Feb 06, 2025

Public workspace Molecular evolution and geographic migration of severe fever with thrombocytopenia syndrome virus V.1

This protocol is a draft, published without a DOI.
  • 1Shandong University;
  • 2FuDan University
Ruyi Sheng
Icon indicating open access to content
QR code linking to this content
Protocol Citation: Ruyi Sheng, cheng tianyu 2025. Molecular evolution and geographic migration of severe fever with thrombocytopenia syndrome virus. protocols.io https://protocols.io/view/molecular-evolution-and-geographic-migration-of-s-dy4q7yvw
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 06, 2025
Last Modified: February 06, 2025
Protocol Integer ID: 119664
Funders Acknowledgements:
Special Key Project of Biosafety Technologies
Grant ID: 2022YFC2604000
Natural Science Foundation of Shandong Province for the National Major Research & Development Program of China
Grant ID: ZR2022MH130
Abstract
In Asia, SFTSV is a pathogen that can trigger a disease with a high fatality rate. Our research comprehensively utilized a large number of SFTSV gene sequences to conduct phylogenetic analysis, explore rearrangement and recombination events, as well as perform discrete phylogeographic analysis.
Materials
Programs used: IQ-TREE, CD - HIT, BioEdit, Tracer, Recombination Detection Program, BEAST
Sequence dataset
Sequence dataset
Download the required sequences from GenBank. The GenBank accession numbers and relevant information of all sequences are presented in Dataset 1.
Process all the data using CD - HIT to remove sequences with a similarity of over 99.9%, and thus obtain Dataset 2.
Phylogenetic analysis
Phylogenetic analysis
Phylogenetic analyses are separately performed on the three segments, employing the ClustalW method in BioEdit for sequence alignment.
Phylogenetic trees are constructed by maximum likelihood (ML) method using IQtree-2.3.1 comparison of the completed sequences.
Use the "ape" package in R 4.1.0 to conduct a comparative analysis of the topological structures of the phylogenetic trees of the L, M, and S segments, and classify the genotypes based on the results of the comparative analysis.
Recombination and reassortment analysis
Recombination and reassortment analysis
Compare the three sequences of the same virus strain based on the genotype data obtained from the "Phylogenetic analysis" section. If the genotypes inferred from the L, M, and S gene segments are different, it is considered a potential reassortant strain.
Use the Recombination Detection Program v4.101 (RDP4) software package to analyze the occurrence of recombination events within the SFTSV genome.
Discrete phylogeographic analysis
Discrete phylogeographic analysis
Use BEAST 2.4.4 for a series of evolutionary analyses of SFTSV, including the evolutionary rate of the gene, the analysis of the origin time, and the origin place and transmission route.
Select the S segment for the construction of the maximum clade credibility (MCC) tree and the geographical migration analysis. 
On the basis of Dataset 1, remove the sequences lacking collection location and collection time and the sequences with recombination events, and organize the remaining sequences into Dataset 3.
After the operation is completed, use Tracer (version 1.7.2) to open the log file to observe the effective sampling of main parameters.
After BEAST operation, the tree file is initially used together with TreeAnnotator (v1.10.4) to integrate all the information (including all branch lengths, branch times, posterior probabilities, etc.) of all sampled evolutionary trees into one evolutionary tree. Select the aging percentage as 10% to generate the MCC tree.
 Make a topological structure comparison between the MCC tree and the ML tree generated for the S segment using the "ape" package in R 4.1.0.