Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts.
Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences. Probability of all possible single-base substitutions for the C2 region predicted N:S values within 95% confidence limits of the corrected within-isolate N:S when the only constraint imposed was viral polymerase error bias for transitions over transversions. These results indicate that bottlenecks coupled with strong negative/purifying selection drive consensus sequences toward neutral sequence space, and that most polymorphism within single-insect isolates is composed of newly-minted mutations sampled prior to selection.
USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757, USA. Electronic address: drake.stenger@ars.usda.gov.
Drake C
DC
Stenger
USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757, USA.
Rodrigo
R
Krugner
Department of Plant Pathology, University of California, Davis, CA 95616, USA.
Shahideh
S
Nouri
Department of Plant Pathology, University of California, Davis, CA 95616, USA.
Inmaculada
I
Ferriol
Department of Plant Pathology, University of California, Davis, CA 95616, USA.
Bryce W
BW
Falk
USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757, USA.
Mark S
MS
Sisterson
D000818:Animals; D003001:Cloning, Molecular; D003062:Codon; D016384:Consensus Sequence; D019143:Evolution, Molecular; D023061:Gene Order; D016679:Genome, Viral; D055106:Genome-Wide Association Study; D007304:Insect Viruses / Q000145:classification / Q000235:genetics*; D007313:Insecta / Q000821:virology; D009154:Mutation; D016366:Open Reading Frames; D010802:Phylogeny; D011110:Polymorphism, Genetic; D020365:RNA Helicases / Q000737:chemistry / Q000235:genetics; D012328:RNA Viruses / Q000145:classification / Q000235:genetics*; D012367:RNA, Viral; D017422:Sequence Analysis, DNA
D003062:Codon; D012367:RNA, Viral; D020365:RNA Helicases
Dicistrovirus; Mutant spectrum; Virus microevolution