HIV-1 drug resistance assay using Ion Torrent Next Generation Sequencing and on-instrument end-to-end analysis software

MT Pyne, KE Simmon, MA Mallory… - Journal of Clinical …, 2022 - Am Soc Microbiol
ABSTRACT HIV-1 antiretroviral therapy management requires sequencing the protease,
reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing …

Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq

DM Dudley, AL Bailey, SH Mehta, AL Hughes, GD Kirk… - Retrovirology, 2014 - Springer
Background Viral resistance to antiretroviral therapy threatens our best methods to control
and prevent HIV infection. Current drug resistance genotyping methods are costly, optimized …

External quality assessment for next-generation sequencing-based HIV drug resistance testing: Unique requirements and challenges

ER Lee, F Gao, P Sandstrom, H Ji - Viruses, 2020 - mdpi.com
Over the past decade, there has been an increase in the adoption of next generation
sequencing (NGS) technologies for HIV drug resistance (HIVDR) testing. NGS far outweighs …

[PDF][PDF] State of the Antiretroviral Therapy in Human Immunodeficiency Virus Drug Resistance: Science and Technology Knowledge Gap.

CA Boucher, MR Bobkova, AM Geretti, CC Hung… - AIDS …, 2018 - researchgate.net
Resistance to antiretroviral therapy (ART) threatens the efficacy of human immunodeficiency
virus type 1 (HIV-1) treatment. We present a review of knowledge gaps in the science and …

Characterization of HIV-1 near full-length proviral genome quasispecies from patients with undetectable viral load undergoing first-line HAART therapy

BM Alves, JD Siqueira, MM Garrido, OM Botelho… - Viruses, 2017 - mdpi.com
Increased access to highly active antiretroviral therapy (HAART) by human
immunodeficiency virus postive (HIV+) individuals has become a reality worldwide. In Brazil …

Highly accurate structure-based prediction of HIV-1 coreceptor usage suggests intermolecular interactions driving tropism

CA Kieslich, P Tamamis, YA Guzman, M Onel… - PloS one, 2016 - journals.plos.org
HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral
glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 …

Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus

SG Aralaguppe, AB Siddik, A Manickam… - Journal of virological …, 2016 - Elsevier
Analysing the HIV-1 near full-length genome (HIV-NFLG) facilitates new understanding into
the diversity of virus population dynamics at individual or population level. In this study we …

Protease and gag diversity and drug resistance mutations among treatment-naive Mexican people living with HIV

S Climaco-Arvizu, V Flores-López… - BMC Infectious …, 2022 - Springer
Abstract Introduction In Mexico, HIV genotyping is performed in people living with HIV
(PLWH) failing their first-line antiretroviral (ARV) regimen; it is not routinely done for all …

[HTML][HTML] Next-generation sequencing and influenza virus: a short review of the published implementation attempts

R Ali, RM Blackburn, Z Kozlakidis - HAYATI Journal of Biosciences, 2016 - Elsevier
Influenza virus represents a major public health concern worldwide after recent pandemics.
To aid the understanding and characterization of the virus in ever-increasing sample …

Identification of minority resistance mutations in the HIV-1 integrase coding region using next generation sequencing

J Fonager, JT Larsson, C Hussing, FN Engsig… - Journal of Clinical …, 2015 - Elsevier
Background The current widely applied standard method to screen for HIV-1 genotypic
resistance is based on Sanger population sequencing (Sseq), which does not allow for the …