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Short Communication |
1 Department of Biochemistry and McGill Cancer Center, McGill University, Montreal, Quebec, Canada H3G 1Y6
2 Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
3 Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
Correspondence
Juan Cristina
cristina{at}cin.edu.uy
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ABSTRACT |
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A figure of the phylogenetic analysis of the complete VP1 region using the p-distance model and the UPGMA method, and a table showing French HAV strains examined in this study are available as supplementary material in JGV Online.
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). Despite an overall physical and epidemiological similarity to enteroviruses, the structure of HAV, its tissue tropism and genetic distance from other members of the family Picornaviridae, indicate that HAV is unique within this family (Ticehurst et al., 1989; Palmenberg, 1989; Wimmer & Murdin, 1991; reviewed by Costa-Mattioli et al., 2003). Hepatitis A viruses have been classified into four human (I, II, III and VII) and three simian (IV, V and VI) genotypes (Robertson et al., 1992; Costa-Mattioli et al., 2003). Recent evidence has suggested that, as other RNA viruses, HAV exists in vivo as distributions of closely related variants referred to as quasispecies (Sanchez et al., 2003a). Quasispecies dynamics is characterized by the continuous generation of variant viral genomes, competition among them and selection of the fittest mutant distributions in any given environment. Understanding the principles that shape the evolution of viral quasispecies is becoming increasingly important to be able to model disease progression and to design preventive and therapeutic strategies to control viral disease (Domingo et al., 2001).
The complexities of genetic data obtained from RNA virus quasispecies populations may not be accurately described by any single analytical tool (Baccam et al., 2001). Over time, RNA virus evolution is conditioned by perturbations of population equilibrium, which may not be equal among individual hosts, and therefore, multiple viral sublineages may rapidly be established that differ in the number of rounds of replication (and history of environmental perturbations), and may co-circulate in the same geographical area.
To study HAV evolution over time in a specific geographical region, we have analysed the highly variable region, VP1, of HAV strains genotype I. The strains studied were isolated in France from 1983 to 2001 (Costa-Mattioli et al., 2002; see also Supplementary Table 1 available in JGV Online). We used two methods, one based on phylogenetic distance, neighbour-joining (NJ; Saitou & Nei, 1987), and the other is a non-hierarchical method developed to study closely related components of mutant spectra of viral quasispecies (PAQ; Baccam et al., 2001).
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). The program PAQ (Baccam et al., 2001) was adapted to compare consensus HAV VP1 sequences and to group HAV VP1 genes that were most similar. The program uses the Hamming distance (number of nucleotide differences) to measure the distances between VP1 gene sequences, and a non-hierarchical clustering method to identify discrete and cohesive partitions of closely related sequences. The optimal output maximizes the number of variants contained within the partition, while minimizing the partition radius and any overlap between partitions. However, PAQ does not select a predetermined number of partitions among groups, and overlap between groups is allowed. The basic assumption of the program is that sequences separated by the fewest genetic differences are more similar and, thus, should be grouped together (Baccam et al., 2001). Application of partitions with a radius of 60, using strain HAV 9F(1994) as an outgroup, generated five distinct, non-overlapping groups, designated clades 1–5 (Table 1
). Interestingly, clades 1–4 were composed of strains isolated from patient's sera, while clade 5 was exclusively composed of strains isolated from sludge (Fig. 1 and Table 1). Whether the HAV environmental strains found clustered in clade 5 represent a potential source of infection or are just more resistant to environmental conditions remains to be determined.
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) among different subpopulations. For instance, the compactness for clades 3 and 5 (values of 83·66 and 54·50, respectively) is significantly lower than that obtained for clades 1 or 4 (values of 681·11 and 719·33, respectively, see Table 1).
To compare the results found with PAQ with those obtained using hierarchical methods of clustering, a matrix for the Kimura two-parameter model (Felsenstein, 1993) was created for all sequences used to compute neighbour-joining trees. The robustness of each node was assessed by bootstrap resampling (500 pseudoreplicates). These methods were implemented by using software from the MEGA2 program (Kumar et al., 1994). Consistent with our previous data (Costa-Mattioli et al., 2002), all the strains analysed were assigned to two well-defined subgenotypes, namely, IA and IB (Fig. 2). In addition, three clades among subgenotype IA and two among subgenotype IB were identified. Taken together these data suggest that there is a high correlation between the lineages identified by the hierarchical (NJ) method and the clades identified by PAQ. Strains isolated from sludge, assigned to a specific clade, also showed a very close genetic relatedness when studied by this hierarchical method (see Fig. 2). A similar relationship among isolates was obtained using the p-distance model and the UPGMA method for constructing phylogenetic trees (Sneath & Sokal, 1973) (not shown; see Supplementary Fig. S1 available in JGV Online).
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), PAUP (Swofford, 1999) or MEGA (Kumar et al., 1994). These methods belong to the category of agglomerative methods, and merge data to form clusters that grow larger in a process termed ‘chaining’. Chaining is adequate at recognizing mutually exclusive clusters but may not be satisfactory at recognizing potential overlapping clusters of sequences. Besides, genetic recombination, in which the frequency is increasing within many RNA viruses (Agol, 2002) including HAV (Costa-Mattioli et al., 2003), may not be adequately modelled under the branching assumptions of phylogenetic reconstruction (Baccam et al., 2001). Recent developments in analyses of RNA viral quasispecies using PAQ have permitted discerning co-circulating lentiviral subpopulations (Baccam et al., 2001, 2003). Although, PAQ was designed specifically to analyse viral quasispecies (Baccam et al., 2001), it can be extended to analyse other types of sequence data, and here we have used it to compare epidemiologically related, consensus HAV sequences. Remarkably, both phylogenetic and partition analyses from the VP1 region identified different subpopulations of HAV variants that coexist in time (during 1993, 1995, 1997 or 1999) and in different environments. Interestingly, clades isolated from different years, reemerged and were even associated with epidemic strains, such as those isolated in 1985 and 1999 (Figs 1 and 2). These data suggest that beyond mutations and genetic recombination, HAV exploits this variation strategy in dominance to promote and ensure their survival.
A high correlation between partition and phylogenetic groupings of variants was also observed by Baccam et al. (2003). In particular, coexisting subpopulations have been extensively documented for HIV type 1 (Shapshak et al., 1999; for review see Papathanasopoulos et al., 2003 and references therein) and Equine infectious anaemia virus (Baccam et al., 2003). Multiple coexisting subpopulations may occupy different regions on a fitness landscape to allow the virus to adapt rapidly to changes in the landscape topology. This may be especially relevant in modelling reservoirs of virus and the emergence of virus variants. The coexisting populations identified in the present study are consistent with the presence in each HAV isolate of a mutant spectrum (Sanchez et al., 2003a), which provides a repertoire of variants that, while constituting a minority in an infected individual, may become dominant following transmission to a new host individual. These findings fit the general picture of quasispecies dynamics (Domingo et al., 2001), with the salient antigenic stability of HAV that is probably related to structural constraints of the viral capsid (Sanchez et al., 2003b).
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ACKNOWLEDGEMENTS |
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REFERENCES |
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Baccam, P., Thompson, R. J., Fedrigo, O., Carpenter, S. & Cornette, J. L. (2001). PAQ: partition analysis of quasispecies. Bioinformatics 17, 16–22.
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Received 26 June 2005;
accepted 4 October 2005.
This article has been cited by other articles:
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  G. Moratorio, M. Costa-Mattioli, R. Piovani, H. Romero, H. Musto, and J. Cristina Bayesian coalescent inference of hepatitis A virus populations: evolutionary rates and patterns J. Gen. Virol., November 1, 2007; 88(11): 3039 - 3042. [Abstract] [Full Text] [PDF]
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