A geopositioned, evidence-graded, pan-species compendium of Mayaro Virus occurrence
Data files
Jun 13, 2023 version files 474.12 KB
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Custom_polys_MAYV_compendium.zip
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Duplicate_entries_MAYV_compendium.csv
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Georefs_MAYV_compendium.csv
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Quality_scores_MAYV_compendium.docx
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RData_check_MAYV_compendium.txt
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README.txt
Dec 14, 2023 version files 474.08 KB
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Custom_polys_MAYV_compendium.zip
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Duplicate_entries_MAYV_compendium.csv
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Georefs_MAYV_compendium.csv
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Quality_scores_MAYV_compendium.docx
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RData_check_MAYV_compendium.txt
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README.md
Abstract
Mayaro Virus (MAYV) is an emerging health threat in the Americas that can cause febrile illness as well as debilitating arthralgia or arthritis. To better understand the geographic distribution of MAYV risk, we developed a georeferenced database of MAYV occurrence based on peer-reviewed literature and unpublished reports. Here we present this compendium, which includes both point and polygon locations linked to occurrence data documented from its discovery in 1954 until 2022. In the associated data descriptor manuscript (https://doi.org/10.1038/s41597-023-02302-z), we describe all methods used to develop the database including data collection, georeferencing, management, and quality-control. We also describe a customized grading system used to assess the quality of each study included in our review. The result is a comprehensive, evidence-graded database of confirmed MAYV occurrence in humans, non-human animals, and arthropods to-date, containing 262 geo-positioned occurrences in total. This database – which can be updated over time – may be useful for local spill-over risk assessment, epidemiological modelling to understand key transmission dynamics and drivers of MAYV spread, as well as identification of major surveillance gaps.
README: A geopositioned, evidence-graded, pan-species compendium of Mayaro Virus occurrence
https://doi.org/10.5061/dryad.cfxpnvx8n
This dataset accompanies a Data Descriptor manuscript that was submitted to the Scientific Data journal. Data are derived from a systematic review of the literature focused on Mayaro virus (MAYV) occurrence.
Dataset Attribution and Usage
Dataset Title: Data for the article "A geopositioned and evidence-graded pan-species compendium of Mayaro Virus occurrence"
Persistent Identifier: https://doi.org/10.5061/dryad.cfxpnvx8n
Dataset Contributors: Michael Celone, Alex Potter, Barbara A. Han, Sean P. Beeman, Bernard Okech, Brett Forshey, James Dunford, George Rutherford, Neida K. Mita-Mendoza, Elizabet Lilia Estallo, Ricardo Khouri, Isadora Cristina de Siqueira, Kyle Petersen, Ryan C. Maves, Assaf Anyamba, Simon Pollett
Contact Information
- Name: Michael Celone
- Affiliations: Uniformed Services University of the Health Sciences
- ORCID ID: 0000-0002-1963-2353
- Email: michael.celone@usuhs.edu
- Alternate Email: mikecelone1@gmail.com
Description of the Data
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Details for File 1: Georefs_MAYV_compendium
Description: A database containing georeferenced locations of MAYV occurrence.
Format(s): .csv
Variables:
- Location_ID: Unique identifier assigned to each georeference.
- Author_Year: First author and publication year for each record.
- Ref_Number: Reference identification number.
- Year_MAYV_Start: Earliest year that MAYV infection was detected.
- Year_MAYV_End: Latest year that MAYV infection was detected.
- Host_Type: Host type for each occurrence: human, non-human animal, or arthropod.
- Location_Description: Relevant information/decisions related to the location of the occurrence record.
- Adm0: Country where MAYV occurrence was detected.
- Adm1: First level administrative unit where MAYV occurrence was detected (if available).
- Adm2: Second level administrative unit where MAYV occurrence was detected (if available).
- GAUL_code: When a MAYV occurrence was georeferenced as an ADM1 or ADM2 administrative polygon, the GAUL code was included.
- Finer_Res: If finer spatial resolution was documented (e.g., a town, city, or exact coordinates) this was recorded.
- Location_Type: Point or polygon location type, depending on the spatial resolution that was provided.
- Admin_Level: Administrative level for each polygon location or -999 was used for point/custom polygon locations.
- X_Coord: Longitude coordinate was recorded in decimal degrees.
- Y_Coord: Latitude coordinate was recorded in decimal degrees.
- Coord_Source: This field describes how the coordinates were determined.
- Uncertainty_km: The amount of uncertainty associated with the record, measured in km.
- Uncertainty_Description: The method used to calculate uncertainty for each georeference.
- Diagnostic_Type: The diagnostic test reported (e.g., polymerase chain reaction [PCR], neutralization test [NT]).
- Positive_n: The number of positive MAYV cases that were reported.
- Denominator: The total number of humans, non-human animals, or arthropod pools in the study.
- Language: The language of the article, either English, Portuguese, or Spanish.
Details for File 2: Quality_scores_MAYV_compendium
Description: A table containing quality scores and references for each included article. We evaluated and graded each study on four quality criteria. For each quality criterion, eligible studies were assigned a quality score of 3 (strong evidence), 2 (moderate evidence), 1 (weak evidence), or unable to judge.
Format(s): .docx
Variables:
- Clarity of research question/objective.
- Description of study methods.
- Description of sampling methods.
- Validity of diagnostic tests.
File 3: Duplicate_entries_MAYV_compendium
Description: A database containing duplicate MAYV georeferences that were excluded from the primary database
Format(s): .csv
Variables:
- Location_ID: Unique identifier assigned to each georeference.
- Author_Year: First author and publication year for each record.
- Ref_Number: Reference identification number.
- Year_MAYV_Start: Earliest year that MAYV infection was detected.
- Year_MAYV_End: Latest year that MAYV infection was detected.
- Host_Type: Host type for each occurrence: human, non-human animal, or arthropod.
- Adm0: Country where MAYV occurrence was detected.
- Adm1: First level administrative unit where MAYV occurrence was detected (if available).
- Adm2: Second level administrative unit where MAYV occurrence was detected (if available).
- Finer_Res: If finer spatial resolution was documented (e.g., a town, city, or exact coordinates) this was recorded.
- Location_Type: Point or polygon location type, depending on the spatial resolution that was provided.
- Admin_Level: Administrative level for each polygon location or -999 was for point locations.
- X_Coord: Longitude coordinate was recorded in decimal degrees.
- Y_Coord: Latitude coordinate was recorded in decimal degrees.
File 4: Custom_polys_MAYV_compendium
- Description: A zip folder with custom polygon locations. The folder contains shapefiles that can be opened in GIS software or statistical packages that handle spatial data. Each polygon is associated with an entry in the Georefs_MAYV_compendium dataset.
Usage notes
Georeferenced Database of Mayaro virus occurrence
A database containing georeferenced locations of Mayaro virus occurrence in humans, non-human animals, and arthropods.
File name: Georefs_MAYV_compendium.csv
Quality Scores and References
A table containing quality scores and references for each article included in our systematic review of human MAYV occurrence. Quality scores are based on a customized grading system of four quality items: clarity of research question/objective; description of study methods; description of sampling methods; and validity of diagnostic tests.
File name: Quality_scores_MAYV_compendium.docx
Duplicate entries
A database containing duplicate Mayaro virus georeferences that were excluded from the primary database.
File name: Duplicate_entries_MAYV_compendium.csv
Shapefiles for custom polygon locations
A zip folder containing a shapefile with custom polygon locations. Each polygon is associated with an entry in the georeferenced dataset. These files can be opened in GIS software or using statistical packages that handle spatial data (e.g., the sf package in R).
File name: Custom_polys_MAYV_compendium.zip