Next Generation Sequencing for Whole Genome Analysis and Surveillance of Influenza A Viruses

• Published in: Journal of clinical virology Vol. 79; pp. 44 - 50
• Main Authors: McGinnis, Jana, Laplante, Jennifer, Shudt, Matthew, George, Kirsten St
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2016
• Subjects: Allergy and Immunology; Antiviral resistance; Epidemiological Monitoring; Genome, Viral; High-Throughput Nucleotide Sequencing - methods; Humans; Infectious Disease; Influenza A virus - classification; Influenza A virus - genetics; Influenza A virus - isolation & purification; Influenza surveillance; Influenza, Human - epidemiology; Influenza, Human - virology; Molecular diagnosis; Molecular epidemiology; Molecular Epidemiology - methods; New York - epidemiology; Next-generation sequencing (NGS); Polymerase Chain Reaction - methods; Sequence Analysis, DNA - methods; Whole genome sequencing (WGS); molecular epidemiology; Next-generation Sequencing (NGS); Whole genome sequencing (WGS); antiviral resistance; influenza surveillance; molecular diagnosis; Molecular epidemiology; Molecular diagnosis; Influenza surveillance; Antiviral resistance; Next-generation sequencing (NGS)
• ISSN: 1386-6532; 1873-5967
• DOI: 10.1016/j.jcv.2016.03.005

Highlights • Influenza A whole genome PCR was optimized for the reliable production of next generation sequencing (NGS) template and the generation of whole genome sequence (WGS) on cultured isolates and primary specimens. • Optimized methods for extraction, amplification, sequencing and data analysis are described. • WGS was implemented to monitor for reassortment and for mutations associated with changes in antiviral susceptibility, antigenicity, virulence and tropism. • Initial applications included the comparison of mixed population analysis with NGS, dideoxy- and pyrosequencing, the comparison of sequences from paired primary and cultured samples, the analysis of sequence changes over several influenza seasons, and phylogenetic analysis of all genomic fragments. • The NGS/WGS method has been successfully implemented for the generation of detailed clinical data and for enhanced comprehensive surveillance: analyses identified variant and mixed populations affecting antigenicity and antiviral susceptibility in both primary specimens and cultured isolates.