Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries
Increased trends of primary drug resistance mutations (DRMs) among treatment-naive HIV-1-infected patients in low- and middle-income countries (LMICs) and the non-availability of pre-antiretroviral therapy (ART) genotypic resistance testing (GRT) may severely affect future therapeutic outcomes. The...
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Veröffentlicht in: | Journal of antimicrobial chemotherapy 2014-12, Vol.69 (12), p.3349-3355 |
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creator | Ekici, Halime Rao, Shwetha D Sönnerborg, Anders Ramprasad, Vedam L Gupta, Ravi Neogi, Ujjwal |
description | Increased trends of primary drug resistance mutations (DRMs) among treatment-naive HIV-1-infected patients in low- and middle-income countries (LMICs) and the non-availability of pre-antiretroviral therapy (ART) genotypic resistance testing (GRT) may severely affect future therapeutic outcomes. The main objective of this study was therefore to develop a simplified, cost- and labour-efficient but high-throughput GRT protocol to be applied in the large-scale surveillance of DRMs in LMICs.
Ninety-six therapy-naive HIV-1-infected patients belonging to three cohorts were included: Indian patients followed at St John's Medical College Hospital, Bangalore, India (n = 49); East Africans (n = 21), who had migrated to Sweden; and Caucasians (n = 26) living in Sweden. GRT by population sequencing (GRT-PS) on individual plasma samples and GRT by next-generation sequencing (GRT-NGS) on equimolar multiplexed samples (n = 24) using Illumina MiSeq were performed.
The multiplexing procedure was shown to be technically feasible and gave high-quality reads independent of whether HIV-1 subtype C or B was analysed. GRT-NGS detected all the DRMs found by GRT-PS. Additional clinically important low-abundance ( |
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Ninety-six therapy-naive HIV-1-infected patients belonging to three cohorts were included: Indian patients followed at St John's Medical College Hospital, Bangalore, India (n = 49); East Africans (n = 21), who had migrated to Sweden; and Caucasians (n = 26) living in Sweden. GRT by population sequencing (GRT-PS) on individual plasma samples and GRT by next-generation sequencing (GRT-NGS) on equimolar multiplexed samples (n = 24) using Illumina MiSeq were performed.
The multiplexing procedure was shown to be technically feasible and gave high-quality reads independent of whether HIV-1 subtype C or B was analysed. GRT-NGS detected all the DRMs found by GRT-PS. Additional clinically important low-abundance (<20% of the viral population) major DRMs (e.g. K101E, K103N, Y181C and M184V) were detected by GRT-NGS but not by GRT-PS. The frequency of low-abundance DRMs was higher among East African compared with Indian and Caucasian individuals.
Our high-throughput next-generation sequencing with a multiplexed amplicon is a cost-efficient and promising approach for the large-scale surveillance of primary DRMs in LMICs where routine pre-ART GRT is not the standard of care. This strategy may be useful in optimizing future therapeutic regimens in those settings.</description><identifier>ISSN: 0305-7453</identifier><identifier>EISSN: 1460-2091</identifier><identifier>DOI: 10.1093/jac/dku278</identifier><identifier>PMID: 25085657</identifier><language>eng</language><publisher>England: Oxford Publishing Limited (England)</publisher><subject>Adult ; Cohort Studies ; Costs ; Developing Countries ; Drug resistance ; Drug Resistance, Viral ; Epidemiological Monitoring ; Female ; Genetics ; Genotyping Techniques - methods ; High-Throughput Nucleotide Sequencing - methods ; HIV ; HIV Infections - virology ; HIV-1 - genetics ; HIV-1 - isolation & purification ; Human immunodeficiency virus ; Human immunodeficiency virus 1 ; Humans ; India ; LDCs ; Male ; Middle Aged ; Middle income ; Plasma - virology</subject><ispartof>Journal of antimicrobial chemotherapy, 2014-12, Vol.69 (12), p.3349-3355</ispartof><rights>The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.</rights><rights>Copyright Oxford Publishing Limited(England) Dec 2014</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c422t-4d9e40df200400d8390afbda376cfc5c33d10e1f5cd1c8821f3bdba66fd82fc93</citedby><cites>FETCH-LOGICAL-c422t-4d9e40df200400d8390afbda376cfc5c33d10e1f5cd1c8821f3bdba66fd82fc93</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,777,781,882,27905,27906</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25085657$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:130244626$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Ekici, Halime</creatorcontrib><creatorcontrib>Rao, Shwetha D</creatorcontrib><creatorcontrib>Sönnerborg, Anders</creatorcontrib><creatorcontrib>Ramprasad, Vedam L</creatorcontrib><creatorcontrib>Gupta, Ravi</creatorcontrib><creatorcontrib>Neogi, Ujjwal</creatorcontrib><title>Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries</title><title>Journal of antimicrobial chemotherapy</title><addtitle>J Antimicrob Chemother</addtitle><description>Increased trends of primary drug resistance mutations (DRMs) among treatment-naive HIV-1-infected patients in low- and middle-income countries (LMICs) and the non-availability of pre-antiretroviral therapy (ART) genotypic resistance testing (GRT) may severely affect future therapeutic outcomes. The main objective of this study was therefore to develop a simplified, cost- and labour-efficient but high-throughput GRT protocol to be applied in the large-scale surveillance of DRMs in LMICs.
Ninety-six therapy-naive HIV-1-infected patients belonging to three cohorts were included: Indian patients followed at St John's Medical College Hospital, Bangalore, India (n = 49); East Africans (n = 21), who had migrated to Sweden; and Caucasians (n = 26) living in Sweden. GRT by population sequencing (GRT-PS) on individual plasma samples and GRT by next-generation sequencing (GRT-NGS) on equimolar multiplexed samples (n = 24) using Illumina MiSeq were performed.
The multiplexing procedure was shown to be technically feasible and gave high-quality reads independent of whether HIV-1 subtype C or B was analysed. GRT-NGS detected all the DRMs found by GRT-PS. Additional clinically important low-abundance (<20% of the viral population) major DRMs (e.g. K101E, K103N, Y181C and M184V) were detected by GRT-NGS but not by GRT-PS. The frequency of low-abundance DRMs was higher among East African compared with Indian and Caucasian individuals.
Our high-throughput next-generation sequencing with a multiplexed amplicon is a cost-efficient and promising approach for the large-scale surveillance of primary DRMs in LMICs where routine pre-ART GRT is not the standard of care. This strategy may be useful in optimizing future therapeutic regimens in those settings.</description><subject>Adult</subject><subject>Cohort Studies</subject><subject>Costs</subject><subject>Developing Countries</subject><subject>Drug resistance</subject><subject>Drug Resistance, Viral</subject><subject>Epidemiological Monitoring</subject><subject>Female</subject><subject>Genetics</subject><subject>Genotyping Techniques - methods</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>HIV</subject><subject>HIV Infections - virology</subject><subject>HIV-1 - genetics</subject><subject>HIV-1 - isolation & purification</subject><subject>Human immunodeficiency virus</subject><subject>Human immunodeficiency virus 1</subject><subject>Humans</subject><subject>India</subject><subject>LDCs</subject><subject>Male</subject><subject>Middle Aged</subject><subject>Middle income</subject><subject>Plasma - virology</subject><issn>0305-7453</issn><issn>1460-2091</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0s2OFCEQB3BiNO44evEBDIkXY4LLR9PdeNtM1N1kEy_qtcNAMcNsN7TQuPo4vqnszrgHL56Ayi8VqvJH6CWj7xhV4vygzbm9KbzrH6EVa1pKOFXsMVpRQSXpGinO0LOcD5TSVrb9U3TGJe1lK7sV-r2JeSHgnDcewoIvr74Rhm0qO5wg-7zoYADnkn6AH8f7R8k-7PBUxsXPI_wEi_d-tyfLPsWy289lwXqaR29iwBm-Fwim-vfY3xf14mPI2MVU-wD2AY_xlmAdLJ68tSMQH0ycAJtYwpI85OfoidNjhhenc42-fvzwZXNJrj9_utpcXBPTcL6QxipoqHWc0oZS2wtFtdtaLbrWOCONEJZRYE4ay0zfc-bE1m512zrbc2eUWCNy7JtvYS7bYU5-0unXELUfTqWbeoNBMtXXna7Rm6OfU6xT5mWYfDZwtySIJQ-so6zpVNOo_9OWSyEUV22lr_-hh1hSqINXJfqOCSV5VW-PyqSYcwL38FtGh7tMDDUTwzETFb86tSzbCewD_RsC8Qf6Gbb3</recordid><startdate>20141201</startdate><enddate>20141201</enddate><creator>Ekici, Halime</creator><creator>Rao, Shwetha D</creator><creator>Sönnerborg, Anders</creator><creator>Ramprasad, Vedam L</creator><creator>Gupta, Ravi</creator><creator>Neogi, Ujjwal</creator><general>Oxford Publishing Limited (England)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>7U7</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>NAPCQ</scope><scope>P64</scope><scope>7X8</scope><scope>ADTPV</scope><scope>AOWAS</scope></search><sort><creationdate>20141201</creationdate><title>Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries</title><author>Ekici, Halime ; 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The main objective of this study was therefore to develop a simplified, cost- and labour-efficient but high-throughput GRT protocol to be applied in the large-scale surveillance of DRMs in LMICs.
Ninety-six therapy-naive HIV-1-infected patients belonging to three cohorts were included: Indian patients followed at St John's Medical College Hospital, Bangalore, India (n = 49); East Africans (n = 21), who had migrated to Sweden; and Caucasians (n = 26) living in Sweden. GRT by population sequencing (GRT-PS) on individual plasma samples and GRT by next-generation sequencing (GRT-NGS) on equimolar multiplexed samples (n = 24) using Illumina MiSeq were performed.
The multiplexing procedure was shown to be technically feasible and gave high-quality reads independent of whether HIV-1 subtype C or B was analysed. GRT-NGS detected all the DRMs found by GRT-PS. Additional clinically important low-abundance (<20% of the viral population) major DRMs (e.g. K101E, K103N, Y181C and M184V) were detected by GRT-NGS but not by GRT-PS. The frequency of low-abundance DRMs was higher among East African compared with Indian and Caucasian individuals.
Our high-throughput next-generation sequencing with a multiplexed amplicon is a cost-efficient and promising approach for the large-scale surveillance of primary DRMs in LMICs where routine pre-ART GRT is not the standard of care. This strategy may be useful in optimizing future therapeutic regimens in those settings.</abstract><cop>England</cop><pub>Oxford Publishing Limited (England)</pub><pmid>25085657</pmid><doi>10.1093/jac/dku278</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Adult Cohort Studies Costs Developing Countries Drug resistance Drug Resistance, Viral Epidemiological Monitoring Female Genetics Genotyping Techniques - methods High-Throughput Nucleotide Sequencing - methods HIV HIV Infections - virology HIV-1 - genetics HIV-1 - isolation & purification Human immunodeficiency virus Human immunodeficiency virus 1 Humans India LDCs Male Middle Aged Middle income Plasma - virology |
title | Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries |
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