Silent Mutations in HIV-1 Reverse Transcriptase in Subtype B HIV-1 containing D67N and K70R Drug Resistance Mutations Restore Viral Fitness and Alleviate Indel Formation — ASN Events
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Silent Mutations in HIV-1 Reverse Transcriptase in Subtype B HIV-1 containing D67N and K70R Drug Resistance Mutations Restore Viral Fitness and Alleviate Indel Formation (#83)

Sushama Telwatte 1 2 , Anna C Hearps 1 , Adam Johnson 1 , Catherine F Latham 1 , Katie Moore 1 , Paul Agius 1 , Mary Tachedjian 3 , Con Sonza , Nicolas Sluis-Cremer 4 , P. Richard Harrigan 5 , Gilda Tachedjian 1 2 6
  1. Burnet Institute, Melbourne, VIC, Australia
  2. Department of Microbiology, Monash University, Melbourne, VIC, Australia
  3. CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Victoria
  4. Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
  5. BC Centre for Excellence, Vancouver, British Columbia, Canada
  6. Department of Immunology and Microbiology, Melbourne University, Melbourne, VIC, Australia

Resistance to combined antiretroviral therapy (cART) in HIV-1 infected individuals is typically due to non-synonymous mutations that change the protein sequence; however, the selection of synonymous or ‘silent’ mutations in the HIV-1 genome with cART has been reported. These silent K65K and K66K mutations in the HIV-1 reverse transcriptase (RT) occur in over 35% of drug-experienced individuals and are highly associated with the thymidine analog mutations D67N and K70R, which confer decreased susceptibility to most HIV-1 RT inhibitor drugs.  However, the basis for the selection of these silent mutations under selective drug pressure is unknown. Using Illumina next-generation sequencing, we demonstrate that D67N/K70R substitutions in HIV-1 RT increase indel frequency by 100-fold at RT codons 65-67, consequently impairing viral fitness. Introduction of either K65K or K66K into HIV-1 containing D67N/K70R reversed the error-prone DNA synthesis at codons 65-67 in RT and improved viral replication fitness but did not impact RT inhibitor drug susceptibility. The fitness advantage conferred by K65K/K66K is likely due to their ability to alleviate decreased RT efficiency on homopolymeric stretches of nucleotides and reverse the introduction of indels due to the emergence of TAMs. These data provide new mechanistic insights into the role of silent mutations selected during cART and have broader implications for the relevance of silent mutations in the evolution and fitness of RNA viruses.

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