The discovery of Citrus yellow vein learing virus Hacienda Heights isolate diversifies the geological origins of the virus in California, United States

Authors: Sun, Yongduo; Yokomi, Raymond - Ray

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2024
Publication Date: 9/18/2024
Citation: Sun, Y., Yokomi, R.K. 2024. The discovery of Citrus yellow vein learing virus Hacienda Heights isolate diversifies the geological origins of the virus in California, United States. Viruses. 16(9): Article 1479. https://doi.org/10.3390/v16091479.
DOI: https://doi.org/10.3390/v16091479

Interpretive Summary: Citrus yellow vein clearing virus (CYVCV) is an exotic graft-transmissible citrus pathogen that was likely introduced to California by unwitting homeowners using CYVCV-infected citrus budwood or propagations to obtain citrus trees for their yard. CYVCV was first detected in 2022 in urban citrus trees in the city of Tulare in the San Joaquin Valley and in a dooryard lemon tree in Hacienda Heights in 2023 in Los Angeles County. This virus is reported to be spread in nature by aphid and whitefly vectors as well as by mechanical transmission with contaminated pruning tools. Therefore, its spread poses a threat to the U.S citrus industry. Sequencing of CYVCV genome obtained from central and southern California and comparing the phylogeny within isolates from California as well as internationally, was performed and provided evidence that the Tulare and Hacienda Heights isolates clearly had separate origins and suggested that they are the result of at least two different introductions. Homeowners need to be better informed about the dangers of propagating or obtaining citrus that are not labeled as pathogen tested or pathogen-free. Sources of certified clean budwood are available at a nominal cost and will result in a superior citrus propagation that does not carry any pathogen that can threaten the US citrus industry.

Technical Abstract: Citrus yellow vein clearing virus (CYVCV) poses an emerging threat to U.S. the citrus industry. Reports from China shows it causes significant reductions in fruit yield and growth, particularly in lemon trees. In 2022, CYVCV was detected in a wide range of citrus cultivars in localized urban properties in Tulare, California, USA. Recently in 2024, a CYVCV-infected lemon tree was detected in Hacienda Heights in Los Angeles County, which is separated from the Tulare foci. Through long-read sequencing technology, the whole genome sequence of the CYVCV isolate from Hacienda Heights (designated as CYVCV-CA-HH1, Accession number PP840891.1), was obtained. Sequence alignments and NeighborNet analysis suggested that the CYVCV-CAHH1 isolate has a different origin than the Tulare CYVCV (CYVCV CA-TL) isolates. The CYVCV CA-TL isolates were grouped with those from South Asia (India and Pakistan) and the Middle East (Türkiye), while the CYVCV-CA-HH1 isolate was grouped with isolates from East Asia (China and South Korea). Phylogenetic analysis further supports this finding, showing that the CYVCV-CA-HH1 isolate shares the most recent common ancestor with a South Korean lineage, which derives from Chinese isolates. Together, our data suggest a diverse geographical origin of CYVCV isolates in California.