First complete genome sequence and detection of garlic yellow curl virus in the Philippines, a member of a novel genus of the family Betaflexiviridae

A newly characterized garlic virus, provisionally named garlic yellow curl virus (GYCV), is a Betaflexiviridae virus first reported in China in 2023. In this study, GYCV was also discovered in the Philippines through transcriptome sequencing of the Batanes White garlic variety from Batanes, the northernmost province of the country. The complete RNA sequence of GYCV from the Philippines (GenBank OR354819) spans 8184 bp, and the genome organization is typical of the subfamily Quinvirinae, which comprises five open reading frames: one replicase gene, three triple gene block protein genes, and one coat protein gene. The complete genome shares its closest relatedness with the first GYCV from China, showing approximately 76% genetic similarity and clustering within the GYCV clade in the phylogenetic tree. Additionally, analysis of the replicase and coat protein genes confirmed the virus's identity with > 72% similarity to GYCV. Among the Betaflexiviridae viruses, the GYCV clade exhibits a higher degree of relatedness to another new and unclassified garlic yellow mosaic-associated virus (GYMaV) recently reported in Brazil and Korea. The presence of GYCV in the Batanes White garlic samples was further confirmed through reverse transcription PCR and subsequent sequencing using primers designed from the generated complete genome. To date, this emerging virus does not belong to any known genera of viruses within the Betaflexiviridae family. This study represents the first detection and complete genome sequencing of GYCV in the Philippines and the second after China. These findings hold significance for virus management and resistance breeding programs aimed at safeguarding the country's garlic industry.