Complete Nucleotide Sequence of a South African Isolate of Grapevine Fanleaf Virus and Its Associated Satellite RNA

Renate Lamprecht,Johan Burger,Dirk Stephan,Monique Spaltman,Thierry Wetzel

doi:10.3390/v5071815

Renate Lamprecht, Johan Burger + Show 3 more

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https://doi.org/10.3390/v5071815

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Journal: Viruses	Publication Date: Jul 17, 2013
Citations: 37	License type: CC BY 4.0

Affiliation: Stellenbosch University, RLP AgroScience (Germany)

Abstract

The complete sequences of RNA1, RNA2 and satellite RNA have been determined for a South African isolate of Grapevine fanleaf virus (GFLV-SACH44). The two RNAs of GFLV-SACH44 are 7,341 nucleotides (nt) and 3,816 nt in length, respectively, and its satellite RNA (satRNA) is 1,104 nt in length, all excluding the poly(A) tail. Multiple sequence alignment of these sequences showed that GFLV-SACH44 RNA1 and RNA2 were the closest to the South African isolate, GFLV-SAPCS3 (98.2% and 98.6% nt identity, respectively), followed by the French isolate, GFLV-F13 (87.3% and 90.1% nt identity, respectively). Interestingly, the GFLV-SACH44 satRNA is more similar to three Arabis mosaic virus satRNAs (85%–87.4% nt identity) than to the satRNA of GFLV-F13 (81.8% nt identity) and was most distantly related to the satRNA of GFLV-R2 (71.0% nt identity). Full-length infectious clones of GFLV-SACH44 satRNA were constructed. The infectivity of the clones was tested with three nepovirus isolates, GFLV-NW, Arabis mosaic virus (ArMV)-NW and GFLV-SAPCS3. The clones were mechanically inoculated in Chenopodium quinoa and were infectious when co-inoculated with the two GFLV helper viruses, but not when co-inoculated with ArMV-NW.

Highlights

The infectivity of the clones was tested with three nepovirus isolates, Grapevine fanleaf virus (GFLV)-NW, Arabis mosaic virus (ArMV)-NW and GFLV-SAPCS3
The clones were mechanically inoculated in Chenopodium quinoa and were infectious when co-inoculated with the two GFLV helper viruses, but not when co-inoculated with ArMV-NW
The full-length nucleotide and amino acid sequences of GFLV-SACH44 RNA1, RNA2 and the satellite RNA (satRNA) were compared to the full-length sequences of other GFLV and ArMV isolates by performing multiple sequence alignments using ClustalW [22]

Summary

Introduction

GFLV-F13 and ArMV-NW are the only isolates that have their full genome, as well as their large satRNAs completely sequenced [10,13,14,15,18,19]. We report the complete sequences of RNA1, RNA2 and the satRNA of a South African GFLV isolate, GFLV-SACH44. Full-length cDNA infectious clones of the GFLV-SACH44 satRNA were constructed and were able to replicate in herbaceous hosts when mechanically co-inoculated with the helper virus isolates, GFLV-NW [18] or GFLV-SAPCS3 [17], but not with ArMV-NW [18,19].

Results

Conclusion