scholarly journals Applying Unique Molecular Identifiers in Next Generation Sequencing Reveals a Constrained Viral Quasispecies Evolution under Cross-Reactive Antibody Pressure Targeting Long Alpha Helix of Hemagglutinin

Viruses ◽  
2018 ◽  
Vol 10 (4) ◽  
pp. 148 ◽  
Author(s):  
Nastasja Hauck ◽  
Josiane Kirpach ◽  
Christina Kiefer ◽  
Sophie Farinelle ◽  
Sophie Maucourant ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Alpha Helix ◽  
Viral Quasispecies ◽  
Next Generation ◽  
Quasispecies Evolution ◽  
Generation Sequencing ◽  
Reactive Antibody

scholarly journals ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing

2014 ◽  
Vol 31 (6) ◽  
pp. 886-896 ◽  
Author(s):  
Duleepa Jayasundara ◽  
I. Saeed ◽  
Suhinthan Maheswararajah ◽  
B.C. Chang ◽  
S.-L. Tang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Viral Quasispecies ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing

2019 ◽  
Vol 21 (5) ◽  
pp. 1766-1775 ◽  
Author(s):  
Marco Cacciabue ◽  
Anabella Currá ◽  
Elisa Carrillo ◽  
Guido König ◽  
María Inés Gismondi
Keyword(s):  
Next Generation Sequencing ◽  
Rna Virus ◽  
Foot And Mouth Disease ◽  
Next Generation Sequencing Data ◽  
Complete Analysis ◽  
Viral Quasispecies ◽  
Next Generation ◽  
Sequencing Data ◽  
Viral Genomes ◽  
Generation Sequencing

Abstract Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workflow proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.

scholarly journals Next-generation sequencing and bioinformatic approaches to detect and analyze influenza virus in ferrets

2014 ◽  
Vol 8 (04) ◽  
pp. 498-509 ◽  
Author(s):  
Zhen Lin ◽  
Amber Farooqui ◽  
Guishuang Li ◽  
Gane KS Wong ◽  
Andrew L Mason ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Next Generation Sequencing ◽  
Viral Quasispecies ◽  
Next Generation ◽  
Sequencing Strategy ◽  
Bioinformatic Approaches ◽  
Next Generation Sequencing Ngs ◽  
Viral Sequences ◽  
Generation Sequencing

Introduction: Conventional methods used to detect and characterize influenza viruses in biological samples face multiple challenges due to the diversity of subtypes and high dissimilarity of emerging strains. Next-generation sequencing (NGS) is a powerful technique that can facilitate the detection and characterization of influenza, however, the sequencing strategy and the procedures of data analysis possess different aspects that require careful consideration. Methodology: The RNA from the lungs of ferrets infected with influenza A/California/07/2009 was analyzed by next-generation sequencing (NGS) without using specific PCR amplification of the viral sequences. Several bioinformatic approaches were used to resolve the viral genes and detect viral quasispecies. Results: The genomic sequences of influenza virus were characterized to a high level of detail when analyzing the short-reads with either the fast aligner Bowtie2, the general purpose aligner BLASTn or de novo assembly with Abyss. Moreover, when using distant viral sequences as reference, these methods were still able to resolve the viral sequences of a biological sample. Finally, direct sequencing of RNA samples did not provide sufficient coverage of the viral genome to study viral quasispecies, and, therefore, prior amplification of the viral segments by PCR would be required to perform this type of analysis. Conclusions: the introduction of NGS for virus research allows routine full characterization of viral isolates; however, careful design of the sequencing strategy and the procedures for data analysis are still of critical importance.

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