Data from: Early-warning surveillance of West Nile and Usutu viruses in wetland and larval habitat waters and mosquito excreta using digital PCR
Data files
Sep 30, 2026 version files 176.84 KB
-
DB_Misarbo.csv
172.48 KB
-
README.md
2.71 KB
-
WNV_Sequence.csv
1.65 KB
Abstract
West Nile virus (WNV) and Usutu virus (USUV) are mosquito-borne pathogens maintained in bird–mosquito cycles and increasingly cause human and equine disease in temperate regions. As most infections are asymptomatic, surveillance based on clinical and veterinary reports provides delayed signals for vector control and equine vaccination strategies. We implemented, in 2024 and 2025, an operational environmental surveillance strategy combining molecular xenomonitoring of adult mosquito excreta with water sampling from wetlands and mosquito breeding sites, coupled to a standardized multiplex reverse transcription digital PCR workflow. Viral detection was performed using a multiplex digital PCR assay with characterized limits of blank, detection, and quantification, and low-level positives were confirmed by Sanger sequencing. This multi-matrix approach detected WNV RNA in southern France weeks before a human or equine case, providing actionable early warnings to guide targeted vector control and preparedness. Across both years, WNV and USUV were detected 29 and 8 times among 396 samples in 2024, and 90 and 14 times among 815 samples in 2025, revealing previously unrecognized, cryptic virus circulation. These results demonstrate that integrating environmental surveillance provides a sensitive, proactive framework for the early detection of emerging Culex-borne arboviruses, offering precious lead time for public one-health strategies.
Data and sequencing from mosquito, mosquito excreta, and breeding site waters
Dataset DOI: 10.5061/dryad.1g1jwsvc6
Description of the data and file structure
These datasets from Mocq et al. (in review) contain 1/ the raw data of mosquito capture, analysis, and identification, with viral dPCR detection, and 2/ the sequencing data from dPCR or Sanger analysis of mosquito, mosquito excreta, or breeding site water sampled in Occitania, France in 2024 or 2025.
Files and variables
File: DB_Misarbo.csv
Description: Raw data.
Variables
- Region, French department, Municipality, Site code: Geographic information describing the sampling site. The Site code is an identifier composed of three segments: a two-character matrix code (ZH = wetland, GL = larval habitat, MX = mosquito excreta), a three-character municipality code (e.g., MTP = Montpellier), and a three-digit site identifier used to distinguish individual sites.
- Sample code: Unique identifier for each sample, combining the Site Code and sampling date in YYYYMMDD format
- Sampling Type: Context of the sampling event: Network = repeatedly sampled site; One-off = site sampled once for exploratory purposes; Vector control operation = samples collected during a vector control operation.
- Longitude, Latitude: Geographic coordinates expressed in decimal degrees.
- Year, Sampling date: Year and date of the sampling event.
- USUV_Pres/Abs, USUV_Pres/Abs, [USUV]_Cop.mL-1, [WNV]_Cop.mL-1: Detection status of Usutu virus (USUV) and West Nile virus (WNV), recorded as positive (POS) or negative (NEG), along with their respective concentrations (copies/mL) when detected. In the presence/absence columns, n/a indicates that the sample was not tested for the corresponding virus (logistical or analytical issues). In the concentration columns, n/a indicates that the virus was not detected.
- Comments: additional information about the sampling site (e.g., Regional Natural Park, Natural reserve)
File: WNV_Sequence.csv
Description: WNV sequencing methods and results. Semicolon-delimited file.
Variables
- Accession number
- Sampling date
- Matrix (Entire Mosquito, mosquito excreta or water)
- Site type (natural/urbanized sites)
- Municipality
- WNV Lineage
- Sequencing method
- Genome coverage (%)
- Sequence identity (%)
- Primer used (for Sanger only)
- Sequences (for Sanger only)
"n/a" stands for "Non applicable"