Wisteria vein mosaic virus: an evolutionary-based case study approach to trace the emergence of new virus threats

Wisteria mosaic disease (WMD) severely affects Wisteria spp. and was originally reported in the US. After the identification of its aetiological agent, Wisteria vein mosaic virus (WVMV), a species of the genus Potyvirus, numerous reports followed worldwide. In 2023 we first identified an Italian isolate of the virus, named WVMV Bari, and more recently completed its full-length sequence, relying on high-throughput barcoding technology. PhyML-SMS phylogenetic inference placed WVMV Bari in the broad cluster known as the ‘bean common mosaic virus supergroup’. In-depth analyses using two-dimensional diversity matrices, built on the coding regions of the ten available WVMV isolates, identified interesting evolutionary traits at the intraspecific level and with close species. A clustering algorithm analysis confirmed the existence of two phylogenetic groups, a major clade comprising WVMV isolates from Wisteria spp. and a minor clade at the species boundary comprising two divergent WVMV isolates and one isolate of kudzu chlorotic ring blotch virus, all found in non-Wisteria, Fabaceae, hosts. A reconstruction of the evolutionary ties that led to this differentiation was attempted. Potential recombination events were found only between non-Wisteria hosts. The divergence time between the two clades was estimated around the 18th century, based on relaxed molecular clock dating. Median Joining network analysis substantiated the existence of the two host-related groups, by highlighting the number of mutations leading to the separation. Kxy, Dxy and Da inter-population parameters and permutation-based tests revealed a high level of genetic differentiation between the two phylogroups. The fixation index (FST) and migrant value (Nm) showed an infrequent gene flow. Negative neutrality tests in Wisteria-affecting variants may prove a recent population expansion or the occurrence of purifying selection. Evidence of negative selection was also found in both phylogroups, based on dN/dS ratio. SLAC analysis identified sites under selection in the taxonomically relevant CP region. Our results highlighted that WVMV is a culpably neglected species whose emergence dynamics raise interesting questions about its taxonomic distinctiveness and its potential to spread in other economically relevant crops, such as legumes. The main intention of our study is to propose an evolution-based analysis approach that serves as a case study to investigate how other emerging viruses may spread.