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Quantitation of HIV-1 RNA levels in plasma and CSF of asymptomatic HIV-1 infected patients from South India using a TaqMan real time PCR assay
Abstract Background Most of the quantitation assays for HIV-1 RNA used currently are designed and optimized for HIV-1 subtype B viruses and hence may not be suitable for India, where the predominant subtype is HIV-1 subtype C. Objectives Development and standardization of HIV-1 TaqMan real time PCR...
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| Published in: | Journal of clinical virology 2007-05, Vol.39 (1), p.9-15 |
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| creator | Kamat, Anupa Ravi, V Desai, Anita Satishchandra, P Satish, K.S Borodowsky, I Subbakrishna, D.K Kumar, Mahendra |
| description | Abstract Background Most of the quantitation assays for HIV-1 RNA used currently are designed and optimized for HIV-1 subtype B viruses and hence may not be suitable for India, where the predominant subtype is HIV-1 subtype C. Objectives Development and standardization of HIV-1 TaqMan real time PCR assay suitable for measuring plasma and CSF viral RNA levels in HIV subtype C infected individuals. Study design A TaqMan real time PCR was developed using primers and probes selected in the gag region for detection of Indian HIV-1 subtype C strain. Plasma ( n = 120) and CSF samples ( n = 46) obtained from HIV infected subjects were used to evaluate the sensitivity and specificity of the assay. A comparative evaluation was carried out with a commercially available quantitative HIV viral load assay (Roche Amplicor Version 1.5). Results The TaqMan assay was able to amplify all HIV-1 group M subtypes except subtype E. Viral loads could be estimated in all the plasma ( n = 120) and 40/46 CSF samples obtained from HIV positive subjects. Sensitivity of this assay was found to be 180 copies/ml. Correlation with the commercially available viral load assay was very good ( r = 0.885). Conclusions A TaqMan real time PCR was standardized for HIV-1 subtype C and it was more sensitive (180 copies/ml) than standard Amplicor monitor assay, Version 1.5 (400 copies/ml). |
| doi_str_mv | 10.1016/j.jcv.2006.12.026 |
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Objectives Development and standardization of HIV-1 TaqMan real time PCR assay suitable for measuring plasma and CSF viral RNA levels in HIV subtype C infected individuals. Study design A TaqMan real time PCR was developed using primers and probes selected in the gag region for detection of Indian HIV-1 subtype C strain. Plasma ( n = 120) and CSF samples ( n = 46) obtained from HIV infected subjects were used to evaluate the sensitivity and specificity of the assay. A comparative evaluation was carried out with a commercially available quantitative HIV viral load assay (Roche Amplicor Version 1.5). Results The TaqMan assay was able to amplify all HIV-1 group M subtypes except subtype E. Viral loads could be estimated in all the plasma ( n = 120) and 40/46 CSF samples obtained from HIV positive subjects. Sensitivity of this assay was found to be 180 copies/ml. Correlation with the commercially available viral load assay was very good ( r = 0.885). Conclusions A TaqMan real time PCR was standardized for HIV-1 subtype C and it was more sensitive (180 copies/ml) than standard Amplicor monitor assay, Version 1.5 (400 copies/ml).</description><identifier>ISSN: 1386-6532</identifier><identifier>EISSN: 1873-5967</identifier><identifier>DOI: 10.1016/j.jcv.2006.12.026</identifier><identifier>PMID: 17368087</identifier><language>eng</language><publisher>Amsterdam: Elsevier B.V</publisher><subject>Allergy and Immunology ; Base Sequence ; Biological and medical sciences ; DNA Primers ; DNA Probes ; Fundamental and applied biological sciences. Psychology ; Genes, gag ; HIV infection in South India ; HIV Infections - blood ; HIV Infections - cerebrospinal fluid ; HIV Infections - virology ; HIV-1 - genetics ; HIV-1 - isolation & purification ; HIV-1 TaqMan viral load assay ; Human immunodeficiency virus 1 ; Human viral diseases ; Humans ; India ; Infectious Disease ; Infectious diseases ; Medical sciences ; Microbiology ; Miscellaneous ; Molecular Sequence Data ; Plasma and CSF viral loads ; Polymerase Chain Reaction - methods ; Reproducibility of Results ; RNA, Viral - blood ; RNA, Viral - cerebrospinal fluid ; Sensitivity and Specificity ; Viral diseases ; Viral diseases of the lymphoid tissue and the blood. Aids ; Viral Load ; Virology</subject><ispartof>Journal of clinical virology, 2007-05, Vol.39 (1), p.9-15</ispartof><rights>2007</rights><rights>2007 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c467t-fa90bc016e3cb72c2acd30d69a742c927aab80f69331d5a03b92f4ae2635d6aa3</citedby><cites>FETCH-LOGICAL-c467t-fa90bc016e3cb72c2acd30d69a742c927aab80f69331d5a03b92f4ae2635d6aa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18735375$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17368087$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kamat, Anupa</creatorcontrib><creatorcontrib>Ravi, V</creatorcontrib><creatorcontrib>Desai, Anita</creatorcontrib><creatorcontrib>Satishchandra, P</creatorcontrib><creatorcontrib>Satish, K.S</creatorcontrib><creatorcontrib>Borodowsky, I</creatorcontrib><creatorcontrib>Subbakrishna, D.K</creatorcontrib><creatorcontrib>Kumar, Mahendra</creatorcontrib><title>Quantitation of HIV-1 RNA levels in plasma and CSF of asymptomatic HIV-1 infected patients from South India using a TaqMan real time PCR assay</title><title>Journal of clinical virology</title><addtitle>J Clin Virol</addtitle><description>Abstract Background Most of the quantitation assays for HIV-1 RNA used currently are designed and optimized for HIV-1 subtype B viruses and hence may not be suitable for India, where the predominant subtype is HIV-1 subtype C. Objectives Development and standardization of HIV-1 TaqMan real time PCR assay suitable for measuring plasma and CSF viral RNA levels in HIV subtype C infected individuals. Study design A TaqMan real time PCR was developed using primers and probes selected in the gag region for detection of Indian HIV-1 subtype C strain. Plasma ( n = 120) and CSF samples ( n = 46) obtained from HIV infected subjects were used to evaluate the sensitivity and specificity of the assay. A comparative evaluation was carried out with a commercially available quantitative HIV viral load assay (Roche Amplicor Version 1.5). Results The TaqMan assay was able to amplify all HIV-1 group M subtypes except subtype E. Viral loads could be estimated in all the plasma ( n = 120) and 40/46 CSF samples obtained from HIV positive subjects. Sensitivity of this assay was found to be 180 copies/ml. Correlation with the commercially available viral load assay was very good ( r = 0.885). Conclusions A TaqMan real time PCR was standardized for HIV-1 subtype C and it was more sensitive (180 copies/ml) than standard Amplicor monitor assay, Version 1.5 (400 copies/ml).</description><subject>Allergy and Immunology</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>DNA Primers</subject><subject>DNA Probes</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes, gag</subject><subject>HIV infection in South India</subject><subject>HIV Infections - blood</subject><subject>HIV Infections - cerebrospinal fluid</subject><subject>HIV Infections - virology</subject><subject>HIV-1 - genetics</subject><subject>HIV-1 - isolation & purification</subject><subject>HIV-1 TaqMan viral load assay</subject><subject>Human immunodeficiency virus 1</subject><subject>Human viral diseases</subject><subject>Humans</subject><subject>India</subject><subject>Infectious Disease</subject><subject>Infectious diseases</subject><subject>Medical sciences</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>Molecular Sequence Data</subject><subject>Plasma and CSF viral loads</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Reproducibility of Results</subject><subject>RNA, Viral - blood</subject><subject>RNA, Viral - cerebrospinal fluid</subject><subject>Sensitivity and Specificity</subject><subject>Viral diseases</subject><subject>Viral diseases of the lymphoid tissue and the blood. Aids</subject><subject>Viral Load</subject><subject>Virology</subject><issn>1386-6532</issn><issn>1873-5967</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><recordid>eNqFkstq3DAUhk1padK0D9BN0abZ2dHFlmwKhTA0zUB6y6TdimNZbuXakiPZA_MSfebIjCHQRbuSEN9_zkHfSZLXBGcEE37RZZ3aZxRjnhGaYcqfJKekFCwtKi6exjsrecoLRk-SFyF0GJOC5eJ5ckIE4yUuxWny59sMdjITTMZZ5Fp0vf2REnT7-RL1eq_7gIxFYw9hAAS2QZvd1UJBOAzj5IYYU2vE2FarSTdojI_aTgG13g1o5-bpF9raxgCag7E_EaA7uP8EFnkNPZrMoNHXzW0sGeDwMnnWQh_0q_U8S75ffbjbXKc3Xz5uN5c3qcq5mNIWKlyr-AWaqVpQRUE1DDe8ApFTVVEBUJe45RVjpCkAs7qibQ6aclY0HICdJefHuqN397MOkxxMULrvwWo3Bylwjssi5v8HkorzsqyKCJIjqLwLwetWjt4M4A-SYLnYkp2MtuRiSxIqo62YebMWn-tBN4-JVU8E3q4ABAV968EqEx65iBRMLM3fHbkoTO-N9jKo6EDpxvgoRTbO_HOM93-lVW-siQ1_64MOnZu9jTIkkSEG5G5Zq2WrsMAYM1axB-dBxiw</recordid><startdate>20070501</startdate><enddate>20070501</enddate><creator>Kamat, Anupa</creator><creator>Ravi, V</creator><creator>Desai, Anita</creator><creator>Satishchandra, P</creator><creator>Satish, K.S</creator><creator>Borodowsky, I</creator><creator>Subbakrishna, D.K</creator><creator>Kumar, Mahendra</creator><general>Elsevier B.V</general><general>Elsevier Science</general><scope>IQODW</scope><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>7T7</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>20070501</creationdate><title>Quantitation of HIV-1 RNA levels in plasma and CSF of asymptomatic HIV-1 infected patients from South India using a TaqMan real time PCR assay</title><author>Kamat, Anupa ; Ravi, V ; Desai, Anita ; Satishchandra, P ; Satish, K.S ; Borodowsky, I ; Subbakrishna, D.K ; Kumar, Mahendra</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c467t-fa90bc016e3cb72c2acd30d69a742c927aab80f69331d5a03b92f4ae2635d6aa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Allergy and Immunology</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>DNA Primers</topic><topic>DNA Probes</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes, gag</topic><topic>HIV infection in South India</topic><topic>HIV Infections - blood</topic><topic>HIV Infections - cerebrospinal fluid</topic><topic>HIV Infections - virology</topic><topic>HIV-1 - genetics</topic><topic>HIV-1 - isolation & purification</topic><topic>HIV-1 TaqMan viral load assay</topic><topic>Human immunodeficiency virus 1</topic><topic>Human viral diseases</topic><topic>Humans</topic><topic>India</topic><topic>Infectious Disease</topic><topic>Infectious diseases</topic><topic>Medical sciences</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>Molecular Sequence Data</topic><topic>Plasma and CSF viral loads</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Reproducibility of Results</topic><topic>RNA, Viral - blood</topic><topic>RNA, Viral - cerebrospinal fluid</topic><topic>Sensitivity and Specificity</topic><topic>Viral diseases</topic><topic>Viral diseases of the lymphoid tissue and the blood. Aids</topic><topic>Viral Load</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kamat, Anupa</creatorcontrib><creatorcontrib>Ravi, V</creatorcontrib><creatorcontrib>Desai, Anita</creatorcontrib><creatorcontrib>Satishchandra, P</creatorcontrib><creatorcontrib>Satish, K.S</creatorcontrib><creatorcontrib>Borodowsky, I</creatorcontrib><creatorcontrib>Subbakrishna, D.K</creatorcontrib><creatorcontrib>Kumar, Mahendra</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of clinical virology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kamat, Anupa</au><au>Ravi, V</au><au>Desai, Anita</au><au>Satishchandra, P</au><au>Satish, K.S</au><au>Borodowsky, I</au><au>Subbakrishna, D.K</au><au>Kumar, Mahendra</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantitation of HIV-1 RNA levels in plasma and CSF of asymptomatic HIV-1 infected patients from South India using a TaqMan real time PCR assay</atitle><jtitle>Journal of clinical virology</jtitle><addtitle>J Clin Virol</addtitle><date>2007-05-01</date><risdate>2007</risdate><volume>39</volume><issue>1</issue><spage>9</spage><epage>15</epage><pages>9-15</pages><issn>1386-6532</issn><eissn>1873-5967</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>Abstract Background Most of the quantitation assays for HIV-1 RNA used currently are designed and optimized for HIV-1 subtype B viruses and hence may not be suitable for India, where the predominant subtype is HIV-1 subtype C. Objectives Development and standardization of HIV-1 TaqMan real time PCR assay suitable for measuring plasma and CSF viral RNA levels in HIV subtype C infected individuals. Study design A TaqMan real time PCR was developed using primers and probes selected in the gag region for detection of Indian HIV-1 subtype C strain. Plasma ( n = 120) and CSF samples ( n = 46) obtained from HIV infected subjects were used to evaluate the sensitivity and specificity of the assay. A comparative evaluation was carried out with a commercially available quantitative HIV viral load assay (Roche Amplicor Version 1.5). Results The TaqMan assay was able to amplify all HIV-1 group M subtypes except subtype E. Viral loads could be estimated in all the plasma ( n = 120) and 40/46 CSF samples obtained from HIV positive subjects. Sensitivity of this assay was found to be 180 copies/ml. Correlation with the commercially available viral load assay was very good ( r = 0.885). Conclusions A TaqMan real time PCR was standardized for HIV-1 subtype C and it was more sensitive (180 copies/ml) than standard Amplicor monitor assay, Version 1.5 (400 copies/ml).</abstract><cop>Amsterdam</cop><pub>Elsevier B.V</pub><pmid>17368087</pmid><doi>10.1016/j.jcv.2006.12.026</doi><tpages>7</tpages></addata></record> |
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| subjects | Allergy and Immunology Base Sequence Biological and medical sciences DNA Primers DNA Probes Fundamental and applied biological sciences. Psychology Genes, gag HIV infection in South India HIV Infections - blood HIV Infections - cerebrospinal fluid HIV Infections - virology HIV-1 - genetics HIV-1 - isolation & purification HIV-1 TaqMan viral load assay Human immunodeficiency virus 1 Human viral diseases Humans India Infectious Disease Infectious diseases Medical sciences Microbiology Miscellaneous Molecular Sequence Data Plasma and CSF viral loads Polymerase Chain Reaction - methods Reproducibility of Results RNA, Viral - blood RNA, Viral - cerebrospinal fluid Sensitivity and Specificity Viral diseases Viral diseases of the lymphoid tissue and the blood. Aids Viral Load Virology |
| title | Quantitation of HIV-1 RNA levels in plasma and CSF of asymptomatic HIV-1 infected patients from South India using a TaqMan real time PCR assay |
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