Meta-transcriptomic analysis reveals an isolate of aphid lethal paralysis virus from Wisteria sinensis in Iran

Viral metagenomic analysis of wisteria leaf sample in Iran detected one dicistrovirus: aphid lethal paralysis virus (ALPV). The complete genome sequence of ALPV-Ir-Wi was 9824 nucleotides (nt) in length (excluding the 3′-poly(A) tail), and contained two ORFs, an intergenic untranslated region of 197 nt flanked by a 538 nt 5′ UTR and a 576 nt 3′ UTR. Comparison with 21 other ALPV genomic sequences from different parts of the world revealed that it most closely resembled the Turkish and Israeli isolates. Pairwise identity analysis showed significant variability in genome sequences among ALPV isolates with genomic nucleotide identities of 78.35–99.15%. In addition to codon mutations, insertions/deletions and recombination also contributed to genetic variability. To explore the genetic variation and molecular evolution of ALPV, ORF2 gene sequences of 18 non-recombinant isolates were analyzed. The isolates belonged to two principal clades (FST=0.614) and showed a considerable genetic diversity (0.140±0.01). Most populations were polyphyletic, indicating that they had not been isolated long enough to reach reciprocal monophyly. There was no significant correlation between genetic and geographical distances or host origins. Pairwise FST and Nm values showed a meaningful differentiation and relatively infrequent gene flow between two compared populations (the Middle East vs. East Asia, the Middle East vs. Africa), and moderate gene flow for East Asian and African populations. Genes in the ALPV genome were subject to strong purifying selection during evolution, and most codons were under negative selection or neutral evolution. The results indicated a relatively stable and conserved genomic composition with a low codon usage bias in all of the assayed ALPV coding sequences. Recombination, natural selection, gene flow, and founder effects were found to be the main evolutionary factors that can affect the genetic structure of ALPV populations.