School of Biological Sciences
Researcher:
Tommy Tsan-Yuk Lam, PhD Student (tylam83@hkusua.hku.hk)
Frederick Chi-Ching Leung, Professor (fcleung@hkucc.hku.hk)
Project Title:
Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia
Project Description:
The global phylogeny of all H5N1 viruses, China’s sequences were predominating at the tree trunk, suggest it is pool of H5N1 viruses. There is a single clade for all Indonesia H5N1 viruses, suggesting a single introduction. Thus, we focused on the Indonesia lineages.
Project Significance:
We performed phylogenetic analyses on all 8 segments. We found that some early viruses which caused outbreaks from 2003-2004 are close to root, and do not form well-supported lineage. However, three well-supported lineages are consistently shown by all 8 gene phylogenies. Except for a group of 25 human and cat isolates (taxa in red) shuffled between G2 and G3 lineages in different gene phylogenies. This preliminarily suggests they are inter-lineage reassortant.
We further analyze the data to validate our preliminary observation. First, we concatenated 8 segments into a single genome alignment. We performed simplot, bootscanning, GARD. We would expect breakpoints were found near those concatenating junction if there were reassortment. The result consistently suggested these 25 isolates were reassortant strain which acquired MP and PB1 from G3 and other 6 segment from G2 lineage.
