Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations

Sushama Telwatte, Anna Clare Hearps, Adam P Johnson, Catherine F Latham, Katie A Moore, Paul A Agius, Mary Tachedjian, Secondo Sonza, Nicolas Sluis-Cremer, P Richard Harrigan, Gilda Tachedjian

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Resistance to combined antiretroviral therapy (cART) in HIV-1-infected individuals is typically due to nonsynonymous 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 nucleoside and nucleotide RT inhibitors. However, the basis for selection of these silent mutations under selective drug pressure is unknown. Using Illumina next-generation sequencing, we demonstrate that the 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. These data provide new mechanistic insights into the role of silent mutations selected during antiretroviral therapy and have broader implications for the relevance of silent mutations in the evolution and fitness of RNA viruses.
Original languageEnglish
Pages (from-to)3256 - 3271
Number of pages16
JournalNucleic Acids Research
Volume43
Issue number6
DOIs
Publication statusPublished - 2015

Cite this

Telwatte, Sushama ; Hearps, Anna Clare ; Johnson, Adam P ; Latham, Catherine F ; Moore, Katie A ; Agius, Paul A ; Tachedjian, Mary ; Sonza, Secondo ; Sluis-Cremer, Nicolas ; Harrigan, P Richard ; Tachedjian, Gilda. / Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations. In: Nucleic Acids Research. 2015 ; Vol. 43, No. 6. pp. 3256 - 3271.
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title = "Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations",
abstract = "Resistance to combined antiretroviral therapy (cART) in HIV-1-infected individuals is typically due to nonsynonymous 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 nucleoside and nucleotide RT inhibitors. However, the basis for selection of these silent mutations under selective drug pressure is unknown. Using Illumina next-generation sequencing, we demonstrate that the 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. These data provide new mechanistic insights into the role of silent mutations selected during antiretroviral therapy and have broader implications for the relevance of silent mutations in the evolution and fitness of RNA viruses.",
author = "Sushama Telwatte and Hearps, {Anna Clare} and Johnson, {Adam P} and Latham, {Catherine F} and Moore, {Katie A} and Agius, {Paul A} and Mary Tachedjian and Secondo Sonza and Nicolas Sluis-Cremer and Harrigan, {P Richard} and Gilda Tachedjian",
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Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations. / Telwatte, Sushama; Hearps, Anna Clare; Johnson, Adam P; Latham, Catherine F; Moore, Katie A; Agius, Paul A; Tachedjian, Mary; Sonza, Secondo; Sluis-Cremer, Nicolas; Harrigan, P Richard; Tachedjian, Gilda.

In: Nucleic Acids Research, Vol. 43, No. 6, 2015, p. 3256 - 3271.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations

AU - Telwatte, Sushama

AU - Hearps, Anna Clare

AU - Johnson, Adam P

AU - Latham, Catherine F

AU - Moore, Katie A

AU - Agius, Paul A

AU - Tachedjian, Mary

AU - Sonza, Secondo

AU - Sluis-Cremer, Nicolas

AU - Harrigan, P Richard

AU - Tachedjian, Gilda

PY - 2015

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N2 - Resistance to combined antiretroviral therapy (cART) in HIV-1-infected individuals is typically due to nonsynonymous 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 nucleoside and nucleotide RT inhibitors. However, the basis for selection of these silent mutations under selective drug pressure is unknown. Using Illumina next-generation sequencing, we demonstrate that the 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. These data provide new mechanistic insights into the role of silent mutations selected during antiretroviral therapy and have broader implications for the relevance of silent mutations in the evolution and fitness of RNA viruses.

AB - Resistance to combined antiretroviral therapy (cART) in HIV-1-infected individuals is typically due to nonsynonymous 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 nucleoside and nucleotide RT inhibitors. However, the basis for selection of these silent mutations under selective drug pressure is unknown. Using Illumina next-generation sequencing, we demonstrate that the 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. These data provide new mechanistic insights into the role of silent mutations selected during antiretroviral therapy and have broader implications for the relevance of silent mutations in the evolution and fitness of RNA viruses.

UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381058/pdf/gkv128.pdf

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DO - 10.1093/nar/gkv128

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SN - 0305-1048

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