Increasing prevalence of K65K and K66K in HIV-1 subtype B reverse transcriptase.
Synonymous substitutions K65K/K66K in HIV-1 reverse transcriptase alleviate fitness and fidelity defects in HIV-1 molecular clones harboring thymidine analogue mutations (TAMs); however, their potential for transmission and persistence is unknown. Here, we investigated the temporal appearance of K65K/K66K relative to TAMs in a HIV-1 cohort, their prevalence over time, and their impact on viral fitness in the context of patient-derived reverse transcriptase sequences.



Retrospective analyses of the temporal appearance and longitudinal prevalence of synonymous substitutions and drug resistance mutations were performed using the British Columbia Centre for Excellence in HIV/AIDS Drug Treatment Program (DTP) database. Plasma-derived HIV-1 from the DTP was used to generate infectious molecular clones. Growth competition assays were performed to determine viral fitness.



The prevalence of K65K/K66K in drug-naïve individuals tripled from 11% in 1997 to 37% in 2014 (P < 0.0001, n = 5221), with K66K mainly accounting for the increase. These mutations emerged in drug-treated individuals without TAMs in 14% of the cohort and conferred a fitness advantage in the context of patient-derived multidrug-resistant (MDR) virus in the absence of drug.



The appearance of K65K/K66K in drug-treated individuals was largely independent of TAMs, suggesting alternative factors are likely associated with their emergence. The increasing K65K/K66K prevalence to over a third of treatment-naïve individuals in the mostly subtype B DTP cohort and their ability to confer a fitness advantage to multidrug-resistant virus might explain the transmission and persistence of virus harbouring K65K/K66K in untreated individuals, and highlights their role in adaptive HIV-1 evolution.
aRetroviral Biology and Antivirals Laboratory, Centre for Biomedical Research, Burnet Institute, Melbourne bDepartment of Microbiology, Monash University, Clayton, Victoria, Australia cBritish Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada dDepartment of Infectious Diseases, Monash University eDepartment of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia fDepartment of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA gUniversity of British Columbia, British Columbia, Canada hSchool of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria, Australia.
Sushama
S
Telwatte
Chanson J
CJ
Brumme
Anna C
AC
Hearps
Catherine F
CF
Latham
Joshua A
JA
Hayward
Secondo
S
Sonza
Nicolas
N
Sluis-Cremer
P Richard
PR
Harrigan
Gilda
G
Tachedjian
D000220:Adaptation, Biological; D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D019943:Amino Acid Substitution; D001955:British Columbia / Q000453:epidemiology; D019143:Evolution, Molecular; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D054303:HIV Reverse Transcriptase / Q000235:genetics*; D015497:HIV-1 / Q000145:classification / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D008137:Longitudinal Studies; D008297:Male; D008875:Middle Aged; D050505:Mutant Proteins / Q000235:genetics*; D020125:Mutation, Missense; D015995:Prevalence; D012189:Retrospective Studies; D055815:Young Adult
D050505:Mutant Proteins; D054303:HIV Reverse Transcriptase