* Department of Biology, University of Puerto RicoRio Piedras, San Juan, Puerto Rico
Department of Zoology, University of Oxford, Oxford, England
Department of Microbiology and Medical Zoology, University of Puerto RicoCiencias Medicas, San Juan, Puerto Rico
Centers for Disease Control and Prevention, San Juan Branch, San Juan, Puerto Rico
|| Centers for Disease Control and Prevention, Fort Collins, Colorado
Correspondence: E-mail: sbennett{at}rrpac.upr.clu.edu.
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Abstract |
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Key Words: dengue virus positive selection epidemiology phylogeny maximum likelihood
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Introduction |
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The ongoing expansion of dengue throughout Asia and the South Pacific is being recapitulated in the Americas (Gubler 1998). Before the 1950s, people were typically exposed to a single strain (hypoendemicity), and epidemics were rare and self-limiting (Gubler 1998). However, geographic expansion of the primary mosquito vector (Aedes aegypti), increasing host densities, particularly in urban centers, and global travel have substantially altered dengue's epidemiologic landscape (Gubler 1998). Now dengue annually infects an estimated 50 million to 100 million people worldwide (WHO 1999), many of whom are exposed to two or more co-circulating DEN serotypes (hyperendemicity), resulting in frequent large-scale epidemics and more frequent severe disease (Gubler 1998).
Determining the contributing factors to the emergence of dengue as a global pandemic, particularly the increasing incidence of DHF and DSS, has proven difficult both because there are no satisfactory models or in vitro correlates with which to study disease transmissibility or pathogenicity directly (Rothman and Ennis 1999), and because most molecular epidemiologic studies to date have had limited scope (Holmes 1998). Associations have been demonstrated between severe manifestations of dengue (DHF/DSS) and both host infection history and viral genotype. Most notably, secondary infections with heterologous serotypes are more likely to develop into DHF/DSS than primary infections (Halstead 1988; Thein et al. 1997; Gubler 1998) so that increasing hyperendemicity could account in part for the rise of DHF/DSS. However, there is also evidence that viral genotype may be a contributing factor in determining dengue disease. For example, attenuated and virulent strains of DEN-2 were first observed simultaneously in the Tonga epidemics of 1974/75 (Gubler et al. 1978), and the introduction of a genetically distinct Asian DEN-2 strain into the Americas has been associated with an increase in DHF/DSS (Rico-Hesse et al. 1997; Leitmeyer et al. 1999). More tentatively, an analysis of selection pressures acting on dengue virus genomes suggested that genotypes of DEN-2 have selectively determined differences in transmissibility, in turn determining their ability to cause epidemics on a global scale (Twiddy et al. 2002).
Puerto Rico provides an ideal natural laboratory to gather a detailed record of viral evolutionary change during disease expansion. The island has a large urban population with high mosquito vector densities and, like many tropical regions, has experienced nearly 20 years of dengue epidemics that are becoming increasingly severe (Gubler 1998). Although dengue fever was recorded in Puerto Rico as early as 1915 (Dietz et al. 1996), continuous transmission of all four serotypes has only occurred since the 1980s (Dietz et al. 1996; Gubler 1998). The first epidemic in Puerto Rico, consisting primarily of DEN-4, was reported in 1981/82, followed by another DEN-4dominated outbreak in 1986, this one marked by high incidences of DHF/DSS (Dietz et al. 1996; fig. 1). DHF/DSS cases have occurred periodically since the 1980s, reaching record levels in the latest DEN-4 epidemic in Puerto Rico in 1998.
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Materials and Methods |
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All samples have low passage histories, reducing the risk of artificial selection in vitro: only those samples derived from chronic (generally low) infections were first cultured in A6/C36 mosquito cells, for one or, at most, two passages, prior to RNA extraction. To further eliminate potential biases due to artificial selection, samples were not processed in temporal (year) order. We extracted sample RNA using QIAamp Viral RNA Mini kits (Qiagen GmbH). For each isolate we amplified, using reverse-transcriptase polymerase chain reaction (RT-PCR), gene regions amounting to 40% of the viral genome (4,016 bp of an 11 kbp genome) and including both 5' and 3' ends (see table 1 for primer sequences). Amplified regions included all the structural genes (capsid: C; membrane: M; and envelope: E), a subset of nonstructural genes (NS1, NS2A, and NS4B), and the noncoding 3' NTR region. Amplifications were divided into separate reactions according to length of the target. Before sequencing, RT-PCR products were purified using Qiagen PCR purification kits (Qiagen GmbH). We sequenced both strands of the amplified products using forward and reverse primers (table 1) in standard dye-labeling reactions. Sequence data were collected on an ABI 377 slab-gel automated sequencer (Applied Biosystems), edited, and compiled with Sequencher 3.1.1 (Gene Codes) and aligned against reference sequences (GenBank number M14931; Zhao et al. 1986, Mackow et al. 1987) using Megalign's clustal algorithm (version 3.1.7, Lasergene). We imported aligned sequences into PAUP* (Swofford 2001) for phylogenetic analysis.
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The evolutionary relationships among DEN-4 isolates were inferred using a ML method (PAUP* package, Swofford [2001]). In all cases trees were estimated using the best fitting model of nucleotide substitution identified by Modeltest 3.06 (Posada and Crandall 1998). The model of DNA substitution that best described DEN-4 evolution in Puerto Rico (including the outgroup and six other foreign samples) was the general time-reversible model that includes six substitution rate parameters (AC = 2.0346, A
G = 12.5935, A
T = 1.7144, C
G = 2.0608, C
T = 31.0427, G
T = 1), with 41.5% of sites variable and a gamma distribution of among-site rate variation (4 categories) with a shape parameter (
) of 1.020 (substitution model GTR + I +
). Phylogenies were generated under successive rounds of tree-bisection/reconnection (TBR) branch swapping, updating parameter estimates at each round. To assess the support for the phylogenetic groupings observed we undertook a bootstrap resampling analysis using 1,000 replicate Neighbor-Joining trees estimated under the ML substitution model determined above. Trees were rooted with the 1981 isolate from Dominica, the oldest sequence available.
We used two methods to assess the extent of adaptive evolution in DEN-4. First, we examined the relative rates of nonsynonymous (dN) and synonymous (dS) substitution across coding portions of the viral genome. To do this, we employed a ML approach to compare models of evolution that allow dN/dS to vary within genes or among lineages of the ML tree of the PR sequences (Yang et al. 2000). In particular, we compared models that allow for positive selection because they incorporate a class of codons where dN/dS can be greater than 1 (models M2, M3, M8) with those that specify neutral evolution because dN is constrained to be less than dS (models M0, M1, and M7). We also used the free ratio (FR) model that allows each branch of the tree to have a different dN/dS ratio. Models were compared using standard likelihood ratio tests. A Bayesian approach was used to identify those individual codons most likely subject to positive selection. This approach calculates the posterior probabilities of dN/dS categories for each amino acid site so that sites with the highest probabilities of falling into dN/dS category>1 are most likely to have been under positive selection. All these analyses were undertaken using the CODEML program from the PAML package (Yang 1997).
We also employed a population genetic approach to test for adaptive evolution in dengue virus. According to standard theory, the average time to fixation of neutral mutations in a haploid population is 2Ne, generations. Consequently, if mutations have been fixed much faster than this, we can conclude that their substitution dynamics are dominated by positive selection rather than drift. To calculate 2Ne generations for DEN-4 in Puerto Rico, we estimated the parameter
(= 2Neµ), the neutral mutation rate per site per generation (µ), and the viral generation time (g).
was estimated from given sampling years (1994 and 1998) using a coalescent method (program Fluctuate; Kuhner, Yamato, and Felsenstein [1998]); the generation time of dengue virus was taken as 14 days comprising intrinsic (within human) and extrinsic (within mosquito) replication times of 7 days duration each (Holmes, Bartley, and Garnett 1998). Although direct estimates of µ are not available for dengue virus, a synonymous rate of 6.89 x 104 substitutions/site/year was recently estimated for DEN-4 (Twiddy, Holmes, and Rambaut 2003). Given a generation time of 14 days, this is equivalent to a µ of 2.64 x 105 mutations per site, per generation. Putatively positively selected amino acid changes were identified as those that fall on the internal branches of the tree that separate sampling times (for example, on the branch leading to the viral isolates sampled in 1998); at the population genetic level, mutations that are absent from an early time-point yet present in all sequences from a later time-point can be assumed to have gone to fixation over the course of the sampling period.
Sequences generated by this study can be accessed on GenBank according to accession numbers AY152036 through AY152363.
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Results |
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Our ML phylogenetic analysis of DEN-4 in Puerto Rico revealed a pattern of evolution marked by strong temporal clustering of isolates by year of sampling (fig. 2). All early (1982) isolates from Puerto Rico were associated with the 1981 isolate from Dominica, and were 0.7% (range: 0.5% to 1%) different from the closest group of subsequent PR isolates from 1986/87. Three of six other foreign isolates shared ancestors with this early introduction group as opposed to later PR isolates (El Salvador 1993, Ecuador 1994, and Mexico 1995, data not shown), reflecting the widespread distribution of the introduced Asian DEN-4 variant from 1981 (Gubler 1998; Foster et al. 2003). Since the initial epidemic in 1982, DEN-4 was virtually absent from Puerto Rico until the 1986 epidemic (fig. 1; Dietz et al. 1996). All viruses sampled in Puerto Rico during and after this re-emergence (1986 onward) fell into a single lineage defined by four silent nucleotide substitutions and one amino acid substitution in the envelope (E) gene (methionine to threonine, aa position 163; fig. 2). With the exception of a single 1994 isolate, two additional silent and two conservative amino acid substitutions (isoleucine to valine, envelope aa position 351; lysine to arginine, NS1 aa position 51) occurred in the formation of the re-emergent PR lineage. Within this re-emergent lineage, sublineages were largely temporally ordered. For example, most of the 1987 isolates fell into a well-defined temporal cluster, distinguished by five silent changes across coding regions examined (gold in fig. 2). Similarly, major temporal clusters were formed by all 1992 (green in fig. 2), most 1994 (blue in fig. 2), and all 1998 isolates (red in fig. 2), respectively. The 1998 year group was defined by several silent changes concentrated in the E gene, and more notably three amino acid replacements in the nonstructural NS2A protein (isoleucine to valine, aa position 14; valine to threonine, aa position 54; and proline to serine, aa position 101).
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To determine whether positive selection has played a significant role in DEN-4 evolution and lineage turnover, we examined rates of nonsynonymous (dN) and synonymous (dS) substitution in individual viral genes using a ML method. Although eight potentially positively selected sites were identified (posterior probability P > 0.99) in the E, NS1, NS4B, and most notably the NS2A genes, where a small class of codons (0.9%) had a mean dN/dS ratio of 4.6, in no case could a model of codon evolution allowing positive selection conclusively reject all competing neutral models (table 2; the results for all model comparisons are available from the authors on request). However, the evolution of the nonstructural gene NS2A was striking in that the branch leading to the 1998 cluster of sequences was distinguished exclusively by three nonconservative amino acid replacements in NS2A (14Ileu to Thr, 54Val to Thr, 101Pro to Ser; fig. 2), in the absence of any synonymous nucleotide changes. This results in an infinitely large dN/dS ratio along this branch, suggestive of positive selection: mean dN/dS for all other internal branches of our phylogeny in NS2A were significantly lower (mean dN/dS = 0.038, P = 0.001, using absolute number nucleotide changes for observed and expected values). Moreover, these mutations appear to have been fixed far more quickly than if they were subject to genetic drift alone. Estimated values of
(2Neµ) are 0.024 (range 0.014 to 0.045) and 0.027 (range 0.016 to 0.052) for the viruses sampled from years 1994 and 1998, respectively. Assuming a neutral mutation rate of 2.64 x 105 mutations per site, per generation, effective population sizes (Ne) were only 454 and 511 for 1994 and 1998, respectively. Taking the mean Ne value across these two sampling times (482), we obtain an expected fixation time under genetic drift of 13,496 days (482 x 14 days/generation x 2) or
37 years. However, the observed fixation time for these mutants is a maximum of 6 years; as these mutations were first detected in 1994, we assume that they appeared sometime between the 1992 and 1994 epidemics, giving a maximum of 6 years time difference to the 1998 strains.
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Discussion |
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There are several non-mutually exclusive explanations for the lineage turnover observed in DEN-4 evolution in Puerto Rico over the last 20 years, aside from incomplete sampling. Novel lineages could arise and proliferate in a population through multiple re-introductions, genetic drift, and/or selection. However, although introductions from other DEN-4 populations may provide a source of variation, evidence suggests that DEN-4 in the Caribbean is characterized by local evolution interrupted occasionally by gene flow (Foster et al. 2003). There was also no evidence that microgeographic population structure within Puerto Rico generated the observed pattern, as virus samples were obtained from similar geographic regions in all cases (data not shown). In addition, the distinct and persistent pattern of lineage turnover is difficult to explain by random sampling processes alone, because we would expect common genotypes to become fixed by genetic drift more often than rare ones. Indeed, the stochastic nature of the dengue virus life-cycle should favor common variants: genetic bottlenecks occur at every mosquito feeding event, along with seasonal reductions in vector populations (Gubler 1987), and annual variation in the abundance of susceptible human hosts. Instead, the dominant Puerto Rican lineage of a given year twice descended from earlier rare genotypes, a pattern that suggests that much of the lineage turnover is driven by selection on viral genotype. In support of this hypothesis, there was an increase in the rate of nonsynonymous substitution (in the absence of any silent changes in NS2A) on the lineage leading to the 1998 epidemic, and these amino acid changes were fixed far more quickly than expected by genetic drift. Moreover, our population genetic estimations for the fixation time of the NS2A mutants are conservative in that these changes may have been fixed much faster than the 6 years separating the 1992 and 1998 samples, and our estimates of Ne may be artificially low if positive selection has purged genetic diversity. Consequently, adaptive evolution in the NS2A gene may have triggered the 1998 epidemic in Puerto Rico, and DEN-4 genotypes bearing these NS2A modifications were also associated with contemporaneous epidemics throughout the Greater and Lesser Antilles (Foster et al. 2003). Conversely, a similar association between amino acid changes and lineage turnover was not observed between 1987 and 1992, where neither clade was defined by amino acid substitutions. In this case, lineage turnover may have resulted from drift-sensitive population bottlenecks, inter-island extinction/recolonization, or selection on other parts of the genome not examined in this study. Although we examined many more nucleotides than previous studies (e.g., Rico-Hesse 1990; Lewis et al. 1993; Lanciotti et al. 1994; Lanciotti, Gubler, and Trent 1997; Rico-Hesse et al. 1997, 1998; Singh et al. 1999; Uzcategui et al. 2001; Twiddy et al. 2002), 60% of the dengue genome was not surveyed, including genes known to be important in virus replication, such as NS5 (Leitmeyer et al. 1999), and virus antigenicity, such as NS1 (Mathew et al. 1998; Jacobs et al. 2000). Because selection is apparently restricted to very few sites, a complete appreciation of the forces driving genetic change in DEN-4 will ultimately require the analysis of full genome sequences.
The apparent positive selection on the NS2A gene is even more anomalous given the relatively strong constraints acting on other regions of the viral genome. In particular, there was no convincing evidence that changes in structural genes, the primary targets of specific immunity, underlie the evolutionary shifts we observed in DEN-4 after its re-emergence in 1986. Most positions within the structural genes were invariant (table 2), and very few of the nonsynonymous substitutions in these regions occurred at internal nodes. Two amino acid changes in E (positions 163 and 351; see fig. 2) defined the DEN-4 that re-emerged in the late 1980s after 3 years of undetectable transmission, both occurring within well-characterized structural epitope domains (summarized in Roehrig [1997]). The E protein, which enables host cell binding and entry, providing a target for the host immune response (Roehrig 1997), is the functional analog of influenza A's hemagglutinin (HA) gene, which, in contrast, appears to be under strong antigenic selection (Bush et al. 1999). In dengue virus, constraints on the E gene may be attributable to its two-host life cycle and resultant multi-cell type tropism (Beaty, Trent, and Roehrig 1988; Strauss and Strauss 1988), so that rates of nucleotide substitution are lower than those seen in many other RNA viruses (Weaver, Rico-Hesse, and Scott 1992; Jenkins et al. 2002). In addition, positive selection is less likely to occur because of intrinsic negative fitness trade-offs (Woelk and Holmes 2002). Indeed, substitution patterns across the four gene regions examined here are consistent with a genome under stabilizing selection, with synonymous changes greatly outnumbering nonsynonymous changes. Against this conservative background, the amino acid changes in NS2A that distinguish the 1998 virus samples appear even more conspicuous, and natural selection on nonstructural genes has been described for other viruses and correlated with epidemic outbreaks (Knowles et al. 2001).
Aside from epidemiologic evidence, the phenotypic traits targeted by natural selection involving NS2A are unclear because we know so little about the gene's function. Dengue viruses in Puerto Rico may be under particularly intense selection to improve replication rate, survival, and, ultimately, transmission rate, because the only vector present, urban-specialist A. aegypti, is relatively inefficient and requires high viral titers to acquire infection (up to 106 infectious units/ml blood in laboratory studies [Gubler 1987; Kuno 1997]). Puerto Rico also lacks potential reservoir (primate) hosts, and its vector exhibits extremely low levels of vertical transmission, such that the disease must cycle directly between mosquitoes and humans to persist (Gubler 1987, 1998). Alternatively, the selection pressure could relate to survival pressure exerted by the human immune system in the guise of cytotoxic T-lymphocytes (CTLs). Epitopes that elicit human T-cell responses ranging from serotype-specific to cross-reactive have been identified throughout the nonstructural regions of the dengue genome (Loke et al. 2001), and phylogenetic evidence for positive selection at or near T-cell epitopes has been noted previously (Twiddy, Woelk, and Holmes 2002). The function of NS2A has been associated with viral replication (Falgout and Markoff 1995; Mackenzie et al. 1998) and the mediation of host immune interactions via NS1 (Rothman et al. 1993; Mathew et al. 1998; Jacobs et al. 2000). As the three amino acid substitutions in NS2A that define the 1998 cluster were all highly nonconservative changes from hydrophobic, non-polar residues to polar, uncharged amino acids, they would at the very least change the 3-dimensional structure of the NS2A protein. To fully determine the repercussions of observed NS2A modifications on viral extended phenotype, future studies must endeavor to characterize the NS2A protein's structure and function, and to survey this gene in phylogenetic studies of epidemic dengue.
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Acknowledgements |
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Footnotes |
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