circulating wild polioviruses with
vaccine-derived strains through well-synchronized mass OPV immunization
campaigns, combined with routine OPV immunization, has been highly
effective (15). Vaccine-derived strains normally disappear
rapidly from the community after cessation of immunization with OPV.
This has been most clearly shown in Cuba, where all OPV is given in two rounds of mass campaigns and where extensive samplings of young children and the environment were found to be consistently negative for
polioviruses at 3 months after the last round of immunization (23). Additional evidence against the long-term persistence of vaccine-derived strains in the community comes from the epidemiology of polio outbreaks among unimmunized populations in countries where
poliovirus is nonendemic. If any residual circulation of vaccine-derived strains had occurred, it was apparently quite limited,
because herd immunity was insufficient to prevent epidemics caused by
imported wild polioviruses (17, 18, 29). However, even in
unimmunized populations, chronic infection of a small number of
immunodeficient persons might continue undetected for some time. Such
persons may represent a potential reservoir for polioviruses after wild
polioviruses have been eradicated and OPV immunization stopped.
Systematic studies of poliovirus excretion among immunodeficient
persons are therefore needed to assess the most appropriate strategy to
eliminate all poliovirus infections of humans.
 |
ACKNOWLEDGMENTS |
We thank George Marchetti for isolating the polioviruses from the
clinical specimens and Milford Hatch for performing the antigenic
characterization of the initial poliovirus isolate. The contributions
of Lina De, Rebeca Rico-Hesse, and Su-Ju Yang to the database of
wild-type poliovirus sequences are appreciated. We thank Larry
Anderson, Steve Cochi, Walter Dowdle, Howard Gary, Milford Hatch, Brian
Mahy, John O'Connor, and Melinda Wharton for constructive suggestions
and review of the manuscript and Andrew Ball, John Modlin, Neal
Nathanson, Larry Schonberger, Gail Wertz, Catherine Wilfert, Jerry
Winkelstein, and Peter Wright for helpful discussions. The cooperation
and assistance of the Missouri State Health Department and the Task
Force for Child Survival and Development are appreciated.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Respiratory and
Enteric Viruses Branch, G-10, Division of Viral and Rickettsial
Diseases, National Center for Infectious Diseases, Centers for Disease
Control and Prevention, Atlanta, GA 30333. Phone: (404) 639-3940. Fax: (404) 639-2648. E-mail: omk1{at}cdc.gov.
 |
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