**3.2. Detection of low-frequency variants**

Low-frequency variants or minority quasispecies are the variants that occur with a frequency of <20–25% in a viral population [59]. Minority quasispecies refers to the memory genomes that were dominant at an earlier phase of quasispecies evolution and can play an important role in conferring drug resistance in viruses such as *Human Immunodeficiency Virus type-1* (HIV-1) and *Influenza virus*. Minority quasispecies of drug-resistant viruses can rapidly reemerge as major populations after the reintroduction of drug pressure. In case of HIV-1, presence of such low-frequency variants has been linked with early failure to the antiretroviral therapy [59, 60]. Emergence of highly pathogenic subtype of *Avian Influenza virus*es (HPAI) has also been explained on the basis of low-frequency variants. Ultra-deep sequencing was used to study the emergence of HPAI from that of less pathogenic (Low Pathogenic Avian Influenza (LPAI)) progenitor viruses [61].
