Processed data, code, configuration files and results of the transmission analysis of two datasets of SARS-CoV-2 genomes. The first dataset contains samples bearing combinations of Alpha and Delta-defining NTD mutations. The second dataset contains samples assigned to the Alpha variant and the BA.1 Omicron lineage with NTD deletion repairs. The GISAID EPI_SETs are available at https://dx.doi.org/10.55876/gis8.230802fh and https://dx.doi.org/10.55876/gis8.230801ex, respectively. The sequence records from each list of target samples were extracted from a FASTA file containing an aligned sequence dataset, and placed on a reference phylogeny. Then, transmission clusters were detected using a breadth-first search approach. Additionally, a fitness metric was estimated for each cluster. Finally, a series of figures (including sample timelines, comparisons of estimated fitness and missing data) were generated. The pipeline used for this analysis, transcluster v2.0.0, is a Snakemake workflow released as free software under the GNU GPLv3 license. Its source code is included here, and is also available in GitHub (https://github.com/PathoGenOmics-Lab/transcluster).

[Description of methods used for collection/generation of data] Worldwide surveys using the GISAID EpiCov database were conducted on 2022-01-16 and 2022-06-15, resulting in the collection of two SARS-CoV-2 genome datasets. Then, transcluster v2.0.0 was run on these datasets. For each dataset, input files containing lists of sample identifiers are contained in the "input" folder. The "output" folder contains the pipeline output files, consisting on a separate folder for each of the input lists, as well as a "summary" folder. Each "config/config.yaml" file describes the pipeline configuration of each run. Further pipeline documentation is available at https://github.com/PathoGenOmics-Lab/transcluster. [Methods for processing the data] Raw genome data from GISAID was processed using transcluster v2.0.0 (https://github.com/PathoGenOmics-Lab/transcluster). The input lists contain the sample identifiers that were selected after filtering by haplotype and sequence quality.

PTI+Salud Global – European Commission – NextGenerationEU/ PRTR (Regulation EU 2020/2094), Generalitat Valenciana and the European Social Fund “ESF Investing in your future” (CIACIF/2022/333), MCIN/AEI/10.13039/501100011033 and the European Union NextGenerationEU/PRTR (CNS2022-135116 and CNS2022-135100).

Peer reviewed