Results:
Discovery of APV in several laboratory lines of pea aphids: We discovered that APV infected some laboratory-held aphid cultures through an RNAseq study (Chevignon, Unpublished data), in which a substantial portion of total reads (15%-26%) mapped to an APV genome in three clonal lines of A. pisum named AS3, AS3AB and ZA17 that hosted different strains of H. defensa (Table S1). Less than 0.2% of reads also mapped to APV in two other lines named A2C and NY26 that hosted other strains of H. defensa (Table S1). After developing a PCR-based diagnostic assay, rescreening confirmed infection of the AS3, AS3AB and ZA17 lines, but did not detect APV in the A2C or NY26 lines which suggested low level infection at the time we made the RNAseq libraries had been lost. PCR screening all of the other aphid cultures in the laboratory indicated that 39% (23/59) carried APV infection. Sequencing a domain within the APV P1 open reading frame suggested the APVs present in our laboratory were very similar with only a few single nucleotide polymorphisms (SNPs) identified. The RNAseq data we generated further enabled us to assemble complete genomes for the APVs in the AS3, AS3AB, ZA17, A2C and NY26 lines. Alignment to other APV genomes in public databases showed high overall similarity (Fig. 1A). A distance matrix computed from amino acid sequences (Table S2) and a maximum likelihood phylogeny (Fig. 1B) indicated the APVs from our laboratory were nearly identical to one another (>99.6-100%) but less similar (< 92.6%) to several APV isolates from China.