title: Performance of LigAmp assay for sensitive detection of drug-resistant hepatitis B virus minor variants in comparison with standard nucleotide sequencing.
abstract: OBJECTIVE
  A virus population often exists as a complex mixture of genetic populations. Antiviral-resistant mutants could be circulating as minority variants in the mixed virus population that are not detected by standard sequencing methods. The role of minor drug-resistant variants and clinical outcome is slowly evolving and there is a need to employ sensitive methods for detection of minority variants that emerge as dominant species and subsequently affect the antiviral efficacy. This study was intended to develop a technique called the ligation amplification assay (LigAmp) to identify minor drug-resistant variants of hepatitis B virus (HBV).
  
  
  METHODS
  A LigAmp HBV assay was developed and clinical samples were tested from chronic hepatitis B subjects on antiviral treatment. Nucleotide sequencing of HBV reverse transcriptase (rt) region was performed and the results were compared with LigAmp assay. The performance of LigAmp assay was validated by clonal sequencing. Virological response was measured using HBV DNA levels and the results were correlated with antiviral-resistant mutations detected by sequencing and LigAmp assays.
  
  
  RESULTS
  A total of 80 reactions of LigAmp assay were performed for rtM204V and rtM204I (ATT) mutant detection. Samples were obtained from 40 chronic hepatitis B subjects. Among these subjects, rtM204V and rtM204I (ATT) mutations were identified by standard sequencing in 10 (25%) and 12 (30%) subjects, respectively. LigAmp detected both rtM204V and rtM204I (ATT) mutations in 13 (32.5%) subjects, rtM204I mutation in 12 (30%) subjects and rtM204V mutation in 1 (2.5%) subject, respectively. LigAmp detected primary resistant mutants in 69.4% of lamivudine non-responders while sequencing detected resistant mutations in only 55.6% subjects (p < 0.001).
  
  
  CONCLUSIONS
  This data shows significantly higher sensitivity of LigAmp for detection of minority rtM204V and rtM204I (ATT) mutations over standard sequencing. Therefore, LigAmp has potential clinical utility for appropriate monitoring and tailoring of HBV therapy.
authors.affiliation: Departments of Clinical Virology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
authors.forename: Ashrafali Mohamed
authors.initials: AM
authors.lastname: Ismail
authors.forename: Jaiprasath
authors.initials: J
authors.lastname: Sachithanandham
authors.forename: Chundmannil Eapen
authors.initials: CE
authors.lastname: Eapen
authors.forename: Rajesh
authors.initials: R
authors.lastname: Kannangai
authors.forename: Priya
authors.initials: P
authors.lastname: Abraham
mesh_terms: D000998:Antiviral Agents / Q000494:pharmacology; D004279:DNA, Viral / Q000235:genetics*; D024882:Drug Resistance, Viral / Q000235:genetics*; D006515:Hepatitis B virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D019694:Hepatitis B, Chronic / Q000175:diagnosis* / Q000188:drug therapy / Q000821:virology; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods; D009154:Mutation / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D000998:Antiviral Agents; D004279:DNA, Viral