Molecular characteristics of a novel alternavirus from Trichoderma harzianum

We analyzed the dsRNA profiles of Trichoderma spp. and identified a novel mycovirus from Trichoderma harzianum strain NFCF419. Phylogenetic and genomic analysis suggested that this virus is a novel member of the family Alternaviridae. Next-generation sequencing (NGS) analysis revealed that this virus consisted of four genome segments. The complete genome sequences of the segments were determined by NGS, and the NGS results were confirmed by manual sequencing of RT-PCR amplicons using specific primer pairs. 5’- and 3’-RACE was performed to determine the terminal sequences of each segment. The genome segments were found to be 3,572 bp (dsRNA1), 2,552 bp (dsRNA2), 2,593 bp (dsRNA3), and 1,484 bp (dsRNA4) in size. The largest segment (dsRNA1) contains a single open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRP). dsRNA2, 3, and 4 each contain a single ORF encoding a putative methyltransferase, a coat protein, and a hypothetical protein with unknown function, respectively. Evaluation of the genome organization, analysis of the deduced amino acid sequence of the RdRP, and phylogenetic analysis indicated that this virus is a new member of the genus Alternavirus in the family Alternaviridae. Accordingly, we designated this novel mycovirus "Trichoderma harzianum alternavirus 1" (ThAV1). This is the first report of a mycovirus of the family Alternaviridae that infects a member of the genus Trichoderma.