Molecular Evolutionary and Epidemiological Dynamics of Genotypes 1G and 2B of Rubella Virus

<div><p>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.</p></div

Maximum clade credibility (MCC) tree depicting TMRCA estimates of respective genotypes.

<p>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.</p

Population pair-wise Fst among different regions for genotype 1G.

<p>Values not significant at <i>p</i><0.01 are indicated with asterisk.</p><p>AFR: African region; EUR: European region; AMR: American region.</p><p>Population pair-wise Fst among different regions for genotype 1G.</p

Estimates of mean substitution rates (×10⁻³ nucleotide substitutions per site per year), TMRCAs (in year) and the dN/dS for genotypes 1G, 2B and for the pooled dataset.

<p>Best-fit models with the highest marginal log likelihood score for respective data sets are in bold.</p><p>n: Number of sequences; SP:Structural protein; NSP:Nonstructural protein; HPD: Highest Posterior Density; TMRCA: Time to the Most Recent Common Ancestor; CoV: Coefficinet of Variation; NA: Not Applicable; dN: Nonsynonymous substitution; dS: Synonymous substitution.</p><p>Estimates of mean substitution rates (×10⁻³ nucleotide substitutions per site per year), TMRCAs (in year) and the dN/dS for genotypes 1G, 2B and for the pooled dataset.</p

Population pair-wise Fst among different regions for genotype 2B.

<p>WPR: Western Pacific region; SEAR: South East Asian region; EUR: European region; AMR: American region. All values are significant at <i>p</i><0.01.</p><p>Population pair-wise Fst among different regions for genotype 2B.</p

The root-to-tip genetic distance based on <i>meq</i> gene versus year of MDV isolation.

<p>The regression coefficient (R²) estimates the fit of the data to a strict molecular clock by testing the degree of influence sampling time has over the amount of pairwise diversity in the data. This analysis suggests the presence of temporal structure for <i>meq</i> gene of MDV.</p

Positive Selection Drives Rapid Evolution of the <i>meq</i> Oncogene of Marek’s Disease Virus

<div><p>Marek’s disease (MD), caused by Marek’s disease virus (MDV), a poultry-borne alphaherpesvirus, is a devastating disease of poultry causing an estimated annual loss of one billion dollars to poultry producers, worldwide. Despite decades of control through vaccination, MDV field strains continue to emerge having increased virulence. The evolutionary mechanism driving the emergence of this continuum of strains to increased MDV virulence, however, remains largely enigmatic. Increase in MDV virulence has been associated with specific amino acid changes within the C-terminus domain of Mareks’s EcoRI-Q (<i>meq</i>)-encoded oncoprotein. In this study, we sought to determine whether the <i>meq</i> gene has evolved adaptively and whether past vaccination efforts have had any significant effect on the reduction or increase of MDV diversity over time. Our analysis suggests that <i>meq</i> is estimated to be evolving at a much faster rate than most dsDNA viruses, and is comparable with the evolutionary rate of RNA viruses. Interestingly, most of the polymorphisms in <i>meq</i> gene appear to have evolved under positive selection and the time of divergence at the <i>meq</i> locus coincides with the period during which the poultry industry had undergone transitions in management practices including the introduction and widespread use of live attenuated vaccines. Our study has revealed that the decades-long use of vaccines did not reduce MDV diversity, but rather had a stimulating effect on the emergence of field strains with increased genetic diversity until the early 2000s. During the years 2004–2005, there was an abrupt decline in the genetic diversity of field isolates followed by a recovery from this bottleneck in the year 2010. Collectively, these data suggest that vaccination seems to not have had any effect on MDV eradication, but rather had a stimulating effect on MDV emergence through adaptation.</p></div

Maximum Clade Credibility (MCC) tree inferred from the Bayesian analysis of the MDV <i>meq</i> gene sequences.

<p>The mean TMRCAs with confident intervals (above the nodes) and the posterior probabilities (below the nodes) are mentioned.</p

Bayesian skyline plot (BSP) inferred from the <i>meq</i> gene sequences.

<p>The BSP above depicts the relative genetic diversity of MDV over time. The plot depicting MDV population had recovered from a recent bottleneck (~2005–2008).</p

Positively selected sites are shown as detected by REL and FUBAR methods.

<p>Positively selected sites are shown as detected by REL and FUBAR methods.</p