Assessing the phylogenetic utility of PRRSV fragments to reconstruct the evolutionary history of the virus

Martí Cortey, Gerard E. Martín-Valls, Enric Mateu

Drift Migration

Quasi-species

MutationSelection

1. Introduction

t0

MutationSelection

t1

1. Introduction

t0

MutationSelection

1. Introduction

t1

MutationSelectionRecombination

Objective: Assess the phylogenetic utility of PRRSV fragments to reconstruct the history of the virus

1. Introduction

How? analyzing the influence of several evolutionary processes and forces along the virus genome

54 genomes from Genotype 1

2. Material and Methods

393 genomes from Genotype 2

Purged and pruned

54 genomes from Genotype 1 237 genomes from Genotype 2

Data mining from GenBank

MutationSq0 AAAAASq1 AAAAASq2 AAAAA

t0

Sq0 AAAAASq1 AACAASq2 AACAA

t1

Sq0 AAAAASq1 ATCAASq2 AACAA

t2

Sq0 AAAAASq1 ATCAASq2 AAGAApresent

frequ

ency

distance

Saturation: Multiple substitutions on a site

3. Results and Discussion

Mutation

Genotype 1

Genotype 2

Little saturationSubstantial saturationExtreme saturation

3. Results and Discussion

Nucleotide saturation

All calculations were carried out with DAMBE package

MutationSelection

3. Results and Discussion

Synonymous or silent substitutions: nucleotide substitution in a codon that does not change the translated aminoacid (estimated by dS).

Non-synonymous substitutions: nucleotide substitution in a codon that change the translated aminoacid (estimated by dN)

Neutral selection:

Negative or purifying selection:

Positive selection:

dN/dS~1 dN-dS~0dN ~ dS

dN/dS>1 dN-dS>0dN ↑ dS ↓

dN/dS<1 dN-dS<0dN ↓ dS ↑

CAA GlutamineCAG Glutamine

CAA GlutamineCAC Histidine

Selection

3. Results and Discussion

N-terminus Overlapping with ORF5a

Mostly NegativeMostly NeutralMostly Positive

Selection

3. Results and Discussion

Genotype 1

Genotype 2

All calculations were carried out with SNAP web utility

Selection

3. Results and Discussion

SelectionRecombination

Genotype 1 16 recombination points

3. Results and Discussion

EU076704

GU047344

JF276431

PRRSV70

All calculations were carried out with GARD package

Recombination

Genotype 2 7 recombination points

3. Results and Discussion

JN662424

KF611905

All calculations were carried out with GARD package

2000 1980 1960 1940year

2005

1974

1953 - 1954

0.002138 subs · site-1 ·year-1Mismatch Distribution3. Results and Discussion

All calculations were carried out with MEGA and BEAST packages

3. Results and Discussion

2006 - 2008

19730.003345 subs · site-1 ·year-1

2000 1985 1970 1955year

All calculations were carried out with MEGA and BEAST packages

3. Results and Discussion

0.001935 subs · site-1 ·year-1

1990

1965

1940yea

r

1915

2015

All calculations were carried out with MEGA and BEAST packages

4. Corollary

1. PRRSV genome is subjected to differential pressures from evolutionary forces.

2. Nucleotide saturation and selection were reported along the genome, heavily influencing the quality of the phylogenetic signal recovered.

3. Recombination is a very common process for PRRSV, different number of breaking points between genotypes were reported suggesting different frequencies of viable recombinant isolates.

4. ORF5 is a reliable molecular marker at the short-term, while Nsp9 is a reliable molecular marker at the long-term. Together, they reconstruct robust phylogenetic groups.

4. Corollary

5. Viral population expansions for Genotype 2 consistently coincide with well-known historical events. The evolutionary results supports a scenario of isolation between the two genotypes lasting a considerable length of time, long before the appearance of PRRS.

6. The short number of Genotype 1 genomes – specifically Nsp9 – hinders the reconstruction of past events within the genotype, and blurry any attempt to trace back older evolutionary scenarios for PRRSV, like when and how the virus appeared and its taxonomic status (Kuhn et al. 2015).

Acknowledgements

Thank you very much for your attention!

Comments and criticisms are welcomed!

The 2015 North American PRRS Symposium wishes to thank the following sponsors for their generous

support: