Molecular epidemiology of the globally spreading genetic lineage IV of peste des petits ruminants virus.

Peste des petits ruminants (PPR) is a highly contagious viral disease of small ruminants caused by the peste des petits ruminants virus (PPRV), which is classified into four distinct genetic lineages (I-IV). A critical concern is the rapid and widespread expansion of lineage IV (LIV) across West Africa over the past decade. In this study, we generated full or partial genome sequence from 26 new PPRV samples, including historical (pre-2000) and recent African LIV isolates, offering the first opportunity to investigate the evolutionary history of LIV in Africa and identify genetic events potentially associated with its recent spread. These new sequences were aligned with 141 publicly available PPRV sequences to perform phylogenomic analyses. Results reveal that the most ancestral LIV group comprises strains circulating in Sub-Saharan Africa (designated clade LIVssa), providing new evidence for an African origin of lineage IV. Our results further indicate that PPRV strains linked to the recent West African expansion of LIV belong to a specific LIVssa subclade, termed NigB. We identified multiple signatures of selection pressure within the LIVssa sublineage, particularly in the NigB subclade. Several amino acid substitutions unique to LIVssa or NigB were detected, some of which may impact protein function and warrant prioritised investigation. While additional genomic data are required to confirm the association between the NigB subclade and the ongoing spread of LIV in West Africa, this expansion is alarming and demands intensified research efforts using integrative approaches. The evolutionary adaptations observed in LIVssa could undermine current disease control strategies in regions where PPR poses significant threats to food security and local economies.