Molecular evolution of peste des petits ruminants virus - PubMed (original) (raw)

. 2014 Dec;20(12):2023-33.

doi: 10.3201/eid2012.140684.

Muhammad Munir, AravindhBabu R Parthiban, Ashley C Banyard, Jingyue Bao, Zhiliang Wang, Chrisostom Ayebazibwe, Gelagay Ayelet, Mehdi El Harrak, Mana Mahapatra, Geneviève Libeau, Carrie Batten, Satya Parida

Molecular evolution of peste des petits ruminants virus

Murali Muniraju et al. Emerg Infect Dis. 2014 Dec.

Abstract

Despite safe and efficacious vaccines against peste des petits ruminants virus (PPRV), this virus has emerged as the cause of a highly contagious disease with serious economic consequences for small ruminant agriculture across Asia, the Middle East, and Africa. We used complete and partial genome sequences of all 4 lineages of the virus to investigate evolutionary and epidemiologic dynamics of PPRV. A Bayesian phylogenetic analysis of all PPRV lineages mapped the time to most recent common ancestor and initial divergence of PPRV to a lineage III isolate at the beginning of 20th century. A phylogeographic approach estimated the probability for root location of an ancestral PPRV and individual lineages as being Nigeria for PPRV, Senegal for lineage I, Nigeria/Ghana for lineage II, Sudan for lineage III, and India for lineage IV. Substitution rates are critical parameters for understanding virus evolution because restrictions in genetic variation can lead to lower adaptability and pathogenicity.

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Figures

Figure 1

Figure 1

Mean ratios of nonsynonymous (dN) to synonymous (dS) substitutions per site of concatenated coding regions of peste des petits ruminants virus genome. Proportion of dS substitutions per potential dS site and proportion of dN substitutions per potential dN site were calculated by using the method of Nei and Gojobori (29) and the suite of nucleotide analysis program (

www.hiv.lanl.gov

). Vertical dashed lines indicate gene junctions with sliding windows of size = 5 codons. dN/dS values ≥ 10 are shown as 10. Numbers along baseline indicate coding regions (basepairs) of individual genes. N, nucleoprotein; P, phosphoprotein; M, matrix; F, fusion; H, hemagglutinin; L, large polymerase.

Figure 2

Figure 2

Time-scaled Bayesian maximum clade credibility phylogeny tree based on peste des petits ruminants virus complete genome sequences. The tree was constructed by using the uncorrelated exponential distribution model and exponential tree prior. Branch tips correspond to date of collection and branch lengths reflect elapsed time. Tree nodes were annotated with posterior probability values and estimated median dates of time to most recent common ancestor (TMRCA). Corresponding 95% highest posterior density (HPD) interval values of TMRCA are indicated as gray bars. Horizontal axis indicates time in years. UAE, United Arab Emirates.

Figure 3

Figure 3

Time-scaled Bayesian MCC phylogeny tree based on peste des petits ruminants virus (PPRV), rinderpest virus (RPV), and measles virus (MV) complete genome sequences. The tree was constructed by using the uncorrelated exponential distribution model and exponential tree prior. Branch tips correspond to date of collection and branch lengths reflect elapsed time. Tree nodes were annotated with posterior probability values, estimated median dates of time to most recent common ancestor (TMRCA). Corresponding 95% highest posterior density (HPD) values of TMRCA are indicated as gray bars. Horizontal axis indicates time in years. UAE, United Arab Emirates.

Figure 4

Figure 4

Bayesian skyline plot showing demographic history of global peste des petits ruminants viruses sampled during 1968–2012. Genetic diversity was estimated by using a partial nucleoprotein gene dataset (n = 159). The thick black line represents median genetic diversity and the blue shaded areas show 95% highest posterior density estimate.

Figure 5

Figure 5

Maximum clade credibility tree constructed for the geospatial analysis of peste des petits ruminants viruses by using complete genome data. Nodes are colored according to the most probable location of their ascendent locations. Posterior probability values are shown along tree nodes. Posterior probability distribution (PPD) values of root location states of the ancestral node are shown along the x-axis at the top left. UAE, United Arab Emirates.

Figure 6

Figure 6

Probability of root locations of the most recent common ancestral peste des petits ruminants (PPRV). MCC trees were obtained by using the continuous time Markov chain and Bayesian stochastic search variable selection procedures. Root location probabilities of the most recent common ancestor using global PPRV isolates (panel A ) are shown graphically alongside lineages I–IV (panels B–E) and were estimated by using a complete dataset of PPRV partial nucleoprotein gene data and individual lineages separately. Probabilities of root locations are shown as percentages along the x-axes. UAE, United Arab Emirates; CAR, Central African Republic.

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