This is the documentation of phylodynamic and transmission dynamics of COVID-19 XBB 1.5 in Indonesia. The interactive output can be accessed HERE
The data were gathered from GISAID. where we filtered variants 'XBB 1.5' and between Oct 2022-Dec 2023. For outside Indonesia, we take the first cases of XBB 1.5. The reference was taken from GenBank, Wuhan Sequence. In this Github the data are consist:
| Data Name | Description |
|---|---|
metadata_covid.csv |
metada of samples |
sample_alignment.constree |
the consensus tree |
sample_alignment.treefile |
best-scoring maximum likelihood tree |
We using MAFFT in Ubuntu with Linux command line
mafft -s sample.fasta > sample_alignment.fasta
Ultrafast bootstrapping in IQ-TREE is a technique used to assess the reliability of individual branches in a phylogenetic tree, offering faster computations than traditional bootstrapping methods. By using the -bb 1000 option, it performs 1000 bootstrap replicates to provide statistical support for the tree's branches, enhancing both efficiency and accuracy.
iqtree -s sample_alignment.fasta -m MFP -bb 1000
Tree dating from tree are using treedater
epicontact package are using for transmission reconstruction
outbreakinfo for XBB 1.5 variants distribution