Changes in population dynamics during long-term evolution of sabin type 1 poliovirus in an immunodeficient patient

Abstract

The evolution of the Sabin strain of type 1 poliovirus in a hypogammaglobulinemia patient for a period of 649 days is described. Twelve poliovirus isolates from sequential stool samples encompassing days 21 to 649 after vaccination with Sabin 1 were characterized in terms of their antigenic properties, virulence in transgenic mice, sensitivity for growth at high temperatures, and differences in nucleotide sequence from the Sabin 1 strain. Poliovirus isolates from the immunodeficient patient evolved gradually toward non-temperature-sensitive and neurovirulent phenotypes, accumulating mutations at key nucleotide positions that correlated with the observed reversion to biological properties typical of wild polioviruses. Analysis of plaque-purified viruses from stool samples revealed complex genetic and evolutionary relationships between the poliovirus strains. The generation of various coevolving genetic lineages incorporating different mutations was observed at early stages of virus excretion. The main driving force for genetic diversity appeared to be the selection of mutations at attenuation sites, particularly in the 5' noncoding region and the VP1 BC loop. Recombination between virus strains from the two main lineages was observed between days 63 and 88. Genetic heterogeneity among plaque-purified viruses at each time point seemed to decrease with time, and only viruses belonging to a unique genotypic lineage were seen from day 105 after vaccination. The relevance of vaccine-derived poliovirus strains for disease surveillance and future polio immunization policies is discussed in the context of the Global Polio Eradication Initiative.

FIG. 1.

Neighbor-joining rooted tree showing phylogenetic sequence relationships in the VP1 coding region between isolates from the immunodeficient patient (circled) and other type 1 vaccine-derived poliovirus strains described previously. The analysis included isolates from immunodeficient patients (iVDPVs), a healthy child (hVDPV), circulating epidemic strains (cVDPVs), and a VAPP case. The accession numbers and literature references are as follows: iVDPV USA, AF083931 and AF083937 (29); iVDPV GER, AJ132960 and AJ132960 (2); iVDPV RUS, AF462418 (8); iVDPV TAI, AF538840, AF538841, AF538843, AY928383, and AY928387 (68); hVDPV IRE (45); cVDPV HIS, AF405634 (30); cVDPV PHI, AB180070 (60); and VAPP ROM (19).

FIG. 2.

Accumulation of nucleotide changes in the VP1 region of type 1 isolates from the immunodeficient patient during a 649-day period after vaccination with Sabin 1. (A) Percentages of synonymous plus nonsynonymous mutations with respect to Sabin type 1. (B) Percentages of synonymous substitutions with respect to Sabin type 1.

FIG. 3.

Neighbor-joining trees representing phylogenetic relationships between the 12 strains and the Sabin type 1 strain across different genomic regions. (A) Complete genome. (B) P1 coding region. (C) P2 coding region. (D) P3 coding region. The numbers at the nodes indicate the percentages of 1,000 bootstrap pseudoreplicates supporting the cluster.

FIG. 4.

Genetic heterogeneity among 10 plaque-purified poliovirus strains at each excretion time point. (A) The average number of mutations between 10-plaque purified viruses (a) or between unique virus variants (b) at each time point was estimated. The values are represented by bubble diagrams with various diameters. (B) Neighbor-joining tree showing phylogenetic relationships between plaque-purified viruses and Sabin 1. A comparison of unique virus variants identified at each time point is shown. The numbers at the nodes indicate the percentages of 1,000 bootstrap pseudoreplicates supporting the cluster. The lowercase letters represent genetic variants. The minor variant found on day 118 is shown as A118.2.

FIG. 5.

Mutations found in domain V of the 5′ NCR in isolates from the immunodeficient patient. (A) Accumulation of nucleotide substitutions in the longer stem of domain V during the period of virus excretion. Mutations with respect to Sabin type 1 strain are underlined. The dates (number of days after vaccination) at which different genetic structures were found are shown. The lowercase letters indicate genetic variants. A continuous line indicates the most likely evolutionary pathway between two genetic structures based on sequencing data in other regions of the genome. The dashed lines indicate alternative sequence evolutionary routes. (B) Predicted secondary structure of domain V of the 5′ NCR of the Sabin 1 type 1 strain (64). The locations of mutations found at nucleotides 476, 480, and 525 are shown.

FIG. 6.

Accumulation of nucleotide substitutions in isolates from the immunodeficient patient. (A) Alignment of nucleotide sequences at polymorphic sites in the 5′ NCR-P1 genomic region (nucleotides 49 to 3386) between isolates from the immunodeficient patient and the Sabin type 1 vaccine strain. Separate virus variants identified on days 49 and 63 were included. The locations of key nucleotide positions (discussed in the text) are shown. The location of nucleotides 2782 to 2787, deleted in variants A49c and A63c, is indicated by an inverted triangle. (B) Nucleotide differences between virus A88 and virus variants A63b and A63c. The dashes indicate that the sequence is the same as that of A88. *, virus A63c had a deletion of nucleotides 2782 to 2787.

FIG. 7.

Likely evolutionary pathways that link the virus isolates from the immunodeficient patient. The two main genetic lineages are represented. Incorporation of mutations at key nucleotide positions in the 5′ NCR (numbers) and relevant amino acid residues in the coding region (letters followed by amino acid numbers) is shown in italics. Isolates are shown in boldface. R indicates recombination across lineages. The lowercase letters represent genetic variants. The dashed arrows show possible links between two isolates in only part of the sequence.