Next-generation sequencing (metagenomic NGS) of CSF is sent for a patient with encephalitis whose standard tests are negative. A novel bunyavirus is identified. Which feature of NGS makes it superior to conventional PCR for this scenario?
- A It is unbiased and can detect any nucleic acid present including previously unknown pathogens ✓
- B It requires knowledge of the pathogen sequence in advance for primer design
- C It has faster turnaround time than PCR
- D It preferentially amplifies low-abundance bacterial sequences over human DNA
Correct answer: A. It is unbiased and can detect any nucleic acid present including previously unknown pathogens
Explanation
Metagenomic NGS sequences all nucleic acids in a sample without prior knowledge of the pathogen, making it uniquely capable of detecting novel, unexpected, or rare pathogens. This is its critical advantage over targeted PCR which requires known sequence for primer design. The main limitations are cost, lengthy bioinformatics processing (typically 24–72 hours), and the challenge of distinguishing pathogen from background human or commensal DNA. Bacteria are not preferentially amplified; if anything, human DNA dominates, requiring depletion strategies.
Reference: Ananthanarayan & Paniker's Textbook of Microbiology, 11th ed.
High-yield for: NEET PGINI-CETNExTFMGEUSMLEPLABMRCP
Written and medically reviewed by the StethoPrep medical team.