The first whole genome sequence and characterization of carnation cryptic virus 3 based on metagenomic analysis of carnation in Iran

Carnation (Dianthus caryophyllus L.) is one of the five most significant and popular cut flowers globally. It is reportedly infected by several viruses in different families. Here we report the first full-length sequence of a carnation cryptic virus 3 (CCV3-IR1 isolate) from carnation in Iran using high-throughput sequencing (HTS). Carnation cryptic virus 3 (CCV3) is a proposed member of the genus Deltapartitivirus in the family Partitiviridae. CCV3-IR1 has two segmented genome consisting of dsRNA1 (1583 bp) and dsRNA2 (1574 bp) which respectively encode the RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). 5 '-Untranslated regions (UTRs) of the two segments have a high degree of sequence identity, starting with a conserved motif (5 '-AGAATTT-3 '). The RdRp-encoded amino acid sequence of the Iranian isolate has six of the eight conserved polypeptide patterns that are thought to be indicators of dsRNA virus RdRps. The Iranian CCV3 RdRp shares the highest amino acid sequence identity with the RdRp of a previously reported CCV3 from D. caryophyllus (DC) in South Korea (100%), while the CCV3 CP shows 99.51% sequence identity to the CP of DC. Negative selection (dN/dS < 1) was detected suggesting good adaptation in the RdRp gene and stability in population. Additionally, nucleotide diversity (pi) and haplotype diversity (Hd) for RdRp and CP genes of all CCV3 isolates revealed a low degree of genetic diversity. Phylogenetic analysis of RdRp and CP amino acid sequences of CCV3-IR1 was clustered it in Deltapartitivirus along with other CCV3 isolates.