Phylogenetic analysis of New Zealand tomato spotted wilt virus  isolates suggests likely incursion history scenarios  and mechanisms for population evolution.
Tomato spotted wilt virus (TSWV) is an internationally significant pathogen with a wide host range, vectored by thrips. We have studied the sequence variation and evolutionary mechanisms at play in parts of the L, M and S subgenomes of 23 New Zealand TSWV isolates collected between 1992 and 2009, aiming to identify the possible geographic origins of isolates. Maximum-likelihood-based phylogenetic analyses of New Zealand and overseas TSWV isolates placed the L and M subgenome sequences of two isolates (MAF04 and PFR04) in distinct clades composed primarily of Korean, Japanese and Chinese isolates, in contrast to the remaining 21 isolates, which clustered with a cosmopolitan group of isolates. The nucleocapsid (N) gene sequences of MAF04 and PFR04 plus MAF02 clustered with Japanese isolates. Consequently, we postulate that these isolates may represent a distinct incursion into New Zealand, but we do not have enough evidence to indicate an incursion pathway. Alternately, these isolates may have arrived with an incursion that included a mixture of TSWV isolates of diverse international origins. The sequences of four of the TSWV isolates contained a number of sites with a mixture of nucleotides, suggesting that these isolates either consisted of several sequence variants or were from plants with mixed infections. One isolate (MAF02) was shown to be a either a reassortant or an S subgenome recombinant. Large amounts of low-level polymorphism were detected with low amino acid change fixation rates (purifying selection). Negative selection was indicated at four amino acid sites in the New Zealand TSWV N gene sequences.
Gail M
GM
Timmerman-Vaughan
Ros
R
Lister
Rebecca
R
Cooper
Joe
J
Tang
D001483:Base Sequence; D018076:DNA, Complementary / Q000235:genetics; D014644:Genetic Variation; D009520:New Zealand; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics; D016865:Reassortant Viruses; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D013997:Time Factors; D017865:Tospovirus / Q000235:genetics*
D018076:DNA, Complementary; D012367:RNA, Viral