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. 2008 May;82(9):4429-40.
doi: 10.1128/JVI.02354-07. Epub 2008 Feb 20.

Calibration of multiple poliovirus molecular clocks covering an extended evolutionary range

Jaume Jorba  1 , Ray Campagnoli, Lina De, Olen Kew
Affiliations

Calibration of multiple poliovirus molecular clocks covering an extended evolutionary range

Jaume Jorba et al. J Virol. 2008 May.

Abstract

We have calibrated five different molecular clocks for circulating poliovirus based upon the rates of fixation of total substitutions (K(t)), synonymous substitutions (K(s)), synonymous transitions (A(s)), synonymous transversions (B(s)), and nonsynonymous substitutions (K(a)) into the P1/capsid region (2,643 nucleotides). Rates were determined over a 10-year period by analysis of sequences of 31 wild poliovirus type 1 isolates representing a well-defined phylogeny derived from a common imported ancestor. Similar rates were obtained by linear regression, the maximum likelihood/single-rate dated-tip method, and Bayesian inference. The very rapid K(t) [(1.03 +/- 0.10) x 10(-2) substitutions/site/year] and K(s) [(1.00 +/- 0.08) x 10(-2)] clocks were driven primarily by the A(s) clock [(0.96 +/- 0.09) x 10(-2)], the B(s) clock was approximately 10-fold slower [(0.10 +/- 0.03) x 10(-2)], and the more stochastic K(a) clock was approximately 30-fold slower [(0.03 +/- 0.01) x 10(-2)]. Nonsynonymous substitutions at all P1/capsid sites, including the neutralizing antigenic sites, appeared to be constrained by purifying selection. Simulation of the evolution of third-codon positions suggested that saturation of synonymous transitions would be evident at 10 years and complete at approximately 65 years of independent transmission. Saturation of synonymous transversions was predicted to be minimal at 20 years and incomplete at 100 years. The rapid evolution of the K(t), K(s), and A(s) clocks can be used to estimate the dates of divergence of closely related viruses, whereas the slower B(s) and K(a) clocks may be used to explore deeper evolutionary relationships within and across poliovirus genotypes.

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Figures

FIG. 1.
FIG. 1.
ML/SRDT tree of P1/capsid region sequence relationships among 31 wild poliovirus type 1 isolates from cases in the period 1981-1991 in the northern Andean region. The tree was rooted to the sequence of isolate VEN81-1, with branch lengths scaled under the SRDT model (69) to the date of specimen collection, as described in Materials and Methods. Statistical support for the tree topology (bootstrap values or Bayesian posterior density values [in parentheses]) is given at the nodes. The sequence of the last indigenous wild poliovirus isolate from the Americas (PER91) is marked by an asterisk. Italicized letters in parentheses identify clusters of isolates (A, VEN81-1, VEN81-2, VEN82, PER83, COL86, VEN88-1, COL89, and COL91-5; B, VEN84; C, VEN88-2, COL90-2, COL90-3, COL90-4, COL91-2, and COL91-3; D, COL91-1, COL91-4, COL91-6, COL91-7, and COL91-8; E, PER88-4; F, PER88-1; G, PER88-3; H, PER88-2; I, ECU89, ECU90-1, COL90-1, PER90-1, and PER91; J, ECU90-2; and K, PER90-2) having identical sequences in the NAg sites shown in Fig. 4.
FIG. 2.
FIG. 2.
Distribution by category of nucleotide substitutions across the P1/capsid region along all observed Andean lineages, based upon the ML/SRDT tree in Fig. 1 and the assignments summarized in Table 1. The reference sequence (set at zero substitutions) was that of VEN81-1. Symbols: Kt, total nucleotide substitutions; Ks, synonymous substitutions; Ka, nonsynonymous substitutions; As, synonymous transitions; Aa, nonsynonymous transitions; Bs, synonymous transversions; Ba, nonsynonymous transversions. NAg sites are shown in gray, and the highly variable (79) and structurally disordered (35) 32 amino-terminal residues of VP1 are represented as a gradient of gray shades.
FIG. 3.
FIG. 3.
ML estimates of distributions of numbers of As (unfilled bars) and Bs (hatched bars) substitutions fixed per site into the P1/capsid regions of all 31 Andean isolates during 10 years of divergence from the VEN81-1 root sequence. The distributions expected for a Poisson model of nucleotide substitution are shown as thin (As) and thick (Bs) lines.
FIG. 4.
FIG. 4.
Sequences of amino acid residues within or bounding NAg sites 1 (VP1 amino acids 95 to 106), 2 (VP2 amino acids 164 to 173, VP2 amino acids 269 to 271, and VP1 amino acids 221 to 226), 3a (VP3 amino acids 56 to 62; VP3 amino acids 70 to 74, and VP1 amino acids 287 to 292), and 3b (VP2 amino acids 71 to 73 and VP3 amino acids 75 to 79). The reference sequence is that of VEN81-1. Residues defining the type 1 poliovirus NAg sites by mutations conferring resistance to neutralization by monoclonal antibodies (4, 56, 60, 83) are indicated in bold. Isolates having identical sequences in the NAg sites are grouped and identified by italicized capital letters, described in the legend to Fig. 1.
FIG. 5.
FIG. 5.
ML estimates of relative frequencies of specific base changes (10−2) (black arrows, transitions; gray arrows, transversions) at all codon positions within the P1/capsid regions of the Andean isolates during divergence from the VEN81-1 root sequence.
FIG. 6.
FIG. 6.
Estimation by linear regression of the rates of fixation of different categories of nucleotide substitutions into the P1/capsid regions of 31 Andean isolates. (A to C) For the abscissa, the time the sample was taken for each isolate (zero time, time of sampling for isolate VEN81-1, assumed to be 1 July 1981) is given. For the ordinate, corrected P1/capsid nucleotide substitution differences were normalized to total sites (Kt) (A), total synonymous (Ks) or nonsynonymous (Ka) sites (B), and total synonymous sites (As and Bs) (C) (zero substitutions, sequence of VEN81-1). Rates were calculated as described in Materials and Methods. (D) Relative rates of fixation of As and Bs substitutions (slope = 0.109; R2 = 0.86).
FIG. 7.
FIG. 7.
Saturation of 3CP transitions (closed circles), 3CP transversions (open circles), and total 3CP substitutions (triangles) in the P1/capsid region over the total period of independent evolution of the northern and southern lineages. (A) Uncorrected pairwise 3CP differences between all 31 isolates (ordinate) were plotted as a function of time of evolutionary separation (estimated from branch lengths of the ML/SRDT tree [Fig. 1]). (B) Pairwise 3CP differences corrected by use of the REV model of nucleotide substitution. (C) Simulation of saturation of 3CP transitions (closed circles), 3CP transversions (open circles), and total 3CP substitutions (triangles) in the P1/capsid region over a 100-year period, calculated by using the mutate program in MATLAB as described in Materials and Methods. The boxed area represents the time interval shown in panels A and B.
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References

    1. Allman, E. S., and J. A. Rhodes. 2004. Mathematical models in biology: an introduction. Cambridge University Press, New York, NY.
    1. Arnold, J. J., and C. E. Cameron. 2004. Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mg2+. Biochemistry 435126-5137. - PMC - PubMed
    1. Blomqvist, S., A. L. Bruu, M. Stenvik, and T. Hovi. 2003. Characterization of a recombinant type 3/type 2 poliovirus isolated from a healthy vaccinee and containing a chimeric capsid protein VP1. J. Gen. Virol. 84573-580. - PubMed
    1. Blondel, B., R. Crainic, O. Fichot, G. Dufraisse, A. Candréa, D. Diamond, M. Girard, and F. Horaud. 1986. Mutations conferring resistance to neutralization with monoclonal antibodies in type 1 poliovirus can be located outside or inside the antibody-binding site. J. Virol. 5781-90. - PMC - PubMed
    1. Brown, B. A., M. S. Oberste, J. P. Alexander, Jr., M. L. Kennett, and M. A. Pallansch. 1999. Molecular epidemiology and evolution of enterovirus 71 strains isolated from 1970 to 1998. J. Virol. 739969-9975. - PMC - PubMed

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