# Custom scripts for Han et al. (2022)
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This repository contains custom codes and data used to analyse the importation risks and within-country transmission dynamics of SARS-CoV-2 variants of concern in the Netherlands. The original manuscript describing this work can be found [here](https://doi.org/10.1101/2022.03.21.22272611), currently cited as a pre-print:

> Han, A.X., Kozanli, E., Koopsen, J., Vennema, H., RIVM COVID-19 molecular epidemiology group, Hajji, K., Kroneman, A., van Walle, I., Klinkenberg, D., Wallinga J., Russell, C.A., Eggink, D., Reusken, C.B.E.M. (2022). Regional importation and asymmetric within-country spread of SARS-CoV-2 variants of concern in the Netherlands. _medRxiv_, 2022.03.21.22272611.

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All sequence data used in this work can be downloaded from [GISAID](https://www.gisaid.org). The accession codes for all Netherlands sequences generated by us can be found in [Supplementary File 1](https://github.com/AMC-LAEB/nl_sars-cov-2_genomic_epi_2022/blob/main/manuscript/supp_file_1.txt). We acknowledged all authors and laboratories that generated the overseas sequences we had used in our analyses as listed in [Supplementary File 2](https://github.com/AMC-LAEB/nl_sars-cov-2_genomic_epi_2022/blob/main/manuscript/supp_file_2.xlsx).  

We are unable to share the BEAST input files we used in our analyses owing to (1) the inclusion of sequence data in those files (we cannot re-share sequences through our repository as per terms of GISAID) and (2) they contain sensitive information including the postal codes of the sampled Dutch residents. We have, however, provided all reconstructed phylogenies.

All codes used to generate the figures in the manuscript can be found in the [Jupyter Notebook](https://github.com/AMC-LAEB/nl_sars-cov-2_genomic_epi_2022/blob/main/figures_nl_sars-cov-2_genomic_epi.ipynb).

Please contact <x.han@amsterdamumc.nl> if you have any questions.