HIV-1 gag genotypic resistance testing using short-read and long-read next-generation sequencing technologies.

INTRODUCTION

Lenacapavir is a new antiretroviral agent that targets the HIV-1 capsid, and is currently indicated for the treatment of patients with multidrug-resistant infection. It was recently approved by the U.S. Food Drug and Administration for use in pre-exposure prophylaxis. A robust sequencing method to determine HIV-1 gag sequences and resistance-associated mutations (RAMs) in people living with HIV-1 (PLWH), both prior and during lenacapavir treatment, is essential.

METHODS AND

RESULTS

In this study, we compared short-read (DeepChek® gag HIV-1) and long-read (PacBio gag SMRT) next-generation sequencing approaches for detecting gag mutations from blood samples of 47 PLWH (24 plasma HIV-1 RNA and 23 cell HIV-1 DNA). We found that both methods exhibited robust performance for sequencing gag from plasma HIV-1 RNA. For cell HIV-1 DNA, low viral load appeared to be a limiting factor for sequencing success for both approaches. Focusing on key positions associated with lenacapavir resistance, we observed concordant interpretation in all but one sample, where the 107S RAM was detected by DeepChek® only. Overall nucleotide concordance between methods remained high (99.2% to 100%).

CONCLUSION

Both NGS methods proved effective for gag genotyping in clinical samples, supporting their use in monitoring resistance to capsid inhibitors, although minor differences in consensus sequences were observed.