Molecular Clock Phylodynamics Project

This is the documentation of phylodynamic and transmission dynamics of COVID-19 XBB 1.5 in Indonesia. The interactive output can be accessed HERE

Data

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

Method

Alignment

We using MAFFT in Ubuntu with Linux command line

mafft -s sample.fasta > sample_alignment.fasta 

Bootstrapping Tree

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

Tree dating from tree are using treedater

Transimssion Reconstruction

epicontact package are using for transmission reconstruction

Variant Distribution

outbreakinfo for XBB 1.5 variants distribution