PMID- 32424187
OWN - NLM
STAT- MEDLINE
DCOM- 20201201
LR  - 20210518
IS  - 2045-2322 (Electronic)
IS  - 2045-2322 (Linking)
VI  - 10
IP  - 1
DP  - 2020 May 18
TI  - A single variant sequencing method for sensitive and quantitative detection of 
      HIV-1 minority variants.
PG  - 8185
LID - 10.1038/s41598-020-65085-y [doi]
LID - 8185
AB  - HIV drug resistance is a major threat to achieving long-term viral suppression in 
      HIV-positive individuals. Drug resistant HIV variants, including minority 
      variants, can compromise response to antiretroviral therapy. Many studies have 
      investigated the clinical relevance of drug resistant minority variants, but the 
      level at which minority variants become clinically relevant remains unclear. A 
      combination of Primer-ID and deep sequencing is a promising approach that may 
      quantify minority variants more accurately compared to standard deep sequencing. 
      However, most studies that used the Primer-ID method have analyzed clinical 
      samples directly. Thus, its sensitivity and quantitative accuracy have not been 
      adequately validated using known controls. Here, we constructed defined 
      proportions of artificial RNA and virus quasispecies and measured their relative 
      proportions using the Primer-ID based, quantitative single-variant sequencing 
      (qSVS) assay. Our results showed that minority variants present at 1% of 
      quasispecies were detected reproducibly with minimal variations between technical 
      replicates. In addition, the measured frequencies were comparable to the expected 
      frequencies. These data validate the accuracy and reproducibility of the qSVS 
      assay in quantifying authentic HIV minority variants, and support the use of this 
      approach to examine the impacts of minority HIV variants on virologic response 
      and clinical outcome.
FAU - Sidhu, Gurjit
AU  - Sidhu G
AD  - Division of Infectious Disease and Global Medicine, Department of Medicine, 
      University of Florida, Gainesville, FL, USA.
FAU - Schuster, Layla
AU  - Schuster L
AD  - Division of Infectious Disease and Global Medicine, Department of Medicine, 
      University of Florida, Gainesville, FL, USA.
AD  - Medosome Biosciences, Alachua, FL, USA.
FAU - Liu, Lin
AU  - Liu L
AD  - Division of Infectious Disease and Global Medicine, Department of Medicine, 
      University of Florida, Gainesville, FL, USA.
AD  - Department of Medicine, St. Luke's Hospital, Chesterfield, MO, USA.
FAU - Tamashiro, Ryan
AU  - Tamashiro R
AD  - Division of Infectious Disease and Global Medicine, Department of Medicine, 
      University of Florida, Gainesville, FL, USA.
FAU - Li, Eric
AU  - Li E
AD  - Division of Infectious Disease and Global Medicine, Department of Medicine, 
      University of Florida, Gainesville, FL, USA.
FAU - Langaee, Taimour
AU  - Langaee T
AD  - Department of Pharmacotherapy and Translational Research, Center for 
      Pharmacogenomics and Precision Medicine, College of Pharmacy, University of 
      Florida, Gainesville, FL, USA.
FAU - Wagner, Richard
AU  - Wagner R
AD  - Medosome Biosciences, Alachua, FL, USA.
FAU - Wang, Gary P
AU  - Wang GP
AD  - Division of Infectious Disease and Global Medicine, Department of Medicine, 
      University of Florida, Gainesville, FL, USA. gary.wang@medicine.ufl.edu.
AD  - Infectious Diseases Section, Medical Service, North Florida/South Georgia 
      Veterans Health System, Gainesville, FL, USA. gary.wang@medicine.ufl.edu.
LA  - eng
GR  - R41 AI122855/AI/NIAID NIH HHS/United States
GR  - R43 DK112540/DK/NIDDK NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20200518
PL  - England
TA  - Sci Rep
JT  - Scientific reports
JID - 101563288
SB  - IM
MH  - HIV-1/*genetics
MH  - *Limit of Detection
MH  - Plasmids/genetics
MH  - *Polymorphism, Single Nucleotide
PMC - PMC7234988
COIS- The authors declare no competing interests.
EDAT- 2020/05/20 06:00
MHDA- 2020/12/02 06:00
PMCR- 2020/05/18
CRDT- 2020/05/20 06:00
PHST- 2019/12/03 00:00 [received]
PHST- 2020/04/20 00:00 [accepted]
PHST- 2020/05/20 06:00 [entrez]
PHST- 2020/05/20 06:00 [pubmed]
PHST- 2020/12/02 06:00 [medline]
PHST- 2020/05/18 00:00 [pmc-release]
AID - 10.1038/s41598-020-65085-y [pii]
AID - 65085 [pii]
AID - 10.1038/s41598-020-65085-y [doi]
PST - epublish
SO  - Sci Rep. 2020 May 18;10(1):8185. doi: 10.1038/s41598-020-65085-y.