RT-qPCR mosquito arbovirus screening results, 2017-2021, South Nation River watershed
Bibliographic record
Abstract
Pool-by-pool RT-qPCR mosquito arbovirus screening results (.xlsx), 2017-2021, South Nation River watershed. Viruses tested include: California serogroup viruses (CSGv), West Nile virus (WNv), eastern equine encephelitis virus (EEEv), and Cache Valley virus (CVv). Includes a sheet with column descriptions. Methods Between 2017 and 2021 (excluding 2020 due to COVID-19), mosquitoes were collected across semi-urban and rural habitats of the South Nation River watershed, eastern Ontario. Pools of 1–50 females per species (≤3 pools, max. 150 individuals) were tested, with some Ceratopogonidae also included. Samples from 2017–2019 were homogenized at the National Microbiology Laboratory (NML) as described in Avramov et al. (1) and RNA-extracted with the QIAamp Viral Mini Kit (QIAGEN™) with minor modifications (2). In 2021, homogenization was performed at Carleton University under the same conditions (1), with RNA extraction by high-throughput phenol–chloroform (1). RT-qPCR screening for CSGv used Wang et al.’s primers/probes (3,4) at NML (2017–2018) and Carleton (2019, 2021). WNv and EEEv were screened at NML (2017–2019) and Carleton (2021) with validated primers/probes (5,6). CVv was screened only at NML in 2017–2018 using Wang et al. (3). Virus-positive pools processed at Carleton underwent RNA re-extraction with the QIAamp Viral Mini Kit, followed by replicate RT-qPCR; Cq < 38 in both replicates defined a positive. All procedures followed institutional biosafety standards. References Avramov M, Gallo V, Gross A, Lapen DR, Ludwig A, Cullingham CI. A cost-effective RNA extraction and RT-qPCR approach to detect California serogroup viruses from pooled mosquito samples. Sci Rep. 2024 Jan 29;14(1):2339. Villeneuve CA, Buhler KJ, Iranpour M, Avard E, Dibernardo A, Fenton H, et al. New records of California serogroup viruses in Aedes mosquitoes and first detection in simulioidae flies from Northern Canada and Alaska. Polar Biol. 2021 Sep 1;44(9):1911–5. Wang H, Nattanmai S, Kramer LD, Bernard KA, Tavakoli NP. A duplex real-time reverse transcriptase polymerase chain reaction assay for the detection of California serogroup and Cache Valley viruses. Diagn Microbiol Infect Dis. 2009 Oct 1;65(2):150–7. Buhler KJ, Dibernardo A, Pilfold NW, Harms NJ, Fenton H, Carriere S, et al. Widespread Exposure to Mosquitoborne California Serogroup Viruses in Caribou, Arctic Fox, Red Fox, and Polar Bears, Canada. Emerg Infect Dis. 2023 Jan;29(1):54–63. Lanciotti RS, Kerst AJ, Nasci RS, Godsey MS, Mitchell CJ, Savage HM, et al. Rapid Detection of West Nile Virus from Human Clinical Specimens, Field-Collected Mosquitoes, and Avian Samples by a TaqMan Reverse Transcriptase-PCR Assay. J Clin Microbiol. 2000 Nov;38(11):4066–71. Lambert AJ, Martin DA, Lanciotti RS. Detection of North American Eastern and Western Equine Encephalitis Viruses by Nucleic Acid Amplification Assays. J Clin Microbiol. 2003 Jan;41(1):379–85.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.061 | 0.028 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".