Faculty Opinions recommendation of Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings.

2011 ◽  
Author(s):  
Jonathan Schapiro
Keyword(s):  
Drug Resistance ◽  
Low Cost ◽  
Resource Limited Settings ◽  
Genotyping Assay ◽  
Resource Limited ◽  
Hiv 1

scholarly journals Optimization of a Low Cost and Broadly Sensitive Genotyping Assay for HIV-1 Drug Resistance Surveillance and Monitoring in Resource-Limited Settings

PLoS ONE ◽  
2011 ◽  
Vol 6 (11) ◽  
pp. e28184 ◽  
Author(s):  
Zhiyong Zhou ◽  
Nick Wagar ◽  
Joshua R. DeVos ◽  
Erin Rottinghaus ◽  
Karidia Diallo ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Low Cost ◽  
Resource Limited Settings ◽  
Genotyping Assay ◽  
Resource Limited ◽  
Hiv 1

scholarly journals HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1125
Author(s):  
Sontaga Manyana ◽  
Lilishia Gounder ◽  
Melendhran Pillay ◽  
Justen Manasa ◽  
Kogieleum Naidoo ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Sanger Sequencing ◽  
Clinical Diagnostics ◽  
Treatment Programs ◽  
People Living With Hiv ◽  
Resource Limited Settings ◽  
Gold Standard Method ◽  
Sequencing Technologies ◽  
Resource Limited ◽  
Hiv 1

Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.

scholarly journals An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

10.3791/51242 ◽  
2014 ◽  
Author(s):  
Justen Manasa ◽  
Siva Danaviah ◽  
Sureshnee Pillay ◽  
Prevashinee Padayachee ◽  
Hloniphile Mthiyane ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Resource Limited Settings ◽  
Monitoring Method ◽  
Resistance Monitoring ◽  
Resource Limited ◽  
Hiv 1

Low cost HIV-1 quantitative RT-PCR assay in resource-limited settings: Improvement and implementation

2012 ◽  
Vol 185 (1) ◽  
pp. 118-123 ◽  
Author(s):  
Azzania Fibriani ◽  
Nadya Farah ◽  
Inri Kusumadewi ◽  
Suzan D. Pas ◽  
Reinout van Crevel ◽  
...  
Keyword(s):  
Low Cost ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Resource Limited Settings ◽  
Resource Limited ◽  
Hiv 1

scholarly journals Development, Validation and Clinical Evaluation of a Low Cost In-House HIV-1 Drug Resistance Genotyping Assay for Indian Patients

PLoS ONE ◽  
2014 ◽  
Vol 9 (8) ◽  
pp. e105790 ◽  
Author(s):  
Arpan Acharya ◽  
Salil Vaniawala ◽  
Parth Shah ◽  
Rabindra Nath Misra ◽  
Minal Wani ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Clinical Evaluation ◽  
Low Cost ◽  
Genotyping Assay ◽  
Indian Patients ◽  
Drug Resistance Genotyping ◽  
Hiv 1

scholarly journals Use of Dried Plasma Spots for HIV-1 Viral Load Determination and Drug Resistance Genotyping in Mexican Patients

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Juan Pablo Rodriguez-Auad ◽  
Othon Rojas-Montes ◽  
Angelica Maldonado-Rodriguez ◽  
Ma. Teresa Alvarez-Muñoz ◽  
Onofre Muñoz ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Viral Load ◽  
Attractive Alternative ◽  
Plasma Samples ◽  
Resistance Mutations ◽  
Resource Limited Settings ◽  
Middle Income ◽  
Subtype B ◽  
Resource Limited ◽  
Hiv 1

Monitoring antiretroviral therapy using measurements of viral load (VL) and the genotyping of resistance mutations is not routinely performed in low- to middle-income countries because of the high costs of the commercial assays that are used. The analysis of dried plasma spot (DPS) samples on filter paper may represent an alternative for resource-limited settings. Therefore, we evaluated the usefulness of analyzing DPS samples to determine VL and identify drug resistance mutations (DRM) in a group of HIV-1 patients. The VL was measured from 22 paired plasma and DPS samples. In these samples, the average VL was 4.7 log10copies/mL in liquid plasma and 4.1 log10copies/mL in DPS, with a correlation coefficient ofR= 0.83. A 1.1 kb fragment of HIVpolcould be amplified in 14/22 (63.6%) of the DPS samples and the same value was amplified in plasma samples. A collection of ten paired DPS and liquid plasma samples was evaluated for the presence of DRM; an excellent correlation was found in the identification of DRM between the paired samples. All HIV-1polsequences that were obtained corresponded to HIV subtype B. The analysis of DPS samples offers an attractive alternative for monitoring ARV therapy in resource-limited settings.

scholarly journals RETRACTED: A low-cost in-house HIV integrase strand transfer inhibitor drug resistance test for resource-limited settings [version 1; peer review: awaiting peer review]

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 306
Author(s):  
Vera M. Onwong'a ◽  
Rachael W. Gachogo ◽  
Moses M. Masika ◽  
Graeme B. Jacobs ◽  
Frank G. Onyambu
Keyword(s):  
Drug Resistance ◽  
Peer Review ◽  
Low Cost ◽  
Strand Transfer ◽  
Hiv Integrase ◽  
Resource Limited Settings ◽  
Resource Limited ◽  
Transfer Inhibitor ◽  
Inhibitor Drug ◽  
Integrase Strand Transfer Inhibitor

At the request of the authors, the article titled 'A low-cost in-house HIV integrase strand transfer inhibitor drug resistance test for resource-limited settings' ([version 1; peer review: awaiting peer review]. F1000Research 2021, 10:260, https://doi.org/10.12688/f1000research.28404.1) has been retracted from F1000Research. Since publication, it has come to the attention of the authors that the primers described in Table 1 were incorrect. As this article contains information which should not be publicly available the content of the article has been removed.  The authors apologise for this honest error, and intend to republish the article with the correct primer information. Unfortunately, Dr Graeme B. Jacobs has passed away since publication of version 1 of this article.

scholarly journals A low-cost in-house HIV integrase strand transfer inhibitor drug resistance test for resource-limited settings

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 260
Author(s):  
Vera M. Onwong'a ◽  
Rachael W. Gachogo ◽  
Moses M. Masika ◽  
Graeme B. Jacobs ◽  
Frank G. Onyambu
Keyword(s):  
Drug Resistance ◽  
Clinical Sample ◽  
Patient Treatment ◽  
Resistance Testing ◽  
People Living With Hiv ◽  
Strand Transfer ◽  
Hiv Integrase ◽  
Resource Limited Settings ◽  
Resource Limited ◽  
Hiv 1

Background: HIV-1 drug resistance testing (DRT) is vital for monitoring of individual patient treatment outcomes and for public health surveillance. Access to HIV-1 DRT is limited in resource-poor settings, including Kenya due to its costly nature. Recent inclusion of integrase strand transfer inhibitors (INSTIs) in first-line treatment for all people living with HIV-1 (PLHIV-1) underscores the need for an INSTI DRT. This study aims to validate a cost-effective in-house DRT method to detect HIV-1 Integrase resistance-associated mutations (RAMs) using HIV positive plasma derived samples Methods: Thirty-six plasma derived samples were used to assess the performance characteristics including accuracy, precision, reproducibility and amplification sensitivity of an in-house method in comparison with a reference assay. Cost estimation per test followed an incremental ingredient costing approach. Clinical application of the in-house test was evaluated on a plasma sample from a patient failing an INSTI-based regimen. Results: Comparison of the in-house and reference assay gave mean nucleotide and amino acid sequence identity of 99.49 %, CI [99.21- 99.77] and 99%, CI [98.58, 99.42] respectively. Complete concordance was observed by both assays in detection of the T97TA INSTI RAM. Precision and reproducibility assessment revealed mean nucleotide sequence identities of 100% and 99.14% respectively. The amplification sensitivity was 100% for samples with VL> 1000 copies/mL (n=8) and 50% for samples with VL<1000 copies/mL. Two major (G118R and E188K) and two accessory INSTI mutations (G149A and E157Q) were detected from the clinical sample of a patient failing an INSTI-based therapy. Cost analysis estimated the cost per test at $50.31. Conclusion: The developed HIV-Integrase assay met the validation acceptance criteria and demonstrates the ability to detect clinically relevant INSTI-resistance-associated mutations, highlighting its potential use as an alternative to commercial INSTI tests in resource-limited settings.

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