Abstract
Genomic Characterization of a Reassortant A/H1N8 Avian Influenza Virus in South American Migratory Shorebirds This Open Science Framework (OSF) project provides the supplementary computational data and analysis outputs associated with the manuscript “Genomic Characterization of a Reassortant A/H1N8 Avian Influenza Virus in South American Migratory Shorebirds.” The study describes the genomic characterization and evolutionary history of a reassortant low-pathogenic avian influenza virus (LPAI) subtype H1N8, isolated from a White-rumped Sandpiper (Calidris fuscicollis) sampled at Parque Nacional da Lagoa do Peixe (PNLP), southern Brazil. The genomic analyses identified a mosaic genome composed of gene segments associated with different South American and North American avian influenza lineages. This OSF repository complements the study's computational repository on GitHub and provides large analysis archives that support the Bayesian phylogenetic, phylodynamic, phylogeographic, host-state and reassortment analyses reported in the manuscript. Repository contents The archived files include: FASTq_222.zip — raw sequencing data associated with isolate PNLP_222. jackknife_history_trees.zip — posterior tree histories generated from the jackknife sensitivity analyses. jackknife_logs.zip — BEAST MCMC log files from the jackknife analyses. NS_NA_logs_trees.zip — Bayesian posterior logs and trees associated with the NS and NA analyses. Relaxed clock.zip — Bayesian analysis outputs generated under the uncorrelated lognormal relaxed molecular-clock framework. Strict clock.zip — Bayesian analysis outputs generated under the strict molecular-clock framework. shared_backbone_logs.zip — Bayesian analysis outputs associated with the shared internal-gene backbone analyses. These files complement the XML configuration files, maximum-likelihood trees, maximum-clade-credibility trees, TreeSort analyses, and Sanger chromatograms available in the associated GitHub repository. The GitHub repository contains the principal analysis inputs and organized supplementary files used throughout the study. Computational reproducibility The complete computational workflow and analysis files are organized in the associated GitHub repository: PNLP_H1N8_Pathogens — GitHub repository The GitHub repository includes the BEAST XML files for relaxed and strict molecular-clock analyses, jackknife analyses, shared-backbone analyses, TreeSort input/output files, ML trees, MCC trees, and Sanger chromatograms. The large BEAST MCMC log and posterior tree archives are additionally deposited in this OSF project to facilitate access to the complete computational outputs of the study.