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Pooled nucleic acid testing strategy for monitoring HIV-1 treatment in resource limited settings.
J Clin Virol 2019; 117:56-60JC

Abstract

BACKGROUND

Virological monitoring (VM) and drug resistance (DR) analysis are crucial for effective HIV management. Due to the high cost of commercial assays, VM and DR analysis is not performed in resource-limited-settings.

OBJECTIVE

The objective of this study is to develop a pooling based algorithm for the combined identification of virologic treatment failure (VTF) by nucleic acid testing (NAT) and DR by sequencing - NAT+DR assay.

STUDY DESIGN

We enrolled 559 participants on first-line therapy and analyzed for VTF. The virologically suppressed participants were followed-up to see the VTF prevalence (>1000 copies/mL) and DR by the NAT+DR pooling. Each pool comprising 5 plasma samples were amplified by targeting reverse transcriptase gene, if found positive, the pool was deconvoluted and samples were individually tested for HIV RNA and DR. Assay characteristics of NAT+DR assay were calculated in comparison with commercial assay.

RESULTS

Of 559 participants, 67 had VTF at baseline and were excluded. Of the remaining 478 participants, 325 returned for follow-up and NAT+DR assay was performed for them. Of 65 pools tested, 13 pools were positive. On deconvolution 14 individuals were found to have VTF. Sensitivity, specificity, positive predictive value and negative predictive value was 100%, relative efficiency was 59% and 87% & 85% cost was saved for identifying VTF and combined identification of VTF and DR, respectively.

CONCLUSIONS

Pooled NAT+DR assay is likely a good strategy to drastically reduce the cost and sustainability of the VM and can thereby facilitate the scale-up of successful HIV treatment programs, and reduce unnecessary switching to second-line drugs in resource-limited-settings.

Authors+Show Affiliations

YR Gaitonde Centre for AIDS Research and Education, Chennai, India.YR Gaitonde Centre for AIDS Research and Education, Chennai, India.YR Gaitonde Centre for AIDS Research and Education, Chennai, India.YR Gaitonde Centre for AIDS Research and Education, Chennai, India.YR Gaitonde Centre for AIDS Research and Education, Chennai, India.YR Gaitonde Centre for AIDS Research and Education, Chennai, India.YR Gaitonde Centre for AIDS Research and Education, Chennai, India.YR Gaitonde Centre for AIDS Research and Education, Chennai, India.YR Gaitonde Centre for AIDS Research and Education, Chennai, India.YR Gaitonde Centre for AIDS Research and Education, Chennai, India; Johns Hopkins School of Medicine, Baltimore, MD, USA.Voluntary Health Services - Infectious Disease Medical Center, Chennai, India.University of California San Diego, CA, USA.YR Gaitonde Centre for AIDS Research and Education, Chennai, India. Electronic address: saravanan@yrgcare.org.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31212189

Citation

J, Boobalan, et al. "Pooled Nucleic Acid Testing Strategy for Monitoring HIV-1 Treatment in Resource Limited Settings." Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology, vol. 117, 2019, pp. 56-60.
J B, Tr D, S G, et al. Pooled nucleic acid testing strategy for monitoring HIV-1 treatment in resource limited settings. J Clin Virol. 2019;117:56-60.
J, B., Tr, D., S, G., E, E., A, P., D, C., ... S, S. (2019). Pooled nucleic acid testing strategy for monitoring HIV-1 treatment in resource limited settings. Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology, 117, pp. 56-60. doi:10.1016/j.jcv.2019.05.012.
J B, et al. Pooled Nucleic Acid Testing Strategy for Monitoring HIV-1 Treatment in Resource Limited Settings. J Clin Virol. 2019;117:56-60. PubMed PMID: 31212189.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Pooled nucleic acid testing strategy for monitoring HIV-1 treatment in resource limited settings. AU - J,Boobalan, AU - Tr,Dinesha, AU - S,Gomathi, AU - E,Elakkiya, AU - A,Pradeep, AU - D,Chitra, AU - Kg,Murugavel, AU - P,Balakrishnan, AU - S,Shantha, AU - Ss,Solomon, AU - N,Kumarasamy, AU - Dm,Smith, AU - S,Saravanan, Y1 - 2019/05/30/ PY - 2019/03/11/received PY - 2019/05/28/revised PY - 2019/05/29/accepted PY - 2019/6/19/pubmed PY - 2019/6/19/medline PY - 2019/6/19/entrez KW - Anti-retro viral treatment KW - Cost effective KW - Drug resistance assay KW - HIV KW - HIV monitoring KW - NAT+DR assay KW - Pooling PCR KW - Viral load SP - 56 EP - 60 JF - Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology JO - J. Clin. Virol. VL - 117 N2 - BACKGROUND: Virological monitoring (VM) and drug resistance (DR) analysis are crucial for effective HIV management. Due to the high cost of commercial assays, VM and DR analysis is not performed in resource-limited-settings. OBJECTIVE: The objective of this study is to develop a pooling based algorithm for the combined identification of virologic treatment failure (VTF) by nucleic acid testing (NAT) and DR by sequencing - NAT+DR assay. STUDY DESIGN: We enrolled 559 participants on first-line therapy and analyzed for VTF. The virologically suppressed participants were followed-up to see the VTF prevalence (>1000 copies/mL) and DR by the NAT+DR pooling. Each pool comprising 5 plasma samples were amplified by targeting reverse transcriptase gene, if found positive, the pool was deconvoluted and samples were individually tested for HIV RNA and DR. Assay characteristics of NAT+DR assay were calculated in comparison with commercial assay. RESULTS: Of 559 participants, 67 had VTF at baseline and were excluded. Of the remaining 478 participants, 325 returned for follow-up and NAT+DR assay was performed for them. Of 65 pools tested, 13 pools were positive. On deconvolution 14 individuals were found to have VTF. Sensitivity, specificity, positive predictive value and negative predictive value was 100%, relative efficiency was 59% and 87% & 85% cost was saved for identifying VTF and combined identification of VTF and DR, respectively. CONCLUSIONS: Pooled NAT+DR assay is likely a good strategy to drastically reduce the cost and sustainability of the VM and can thereby facilitate the scale-up of successful HIV treatment programs, and reduce unnecessary switching to second-line drugs in resource-limited-settings. SN - 1873-5967 UR - https://www.unboundmedicine.com/medline/citation/31212189/Pooled_nucleic_acid_testing_strategy_for_monitoring_HIV-1_treatment_in_resource_limited_settings L2 - https://linkinghub.elsevier.com/retrieve/pii/S1386-6532(19)30131-3 DB - PRIME DP - Unbound Medicine ER -