COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses

Zhiyuan Chen¹, Joseph L.-H. Tsui², Bernardo Gutierrez^2,3, Simon Busch Moreno², Louis du Plessis^4,5, Xiaowei Deng⁶, Jun Cai¹, Sumali Bajaj², Marc A. Suchard⁷, Oliver G. Pybus^{2,8,9,‡,†}, Philippe Lemey^10,‡,†, Moritz U. G. Kraemer^2,9,‡,†, Hongjie Yu^{1,10,11,‡,†}

1. Department of Epidemiology, School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, China
2. Department of Biology, University of Oxford, Oxford, UK
3. Colegio de Ciencias Biologicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
4. Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
5. Swiss Institute of Bioinformatics, Lausanne, Switzerland
6. Department of Epidemiology, National Vaccine Innovation Platform, School of Public Health, Nanjing Medical University, Nanjing, China
7. Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
8. Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
9. Pandemic Sciences Institute, University of Oxford, Oxford, UK
10. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
11. Shanghai Institute of Infectious Disease and Biosecurity, Fudan University; Shanghai, China
12. Department of Infectious Diseases, Huashan Hospital, Fudan University; Shanghai, China

^‡ Contributed equally to this work
^† Correspondence: [email protected]; [email protected]; [email protected]; [email protected]

Before starting

1. This repository contains code and data used in the paper entitled "COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses"
2. All code and data contained within this repository are released under the CC BY-NC-SA License.
3. Because of GISAID terms of use, sequence data are not provided. All sequence identifiers are provided and sequences can be downloaded from NCBI or GISAID.

Repository structure and usage

The structure of this repository is shown below.

global_influenza_project/
├── data
│   ├── air_traffic_data
│   ├── epi_data
│   ├── genomic_data
│   ├── genomic_data_subsample
│   └── map_data
├── phylogenetic_analysis
├── phylogeographic_analyses
│   ├── step1
│   └── step2
├── analysis_main_figures
│   ├── Epi_analysis_Fig1.r
│   ├── Air_traffic_analysis_Fig2.r
│   ├── Flu_movement_analysis_Fig3.r
│   └── Flu_genetic_diveristy_Fig4.r
├── analysis_others
│   ├── glm_log_file
│   ├── trunk
│   ├── jump_history
│   ├── dwell_time
│   ├── mcc_tree
│   ├── diversity
│   ├── pop_size
│   └── nature_selection
├── regression_analysis
│   ├── bayesian_model_v2.py
│   └── forest_plots_epoch
├── acknowledgement_table
└── README.md

License

CC BY-NC-SA 4.0

Attribution-NonCommercial-ShareAlike 4.0 International This license requires that reusers give credit to the creator. It allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, for noncommercial purposes only. If others modify or adapt the material, they must license the modified material under identical terms.

BY: Credit must be given to you, the creator.

NC: Only noncommercial use of your work is permitted. Noncommercial means not primarily intended for or directed towards commercial advantage or monetary compensation.

SA: Adaptations must be shared under the same terms.

COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses © 2024 by Zhiyuan Chen is licensed under CC BY-NC-SA 4.0

Copyright (c) 2024 Zhiyuan Chen, Fudan University & University of Oxford