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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #318862

Title: 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

item Stenger, Drake
item Krugner, Rodrigo
item NOURI, SHAHIDEH - University Of California
item FERRIOL, INMACULADA - University Of California
item FALK, BRUCE - University Of California
item Sisterson, Mark

Submitted to: Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/27/2016
Publication Date: 9/6/2016
Citation: Stenger, D.C., Krugner, R., Nouri, S., Ferriol, I., Falk, B.W., Sisterson, M.S. 2016. 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. Virology. 498:209-217.

Interpretive Summary: Viruses cause significant disease of plants, animals, and humans. To understand how viruses evolve in response to efforts to control disease, a basic understanding of virus population genetics is needed. Here, the basic population structure of an insect virus under field conditions was determined and analyzed. Using a single-point-in-time sampling strategy, possible effects of differential selection and/or differences in evolutionary history among isolates were minimized, allowing revelation of basic forces driving virus population structure under field conditions. Analysis of genetic variation within and among single insects infected with an RNA virus demonstrated that although virus populations are subjected to strong negative selection, the specific sequence dominating a virus population within an individual host was not predictable as there are a large number of possible mutations that are silent. Analysis of genetic variation within single insects reveals an additional stochastic outcome: the spectrum of mutants within each single insect was distinct and dominated by mutations that change the encoded protein coding sequence. However, as the proportion of mutations causing changes in protein coding sequences was similar to that expected solely by mis-incorporation of the viral polymerase in the absence of selection, diversity of within-isolate mutations does not support diversifying/positive selection for change; rather the spectrum of virus mutants within a host represents newly-minted errors that have yet to undergo the sieve of selection. Thus, the combined effects of deterministic and stochastic forces shape virus populations and must be accounted for when devising strategies aimed at mitigating disease.

Technical Abstract: Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects was examined. To minimize effects of different evolutionary histories and/or selection pressures, all glassy-winged sharpshooter (Homalodisca vitripennis; synonym H. coagulata) hosts were randomly collected from a single point in space and time. Despite low diversity (p = 0.0020), 28 haplotypes were identified among 30 single-insect consensus sequences with polymorphic sites randomly distributed among genomic regions. Synonymous substitutions were >4-fold more common than nonsynonymous substitutions, indicating consensus sequences were subject to strong negative/purifying selection. The mutant spectrum resident in the C2 helicase region within ten single-insect isolates was unique for each isolate and dominated by nonsynonymous singletons. To estimate the nonsynonymous/synonymous (Non/Syn) substitution rate within single-insect isolates, bootstrapping was used to correct for RT-PCR error. The corrected Non/Syn substitution rate within single insect isolates was ~one log unit greater (1.675; 95% confidence limits of 1.359 and 2.051) than that of the same region among consensus sequences (0.154). The within-isolate Non/Syn substitution rate (1.646) expected due to virus polymerase error, in the absence of selection, was similar to the observed value when the only constraint imposed was a 9:1 bias for transitions over transversions. Collectively, the results indicate 1) bottlenecks coupled with strong negative/purifying selection drive consensus sequences towards a large neutral sequence space, and 2) the high Non/Syn substitution rate within an isolate reflects newly-minted errors sampled prior to selection, rather than positive selection driving group diversification.