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SARS-CoV-2 wastewater surveillance data and metadata in the Open Data Model format. Part 1: Québec City
<p>SARS-CoV-2 wastewater surveillance data and metadata in the Open Data Model format. Part 1: Québec City Authors</p> <ul> <li>Therrien, J-D<sup>1</sup></li> <li>Maere, T.<sup>1</sup></li> <li>Sanchez-Quete, F.<sup>2</sup></li> <li>Tsitouras, A.<sup>2</sup></li> <li>Goitom, E.<sup>3</sup></li> <li>Cloutier, F.<sup>4</sup></li> <li>Dufour, D.<sup>4</sup></li> <li>Proulx, F. <sup>4</sup></li> <li>Nicolaï, N.<sup>1</sup></li> <li>Philippe, R.<sup>1</sup></li> <li>Tohidi, M.<sup>1</sup></li> <li>Dorner, S.<sup>3</sup></li> <li>Frigon, D.<sup>2</sup></li> <li>Vanrolleghem, P.A.<sup>1</sup></li> </ul> <p>Affiliations</p> <ul> <li><sup>1</sup> model<em>EAU</em>, Département de génie civil et de génie des eaux, Université Laval</li> <li><sup>2</sup> Microbial Community Engineering Lab (MiCEL), Department of Civil Engineering, McGill University</li> <li><sup>3</sup> Polytechnique Montréal</li> <li><sup>4</sup> Ville de Québec</li> </ul> <p>General Remarks</p> <p>Wastewater-based surveillance of SARS-CoV-2 virus can detect between 1 and 30 infected individuals per 100,000 (including asymptomatic ones) by analyzing the population's sewage. As such, this method is very attractive since it costs only a fraction of clinical testing (as low as 1%). Human faeces may contain the virus a few days before a person becomes ill. Thus, this approach allows for detection of outbreaks 2-7 days before the increase in reported cases stemming from clinical screening tests (Bibby et al., 2021). Wastewater-based surveillance complements clinical testing by geolocating outbreaks, which may help targeting intensive screening programs. Moreover, it provides a quick indication of whether new public health measures (e.g., masks, social distancing, confinement, and curfew) are effective.</p> <p>Sampling</p> <p>The reported dataset contains open data collected in the province of Québec as part of the SARS-CoV-2 wastewater-based surveillance program <a href="https://www.centreau.ulaval.ca/en/covid/">CentrEau</a>-COVID. Four of the largest cities in the province (Montréal, Laval, Québec City, and Trois-Rivières), as well as the municipalities of four rural regions (Mauricie, Centre-du-Québec, Bas-St-Laurent, and Gaspésie) participated in the program. The entire dataset includes 31 sampling sites covering approximately half the population of the province of Québec (population size of 8.5 million). The timeframe covered by the dataset varies for each site. The earliest surveillance program was launched in March 2020, others followed soon after. Samples were collected using various methods, such as 24h composite samples, grab samples, and passive sampling using variations on the Moore swab method (Schang et al., 2020)</p> <p>Analysis</p> <p>Prior to the analysis of the samples for SARS-CoV-2, physiochemical parameters such as total suspended solids (TSS), turbidity, conductivity, ammonium concentration, and pH were measured. The samples were subsequently concentred by filtration using a MEC filter (0.45 um), followed by total RNA extraction using the Qiagen AllPrep PowerViral DNA/RNA Kit (Qiagen, USA) with some modifications (beta-mercaptoethanol concentration raised to 10% and lysis performed at 55 °C for 30 minutes) (Ahmed et al., 2020). SARS-CoV-2 viral RNA was detected by a one-step RT-qPCR. To assess the RNA recovery rate of the procedure, samples were spiked before extraction with a known concentration of Bovine Respiratory Syncytial Virus (BRSV) using the Zoetis INFORCE 3 vaccine (Zoetis, USA). In addition to SARS-CoV-2, samples were assessed for Pepper Mild Mottle Virus (PMMoV), the daily load of which is hypothesized to represent the fecal load contributions to the samples at a given site and time. PCR conditions and primer used to collect viral data are described in the files <code>primers.md</code> and <code>PCR conditions.md</code>.</p> <p>Compilation</p> <p>The measurements on wastewater samples carried out by the participating laboratories of this study are found in the <code>WWMeasure</code> table. The values provided by municipalities come from laboratories accredited by the Centre d'expertise en analyse environnementale du Québec (CEAEQ), in compliance with the latter's quality assurance protocols. The COVID-19-related public health data found in the <code>CPHD</code> table were collected from the Institut National de Santé Publique du Québec (INSPQ)'s public reports. Wastewater data taken in-situ at the sampling sites (e.g., the flow at pumping stations or water resource recovery facilities (WRRFs)) are found in the <code>SiteMeasure</code> table and were taken by the institutions responsible for managing the sites. All of the data, stemming from multiple sources, were combined into the <a href="https://github.com/Big-Life-Lab/ODM">Open Data Model (ODM)</a> standard format using the <a href="https://github.com/modelEAU/ODM-Import">ODM-Import python package</a> (see also Structure).</p> <p>Validation</p> <p>Wastewater and sample data were manually assessed for quality by our research collaborators. Data points for which the quality appeared to be uncertain were tagged with the value <code>True</code> in the <code>qualityFlag</code> column. Conversely, data deemed of good quality have a quality flag of <code>False</code>. Data that were not checked have a quality flag of <code>NA</code>. Textual comments describing the issues with the data points in more detail are also included in the dataset using the <code>notes</code> column of the relevant tables. Note that data validation was carried out by the data custodians responsible for each city in the dataset according to available resources. As the project continues and data validation is undertaken on more sections of the dataset, data may be re-analyzed, flagged, or commented as needed. Revisions to the dataset will be reported to the best of our ability.</p> <p>Structure</p> <p>The data contained in this dataset has been structured according to the <a href="https://github.com/Big-Life-Lab/ODM">Open Data Model (ODM) for Wastewater-Based Surveillance</a>. This model provides a standardized dictionary to collect and share data and metadata stemming from wastewater-based surveillance programs. By convention, it splits all data into 10+ thematic tables with each record representing a unique measurement, i.e., long format. For convenience, the <code>wide</code> folder presents the data found in all the other tables in a wide format, i.e., multiple measurements are aligned by <code>timestamp</code>, with each column representing a different parameter.</p> <p>Acknowledgements</p> <p>The authors would like to acknowledge that this dataset was collected thanks to the financial support of the Fonds de Recherche du Québec, the Molson Foundation, the Trottier Family Foundation, CentrEau and NSERC. The authors would also like to acknowledge the efforts of Douglas Manuel (Ottawa Hospital) and Howard Swerdfeger (Public Health Agency of Canada) for their original idea for the Open Data Model and continued development.</p> <p>References</p> <ol> <li> <p>Ahmed, W., Bertsch, P.M., Bivins, A., Bibby, K., Farkas, K., Gathercole, A., Haramoto, E., Gyawali, P., Korajkic, A., McMinn, B.R., Mueller, J.F., Simpson, S.L., Smith, W.J.M., Symonds, E.M., Thomas, K. v., Verhagen, R., Kitajima, M., 2020. Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater. Science of the Total Environment 739. <a href="https://doi.org/10.1016/j.scitotenv.2020.139960">https://doi.org/10.1016/j.scitotenv.2020.139960</a></p> </li> <li> <p>Bibby, K., Bivins, A., Wu, Z., North, D., 2021. Making waves: Plausible lead time for wastewater based epidemiology as an early warning system for COVID-19. Water Research 202, 117438. <a href="https://doi.org/10.1016/j.watres.2021.117438">https://doi.org/10.1016/j.watres.2021.117438</a></p> </li> <li> <p>Schang, C., Crosbie, N., Nolan, M., Poon, R., Wang, M., Jex, A., Scales, P., Schmidt, J., Thorley, B.R., Henry, R., Kolotelo, P., Langeveld, J., Schilperoort, R., Shi, B., Einsiedel, S., Thomas, M., Black, J., Wilson, S., McCarthy, D.T., 2020. Passive sampling of viruses for wastewater-based epidemiology: a case-study of SARS-CoV-2 [WWW Document]. URL <a href="https://www.researchgate.net/publication/347103410\_Passive\_sampling\_of\_viruses\_for\_wastewater-based\_epidemiology\_a\_case-study\_of\_SARS-CoV-2?channel=doi&linkId=5fd800f392851c13fe892393&showFulltext=true">https://www.researchgate.net/publication/347103410\_Passive\_sampling\_of\_viruses\_for\_wastewater-based\_epidemiology\_a\_case-study\_of\_SARS-CoV-2?channel=doi&linkId=5fd800f392851c13fe892393&showFulltext=true</a> (accessed 1.18.21).</p> </li> </ol>
Data on carbon, nitrogen, and phosphorus forms in a north temperate river, Rivière du Nord, Québec, Canada, from 2017 to 2019
<p>The Rivière du Nord was sampled at 13 sites along its mainstem once per season from summer 2017 to winter 2020. Sites are numbered by river kilometer (RKm) with the outlet being RKm 0. The dataset includes concentrations (ug/L or mg/L as noted) of total organic carbon, dissolved organic carbon, particulate organic carbon, total nitrogen, total dissolved nitrogen, nitrate, ammonium, dissolved organic nitrogen, total phosphorus, total dissolved phosphorus and particulate phosphorus. It also includes fluorescence metrics derived from PARAFAC EEMs: fluorescence intensities (in Raman units) of 5 dissolved organic matter components (C1-C5), and 5 indices (SUVA-254, CDOM, FI, b:a, HIX). We sampled an additional 12 sites to act as endmembers (5 mainly forested sites, 5 mainly agricultural sites, and 2 wastewater treatment plant measures).</p> <p>Data were used to calculate C:N:P stoichiometry in the paper "Different forms of carbon, nitrogen, and phosphorus influence ecosystem stoichiometry in a north temperate river across seasons and land uses" (<a href="https://doi.org/10.1002/lno.11960">https://doi.org/10.1002/lno.11960</a>).</p> <p>Data were used to quantify changes in organic matter composition in the paper "Contrasting seasons and land uses alter riverine dissolved organic matter composition" (<a href="https://doi.org/10.1007/s10533-022-00979-9">https://doi.org/10.1007/s10533-022-00979-9</a>). </p>
FIG. 8 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 8. — SEM images of Kobayasiella pseudostauron (Lange-Bertalot) Lange-Bertalot: A, B, external views of the complete valve; C, D, external views of the central area showing a stauros fascia and the multiseriate poroid covers over the striae between virgae; E, external view of the valve apex showing a curved proximal fissure opening into an irregular surface depression; F, magnified view of the terminal raphe fissure; G, internal view of a broken valve showing T-shaped proximal fissure and elongated helictoglossa. Scale bars: A, B, G, 5 µm; C-E, 2 µm.
FIG. 2 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 2. — Light micrograph diminution series of Kobayasiella Lange-Bertalot species: A-P, Kobayasiella parasubtilissima (Kobayasi & Nagumo) Lange-Bertalot; Q-AB, Kobayasiella madumensis (Jørgensen) Lange-Bertalot; AC-AO, Kobayasiella subtilissima (Cleve) Lange-Bertalot. Scale bar: 10 µm.
FIG. 5 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 5. — SEM images of Kobayasiella madumensis (Jørgensen) Lange-Bertalot: A, external view of the complete valve; B, internal view of the complete valve; C, external view of the axial and central areas showing the multiseriate poroid covers between irregular formed virgae; D, internal view of the central area showing Y-shaped proximal fissures; E, central area with differentially thickened axial ridges; F, external view of the valve apex showing an elevated terminal area with a partially curved proximal fissure; G, internal valve view of the apex. Helictoglossa expanded onto a highline apex. Areolae interrupted around the apex. Scale bars: A, B, 10 µm; C, D, F, 3 µm; E, 500 nm; G, 2 µm.
FIG. 9 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 9. — SEM images of Kobayasiella micropunctata (Germain) Lange-Bertalot: A, B, external views of the complete valve; C, external view of the central area showing the multiseriate poroid covers over the striae between virgae; D, external view of the valve apex showing a hooked terminal fissure opening into an irregular surface depression; E, internal view of the apex with magnified view of the terminal elongated helictoglossa; F, internal view of a copula showing two rows of pores occluded with small round pores. Scale bars: A, B, 5 µm; C, D, 2 µm; E, 1 µm; F, 500 nm.
FIG. 15 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 15. — SEM images of Nupela tenuicephala (Hustedt) Lange-Bertalot: A, B, external views of complete valves with recessed depressions covered with multiporoid volae; C, internal view of the whole valve; D, external view of the central area showing the expanded proximal raphe fissures and multiseriate poroid covers over the areolae; E, internal view of the central area with bent proximal fissures; F, internal views of the apex, helictoglossa small and elevated. Areolae interrupted around the apex. Scale bars: A-C, 5 µm; D, 2 µm; E, F, 1 µm.
FIG. 14 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 14. — SEM images of Sellaphora vincentiana sp. nov.: A, C, E, external views of the complete valve; B, F, external view of the central area showing a linear expanded proximal fissure and recessed poroid covers over the areolae; D, external view of the apex with a bent fissure onto the mantle. Scale bars: A, C, 3 µm; B, D, 1 µm; E, F, 500 nm.
FIG. 1 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 1. — Lake sampling locations and surface deposits in Tursujuq National Park. Insert shows the position of Tursujuq Park in Nunavik, Québec, eastern North America.
FIG. 4 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 4. — SEM images of Kobayasiella parasubtilissima (Kobayasi & Nagumo) Lange-Bertalot: A, external view of the complete valve; B, internal view of the valve areolae recessed between virgae; C, section of girdle band showing one row of evident pore and a second row of scattered less evident pores with volae covers; D, external view of the axial and central areas showing the multiseriate poroid covers between the virgae; E, internal view of the central area showing T-shaped proximal fissures; F, central area with a weak central depression; G, external view of the valve apex, showing a partially curved proximal fissure opening into a small round surface depression; H, internal valve view of the apex. Helictoglossa expanded onto a highline apex. Areolae continuous around the apex. Scale bars: A, 10 µm; B-E, H, 1 µm; F, 600 nm; G, 3 µm.
FIG. 11 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 11. — SEM images of Adlafia bryophila (J.B.Petersen) Lange-Bertalot: A, external view of the complete valve; B, internal view of the complete valve; C, external view of the central area showing the multiseriate poroid covers over the areolae; D, internal view of the central area showing hooked proximal fissures to one side. Copula with one row of large occluded pores; E, external view of the apex with a curved fissure onto the mantle. A curved ridge follows the fissure; F, internal view of the apex with a small elevated helictoglossa. Areolae are continuous around the apex. Scale bars: A, B, 5 µm; C, D, 2 µm; E, F, 1 µm.
FIG. 3 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 3. — Light micrograph diminution series of Kobayasiella Lange-Bertalot species: A-J, Kobayasiella tursujuqensis sp. nov.; K-T. Kobayasiella pseudostauron (Lange-Bertalot) Lange-Bertalot. Scale bar: 10 µm.
FIG. 6 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 6. — SEM images of Kobayasiella subtilissima (Cleve) Lange-Bertalot:A, external view of the complete valve; B, internal view of the complete valve; C, external view of central area showing the multiseriate poroid covers between irregular formed virgae; D, internal view of the central area showing T-shaped proximal fissures and irregular orientated areolae; E, external view of the valve apex showing a partially curved proximal fissure opening into an elliptic surface depression; F, internal valve view of the apex. Helictoglossa expanded onto a highline apex. Areolae continue around the apex. Scale bars: A, B, 5 µm; C, 1 µm; D, F, 3 µm; E, 2 µm.
FIG. 10 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
FIG. 10. — Light micrograph diminution series of Adlafia Moser, Lange-Bertalot & Metzeltin, Sellaphora Mereschkowski and Nupela Vyverman & Compère species: A-R, Adlafia bryophila (J.B.Petersen) Lange-Bertalot; S-AG, Adlafia umiujaqensis sp. nov.; AH-AT, Adlafia ossiformis sp. nov.; AU-BJ, Sellaphora vincentiana sp. nov.; BK-BY, Nupela tenuicephala (Hustedt) Lange-Bertalot. Scale bar: 10 µm.
Exploration and diet specialization in eastern chipmunks - Québec - Canada
<p>Individual diet specialization (IDS) is widespread and can affect the ecological and evolutionary dynamics of populations in significant ways. Extrinsic factors (e.g., food abundance) and individual variation in energetic needs, morphology, or physiology, have been suggested as drivers of IDS. Behavioral traits like exploration and boldness can also impact foraging decisions, although their effects on IDS have not yet been investigated. Specifically, variation among individuals in exploratory behavior and their position along <span>the exploration/exploitation trade-off </span>may <span>affect their foraging behavior, acquisition of food items and home-range size, which may in turn influence</span> the diversity of their diet. Here we analyzed stable carbon and nitrogen isotopes in hair of wild eastern chipmunks, <em>Tamias striatus,</em> to investigate the influence of individual differences in exploration on IDS. We found that exploration profile, sex, and yearly fluctuations in food availability explained differences in the degree of dietary specialization and in plasticity in stable carbon and stable nitrogen over time. Thus, consistent individual differences in exploration can be an important driver of within-population niche specialization and could therefore affect within-species competition. Our results highlight the need for a more thorough investigation of the mechanisms underlying the link between individual behavioral differences and diet specialization in wild animal populations.</p>
Linked collectors and determiners for: Potential indicator species of climate changes occurring in Québec, Part 1: the small brown lacewing fly Micromus posticus (Walker) (Neuroptera: Hemerobiidae).
Natural history specimen data linked to collectors and determiners held within, "Potential indicator species of climate changes occurring in Québec, Part 1: the small brown lacewing fly Micromus posticus (Walker) (Neuroptera: Hemerobiidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8260db39-8776-4ad6-bd80-46e4e1168bf7">https://bionomia.net/dataset/8260db39-8776-4ad6-bd80-46e4e1168bf7</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8260db39-8776-4ad6-bd80-46e4e1168bf7">https://gbif.org/dataset/8260db39-8776-4ad6-bd80-46e4e1168bf7</a>. Formatted as a Frictionless Data package.
Life cycle inventory database for consumption in Québec – Food consumption
<p>These inventory datasets are essential for calculating the carbon footprint of an individual’s consumption in Quebec.</p> <p>Led by the CIRAIG, in collaboration with PolyCarbone and ESG-UQAM, this project aims to develop an inventory database of the life cycle of consumption in Quebec. These inventory datasets are essential for calculating the carbon footprint of an individual’s consumption in Quebec. The inventory is developed with a life cycle approach. Ultimately, it allows for evaluating carbon footprints at every step of the consumption life cycle (extraction of primary sources, transformation, transport, use of goods and services, end of life). The inventory is developed in a modular fashion for the different areas of individual consumption as Food; Transport; Housing; Clothing; Travel; Communications; Entertainment and Culture; Financial and Administrative Management; Health, Hygiene, and Beauty. These areas are developed and detailed as a priority, as they contribute most to an individual’s carbon footprint in Quebec. Other non-priority areas are roughly modelled in order to provide a complete (but more uncertain) portrait of individual consumption. The project is underway and the deliverables will be made available online as things progress. It is not, however, an objective of the project to create a carbon footprint calculation tool at the moment.</p> <p>https://ciraig.org/index.php/project/life-cycle-inventory-database-for-consumption-in-quebec/</p> <p> </p>
Exploration and diet specialization in eastern chipmunks - Québec - Canada
Open the record for dataset details and reuse information.
Supplementary data 'Mitochondrial genome sequence of the protist Ancyromonas sigmoides Kent, 1881 (Ancyromonadida) from the Sugluk Inlet, Hudson Strait, Nunavik, Québec'
<p>Fasta file with the transcripts obtained from RNAseq sequencing of Ancryomonas sigmoides (kmer 35) and file with datamining results.</p><p>Fasta file of the transcript matching the cox1 gene.</p><p>Scaffolds of the kmer 85 assembly of the genomic data of Ancryomonas sigmoides.</p><p>Databse used for datamining (fasta file)</p>
APPENDIX 4 in Small naviculoid species of Kobayasiella Lange-Bertalot, Adlafia Moser, Lange-Bertalot & Metzeltin, Nupela Vyverman & Compère and Sellaphora Mereschowsky from Tursujuq National Park, Hudson Bay region, Nunavik, Québec
APPENDIX 4. — Relative abundance of species as a function of DIC values.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
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OpenNeuro
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