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Molecular evolutionary and epidemiological dynamics of genotypes 1G and 2B of rubella virus.

Padhi A, Ma L - PLoS ONE (2014)

Bottom Line: The overall nucleotide substitution rate of this non-vector-borne RV is in the order of 10-3 substitutions/site/year, which is considerably higher than the substitution rates previously reported for the vector-borne alphaviruses within the same family.Currently circulating strains of RV share a common ancestor that existed within the last 150 years, with 95% Highest Posterior Density values ranging from 1868 to 1926 AD.Such a viral dispersal pattern could be related to the migration of infected individuals across the regions coupled with a low coverage of MMR vaccination.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America.

ABSTRACT
Rubella Virus (RV), which causes measles-like rashes in children, puts millions of infants at risk of congenital defects across the globe. Employing phylogenetic approaches to the whole genome sequence data and E1 glycoprotein sequence data, the present study reports the substitution rates and dates of emergence of all thirteen previously described rubella genotypes, and gains important insights into the epidemiological dynamics of two geographically widely distributed genotypes 1G and 2B. The overall nucleotide substitution rate of this non-vector-borne RV is in the order of 10-3 substitutions/site/year, which is considerably higher than the substitution rates previously reported for the vector-borne alphaviruses within the same family. Currently circulating strains of RV share a common ancestor that existed within the last 150 years, with 95% Highest Posterior Density values ranging from 1868 to 1926 AD. Viral strains within the respective genotypes began diverging between the year 1930 s and 1980 s. Both genotype 1G and 2B have shown a decline in effective number of infections since 1990 s, a period during which mass immunization programs against RV were adapted across the globe. Although both genotypes showed some extent of spatial genetic structuring, the analyses also depicted an inter-continental viral dispersal. Such a viral dispersal pattern could be related to the migration of infected individuals across the regions coupled with a low coverage of MMR vaccination.

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Related in: MedlinePlus

Maximum clade credibility (MCC) tree depicting TMRCA estimates of respective genotypes.Posterior probability of each node is shown. The horizontal bar at each node is the 95% HPD interval for the TMRCA of the respective node. Time-scale (in year) is shown at the bottom of the tree.
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pone-0110082-g001: Maximum clade credibility (MCC) tree depicting TMRCA estimates of respective genotypes.Posterior probability of each node is shown. The horizontal bar at each node is the 95% HPD interval for the TMRCA of the respective node. Time-scale (in year) is shown at the bottom of the tree.

Mentions: By employing the Bayesian coalescent and ML-based phylogenetic approaches to the whole genome sequence data and 739-bp E1 nucleotide sequence data, the present study reports the estimated rate and date of emergence of each rubella viral genotype (Fig. 1; Table 1) and infers the population dynamics of genotypes 1G and 2B (Fig. 2A & B; 3A & B; Table 1). Two molecular clock models (strict and relaxed) with different coalescent priors were fitted to infer the rate and date of emergence of rubella viral genotypes. The Bayes factor (BF) using either a constant population size, BSP, or GMRF skyride coalescent prior favored the relaxed over the strict clock model (Table 1). With exception of 1G, under the relaxed molecular clock, the CoV for all the data sets did not encompass zero, indicating a large scale rate variation across the lineages (Table 1). We found a large degree of overlap (within the 95%HPD) in the evolutionary rate estimated from the whole genome, SP, NSP, as well as from the partial E1 nucleotide sequences (739-bp) (Table 1). Based on the relaxed clock assumption, the estimated evolutionary rates of RV inferred from the whole genome, SP, NSP and partial E1 nucleotide sequences are all within the range of 0.57–1.15×10−3 substitutions per site per year. According to our estimate, the currently circulating strains of RV share a common ancestor that existed within the last 150 years, with 95% HPD values ranging from 1863 to 1930 AD (Table 1; Fig. 1). While clade 1, which is comprised of ten genotypes, appeared to be monophyletic, clustering of the three genotypes that were previously designated to be within clade 2 is not supported (posterior probability <0.99). However, clustering of the RV strains within their respective genotypes in clade 2 is strongly supported with a posterior probability of 1.0, and the cluster began diverging between the year 1940 s and 1980 s (Fig. 1). All the 10 genotypes within clade 1 were descended from their most recent common ancestor between the year 1930 s and 1980 s (Fig. 1).


Molecular evolutionary and epidemiological dynamics of genotypes 1G and 2B of rubella virus.

Padhi A, Ma L - PLoS ONE (2014)

Maximum clade credibility (MCC) tree depicting TMRCA estimates of respective genotypes.Posterior probability of each node is shown. The horizontal bar at each node is the 95% HPD interval for the TMRCA of the respective node. Time-scale (in year) is shown at the bottom of the tree.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4201520&req=5

pone-0110082-g001: Maximum clade credibility (MCC) tree depicting TMRCA estimates of respective genotypes.Posterior probability of each node is shown. The horizontal bar at each node is the 95% HPD interval for the TMRCA of the respective node. Time-scale (in year) is shown at the bottom of the tree.
Mentions: By employing the Bayesian coalescent and ML-based phylogenetic approaches to the whole genome sequence data and 739-bp E1 nucleotide sequence data, the present study reports the estimated rate and date of emergence of each rubella viral genotype (Fig. 1; Table 1) and infers the population dynamics of genotypes 1G and 2B (Fig. 2A & B; 3A & B; Table 1). Two molecular clock models (strict and relaxed) with different coalescent priors were fitted to infer the rate and date of emergence of rubella viral genotypes. The Bayes factor (BF) using either a constant population size, BSP, or GMRF skyride coalescent prior favored the relaxed over the strict clock model (Table 1). With exception of 1G, under the relaxed molecular clock, the CoV for all the data sets did not encompass zero, indicating a large scale rate variation across the lineages (Table 1). We found a large degree of overlap (within the 95%HPD) in the evolutionary rate estimated from the whole genome, SP, NSP, as well as from the partial E1 nucleotide sequences (739-bp) (Table 1). Based on the relaxed clock assumption, the estimated evolutionary rates of RV inferred from the whole genome, SP, NSP and partial E1 nucleotide sequences are all within the range of 0.57–1.15×10−3 substitutions per site per year. According to our estimate, the currently circulating strains of RV share a common ancestor that existed within the last 150 years, with 95% HPD values ranging from 1863 to 1930 AD (Table 1; Fig. 1). While clade 1, which is comprised of ten genotypes, appeared to be monophyletic, clustering of the three genotypes that were previously designated to be within clade 2 is not supported (posterior probability <0.99). However, clustering of the RV strains within their respective genotypes in clade 2 is strongly supported with a posterior probability of 1.0, and the cluster began diverging between the year 1940 s and 1980 s (Fig. 1). All the 10 genotypes within clade 1 were descended from their most recent common ancestor between the year 1930 s and 1980 s (Fig. 1).

Bottom Line: The overall nucleotide substitution rate of this non-vector-borne RV is in the order of 10-3 substitutions/site/year, which is considerably higher than the substitution rates previously reported for the vector-borne alphaviruses within the same family.Currently circulating strains of RV share a common ancestor that existed within the last 150 years, with 95% Highest Posterior Density values ranging from 1868 to 1926 AD.Such a viral dispersal pattern could be related to the migration of infected individuals across the regions coupled with a low coverage of MMR vaccination.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America.

ABSTRACT
Rubella Virus (RV), which causes measles-like rashes in children, puts millions of infants at risk of congenital defects across the globe. Employing phylogenetic approaches to the whole genome sequence data and E1 glycoprotein sequence data, the present study reports the substitution rates and dates of emergence of all thirteen previously described rubella genotypes, and gains important insights into the epidemiological dynamics of two geographically widely distributed genotypes 1G and 2B. The overall nucleotide substitution rate of this non-vector-borne RV is in the order of 10-3 substitutions/site/year, which is considerably higher than the substitution rates previously reported for the vector-borne alphaviruses within the same family. Currently circulating strains of RV share a common ancestor that existed within the last 150 years, with 95% Highest Posterior Density values ranging from 1868 to 1926 AD. Viral strains within the respective genotypes began diverging between the year 1930 s and 1980 s. Both genotype 1G and 2B have shown a decline in effective number of infections since 1990 s, a period during which mass immunization programs against RV were adapted across the globe. Although both genotypes showed some extent of spatial genetic structuring, the analyses also depicted an inter-continental viral dispersal. Such a viral dispersal pattern could be related to the migration of infected individuals across the regions coupled with a low coverage of MMR vaccination.

Show MeSH
Related in: MedlinePlus