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, ai...

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Bibliographic Details
Published in:Archives of virology 2014-05, Vol.159 (5), p.993-1003
Main Authors: Timmerman-Vaughan, Gail M, Lister, Ros, Cooper, Rebecca, Tang, Joe
Format: Article
Language:English
Subjects:
Base Sequence
Biomedical and Life Sciences
Biomedicine
DNA, Complementary - genetics
Evolution
Genetic Variation
Genomes
host range
Infectious Diseases
Medical Microbiology
mixed infection
New Zealand
nucleocapsid
nucleotide sequences
Original Article
pathogens
Phylogenetics
Phylogeny
Plant Diseases - virology
Polymorphism
Reassortant Viruses
Reverse Transcriptase Polymerase Chain Reaction
RNA, Viral - genetics
Sequence Alignment
Time Factors
Tomato spotted wilt virus
Tospovirus - genetics
Virology
Viruses
wilting
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Summary: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.
ISSN:0304-8608
1432-8798
DOI:10.1007/s00705-013-1909-y