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Circulation of multiple subtypes (A, G and CRFs 02_AG) of human immunodeficiency virus type 1 (HIV-1) in selected districts of Punjab province, Pakistan. Arch Virol 2019; 164:3081-3087. [PMID: 31576459 DOI: 10.1007/s00705-019-04422-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/30/2019] [Indexed: 10/25/2022]
Abstract
Owing to consistent genetic mutation and recombination, various escape mutants and/or drug-resistant mutants of human immunodeficiency virus (HIV-1) are now emerging worldwide. Therefore, an understanding of the genetic characteristics of prevailing strains, particularly with regard to drug-resistance-associated substitutions, is essential for devising and implementing treatments and disease control interventions in endemic settings such as Pakistan. We processed a total of 130 plasma samples originating from HIV-treatment centers in selected districts of Punjab province, Pakistan. The samples were first screened using an HIV-1 Ag/Ab Combo test followed by amplification of the pol gene (1084 bp) from samples that were positive either for the antigen or for both the antigen and antibodies simultaneously. Screening revealed that a total of 45 samples were positive (34.62%; 95% CI: 26.99-43.13) for either antigen or both antigen and antibodies (n = 18, 40%; 95% CI: 27.02-54.55) or for antibodies alone (n = 27, 60%; 95% CI: 45.45-72.98). A largest number of positive samples was from the district of Lahore (n = 19/43, 44.18%; 95% CI: 30.44-58.9) followed by Faisalabad (n= 12/36, 33.33%; 95% CI: 20.21-49.66), Gujranwala (n = 05/23, 21.7%; 95% CI: 9.66-41.9) and Sargodha (n = 09/28, 32.1%; 95% CI: 17.93-50.66). The probability of occurrence of HIV infection was significantly associated with individuals having a history of injecting drug use (68.08%; OR = 11.15; 95% CI: 53.84-79.61, p = 0.0001). Phylogenetic analysis based on the pol gene showed that the sequences from this study clustered into three distinct clades representing recombinant form 02_AG (n = 14, 77.0%; 95% CI: 54.79-91.00), and subtypes A (n = 2, 11.1%; 95% CI: 3.1-32.8) and G (n = 2, 11.1%; 95% CI: 3.1-32.8). Although we screened 18 samples for drug-resistance-associated mutations, except for an accessory mutation (M46K) in the protease (PR) region in one subject, we found a lack of drug-resistance-associated substitutions in the PR region. On the other hand, we found two subjects (2/18) carrying a resistance-associated mutation (V106I) conferring a low level of resistance against non-nucleoside reverse transcriptase inhibitors. The present study shows that multiple subtypes of HIV-1 are present in the affected population. Continuous disease surveillance coupled with evaluation of drug resistance at higher resolution should be done in future studies.
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Sinha S, Gupta K, Khan NH, Mandal D, Kohli M, Das BK, Pandey RM. Higher Frequency of HIV-1 Drug Resistance and Increased Nucleoside Reverse Transcriptase Inhibitor Mutations among the HIV-1 Positive Antiretroviral Therapy-Naïve patients Coinfected With Mycobacterium tuberculosis Compared With Only HIV Infection in India. Infect Dis (Lond) 2018; 11:1178633718788870. [PMID: 30046244 PMCID: PMC6056791 DOI: 10.1177/1178633718788870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/24/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Emergence of human immunodeficiency virus (HIV) drug resistance mutations
prior to highly active antiretroviral therapy is a serious problem in
clinical management of HIV/AIDS. Risk factors for appearance of drug
resistance mutations are not known. We hypothesize that
Mycobacterium tuberculosis infection may contribute to
rapid emergence of such mutations in antiretroviral therapy–naïve
patients. Methods: A total of 115 patients were recruited in this study of which 75 were HIV+TB+
coinfected (group 1) and 40 were HIV+TB− (group 2). Blood samples from all
the patients were collected and CD4+ cell counts; HIV-1 plasma viral load
and sequencing of protease and two-third region of reverse transcriptase of
HIV-1 was performed and analyzed for drug resistance pattern. Results: For patients with HIV+TB+, 10.6% (8/75) had mutations to non-nucleoside
reverse transcriptase inhibitors (NNRTIs), 4% (3/75) to nucleoside reverse
transcriptase inhibitors, and only 2.6% (2/75) patients had mutations to
protease inhibitors. Interestingly, for group 2 (HIV+TB−), there were only
NNRTI mutations found among these patients, and only 3 patients (7.5%) had
these drug-resistant mutations. Clade typing and phylogenetic tree analysis
showed HIV-1 subtype C predominance in these patients. Conclusions: Our study showed that higher percentage of HIV drug resistance mutations was
found among HIV+TB+ individuals compared with tuberculosis-uninfected
patients. Tuberculosis coinfection may be a risk factor for emergence of
high frequency of drug resistance mutations. Studies with a larger sample
size will help to confirm these findings from the Indian population.
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Affiliation(s)
- Sanjeev Sinha
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Kartik Gupta
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Nawaid Hussain Khan
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Dibyakanti Mandal
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - Mikashmi Kohli
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - B K Das
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
| | - R M Pandey
- Department of Biostatistics, All India Institute of Medical Sciences (AIIMS), New Delhi, New Delhi, India
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Rosemary A, Chika O, Jonathan O, Godwin I, Georgina O, Azuka O, Zaidat M, Philippe C, Oliver E, Oche A, David O, Jay S, Ibrahim D, Mukhtar A, Joshua D, Chunfu Y, Elliot R, Beth C, Phyllis K, Emmanuel I. Genotyping performance evaluation of commercially available HIV-1 drug resistance test. PLoS One 2018; 13:e0198246. [PMID: 29953436 PMCID: PMC6023177 DOI: 10.1371/journal.pone.0198246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/16/2018] [Indexed: 11/18/2022] Open
Abstract
Background ATCC HIV-1 drug resistance test kit was designed to detect HIV-1 drug resistance (HIVDR) mutations in the protease and reverse transcriptase genes for all HIV-1 group M subtypes and circulating recombinant forms. The test has been validated for both plasma and dried blood spot specimen types with viral load (VL) of ≥1000 copies/ml. We performed an in-country assessment on the kit to determine the genotyping sensitivity and its accuracy in detecting HIVDR mutations using plasma samples stored under suboptimal conditions. Methods Among 572 samples with VL ≥1000 copies/ml that had been genotyped by ViroSeq assay, 183 were randomly selected, including 85 successful genotyped and 98 unsuccessful genotyped samples. They were tested with ATCC kits following the manufacturer’s instructions. Sequence identity and HIVDR patterns were analysed with Stanford University HIV Drug Resistance HIVdb program. Results Of the 183 samples, 127 (69.4%) were successfully genotyped by either method. While ViroSeq system genotyped 85/183 (46.5%) with median VL of 32,971 (IQR: 11,150–96,506) copies/ml, ATCC genotyped 115/183 (62.8%) samples with median VL of 23,068 (IQR: 7,397–86,086) copies/ml. Of the 98 unsuccessful genotyped samples with ViroSeq assay, 42 (42.9%) samples with lower median VL of 13,906 (IQR: 6,122–72,329) copies/ml were successfully genotyped using ATCC. Sequence identity analysis revealed that the sequences generated by both methods were >98% identical and yielded similar HIVDR profiles at individual patient level. Conclusion This study confirms that ATCC kit showed greater sensitivity in genotyping plasma samples stored in suboptimal conditions experiencing frequent and prolonged power outage. Thus, it is more sensitive particularly for subtypes A and A/G HIV-1 in resource-limited settings.
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Affiliation(s)
- Audu Rosemary
- Nigerian Institute of Medical Research, Lagos, Nigeria
- * E-mail:
| | | | | | | | | | | | - Musa Zaidat
- Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | - Ezechi Oliver
- Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Agbaji Oche
- Jos University Teaching Hospital, Jos, Nigeria
| | | | - Samuel Jay
- AIDS Prevention Initiative in Nigeria, Abuja, Nigeria
| | | | - Ahmed Mukhtar
- Centers for Disease Control and Prevention, Abuja, Nigeria
| | - DeVos Joshua
- Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Yang Chunfu
- Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Raizes Elliot
- Division of Global HIV & TB, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Chaplin Beth
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Kanki Phyllis
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
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Heger E, Kaiser R, Knops E, Neumann-Fraune M, Schuelter E, Pironti A, Lengauer T, Walter H, Sierra S. Results of the first international HIV-1 coreceptor proficiency panel test. J Clin Virol 2017. [PMID: 28633097 DOI: 10.1016/j.jcv.2017.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Quality Assurance (QA) programs are essential to evaluate performance in diagnostics laboratories. OBJECTIVES We present the results from the first QA for HIV-1 genotypic tropism testing, organized and coordinated by the Institute of Virology at the University of Cologne. STUDY DESIGN 12 cell culture-derived viral strains of different HIV-1 clades from the NIH AIDS Reagent Program were sent to the participants to be processed with their standard diagnostic methods Fasta files containing the V3 region sequence were centrally analyzed at the Institute of Virology, Cologne. All samples were sent in parallel for phenotypic testing. RESULTS 36 laboratories from 16 countries reported genotypic results. The sequence-generation efficacy was 95.1%, while the phenotypic assays ESTA® and PhenXR only achieved results for 58.3% of the samples. All four X4 samples were identified by 31/36 laboratories, two laboratories amplified 3/4×4 samples, and three detected 2/4×4 samples. There was high concordance among the genotypic and phenotypic results, although differences in FPR values were detected. Most deficiencies in sequence editing did not result in wrong classification of X4 viruses as R5, with the exception of sample NRZ05 by laboratory 38, but in an overestimation of CXCR4 use. CONCLUSIONS This demonstrates that genotypic tropism prediction is a safe procedure for clinical purposes. As we used homogeneous cell culture samples and all sequence fasta files were centrally analyzed, variations in FPR values can only be attributed to sample preparation, RT-PCR or sequence editing protocols.
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Affiliation(s)
- Eva Heger
- Institute of Virology, University of Cologne, 50935 Cologne, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935 Cologne, Germany.
| | - Elena Knops
- Institute of Virology, University of Cologne, 50935 Cologne, Germany
| | | | - Eugen Schuelter
- Institute of Virology, University of Cologne, 50935 Cologne, Germany
| | - Alejandro Pironti
- Computational Biology and Applied Algorithmics, MPI for Informatics, 66123 Saarbrücken, Germany
| | - Thomas Lengauer
- Computational Biology and Applied Algorithmics, MPI for Informatics, 66123 Saarbrücken, Germany
| | - Hauke Walter
- Institute for Virology, University of Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Saleta Sierra
- Institute of Virology, University of Cologne, 50935 Cologne, Germany
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Bissio E, Barbás MG, Kademián S, Bouzas MB, Salomón H, Cudolá A, Giuliano SF, Falistocco C. Prevalence of rilpivirine resistance in people starting antiretroviral treatment in Argentina. Antivir Ther 2017; 22:625-629. [PMID: 28234630 DOI: 10.3851/imp3147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Rilpivirine-based regimens are now preferred or alternative first-line regimens according to many HIV treatment guidelines. Recently, a surveillance study conducted in Argentina determined that prevalence of pretreatment resistance to first-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) was 10%. The aim of this study was to analyse the prevalence of resistance mutations to newer generation NNRTIs in the population starting ART in Argentina. METHODS We analysed the prevalence of resistance mutations to rilpivirine and etravirine (according to the IAS list), obtained through a nationally representative pretreatment HIV-drug resistance (PDR) surveillance study performed in Argentina in 2014-2015. Briefly, 25 ART-dispensing sites throughout the country were randomly chosen to enrol 330 adults starting ART. Samples were processed with Trugene (Siemens)® and analysed using the Stanford algorithm. RESULTS All 270 samples corresponding to participants with no prior exposure to antiretroviral drugs were included in this analysis. Median (IQR) age was 35 years (28-43); 66.7% were male; median (IQR) CD4+ T-cell count was 284 cells/mm3 (112-489). The prevalence of resistance to any antiretroviral was 16% (±5%) and prevalence of NNRTI RAMs was 13% (±4%). The prevalence of resistance to rilpivirine was 8% (±3%). Prevalence of resistance to etravirine was 4% (±3%). The most frequent mutations conferring resistance to rilpivirine were: E138A (n=6) and G190A (n=4). CONCLUSIONS This PDR surveillance study showed concerning levels of HIV drug resistance (HIVDR) in Argentina, not only for first-generation NNRTIs but also to rilpivirine. In our setting, performing resistance testing would be necessary before prescription of ART even if a second-generation NNRTI-based regimen was used as first-line therapy.
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Affiliation(s)
- Emiliano Bissio
- Fundación Centro de Estudios Infectológicos (FUNCEI), Buenos Aires, Argentina
| | | | | | - Maria B Bouzas
- Unidad de Virología, División Análisis Clínicos, Hospital de Infecciosas F. J. Muñiz, Buenos Aires, Argentina
| | - Horacio Salomón
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Silvina Fernández Giuliano
- Unidad de Virología, División Análisis Clínicos, Hospital de Infecciosas F. J. Muñiz, Buenos Aires, Argentina
| | - Carlos Falistocco
- Dirección de Sida, Ministerio de Salud de la Nación, Buenos Aires, Argentina
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Brumme CJ, Poon AFY. Promises and pitfalls of Illumina sequencing for HIV resistance genotyping. Virus Res 2016; 239:97-105. [PMID: 27993623 DOI: 10.1016/j.virusres.2016.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 12/13/2022]
Abstract
Genetic sequencing ("genotyping") plays a critical role in the modern clinical management of HIV infection. This virus evolves rapidly within patients because of its error-prone reverse transcriptase and short generation time. Consequently, HIV variants with mutations that confer resistance to one or more antiretroviral drugs can emerge during sub-optimal treatment. There are now multiple HIV drug resistance interpretation algorithms that take the region of the HIV genome encoding the major drug targets as inputs; expert use of these algorithms can significantly improve to clinical outcomes in HIV treatment. Next-generation sequencing has the potential to revolutionize HIV resistance genotyping by lowering the threshold that rare but clinically significant HIV variants can be detected reproducibly, and by conferring improved cost-effectiveness in high-throughput scenarios. In this review, we discuss the relative merits and challenges of deploying the Illumina MiSeq instrument for clinical HIV genotyping.
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Affiliation(s)
- Chanson J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada.
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Bissio E, Barbás MG, Bouzas MB, Cudolá A, Salomón H, Espínola L, Fernández Giuliano S, Kademián S, Mammana L, Ornani MLS, Ravasi G, Vila M, Zapiola I, Falistocco C. Pretreatment HIV-1 drug resistance in Argentina: results from a surveillance study performed according to WHO-proposed new methodology in 2014-15. J Antimicrob Chemother 2016; 72:504-510. [PMID: 27789684 DOI: 10.1093/jac/dkw445] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 09/15/2016] [Accepted: 09/20/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND In Argentina, current national guidelines recommend starting with NNRTI-based regimens. Recently, there have been some local reports regarding concerning levels of NNRTI-transmitted resistance, but surveillance has never been carried out at a national level. OBJECTIVES To determine the prevalence of HIV drug resistance in people starting ART in Argentina using a WHO-proposed methodology. METHODS This was a cross-sectional, nationally representative study. Twenty-five antiretroviral-dispensing sites throughout the country were randomly chosen to enrol at least 330 persons starting ART, to generate a point prevalence estimate of resistance-associated mutations (RAMs) with a 5% CI (for the total population and for those without antiretroviral exposure). All consecutive patients older than 18 years starting or restarting ART in the chosen clinics were eligible. Samples were processed with Trugene and analysed using the Stanford algorithm. RESULTS Between August 2014 and March 2015, we obtained 330 samples from people starting ART. The mean ± SD age was 35 ± 11 years, 63.4% were male, 16.6% had prior antiretroviral exposure and the median (IQR) CD4 count was 275 cells/mm3 (106-461). The prevalence of RAMs found was 14% (±4%) for the whole population (3% NRTI-RAMs; 11% NNRTI-RAMs and 2% PI-RAMs) and 13% (±4%) for those without prior antiretroviral exposure (3%, 10% and 2%, respectively). The most common mutation was K103N. CONCLUSIONS This surveillance study showed concerning levels of HIV drug resistance in Argentina, especially to NNRTIs. Due to this finding, Argentina's Ministry of Health guidelines will change, recommending performing a resistance test for everyone before starting ART. If this is taken up properly, it also might function as a continuing surveillance tool.
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Affiliation(s)
- E Bissio
- Fundación Centro de Estudios Infectológicos (FUNCEI), Ciudad de Buenos Aires, Argentina
| | - M G Barbás
- Laboratorio Central de Córdoba, Ciudad de Córdoba, Argentina
| | - M B Bouzas
- Hospital Muñiz, Ciudad de Buenos Aires, Argentina
| | - A Cudolá
- Laboratorio Central de Córdoba, Ciudad de Córdoba, Argentina
| | - H Salomón
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - L Espínola
- Dirección de Sida, Ministerio de Salud de la Nación, Ciudad de Buenos Aires, Argentina
| | | | - S Kademián
- Laboratorio Central de Córdoba, Ciudad de Córdoba, Argentina
| | - L Mammana
- Hospital Muñiz, Ciudad de Buenos Aires, Argentina
| | - M L Suárez Ornani
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - G Ravasi
- Pan American Health Organization, Washington, DC, USA
| | - M Vila
- Pan American Health Organization, Ciudad de Buenos Aires, Argentina
| | - I Zapiola
- Hospital Muñiz, Ciudad de Buenos Aires, Argentina
| | - C Falistocco
- Dirección de Sida, Ministerio de Salud de la Nación, Ciudad de Buenos Aires, Argentina
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McAllister G, Shepherd S, Templeton K, Aitken C, Gunson R. Long term stability of HBsAg, anti-HBc and anti-HCV in dried blood spot samples and eluates. J Clin Virol 2015; 71:10-7. [PMID: 26370308 DOI: 10.1016/j.jcv.2015.07.303] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/23/2015] [Accepted: 07/25/2015] [Indexed: 11/15/2022]
Abstract
BACKGROUND Dried blood spots (DBS) are a useful specimen collection tool in situations where venous access is problematic, however, detection of biomarkers from this specimen type is subject to variation depending on storage conditions and storage time. OBJECTIVES The objective of this study is to assess the detection of HBsAg, anti-HBc and anti-HCV from DBS after storage. STUDY DESIGN DBS specimens were stored at -70°C, -20°C, 4°C, 22 to 28°C and 37°C either with or without desiccant. Eluates were also prepared from DBS specimens and stored at -20°C and -70°C. DBS cards and eluates were tested for HBsAg, anti-HBc and anti-HCV at baseline on day 0 and thereafter at intervals of 14, 70 and 200 days. RESULTS Loss of detection of both HBsAg and anti-HBc was evident by the first time point (14 days) in all storage conditions except for the samples (DBS and eluates) stored at -20°C or -70°C. Both HBsAg and anti-HBc stored under these conditions showed minimal variation up to the final time point (200 days) of storage. The detection of anti-HCV did not differ between the 22 to 28°C, 4°C, -20°C and -70°C DBS nor the -20°C or the -70°C stored eluates over the 200 day time period. CONCLUSION We suggest that extended storage of DBS intended for downstream testing is best carried out by freezing either the DBS, or eluate, at -20°C or -70°C as soon as possible following collection for optimal detection of HBsAg, anti-HBc and anti-HCV.
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Affiliation(s)
- Georgina McAllister
- East of Scotland Specialist Virology Centre, Edinburgh Royal Infirmary, 51 Little France Crescent, Edinburgh, Scotland, UK.
| | - Samantha Shepherd
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, Scotland, UK
| | - Kate Templeton
- East of Scotland Specialist Virology Centre, Edinburgh Royal Infirmary, 51 Little France Crescent, Edinburgh, Scotland, UK
| | - Celia Aitken
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, Scotland, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, Scotland, UK
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Acharya A, Vaniawala S, Shah P, Misra RN, Wani M, Mukhopadhyaya PN. Development, validation and clinical evaluation of a low cost in-house HIV-1 drug resistance genotyping assay for Indian patients. PLoS One 2014; 9:e105790. [PMID: 25157501 PMCID: PMC4144911 DOI: 10.1371/journal.pone.0105790] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023] Open
Abstract
Human Immunodeficiency Virus-1 (HIV-1) drug resistance genotyping assay is a part of clinical management of HIV-1 positive individuals under treatment with highly active antiretroviral therapy (HAART). Routine monitoring of drug resistance mutations in resource limited settings like India is not possible due to high cost of commercial drug resistance assays. In this study we developed an in-house, cost effective HIV-1 drug resistance genotyping assay for Indian patients and validated it against the US-FDA-approved ViroSeq HIV-1 drug resistance testing system. A reference panel of 20 clinical samples was used to develop and validate the assay against ViroSeq HIV-1 drug resistance testing system which was subsequently used to genotype a clinical panel of 225 samples. The Stanford HIV database was used to identify drug resistant mutations. The analytical sensitivity of the assay was 1000 HIV-1 RNA copies/ml of plasma sample while precision and reproducibility was 99.68±0.16% and 99.76±0.18% respectively. One hundred and one drug resistant mutations were detected by the in-house assay compared to 104 by ViroSeq system in the reference panel. The assay had 91.55% success rate in genotyping the clinical panel samples and was able to detect drug resistant mutations related to nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse-transcriptase inhibitor (NNRTI) as well as protease inhibitor (PI) classes of antiretroviral drugs. It was found to be around 71.9% more cost effective compared to ViroSeq genotyping system. This evaluation of the assay on the clinical panel demonstrates its potential for monitoring clinical HIV-1 drug resistance mutations and population-based surveillance in resource limited settings like India.
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Affiliation(s)
- Arpan Acharya
- Department of Molecular Biology, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Salil Vaniawala
- Department of Molecular Diagnostics, SN Genelab, Surat, Gujarat, India
| | - Parth Shah
- Department of Molecular Diagnostics, Supratech Micropath Laboratory & Research Institute, Ahmedabad, Gujarat, India
| | - Rabindra Nath Misra
- Department of Microbiology, Padmashree Dr. D. Y. Patil Medical College & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Minal Wani
- Department of Molecular Biology, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Pratap N. Mukhopadhyaya
- Department of Microbiology, Interdisciplinary Science, Technology and Research Academy, AISC, Pune, Maharashtra, India
- * E-mail:
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Ji H, Li Y, Graham M, Liang BB, Pilon R, Tyson S, Peters G, Tyler S, Merks H, Bertagnolio S, Soto-Ramirez L, Sandstrom P, Brooks J. Next-generation sequencing of dried blood spot specimens: a novel approach to HIV drug-resistance surveillance. Antivir Ther 2011; 16:871-8. [DOI: 10.3851/imp1839] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Johannessen A, Holberg-Petersen M, Lövgaarden G, Naman E, Ormaasen V, Matee MI, Gundersen SG, Bruun JN. HIV type-1 drug resistance testing on dried blood spots is feasible and reliable in patients who fail antiretroviral therapy in rural Tanzania. Antivir Ther 2010; 15:1003-9. [DOI: 10.3851/imp1660] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Jordan MR, Bennett DE, Bertagnolio S, Gilks CF, Sutherland D. World Health Organization surveys to monitor HIV drug resistance prevention and associated factors in sentinel antiretroviral treatment sites. Antivir Ther 2008. [DOI: 10.1177/135965350801302s07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The World Health Organization (WHO) estimates that >2 million people will have started antiretroviral therapy (ART) by the end of 2006. As the development of some HIV drug resistance (HIVDR) is inevitable in populations taking ART, the emergence of HIVDR must be balanced against the benefits of providing ART, including improved health outcomes and decreased HIV/AIDS-associated morbidity and mortality. ART programmes should operate to minimize the emergence of HIVDR in populations receiving therapy and HIVDR itself must be monitored to ensure ongoing regimen efficacy. ART regimens in resource-limited settings are usually selected at the national level following a public health approach: generally only one first-line regimen with alternate regimen(s) incorporating within-class drug substitutions are available in the public sector. The WHO has developed a population-based HIVDR assessment and prevention strategy, which includes standardized HIVDR monitoring surveys in populations receiving first-line ART at sentinel sites. The WHO surveys monitor HIVDR prevention in sentinel sites by utilizing a standardized, minimum-resource prospective survey methodology to assess the success of adult and paediatric ART sites in preventing HIVDR emergence during the first year of ART. The surveys also identify associated factors that can be addressed at the level of the ART site or programme. WHO HIVDR monitoring surveys are designed to be integrated easily into a country's ongoing, routine HIV-related evaluation activities. Performed regularly at representative sites, the data generated will inform evidence-based decision making regarding national and global ART regimen selection and minimize the emergence of HIVDR at a population level.
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Bennett DE, Myatt M, Bertagnolio S, Sutherland D, Gilks CF. Recommendations for surveillance of transmitted HIV drug resistance in countries scaling up antiretroviral treatment. Antivir Ther 2008. [DOI: 10.1177/135965350801302s04] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background The World Health Organization (WHO) HIV drug resistance (HIVDR) threshold survey method was developed for surveillance of transmitted HIVDR in resource-limited countries. The method is being implemented with minimal resources as a routine public health activity to produce comparable results in multiple countries and areas within countries. Transmitted drug resistant HIV strains will be seen first in cities or health districts where antiretroviral treatment (ART) has been widely available for years. WHO recommends countries begin surveillance in these areas. Methods Each survey requires ≤47 specimens from individuals consecutively diagnosed with HIV to categorize resistance to each relevant drug class as <5%, 5–15% or >15%. Use of routinely collected information and remnant specimens is recommended to minimize costs. Site and individual eligibility criteria are designed to minimize inclusion of ARV-experienced individuals and individuals infected before ART was available. Results Surveys have been implemented in 21 countries. In this supplement, seven countries report results of <5% transmitted HIVDR in areas where ART has been available for the longest time period. The main challenges in implementation are acquiring sufficient numbers of eligible specimens and optimizing specimen handling. Conclusion The WHO HIVDR threshold survey method is feasible in resource-limited countries and produces information relevant to ART and drug resistance prevention planning.
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Affiliation(s)
| | - Mark Myatt
- Division of Epidemiology, Institute of Ophthalmology, University College London, London, UK
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Bennett DE, Bertagnolio S, Sutherland D, Gilks CF. The World Health Organization's global strategy for prevention and assessment of HIV drug resistance. Antivir Ther 2008. [DOI: 10.1177/135965350801302s03] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Antiretroviral treatment (ART) for HIV is being scaled up rapidly in resource-limited countries. Treatment options are simplified and standardized, generally with one potent first-line regimen and one potent alternate first-line regimen recommended. Widespread HIV drug resistance (HIVDR) was initially feared, but reports from resource-limited countries suggest that initial ART programmes are as effective as in resource-rich countries, which should limit HIV drug resistance if programme effectiveness continues during scale-up. ART interruptions must be minimized to maintain viral suppression on the first-line regimen for as long as possible. Lack of availability of appropriate second-line drugs is a concern, as is the additional accumulation of resistance mutations in the absence of viral load testing to determine failure. The World Health Organization (WHO) recommends a minimum-resource strategy for prevention and assessment of HIVDR in resource-limited countries. The WHO's Global Network HIVResNet provides standardized tools, training, technical assistance, laboratory quality assurance, analysis of results and recommendations for guidelines and public health action. National strategies focus on assessments to guide immediate public health action to improve ART programme effectiveness in minimizing HIVDR and to guide regimen selection. Globally, WHO HIVResNet collects and analyses data to support evidence-based international policies and guidelines. Financial support is provided by major international organizations and technical support from HIVDR experts worldwide. As of December 2007, 25 countries were planning or implementing the strategy; seven countries report results in this supplement.
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