Next-generation sequencing (whole-genome sequencing) of influenza viruses from outbreak clusters compared with Sanger sequencing offers the primary advantage of:

• A Faster turnaround time (results within 2 hours)
• B Requiring less specimen volume and no RNA extraction
• C Detecting influenza without prior knowledge of the viral strain
• D Simultaneous detection of all mutations across the entire genome for transmission cluster analysis ✓

Explanation

Whole-genome sequencing (WGS) provides complete genomic data in a single run, enabling simultaneous detection of mutations in all gene segments (HA, NA, PB1, PB2, PA, NP, M, NS). This allows precise phylogenetic clustering to confirm transmission chains, detect antiviral resistance (NA mutations for oseltamivir), and identify reassortant strains — none of which are possible with Sanger sequencing of single target regions. WGS typically takes longer than point-of-care rapid tests; metagenomic sequencing can work without prior knowledge, but standard WGS requires amplicon panels.

Reference: Ananthanarayan & Paniker's Textbook of Microbiology, 11th ed.

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Written and medically reviewed by the StethoPrep medical team.