Phylogeographic analysis of hepatitis A virus in Russia

Introduction

Aim and objectives
The aim of the work is to reconstruct the phylogenetics, geographic structure and migration events of HAV in Russia.
The hypothesis is that IIIA subgenotype originates from India while IA is expanding from Europe.
Objectives:
Phylogeographic analysis using Bayesian approach (BEAST)
Phylogeographic analysis with ML approach (augur) and GenGis
Obtaining full genomes of HAV
Have fun with full genomes

The dataset
Central Research Institute of Epidemiology kindly provided us with the unique collection of HAV isolates obtained all over Russian Federation and CIS countries.
Samples (more than 500 isolates) were collected from 1999 to 2015 and characterized by one of the two most variable fragments of HAV genome (VP1 and 2C regions) or by both of them.
The dataset includes 124 unique sequences of 2C/3A region, length ≈ 650 bp, and 217 sequences of VP1/2A region, length ≈ 400 bp. For each sample, date and location of collection is indicated.
Whole-genome sequences of HAV from GenBank were used (accession numbers KC182588, KC182589, HM769724, LC049342, LC049339, LC049338, AB909123, AB623053, JQ655151, AB973400, FJ360735, FJ360734, FJ360733, FJ360732, FJ360731, FJ360730, AB279734, AB279733, AB279732).

Methods
Software:
MEGA – alignment, tree reconstruction
IQTree – model selection
BEAST – phylogeography, model selection
Spread3 – visualization of phylogeography
Chelper – primer design for sequencing of whole genomes
Planned:
GenGis – estimating directions of migration
Augur – phylogeography based on ML, not Bayes
This python package which name I don’t know – geographic clusterization
Whole genome sequencing will be performed with Mi-seq

BEAST and VEME2018
The 23rd International Workshop on Virus Evolution and Molecular Epidemiology (VEME2018) was hosted in Berlin, Germany. It was devoted to phylogenetic inference and BEAST.
Markov chain Monte Carlo

Results

Results: IA phylogeography

Results: IIIA phylogeography

Discussion and problems
Sampling issues
Uncertainty in time and place of sample collection (current solution – setting random jitter in BEAST)
Low mutation rate => low resolution

Plans
Verify BEAST results with other approaches (augur, GenGis)
Obtain whole genomes of HAV
Analyze the whole genomes and add partial sequences from Genbank if possible

Conclusions (obtained, desired)
So far, the results of BEAST estimation of phylogeography agree with literature data
Desired :