title: Evaluation of GS Junior and MiSeq next-generation sequencing technologies as an alternative to Trugene population sequencing in the clinical HIV laboratory.
abstract: Population HIV-1 sequencing is currently the method of choice for the identification and follow-up of HIV-1 antiretroviral drug resistance. It has limited sensitivity and results in a consensus sequence showing the most prevalent nucleotide per position. Moreover concomitant sequencing and interpretation of the results for several samples together is laborious and time consuming. In this study, the practical use of GS Junior and MiSeq bench-top next generation sequencing (NGS) platforms as an alternative to Trugene Sanger-based population sequencing in the clinical HIV laboratory was assessed. DeepChek(®)-HIV TherapyEdge software was used for processing all the protease and reverse transcriptase sequences and for resistance interpretation. Plasma samples from nine HIV-1 carriers, representing the major HIV-1 subtypes in Israel, were compared. The total number of amino acid substitutions identified in the nine samples by GS Junior (232 substitutions) and MiSeq (243 substitutions) was similar and higher than Trugene (181 substitutions), emphasizing the advantage of deep sequencing on population sequencing. More than 80% of the identified substitutions were identical between the GS Junior and MiSeq platforms, most of which (184 of 199) at similar frequency. Low abundance substitutions accounted for 20.9% of the MiSeq and 21.9% of the GS Junior output, the majority of which were not detected by Trugene. More drug resistance mutations were identified by both the NGS platforms, primarily, but not only, at low abundance. In conclusion, in combination with DeepChek, both GS Junior and MiSeq were found to be more sensitive than Trugene and adequate for HIV-1 resistance analysis in the clinical HIV laboratory.
authors.affiliation: National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel. Electronic address: dr.daniela.ram@gmail.com.
authors.forename: Daniela
authors.initials: D
authors.lastname: Ram
authors.affiliation: Bioinformatics Unit, The Nancy and Stephen Grand National Center for Personalized Medicine, Weizmann Institute, Rehovot, Israel. Electronic address: Dena.Leshkowitz@weizmann.ac.il.
authors.forename: Dena
authors.initials: D
authors.lastname: Leshkowitz
authors.affiliation: ABL TherapyEdge Spain SL, Barcelona, Spain. Electronic address: dimitri@therapyedge.com.
authors.forename: Dimitri
authors.initials: D
authors.lastname: Gonzalez
authors.affiliation: DYN LABS Ltd., Caesarea, Israel. Electronic address: Relly@dyn.co.il.
authors.forename: Relly
authors.initials: R
authors.lastname: Forer
authors.affiliation: Infectious Disease Unit, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Israel. Electronic address: Itsik.Levi@sheba.health.gov.il.
authors.forename: Itzchak
authors.initials: I
authors.lastname: Levy
authors.affiliation: Infectious Disease Unit, Meir Medical Center, Kfar Saba, Israel. Electronic address: michalch@clalit.org.il.
authors.forename: Michal
authors.initials: M
authors.lastname: Chowers
authors.affiliation: Autoimmune Disease Unit, Rambam Medical Center, Haifa, Israel. Electronic address: m_lorber@rambam.health.gov.il.
authors.forename: Margalit
authors.initials: M
authors.lastname: Lorber
authors.affiliation: National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel; Tel-Aviv University, Tel-Aviv, Israel. Electronic address: Musa.Hindiyeh@sheba.health.gov.il.
authors.forename: Musa
authors.initials: M
authors.lastname: Hindiyeh
authors.affiliation: National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel; Tel-Aviv University, Tel-Aviv, Israel. Electronic address: Ella.Mendelson@sheba.health.gov.il.
authors.forename: Ella
authors.initials: E
authors.lastname: Mendelson
authors.affiliation: National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel. Electronic address: orna.mor@sheba.health.gov.il.
authors.forename: Orna
authors.initials: O
authors.lastname: Mor
mesh_terms: D019943:Amino Acid Substitution; D019411:Clinical Laboratory Techniques / Q000379:methods*; D006678:HIV / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D015658:HIV Infections / Q000821:virology*; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007557:Israel; D008826:Microbial Sensitivity Tests / Q000379:methods*; D020125:Mutation, Missense; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D054303:HIV Reverse Transcriptase; D016333:HIV Protease
keywords: DeepChek(®)-HIV TherapyEdge; GS Junior; HIV-1 mutations; MiSeq; Next generation sequencing (NGS); Trugene