Variation in Alfalfa mosaic virus isolates from New Zealand

Alfalfa mosaic virus (AMV) is a virus that infects numerous hosts in New Zealand and worldwide. AMV has been in New Zealand since 1951, and infects white clover and other important economic crops. These crops have the potential for their output to be greatly impacted on negatively. The aim of this project was to investigate the variation in AMV isolates from a range of different hosts that came from New Zealand. This was done by determining how many different isolates could be found in New Zealand, seeing the variation within the New Zealand isolates and the rest of the world, which in turn helped in the categorising of the isolates into the subgroups, and lastly looking to see whether AMV had one or more than one strain(s) in New Zealand. In addition, a preliminary investigation on mixed infection between AMV and other viruses in host white clover was looked at. The identification and characterisation of the partial New Zealand isolates’ RNA 1 and RNA 3 sequence was done by enzyme linked immune-sorbent assay (ELISA), reverse transcription polymerase chain reaction, and sequencing. The sequenced isolates underwent further analysis by doing multiple alignments and constructing phylogeny trees. As for the mixed infection experiment, white clover from pasture fields and lawn were picked, and AMV and a range of other viruses underwent ELISA testing. In total nineteen AMV isolates were identified and characterised from a variety of different hosts from all over New Zealand. From all of the isolates both partial RNA’s were obtained except for four samples. The variation in the isolates was between 0.0-9.0% for RNA 1 and 0.6-12.5% for RNA 3. The New Zealand isolates fell into both subgroups in RNA 1 and RNA 3 with the majority of them being subgroup I isolates. From the isolates obtained, it was determined that there were possibly at least six strains of AMV that has been introduced into New Zealand since it was first discovered. In the mixed infection experiment, the types of viruses seen between the pasture and lawn varied greatly. The mixed infections seen with AMV and another virus(es) were: AMV + ClYVV, AMV + BWYV, and AMV + ClYVV + SbDV; with the triple infection being statistically significant