Characterization of Genetic Diversity in the Capsid Protein Gene of Grapevine Fleck Virus and Development of a New Real-Time RT-PCR Assay

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2024 Sep 28

PMID 39339933

Authors

Juliana Osse de Souza

Vicki Klaassen

Kristian Stevens

Teresa M Erickson

Claire Heinitz

Maher Al Rwahnih

Affiliations

Soon will be listed here.

Abstract

The grapevine fleck virus (GFkV) is a ubiquitous grapevine-infecting virus found worldwide, is associated with the grapevine fleck complex, and is often found in mixed infections with viruses of the grapevine leafroll complex and/or vitiviruses. Although GFkV has been studied for a long time, limited sequence information is available in the public databases. In this study, the GFkV sequence data available in GenBank and data generated at the Foundation Plant Services, University of California, Davis, were used to perform nucleotide sequence comparisons, construct a phylogenetic tree, and develop a new RT-qPCR assay. Sequence comparisons showed high genetic diversity among the GFkV isolates, and the phylogenetic analyses revealed a new group comprised of GFkV isolates identified in the present study. A new assay, referred to as GFkV-CP, was designed and validated using an existing GFkV positive control together with 11 samples known to be infected with combinations of different marafiviruses and maculaviruses but not GFkV. In addition, the newly designed assay was used in a field survey to screen grapevines from diverse geographical locations that are maintained at the United States Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR) in Winters, CA.

References

Osman F, Leutenegger C, Golino D, Rowhani A . Comparison of low-density arrays, RT-PCR and real-time TaqMan RT-PCR in detection of grapevine viruses. J Virol Methods. 2008; 149(2):292-9. DOI: 10.1016/j.jviromet.2008.01.012. View

Sabanadzovic S, Castellano M, Digiaro M, Martelli G . Grapevine fleck virus-like viruses in Vitis. Arch Virol. 2000; 145(3):553-65. DOI: 10.1007/s007050050046. View

Osman F, Rowhani A . Application of a spotting sample preparation technique for the detection of pathogens in woody plants by RT-PCR and real-time PCR (TaqMan). J Virol Methods. 2005; 133(2):130-6. DOI: 10.1016/j.jviromet.2005.11.005. View

Bisson L, Waterhouse A, Ebeler S, Walker M, Lapsley J . The present and future of the international wine industry. Nature. 2002; 418(6898):696-9. DOI: 10.1038/nature01018. View

Diaz-Lara A, Klaassen V, Stevens K, Sudarshana M, Rowhani A, Maree H . Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design. PLoS One. 2018; 13(12):e0208862. PMC: 6291115. DOI: 10.1371/journal.pone.0208862. View

Muhire B, Varsani A, Martin D . SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One. 2014; 9(9):e108277. PMC: 4178126. DOI: 10.1371/journal.pone.0108277. View

Darriba D, Posada D, Kozlov A, Stamatakis A, Morel B, Flouri T . ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. Mol Biol Evol. 2019; 37(1):291-294. PMC: 6984357. DOI: 10.1093/molbev/msz189. View

Diaz-Lara A, Stevens K, Klaassen V, Hwang M, Al Rwahnih M . Sequencing a Strawberry Germplasm Collection Reveals New Viral Genetic Diversity and the Basis for New RT-qPCR Assays. Viruses. 2021; 13(8). PMC: 8402890. DOI: 10.3390/v13081442. View

Abou Ghanem-Sabanadzovic N, Sabanadzovic S, Martelli G . Sequence analysis of the 3' end of three Grapevine fleck virus-like viruses from grapevine. Virus Genes. 2003; 27(1):11-6. DOI: 10.1023/a:1025164200412. View

10.

Bouckaert R, Vaughan T, Barido-Sottani J, Duchene S, Fourment M, Gavryushkina A . BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2019; 15(4):e1006650. PMC: 6472827. DOI: 10.1371/journal.pcbi.1006650. View

11.

Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Saldarelli P, Martelli G . Complete nucleotide sequence and genome organization of Grapevine fleck virus. J Gen Virol. 2001; 82(Pt 8):2009-2015. DOI: 10.1099/0022-1317-82-8-2009. View

12.

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

13.

Duffy S . Why are RNA virus mutation rates so damn high?. PLoS Biol. 2018; 16(8):e3000003. PMC: 6107253. DOI: 10.1371/journal.pbio.3000003. View

14.

Bruisson S, Lebel S, Walter B, Prevotat L, Seddas S, Schellenbaum P . Comparative detection of a large population of grapevine viruses by TaqMan RT-qPCR and ELISA. J Virol Methods. 2016; 240:73-77. DOI: 10.1016/j.jviromet.2016.12.003. View

15.

Diaz-Lara A, Stevens K, Klaassen V, Golino D, Al Rwahnih M . Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting spp. Plants (Basel). 2020; 9(2). PMC: 7076543. DOI: 10.3390/plants9020273. View

16.

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View