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Genomic profiling of Nipah virus using NGS driven RNA-Seq expression data.

Md Zakiul Hassan¹, Md Shakil Ahmed¹, Md Marufuzzaman Khan²

¹Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh.

|April 8, 2020

Summary

Nipah virus (NiV) gene expression analysis identified 2707 differentially expressed genes (DEGs). Top DEGs like EPST1 and MX1 may serve as biomarkers for NiV infection, aiding vaccine and drug development.

Keywords:

NGS RNA-Seq Nipah virus Phylogenetic gene tree Protein-protein interaction network limma

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Area of Science:

Virology
Genomics
Bioinformatics

Background:

Nipah virus (NiV) is a highly fatal paramyxovirus.
Understanding NiV's genetic mechanisms is crucial for control.

Purpose of the Study:

To identify differentially expressed genes (DEGs) in NiV infection.
To explore potential biomarkers and therapeutic targets for NiV.

Main Methods:

Next-generation sequencing (NGS) RNA-Seq data analysis.
Differential gene expression analysis using the R package limma.
Gene-gene interaction and protein-protein interaction network construction using Cytoscape, Ensembl, and STRING.

Main Results:

Identified 2707 DEGs (p-value <0.05) in NiV.
Top up-regulated DEGs include EPST1, MX1, IFIT3, RSAD2, OAS1, OASL, CMPK2.
Top down-regulated DEGs include SLFN13, SPAC977.17.
No significant gene association found between NiV and Tularemia or Ebola viruses.

Conclusions:

Identified key DEGs in NiV infection.
These DEGs show potential as biomarkers for NiV.
DEGs are candidates for developing NiV vaccines or drugs.