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Deep sequencing of HIV-1 RNA and DNA in newly diagnosed patients with baseline drug resistance showed no indications for hidden resistance and is biased by strong interference of hypermutation

Kenny Dauwe UGent, Delfien Staelens UGent, Leen Vancoillie UGent, Virginie Mortier UGent and Chris Verhofstede UGent (2016) JOURNAL OF CLINICAL MICROBIOLOGY. 54(6). p.1605-1615
abstract
Deep sequencing of plasma RNA or proviral DNA may be an interesting alternative to population sequencing for the detection of baseline transmitted HIV-1 drug resistance. Using a Roche 454 GS Junior HIV-1 prototype kit, we performed deep sequencing of the HIV-1 protease and reverse transcriptase genes on paired plasma and buffy coat samples from newly diagnosed HIV-1-positive individuals. Selection was based on the outcome of population sequencing and included 12 patients with either a revertant amino acid at codon 215 of the reverse transcriptase or a singleton resistance mutation, 4 patients with multiple resistance mutations, and 4 patients with wild-type virus. Deep sequencing of RNA and DNA detected 6 and 43 mutations, respectively, that were not identified by population sequencing. A subsequently performed hypermutation analysis, however, revealed hypermutation in 61.19% of 3,188 DNA reads with a resistance mutation. The removal of hypermutated reads dropped the number of additional mutations in DNA from 43 to 17. No hypermutation evidence was found in the RNA reads. Five of the 6 additional RNA mutations and all additional DNA mutations, after full exclusion of hypermutation bias, were observed in the 3 individuals with multiple resistance mutations detected by population sequencing. Despite focused selection of patients with T215 revertants or singleton mutations, deep sequencing failed to identify the resistant T215Y/F or M184V or any other resistance mutation, indicating that in most of these cases there is no hidden resistance and that the virus detected at diagnosis by population sequencing is the original infecting variant.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
LONG-TERM PERSISTENCE, REAL-TIME PCR, TREATMENT-NAIVE INDIVIDUALS, IMMUNODEFICIENCY-VIRUS TYPE-1, REVERSE-TRANSCRIPTASE, GENOTYPIC RESISTANCE, PRIMARY INFECTION, LOW-FREQUENCY, TRANSMISSION, MUTATIONS
journal title
JOURNAL OF CLINICAL MICROBIOLOGY
J. Clin. Microbiol.
volume
54
issue
6
pages
1605 - 1615
Web of Science type
Article
Web of Science id
000376529200030
JCR category
MICROBIOLOGY
JCR impact factor
3.712 (2016)
JCR rank
33/124 (2016)
JCR quartile
2 (2016)
ISSN
0095-1137
DOI
10.1128/JCM.00030-16
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
7275057
handle
http://hdl.handle.net/1854/LU-7275057
date created
2016-06-20 16:42:02
date last changed
2016-12-19 15:42:16
@article{7275057,
  abstract     = {Deep sequencing of plasma RNA or proviral DNA may be an interesting alternative to population sequencing for the detection of baseline transmitted HIV-1 drug resistance. Using a Roche 454 GS Junior HIV-1 prototype kit, we performed deep sequencing of the HIV-1 protease and reverse transcriptase genes on paired plasma and buffy coat samples from newly diagnosed HIV-1-positive individuals. Selection was based on the outcome of population sequencing and included 12 patients with either a revertant amino acid at codon 215 of the reverse transcriptase or a singleton resistance mutation, 4 patients with multiple resistance mutations, and 4 patients with wild-type virus. Deep sequencing of RNA and DNA detected 6 and 43 mutations, respectively, that were not identified by population sequencing. A subsequently performed hypermutation analysis, however, revealed hypermutation in 61.19\% of 3,188 DNA reads with a resistance mutation. The removal of hypermutated reads dropped the number of additional mutations in DNA from 43 to 17. No hypermutation evidence was found in the RNA reads. Five of the 6 additional RNA mutations and all additional DNA mutations, after full exclusion of hypermutation bias, were observed in the 3 individuals with multiple resistance mutations detected by population sequencing. Despite focused selection of patients with T215 revertants or singleton mutations, deep sequencing failed to identify the resistant T215Y/F or M184V or any other resistance mutation, indicating that in most of these cases there is no hidden resistance and that the virus detected at diagnosis by population sequencing is the original infecting variant.},
  author       = {Dauwe, Kenny and Staelens, Delfien and Vancoillie, Leen and Mortier, Virginie and Verhofstede, Chris},
  issn         = {0095-1137},
  journal      = {JOURNAL OF CLINICAL MICROBIOLOGY},
  keyword      = {LONG-TERM PERSISTENCE,REAL-TIME PCR,TREATMENT-NAIVE INDIVIDUALS,IMMUNODEFICIENCY-VIRUS TYPE-1,REVERSE-TRANSCRIPTASE,GENOTYPIC RESISTANCE,PRIMARY INFECTION,LOW-FREQUENCY,TRANSMISSION,MUTATIONS},
  language     = {eng},
  number       = {6},
  pages        = {1605--1615},
  title        = {Deep sequencing of HIV-1 RNA and DNA in newly diagnosed patients with baseline drug resistance showed no indications for hidden resistance and is biased by strong interference of hypermutation},
  url          = {http://dx.doi.org/10.1128/JCM.00030-16},
  volume       = {54},
  year         = {2016},
}

Chicago
Dauwe, Kenny, Delfien Staelens, Leen Vancoillie, Virginie Mortier, and Chris Verhofstede. 2016. “Deep Sequencing of HIV-1 RNA and DNA in Newly Diagnosed Patients with Baseline Drug Resistance Showed No Indications for Hidden Resistance and Is Biased by Strong Interference of Hypermutation.” Journal of Clinical Microbiology 54 (6): 1605–1615.
APA
Dauwe, K., Staelens, D., Vancoillie, L., Mortier, V., & Verhofstede, C. (2016). Deep sequencing of HIV-1 RNA and DNA in newly diagnosed patients with baseline drug resistance showed no indications for hidden resistance and is biased by strong interference of hypermutation. JOURNAL OF CLINICAL MICROBIOLOGY, 54(6), 1605–1615.
Vancouver
1.
Dauwe K, Staelens D, Vancoillie L, Mortier V, Verhofstede C. Deep sequencing of HIV-1 RNA and DNA in newly diagnosed patients with baseline drug resistance showed no indications for hidden resistance and is biased by strong interference of hypermutation. JOURNAL OF CLINICAL MICROBIOLOGY. 2016;54(6):1605–15.
MLA
Dauwe, Kenny, Delfien Staelens, Leen Vancoillie, et al. “Deep Sequencing of HIV-1 RNA and DNA in Newly Diagnosed Patients with Baseline Drug Resistance Showed No Indications for Hidden Resistance and Is Biased by Strong Interference of Hypermutation.” JOURNAL OF CLINICAL MICROBIOLOGY 54.6 (2016): 1605–1615. Print.