Genome Sequence of Pineapple Secovirus B, a Second Sadwavirus Reported Infecting Ananas Comosus

Abstract The complete genome sequence of a member of a novel species of Sadwavirus (family Secoviridae) infecting pineapple on the island of Oahu, Hawaii was determined by high throughput sequencing. The genome comprised two RNA molecules of 5,956 nt and 3,808 nt in length, excluding the poly-A tails at the 3’ end and each encoding a single large polyprotein. The RNA-1 polyprotein contained five conserved domains, all associated with replication, while the RNA-2 polyprotein is cleaved into the movement protein and coat protein. Analysis of the Pro-Pol region revealed less than 75% amino acid identity with pineapple secovirus A, chocolate lily virus A, and Dioscorea mosaic-associated virus, all members and candidate members of the proposed subgenus Cholivirus. Two specific primer sets derived from HTS data were used in RT-PCR assays, confirming the presence of this new virus infecting pineapple. The name “pineapple secovirus B” is proposed for this putative new virus.