Data for modeling phylogeographic dynamics of Sindbis virus in Africa (doi:10.60507/FK2/VUMWZI)

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Data for modeling phylogeographic dynamics of Sindbis virus in Africa

doi:10.60507/FK2/VUMWZI

bonndata

2026-07-08

1

Nabatanzi, Maureen, 2026, "Data for modeling phylogeographic dynamics of Sindbis virus in Africa", https://doi.org/10.60507/FK2/VUMWZI, bonndata, V1

Data for modeling phylogeographic dynamics of Sindbis virus in Africa

doi:10.60507/FK2/VUMWZI

Nabatanzi, Maureen (University of Bonn)

MAFFT

R

458328858

bonndata

Nabatanzi, Maureen

Nabatanzi, Maureen

2026-03-06

https://doi.org/10.60507/FK2/VUMWZI

Agricultural Sciences, Earth and Environmental Sciences, Medicine, Health and Life Sciences

This dataset comprises Sindbis virus (SINV) sequences, their locations of sample collection and ecological variables used to conduct continuous phylogeographic and phylodynamic analysis of SINV dispersal in Africa. There are 23 complete and near-complete SINV genomes sampled across Africa between 1952 and 2022. Ecological variables comprise 26 potential predictors with suspected associations with viral discovery and dispersal. Sequences and location data were used to generate time-calibrated phylogenies, its spatiotemporal dispersal history and dispersal dynamics. We assessed the impact of the predictors on viral dispersal position, direction, and velocity.

1952-08-01-2022-01-01

2025-08-01-2025-12-01

Genome sequences

GPS Coordinates

Raster data

a) CRU-TS 4.09 (Harris et al., 2020) downscaled with WorldClim 2.1 (Fick and Hijmans, 2017). Fick, S.E. and R.J. Hijmans, 2017. WorldClim 2: new 1km spatial resolution climate surfaces for global land areas. International Journal of Climatology 37 (12): 4302-4315.https://www.worldclim.org/data/monthlywth.html b) Nabatanzi, Maureen, 2026, "Ecological niche and presence maps for Wesselsbron, Sindbis and Middelburg viruses and their vectors in Africa", https://doi.org/10.60507/FK2/FWVXDH, bonndata, v1 c) Center For International Earth Science Information Network-CIESIN-Columbia University. (2018). <i>Gridded Population of the World, Version 4 (GPWv4): Population Count Adjusted to Match 2015 Revision of UN WPP Country Totals, Revision 11</i> (Version 4.11) [Data set]. Palisades, NY: NASA Socioeconomic Data and Applications Center (SEDAC). https://doi.org/10.7927/H4PN93PB Date Accessed: 2025-11-10 d) World Health Organization. IHR eSPAR scores (2020). Available at https://extranet.who.int/e-spar/ e) https://www.nature.com/articles/nature25181 f) BirdLife International (2025) Digital boundaries of Important Bird and Biodiversity Areas (IBAs) and Key Biodiversity Areas (KBAs) identified for birds. September 2025 version. BirdLife International, Cambridge, UK. Available at: https://datazone.birdlife.org/contact-us/request-our-data g) Adriana De Palma; Sara Contu; Gareth E Thomas; Connor Duffin; Sabine Nix; Andy Purvis (2024). The Biodiversity Intactness Index developed by The Natural History Museum, London, v2.1.1 (Open Access, Limited Release) (from The Biodiversity Intactness Index developed by The Natural History Museum, London, v2.1.1 (Open Access, Limited Release)) [Data set resource]. Natural History Museum. https://data.nhm.ac.uk/dataset/bii-developed-by-nhm-v2-1-1-limited-release/resource/c4c281c4-befa-4e1b-a162-ba2f25e5ae82 h) Friedl, M., Sulla-Menashe, D. (2022). MODIS/Terra+Aqua Land Cover Type Yearly L3 Global 500m SIN Grid V061. NASA EOSDIS Land Processes Distributed Active Archive Center. Accessed 2025-11-11 from https://doi.org/10.5067/MODIS/MCD12Q1.061. Accessed November 11, 2025. i) Hurtt, G. C., L. Chini, R. Sahajpal, S. Frolking, B. L. Bodirsky, K. Calvin, J. C. Doelman, J. Fisk, S. Fujimori, K. Klein Goldewijk, T. Hasegawa, P. Havlik, A. Heinimann, F. Humpenöder, J. Jungclaus, J. O. Kaplan, J. Kennedy, T. Krisztin, D. Lawrence, P. Lawrence, L. Ma, O. Mertz, J. Pongratz, A. Popp, B. Poulter, K. Riahi, E. Shevliakova, E. Stehfest, P. Thornton, F. N. Tubiello, D. P. van Vuuren and X. Zhang (2020). "Harmonization of global land use change and management for the period 850–2100 (LUH2) for CMIP6." Geosci. Model Dev. 13(11): 5425-5464. j) Maus, Victor; da Silva, Dieison M; Gutschlhofer, Jakob; da Rosa, Robson; Giljum, Stefan; Gass, Sidnei L B; Luckeneder, Sebastian; Lieber, Mirko; McCallum, Ian (2022): Global-scale mining polygons (Version 2) [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.942325 k) Kummu, M., Kosonen, M. & Masoumzadeh Sayyar, S. 2025. Downscaled gridded global dataset for gross domestic product (GDP) per capita PPP over 1990–2022. Scientific Data 12: 178. https://doi.org/10.1038/s41597-025-04487-x l) Joint Research Centre - JRC - European Commission, & Center for International Earth Science Information Network - CIESIN - Columbia University. (2021). Global Human Settlement Layer: Population and Built-Up Estimates, and Degree of Urbanization Settlement Model Grid. Retrieved from: https://doi.org/10.7927/h4154f0w m) NSAL, F. a. A. O.-. (2024). GLW 4: Gridded Livestock Density (Global - 2020 - 10 km) [mapDigital]. Retrieved from: https://data.apps.fao.org/catalog/iso/9d1e149b-d63f-4213-978b-317a8eb42d02 n) National Center for Biotechnology Information, NCBI Virus [Internet]. National Library of Medicine. 2024. Available from: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide

<a href="http://creativecommons.org/licenses/by/4.0">CC BY 4.0</a>

Nabatanzi, Maureen, 2026, "Ecological niche and presence maps for Wesselsbron, Sindbis and Middelburg viruses and their vectors in Africa", https://doi.org/10.60507/FK2/FWVXDH, bonndata, V1

Nabatanzi, Maureen, 2026, "Ecological niche and presence maps for Wesselsbron, Sindbis and Middelburg viruses and their vectors in Africa", https://doi.org/10.60507/FK2/FWVXDH, bonndata, V1

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AccessCity.tif

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Accessibility as travel time in minutes required to reach the nearest city if walking-only or using motorized transport in 2015.

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AccessHealth.tif

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Accessibility as time in walking minutes to nearest healthcare facility in 2015.

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BII.tif

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Biodiversity Intactness Index (BII) are percentage values between 0 and 100, indicating the intactness of the ecosystem in 2020.

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Bio1.tif

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Annual Mean Temperature (°C) for 2022

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Bio12.tif

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Annual Precipitation (mm), the sum of 12 months precipitation for 2022

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Bio5.tif

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Maximum Temperature (°C) of Warmest Month for 2022

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Built.tif

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Built-Up areas given by the proportion of the building footprint area within the total size of the grid cell for 2014

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Cropland.tif

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Sum of annual crops, perennial crops, annual crops, perennial crops and nitrogen-fixing crops in 2015.

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CulexP.tif

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Culex pipiens presence for 2015. Values range from highest certainty (4) to least certainty (0) of presence.

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CulexU.tif

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Culex univittatus presence for 2015. Values range from highest certainty (4) to least certainty (0) of presence.

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DistanceKBA.tif

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Distance to nearest Key Biodiversity Area created from KBA dataset by computing Euclidean distances from each cell to the nearest KBA cell; 2025.

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Forest.tif

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Sum of forested primary land and potentially forested secondary land in 2015.

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GDP.tif

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Gross Domestic Product per capita for 2020.

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Humanpop.tif

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Human population distribution by number of people per grid cell for 2015

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IBA.tif

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Important Bird and Biodiversity Areas (IBAs); boundaries of sites that are significant for the long-term viability of naturally occurring bird populations in 2025.

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IHR.tif

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International Health Regulations (IHR) capacity score given by the electronic IHR States Parties Self-Assessment Annual Reporting Tool (eSPAR). An annual self-assessment of country capacity and compliance with the IHR. eSPAR total average capacity scores for 2020.

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KBA.tif

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Key Biodiversity Areas (KBA); boundaries of sites of significance for the global persistence of biodiversity in 2025.

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Livestock.tif

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Livestock density in 2020. Animals or birds/pixel.

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Mammals.tif

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Grid cell values represent the number of mammalian species. Data from International Union for Conservation of Nature (IUCN) are dated April 2013.

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Mining.tif

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Land used by mining industry between 2000 - 2017.

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NonForest.tif

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Forested primary land and potentially non-forested secondary land in 2015.

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Pastureland.tif

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Sum of managed pasture and rangeland in 2015

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Readme.txt

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Roads.tif

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Total road density in meters per km² in 2018.

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S1_Video.mp4

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Video animation of the results of continuous phylogeographic spread of SINV in Africa

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SINV_aligned.fasta

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Complete and near-complete genome sequences of SINV sampled in Africa between 1952 and 2022 and downloaded from the National Center for Biotechnology Information (NCBI) on 9/08/2025. They were aligned in MAFFT (version 7), an online multiple sequence alignment program, and can be opened with a text editor and most sequence alignment software.

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Smod.tif

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Human settlement model grid for 2015. Grid cells assigned with 2-digit codes in the following classes: 30 = "Urban Centre"; 23 = "Dense Urban Cluster"; 22 = "Semi-dense Urban Cluster"; 21 = "Suburban or peri-urban grid cells"; 13 = "Rural cluster"; 12 = "Low Density Rural grid cells"; 11 = "Very low density rural grid cells"; 10 = "Water grid cells"

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Traits.txt

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Traits file comprising sequence identifiers and their geo-location of sampling

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Urban.tif

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Urban land as a unit fraction of a grid cell in 2015.

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Wetlands.tif

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MCD12Q1_V61 Land Cover Type 1: Annual International Geosphere-Biosphere Programme (IGBP) dataset for 2020; class 11.

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