Data and code from: Molecular surveillance supports differing roles in West Nile virus transmission between Culex pipiens and Culex restuans (Diptera: Culicidae) in Chicago, Illinois
Data files
Apr 30, 2026 version files 163.03 KB
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ALLSampleOrganization_All_Quarters.csv
61.90 KB
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BaseHexMap.csv
828 B
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Categorized_binGroup.csv
454 B
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Comp_Haversine.csv
59.12 KB
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MIRcalcAll.csv
9.31 KB
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Pub_Comp.qmd
6.38 KB
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Pub_Haversine.qmd
2.68 KB
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Pub_Prev.qmd
10.08 KB
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README.md
6.93 KB
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RestID_Full.csv
5.06 KB
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Yearless_IPS.csv
295 B
Abstract
The Chicago metropolitan area is a hotspot for human West Nile virus (WNV) cases. Despite extensive surveillance and research, predicting WNV cases in Chicago on a local scale is a major challenge. Most studies and mosquito surveillance efforts do not differentiate between the cryptic species Culex pipiens Linnaeus and Culex restuans (Theobald), key vectors of WNV, due to the challenge of distinguishing them morphologically. This obscures each species’ respective role in transmission and may blunt the accuracy of local case forecasting. We used species-specific PCR diagnosis to identify Chicago mosquitoes across 21 sites in July and August of 2021 and 2022. We found that the percentage of Cx. restuans collected fell between July and August, with Culex pipiens often serving as the sole species recorded from sites in August. We found that the balance between our target species could vary, sometimes dramatically, across years. Following species identification, we pooled our specimens and determined infection prevalence using quantitative reverse transcription polymerase chain reaction (RT-qPCR). We found that both species were infected with WNV and observed no significant difference in their infection rates between months. We assess the accuracy of a human case prediction model. We found no evidence to support the molecular separation of these species in routine Chicago WNV surveillance.
Description of the data and file structure
Code and Dataframe Guide:
Code can be found at https://github.com/BugmanBen/Thesis_Code
ALLSampleOrganization_All_Quarters.csv
CSV containing a row for every sample tested as part of our work to identify the species identity of Culex collected in Chicago. Samples identified as Cx. restuans, pipiens, salinarius, or Unknown.
| Variable | Definition |
|---|---|
| TRAP ID | site name |
| Month | month data |
| Year | year data |
| Abdomen Species ID | molecular species identification |
BaseHexMap.csv
CSV containing the category, latitude, longitude, residual, and human cases of each trapping site. Site data provided by the Northwest Mosquito Abatement District.
| Variable | Definition |
|---|---|
| Trap.ID | site name |
| Cases | site human cases |
| Category | site categorization |
| X | longitude |
| Y | latitude |
Categorized_binGroup.csv
CSV containing the MLE estimations, site categorization, high, and low confidence intervals for our target species across our two sampling months as calculated by the R Package 'binGroup' (Bilder et al. 2010), using 95% bias- and skewness-corrected confidence intervals as recommended by Biggerstaff 2008.
| Variable | Definition |
|---|---|
| Species | species identification (P = Cx. pipiens, R = Cx. restuans) |
| Month | month data (J = July, A = August) |
| Category | site categorization (L = lower, E = expected, H = higher) |
| PointEst | binGroup MLE estimate |
| Lower | lower confidence interval |
| Upper | upper confidence interval |
| Scale | infection rate scale |
Comp_Haversine.csv
CSV containing the haversine formula-estimated distance between sites and the difference between their proportion Cx. pipiens.
| Variable | Definition |
|---|---|
| Site1 | site 1 |
| Site2 | site 2 |
| Diff in Prop | difference in percentage Cx. pipiens between sites |
| Quarter | month-year of sampling |
| Distance | Haversine formula–calculated distance between sites (km) |
| Difference | proportion difference in percentage Cx. pipiens between sites |
MIRcalcAll.csv
CSV containing the collection details and the minimum infection rate of sites.
| Variable | Definition |
|---|---|
| Month | month data |
| Species | species data |
| Hex | sampling site |
| Category | site categorization |
| Year | year data |
| summed_MQ | total mosquitoes |
| Positive | number of positive pools |
| TotalSamples | total pools |
| FracPos | fraction positive pools |
| MIR | minimum infection rate |
| Category_fac | factor of site category |
| Month_f | factor of the month data |
Pub_Comp.qmd
qmd file of R code that wrangles composition data, produces a graph of site composition by collection month and year, a map of site categorization and composition, and a raw count of all analyzed specimens by species identity. Finally, contains stepwise clustered binomial model reduction analysis of key variables across the entire dataset and then between July sampling events.
Pub_Haversine.qmd
qmd file of distance vs. differences in site composition or minimum infection rate.
Pub_Prev.qmd
qmd file containing MIR clustered binomial model reduction analysis of species identity, collection period, site category, and MIR. Produces graphs of MIR by species and category, positivity of sites map, an MLE comparison between species and collection month as generated by binGroup (Bilder et al. 2010), and an MLE comparison between species, site category, and collection month as generated by binGroup (Bilder et al. 2010).
RestID_Full.csv
csv file containing collection information and site composition.
| Variable | Definition |
|---|---|
| Month | month data |
| Category.x | site category |
| Trap.ID | site name |
| Year | year data |
| Num.Rest | number of Cx. restuans collected |
| Num.Pip | number of Cx. pipiens collected |
| PropPip | percentage Cx. pipiens collected |
| X | longitude |
| Y | latitude |
Yearless_IPS.csv
csv file of species, month, point estimate, and lower and upper confidence intervals as generated by binGroup (Bilder et al. 2010), using a 95% bias-
and skewness-corrected confidence intervals as recommended by Biggerstaff 2008.
| Variable | Definition |
|---|---|
| Species | species data |
| Month | month data |
| PointEst | binGroup MLE estimate |
| Lower | lower confidence interval |
| Upper | upper confidence interval |
| Scale | infection rate scale |
| CI | type of confidence interval (bsc = bias- and skewness-corrected, sc = skewness-corrected) |
We collected adult female mosquitoes via gravid traps set within the Northwest Mosquito Abatement District in Cook County, IL, USA, in July and August of 2021 and 2022. The samples were mailed to our lab at the University of Maryland, College Park, and frozen at -80 °C. We dissected the samples and extracted DNA from them to molecularly identify them as Culex pipiens, restuans, or salinarius. We then pooled these specimens by species, collection month, collection year, and collection site. We tested these pools for West Nile virus using RT-qPCR to determine the local abundance of these species and their infection rates in the middle and late summer.