Genetic and epidemiological insights into the emergence of peste des petits ruminants virus (PPRV) across Asia and Africa

Abstract

Small ruminants are important components in the livelihood of millions of households in many parts of the world. The spread of the highly contagious peste des petits ruminants (PPR) disease, which is caused by an RNA virus, PPRV, across Asia and Africa remains a major concern. The present study explored the evolutionary and epidemiological dynamics of PPRV through the analyses of partial N-gene and F-gene sequences of the virus. All the four previously described PPRV lineages (I-IV) diverged from their common ancestor during the late-19 th to early-20 th century. Among the four lineages, PPRV-IV showed pronounced genetic structuring across the region; however, haplotype sharing among the geographic regions, together with the presence of multiple genetic clusters within a country, indicates the possibility of frequent mobility of the diseased individuals across the region. The gradual decline in the effective number of infections suggests a limited genetic variation, which could be attributed to the effective vaccination that has been practiced since 1990s. However, the movement of infected animals across the region likely contributes to the spread of PPRV-IV. No evidence of positive selection was identified from this study.

Peste Des Petits Ruminants in Benin: Persistence of a Single Virus Genotype in the Country for Over 42 Years

“…Accordingly, the evolutionary rate of PPRV at the genomic scale was estimated to be 7.8 × 10 −4 nucleotide substitutions per site, per year (95% HPD values = 7.3–8.4 × 10 −4 subs/site/year) and the time to common ancestor of this sample of PPRV was estimated to be between 1891–1905 (95% HPD values). These rate and divergence time estimates are broadly similar to those estimated previously for PPRV (Muniraju et al., ; Padhi and Ma, ), although for our analysis we has used a larger number of full genome sequences which have become available since their publications. Similarly, the divergence time of the genotype II viruses (of which Benin/B1/1969 is the basal lineage) was estimated to be between 1960–1963, while Benin/10/2011 is estimated to have diverged from Ghana/2010 and SnDK/Senegal/2013 between 1996–1999.…”

“…The persistence of lineage II in Benin is of note when compared to other countries/regions in Africa. In Senegal, viruses isolated in the 1960s are from lineage I and have now been replaced by lineage II viruses (Dundon et al, 2015;Kwiatek et al, 2007Kwiatek et al, , 2011Salami et al, 2014). A similar situation has also occurred in Sudan and Ethiopia where lineages III viruses that were present in the 1970-1990s have now been replaced by lineage IV viruses (Kwiatek et al, 2011;Libeau et al, 2014;Muniraju et al, 2016).…”

First serological and molecular evidence of PPRV occurrence in Ghardaïa district, center of Algeria

“…Phylogenetic analysis revealed that the strain involved in the Ghardaïa outbreak is very close to those identified in Morocco and Tunisia; this is compatible with the recent establishment and spread of the Asian PPRV lineage IV in Africa and its emergence in other parts of Africa (Kwiatek et al 2011;Libeau et al 2014;Padhi and Ma 2014).…”

“…Traditionally, lineages I and II are found in West Africa, lineage III in East Africa and the Middle East, and lineage IV in Asia. Recent studies have shown changes in this distribution including the emergence of PPRV lineage IV in northeastern and northern Africa (Kwiatek et al 2011;Albina et al 2013;Libeau et al 2014;Padhi and Ma 2014).…”

Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014

“…Recent phylogenetic analysis revealed that the Chinese Tibetan strains and the Chinese 2013-2014 strains were separately grouped into two clusters in lineage IV (Wu et al, 2015). Historically, PPRV molecular epidemiology has focused on the partial N (255 nt region; nucleotide site 1360-1614 of PPRV genome) or partial F gene (322 nt region; nucleotide site 5779-6100 of PPRV genome) sequences, preventing the in-depth evolutionary analysis among strains (Cosseddu et al, 2013;Munir et al, 2011;Ozkul et al, 2002;Padhi and Ma, 2014;Soltan and Abd-Eldaim, 2014). Genome sequences for PPRV have recently been used for an evolutionary study on a global scale (Muniraju et al, 2014c).…”