Supplement for: Novel clade 2.3.4.4b H5N1 avian influenza virus reassortants identified from migratory birds in China: posing risks to birds and public health
Novel clade 2.3.4.4b H5N1 avian influenza virus reassortants identified from migratory birds in China: posing risks to birds and public health
Jing Yang1, Chunge Zhang1, Yue Yuan1, Ju Sun1, Lu Lu1, Honglei Sun, Heting Sun, Dong Chu, Siyuan Qin, Jianjun Chen, Xiyan Hao, Chengbo Zhang, Weifeng Shi, Wenjun Liu, George F. Gao, Paul Digard, Samantha Lycett, and Yuhai Bi*
(In submission)
Will be available after manuscript published.
- The MCC.tree appendices were generated from the BEAST v1.10.4 by Dr. LuLu.
- Time-scaled MCC tree of the eight gene segment of HPAIV H5N1 sequences found in the study and the related sequences from GISAID and NCBI influenza database. Discrete traits and continuous traits were reconstructed on time-scaled phylogeny. The 3 types of traits are: host type, HA/NA type, and geographic coordinates.
- Appendix file 1: Time-scaled MCC tree of the PB2 gene sequences
- Appendix file 2: Time-scaled MCC tree of the PB1 gene sequences.
- Appendix file 3: Time-scaled MCC tree of the PA gene sequences.
- Appendix file 4: Time-scaled MCC tree of the HA gene sequences.
- Appendix file 5: Time-scaled MCC tree of the NP gene sequences.
- Appendix file 6: Time-scaled MCC tree of the NA gene sequences.
- Appendix file 7: Time-scaled MCC tree of the MP gene sequences.
- Appendix file 8: Time-scaled MCC tree of the NS gene sequences.
- Appendix file 9: Summary of sequences used in each tree of Appendix file 1-8.
- The maximum likelihood trees were estimated by Dr. Jing Yang.
- Appendix_Figure2_global_H5_phylogeny.pdf.
Phylogenetic tree of global H5 HA genes. HA sequences from our lab are shown in green text and labeled with solid green circles. The vaccine strains are shown in orange text and labeled with solid orange triangles. Human strains are shown in red text and labeled with red asterisks. H5 clade references are shown in blue text and labeled by blue asterisks. The rightmost bars label different clades. The unit of scale bar is the number of mutations per site.
- Appendix_Figure3_phylogeny_of_NA_genes_of_global_H5N1.pdf
Phylogenetic tree of NA gene of global H5N1. The NA sequences generated in this study are shown in green text and labeled with solid green circles. The NA genes identified from mainland China (except for NA genes from this study) are shown in blue text and labeled with blue asterisks. H5N1 NA genes collected in 2020 and 2021 are labeled with light and dark orange triangles, respectively. The rightmost bars label different clades. The unit of scale bar is the number of mutations per site.