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Kingwara L, Karanja M, Ngugi C, Kangogo G, Bera K, Kimani M, Bowen N, Abuya D, Oramisi V, Mukui I. From Sequence Data to Patient Result: A Solution for HIV Drug Resistance Genotyping With Exatype, End to End Software for Pol-HIV-1 Sanger Based Sequence Analysis and Patient HIV Drug Resistance Result Generation. J Int Assoc Provid AIDS Care 2021; 19:2325958220962687. [PMID: 32990139 PMCID: PMC7536479 DOI: 10.1177/2325958220962687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Introduction: With the rapid scale-up of antiretroviral therapy (ART) to treat HIV
infection, there are ongoing concerns regarding probable emergence and
transmission of HIV drug resistance (HIVDR) mutations. This scale-up has to
lead to an increased need for routine HIVDR testing to inform the clinical
decision on a regimen switch. Although the majority of wet laboratory
processes are standardized, slow, labor-intensive data transfer and
subjective manual sequence interpretation steps are still required to
finalize and release patient results. We thus set out to validate the
applicability of a software package to generate HIVDR patient results from
raw sequence data independently. Methods: We assessed the performance characteristics of Hyrax Bioscience’s Exatype (a
sequence data to patient result, fully automated sequence analysis software,
which consolidates RECall, MEGA X and the Stanford HIV database) against the
standard method (RECall and Stanford database). Exatype is a web-based HIV
Drug resistance bioinformatic pipeline available at sanger.exatype.com. To validate the exatype, we used a test set of
135 remnant HIV viral load samples at the National HIV Reference Laboratory
(NHRL). Result: We analyzed, and successfully generated results of 126 sequences out of 135
specimens by both Standard and Exatype software. Result production using
Exatype required minimal hands-on time in comparison to the Standard (6
computation-hours using the standard method versus 1.5 Exatype
computation-hours). Concordance between the 2 systems was 99.8% for 311,227
bases compared. 99.7% of the 0.2% discordant bases, were attributed to
nucleotide mixtures as a result of the sequence editing in Recall. Both
methods identified similar (99.1%) critical antiretroviral
resistance-associated mutations resulting in a 99.2% concordance of
resistance susceptibility interpretations. The Base-calling comparison
between the 2 methods had Cohen’s kappa (0.97 to 0.99), implying an almost
perfect agreement with minimal base calling variation. On a predefined
dataset, RECall editing displayed the highest probability to score mixtures
accurately 1 vs. 0.71 and the lowest chance to inaccurately assign mixtures
to pure nucleotides (0.002–0.0008). This advantage is attributable to the
manual sequence editing in RECall. Conclusion: The reduction in hands-on time needed is a benefit when using the Exatype HIV
DR sequence analysis platform and result generation tool. There is a minimal
difference in base calling between Exatype and standard methods. Although
the discrepancy has minimal impact on drug resistance interpretation,
allowance of sequence editing in Exatype as RECall can significantly improve
its performance.
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Affiliation(s)
- Leonard Kingwara
- National Public Health Laboratory (NPHL), Nairobi, Kenya.,National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Muthoni Karanja
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Catherine Ngugi
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Geoffrey Kangogo
- National Public Health Laboratory (NPHL), Nairobi, Kenya.,National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Kipkerich Bera
- National Public Health Laboratory (NPHL), Nairobi, Kenya
| | - Maureen Kimani
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Nancy Bowen
- National Public Health Laboratory (NPHL), Nairobi, Kenya
| | - Dorcus Abuya
- National Public Health Laboratory (NPHL), Nairobi, Kenya.,National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Violet Oramisi
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Irene Mukui
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
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Shade SB, Marseille E, Kirby V, Chakravarty D, Steward WT, Koester KK, Cajina A, Myers JJ. Health information technology interventions and engagement in HIV care and achievement of viral suppression in publicly funded settings in the US: A cost-effectiveness analysis. PLoS Med 2021; 18:e1003389. [PMID: 33826617 PMCID: PMC8059802 DOI: 10.1371/journal.pmed.1003389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 04/21/2021] [Accepted: 03/25/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The US National HIV/AIDS Strategy (NHAS) emphasizes the use of technology to facilitate coordination of comprehensive care for people with HIV. We examined cost-effectiveness from the health system perspective of 6 health information technology (HIT) interventions implemented during 2008 to 2012 in a Ryan White HIV/AIDS Program (RWHAP) Special Projects of National Significance (SPNS) Program demonstration project. METHODS/FINDINGS HIT interventions were implemented at 6 sites: Bronx, New York; Durham, North Carolina; Long Beach, California; New Orleans, Louisiana; New York, New York (2 sites); and Paterson, New Jersey. These interventions included: (1) use of HIV surveillance data to identify out-of-care individuals; (2) extension of access to electronic health records (EHRs) to support service providers; (3) use of electronic laboratory ordering and prescribing; and (4) development of a patient portal. We employed standard microcosting techniques to estimate costs (in 2018 US dollars) associated with intervention implementation. Data from a sample of electronic patient records from each demonstration site were analyzed to compare prescription of antiretroviral therapy (ART), CD4 cell counts, and suppression of viral load, before and after implementation of interventions. Markov models were used to estimate additional healthcare costs and quality-adjusted life-years saved as a result of each intervention. Overall, demonstration site interventions cost $3,913,313 (range = $287,682 to $998,201) among 3,110 individuals (range = 258 to 1,181) over 3 years. Changes in the proportion of patients prescribed ART ranged from a decrease from 87.0% to 72.7% at Site 4 to an increase from 74.6% to 94.2% at Site 6; changes in the proportion of patients with 0 to 200 CD4 cells/mm3 ranged from a decrease from 20.2% to 11.0% in Site 6 to an increase from 16.7% to 30.2% in Site 2; and changes in the proportion of patients with undetectable viral load ranged from a decrease from 84.6% to 46.0% in Site 1 to an increase from 67.0% to 69.9% in Site 5. Four of the 6 interventions-including use of HIV surveillance data to identify out-of-care individuals, use of electronic laboratory ordering and prescribing, and development of a patient portal-were not only cost-effective but also cost saving ($6.87 to $14.91 saved per dollar invested). In contrast, the 2 interventions that extended access to EHRs to support service providers were not effective and, therefore, not cost-effective. Most interventions remained either cost-saving or not cost-effective under all sensitivity analysis scenarios. The intervention that used HIV surveillance data to identify out-of-care individuals was no longer cost-saving when the effect of HIV on an individual's health status was reduced and when the natural progression of HIV was increased. The results of this study are limited in that we did not have contemporaneous controls for each intervention; thus, we are only able to assess sites against themselves at baseline and not against standard of care during the same time period. CONCLUSIONS These results provide additional support for the use of HIT as a tool to enhance rapid and effective treatment of HIV to achieve sustained viral suppression. HIT has the potential to increase utilization of services, improve health outcomes, and reduce subsequent transmission of HIV.
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Affiliation(s)
- Starley B. Shade
- Institute for Global Health Sciences, Department of Epidemiology and Biostatistics, University of California, San Francisco, California, United States of America
- Center for AIDS Prevention Studies, University of California, San Francisco, California, United States of America
- * E-mail:
| | | | - Valerie Kirby
- Center for AIDS Prevention Studies, University of California, San Francisco, California, United States of America
| | - Deepalika Chakravarty
- Center for AIDS Prevention Studies, University of California, San Francisco, California, United States of America
| | - Wayne T. Steward
- Center for AIDS Prevention Studies, University of California, San Francisco, California, United States of America
| | - Kimberly K. Koester
- Center for AIDS Prevention Studies, University of California, San Francisco, California, United States of America
| | - Adan Cajina
- Demonstration and Evaluation Branch, HIV/AIDS Bureau, Health Resources and Services Administration, Rockville, Maryland, United States of America
| | - Janet J. Myers
- Center for AIDS Prevention Studies, University of California, San Francisco, California, United States of America
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3
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Rautenberg TA, George G, Bwana MB, Moosa MS, Pillay S, McCluskey SM, Aturinda I, Ard K, Muyindike W, Moodley P, Brijkumar J, Johnson BA, Gandhi RT, Sunpath H, Marconi VC, Siedner MJ. Comparative analyses of published cost effectiveness models highlight critical considerations which are useful to inform development of new models. J Med Econ 2020; 23:221-227. [PMID: 31835974 PMCID: PMC7105898 DOI: 10.1080/13696998.2019.1705314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Background: Comparative analyses of published cost effectiveness models provide useful insights into critical issues to inform the development of new cost effectiveness models in the same disease area.Objective: The purpose of this study was to describe a comparative analysis of cost-effectiveness models and highlight the importance of such work in informing development of new models. This research uses genotypic antiretroviral resistance testing after first line treatment failure for Human Immunodeficiency Virus (HIV) as an example.Method: A literature search was performed, and published cost effectiveness models were selected according to predetermined eligibility criteria. A comprehensive comparative analysis was undertaken for all aspects of the models.Results: Five published models were compared, and several critical issues were identified for consideration when developing a new model. These include the comparator, time horizon and scope of the model. In addition, the composite effect of drug resistance prevalence, antiretroviral therapy efficacy, test performance and the proportion of patients switching to second-line ART potentially have a measurable effect on model results. When considering CD4 count and viral load, dichotomizing patients according to higher cost and lower quality of life (AIDS) versus lower cost and higher quality of life (non-AIDS) status will potentially capture differences between resistance testing and other strategies, which could be confirmed by cross-validation/convergent validation. A quality adjusted life year is an essential outcome which should be explicitly explored in probabilistic sensitivity analysis, where possible.Conclusions: Using an example of GART for HIV, this study demonstrates comparative analysis of previously published cost effectiveness models yields critical information which can be used to inform the structure and specifications of new models.
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Affiliation(s)
- T. A. Rautenberg
- Division of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Applied Health Economics, Griffith University, Nathan, Australia
| | - G. George
- Division of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - M. B. Bwana
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - M. S. Moosa
- Division of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - S. Pillay
- Division of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - S. M. McCluskey
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - I. Aturinda
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - K. Ard
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - W. Muyindike
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - P. Moodley
- Division of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - J. Brijkumar
- Division of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - B. A. Johnson
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
| | - R. T. Gandhi
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - H. Sunpath
- Division of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - V. C. Marconi
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - M. J. Siedner
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
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4
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Abstract
Approximately 20% of people with HIV in the United States prescribed antiretroviral therapy are not virally suppressed. Thus, optimal management of virologic failure has a critical role in the ability to improve viral suppression rates to improve long-term health outcomes for those infected and to achieve epidemic control. This article discusses the causes of virologic failure, the use of resistance testing to guide management after failure, interpretation and relevance of HIV drug resistance patterns, considerations for selection of second-line and salvage therapies, and management of virologic failure in special populations.
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Affiliation(s)
- Suzanne M McCluskey
- Division of Infectious Diseases, Harvard Medical School, Massachusetts General Hospital, 55 Fruit Street, GRJ5, Boston, MA 02114, USA.
| | - Mark J Siedner
- Division of Infectious Diseases, Harvard Medical School, Massachusetts General Hospital, 55 Fruit Street, GRJ5, Boston, MA 02114, USA
| | - Vincent C Marconi
- Division of Infectious Diseases, Department of Global Health, Emory University School of Medicine, Rollins School of Public Health, Health Sciences Research Building, 1760 Haygood Dr NE, Room W325, Atlanta, GA 30322, USA
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5
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Li H, Chang S, Han Y, Zhuang D, Li L, Liu Y, Liu S, Bao Z, Zhang W, Song H, Li T, Li J. The prevalence of drug resistance among treatment-naïve HIV-1-infected individuals in China during pre- and post- 2004. BMC Infect Dis 2016; 16:605. [PMID: 27782811 PMCID: PMC5080753 DOI: 10.1186/s12879-016-1928-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 10/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The widespread use of antiretroviral therapies has led to considerable concerns about the prevalence of drug-resistant, as transmission of drug-resistant (TDR) strains poses a challenge for the control of the HIV-1 epidemic. METHODS We conducted an epidemiological study enrolling treatment-naïve HIV-1-positive subjects at the Peking Union Medical College Hospital since 1991. Drug resistance was determined by submitting the sequences to the Stanford University Network HIV-1 database. RESULTS Of 521 participants, 478 samples were amplified and sequenced successfully. HIV Transmitted drug resistance prevalence in China was determined to be 6.7 %. We did not find significant differences in the TDR rate by demographic characteristics. No significant time trend in the prevalence of overall TDR was observed (p > 0.05). CONCLUSIONS We identified an intermediate prevalence of transmitted drug resistance (TDR), exhibiting a stable time trend. These findings enhance our understanding of HIV-1 drug resistance prevalence and time trend, and provide some guidelines for the comprehensive public health strategy of TDR prevention.
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Affiliation(s)
- Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Shuai Chang
- Institute of Disease Control and Prevention, Academy of Military Medical Science, Beijing, 100071, China.,Department of Clinical Laboratory, PLA Army General Hospital, Beijing, 100700, China
| | - Yang Han
- Department of Infectious Disease, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing, Dongcheng district, Beijing, 100730, China
| | - Daomin Zhuang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Siyang Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Zuoyi Bao
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China
| | - Wenfu Zhang
- Institute of Disease Control and Prevention, Academy of Military Medical Science, Beijing, 100071, China
| | - Hongbin Song
- Institute of Disease Control and Prevention, Academy of Military Medical Science, Beijing, 100071, China
| | - Taisheng Li
- Department of Infectious Disease, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan Wangfujing, Dongcheng district, Beijing, 100730, China.
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, No. 20 East Street, Fengtai district, Beijing, 100071, China.
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Economic Evaluations of Pharmacogenetic and Pharmacogenomic Screening Tests: A Systematic Review. Second Update of the Literature. PLoS One 2016; 11:e0146262. [PMID: 26752539 PMCID: PMC4709231 DOI: 10.1371/journal.pone.0146262] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/15/2015] [Indexed: 01/29/2023] Open
Abstract
Objective Due to extended application of pharmacogenetic and pharmacogenomic screening (PGx) tests it is important to assess whether they provide good value for money. This review provides an update of the literature. Methods A literature search was performed in PubMed and papers published between August 2010 and September 2014, investigating the cost-effectiveness of PGx screening tests, were included. Papers from 2000 until July 2010 were included via two previous systematic reviews. Studies’ overall quality was assessed with the Quality of Health Economic Studies (QHES) instrument. Results We found 38 studies, which combined with the previous 42 studies resulted in a total of 80 included studies. An average QHES score of 76 was found. Since 2010, more studies were funded by pharmaceutical companies. Most recent studies performed cost-utility analysis, univariate and probabilistic sensitivity analyses, and discussed limitations of their economic evaluations. Most studies indicated favorable cost-effectiveness. Majority of evaluations did not provide information regarding the intrinsic value of the PGx test. There were considerable differences in the costs for PGx testing. Reporting of the direction and magnitude of bias on the cost-effectiveness estimates as well as motivation for the chosen economic model and perspective were frequently missing. Conclusions Application of PGx tests was mostly found to be a cost-effective or cost-saving strategy. We found that only the minority of recent pharmacoeconomic evaluations assessed the intrinsic value of the PGx tests. There was an increase in the number of studies and in the reporting of quality associated characteristics. To improve future evaluations, scenario analysis including a broad range of PGx tests costs and equal costs of comparator drugs to assess the intrinsic value of the PGx tests, are recommended. In addition, robust clinical evidence regarding PGx tests’ efficacy remains of utmost importance.
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Duwal S, Winkelmann S, Schütte C, von Kleist M. Optimal Treatment Strategies in the Context of 'Treatment for Prevention' against HIV-1 in Resource-Poor Settings. PLoS Comput Biol 2015; 11:e1004200. [PMID: 25927964 PMCID: PMC4423987 DOI: 10.1371/journal.pcbi.1004200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 02/18/2015] [Indexed: 12/15/2022] Open
Abstract
An estimated 2.7 million new HIV-1 infections occurred in 2010. `Treatment-for-prevention’ may strongly prevent HIV-1 transmission. The basic idea is that immediate treatment initiation rapidly decreases virus burden, which reduces the number of transmittable viruses and thereby the probability of infection. However, HIV inevitably develops drug resistance, which leads to virus rebound and nullifies the effect of `treatment-for-prevention’ for the time it remains unrecognized. While timely conducted treatment changes may avert periods of viral rebound, necessary treatment options and diagnostics may be lacking in resource-constrained settings. Within this work, we provide a mathematical platform for comparing different treatment paradigms that can be applied to many medical phenomena. We use this platform to optimize two distinct approaches for the treatment of HIV-1: (i) a diagnostic-guided treatment strategy, based on infrequent and patient-specific diagnostic schedules and (ii) a pro-active strategy that allows treatment adaptation prior to diagnostic ascertainment. Both strategies are compared to current clinical protocols (standard of care and the HPTN052 protocol) in terms of patient health, economic means and reduction in HIV-1 onward transmission exemplarily for South Africa. All therapeutic strategies are assessed using a coarse-grained stochastic model of within-host HIV dynamics and pseudo-codes for solving the respective optimal control problems are provided. Our mathematical model suggests that both optimal strategies (i)-(ii) perform better than the current clinical protocols and no treatment in terms of economic means, life prolongation and reduction of HIV-transmission. The optimal diagnostic-guided strategy suggests rare diagnostics and performs similar to the optimal pro-active strategy. Our results suggest that ‘treatment-for-prevention’ may be further improved using either of the two analyzed treatment paradigms. HIV-1 continues to spread globally. Antiviral treatment cannot cure patients, but it slows disease progression and may prevent HIV transmission by decreasing the amount of transmittable viruses in treated individuals. ‘Treatment-for-prevention’ argues for immediate treatment initiation and may reduce transmission by 96% (CI: 73–99%), according to the results of a large clinical study (HPTN052). In order to ensure long-lasting treatment success, early therapy initiation demands more sophisticated treatment strategies & exceeding funds. However, countries facing the highest HIV burden are among the poorest. Within this work, we provide a mathematical framework that allows assessing different treatment paradigms using optimal control theory together with stochastic modelling of within-host viral dynamics and drug resistance development. We use this framework to compute and evaluate two distinct optimal long-term treatment strategies for resource-constrained settings: (i) a diagnostic-guided and (ii) a pro-active treatment strategy. The cost of a strategy is evaluated from a national economic perspective, valuating a severe patient health status in terms of an economic loss. The optimal strategies are compared with current clinical treatment protocols and no treatment in terms of costs, life expectation and reduction of secondary cases. Our simulations indicate that the pro-active treatment strategy performs comparably to the diagnostic-guided treatment strategy. Both strategies perform better than current clinical protocols, suggesting directions for improvement.
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Affiliation(s)
- Sulav Duwal
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
- Junior Research Group “Systems Pharmacology & Disease Control”
| | - Stefanie Winkelmann
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
| | - Christof Schütte
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
- Zuse Institute Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
- Junior Research Group “Systems Pharmacology & Disease Control”
- * E-mail:
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8
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Shao J, Wang J, Abubakar YF, Zhou D, Chen J, Shen Y, Wang Z, Lu H. Genetic relatedness of human immunodeficiency virus-1 (HIV-1) strains in a 12-year-old daughter and her father in a household setting. Arch Virol 2014; 159:1385-91. [PMID: 24385159 DOI: 10.1007/s00705-013-1963-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/22/2013] [Indexed: 11/25/2022]
Abstract
Modalities of intra-familial transmission of HIV-1 are not always clear. Here we describe an uncommon case of HIV transmission in a family setting, analyzed using clinical, epidemiological and nucleic-acid-based methods, and assess risk factors for intrafamilial transmission of HIV-1 infection. All sequences from the father and the daughter were grouped in the same cluster with a 100 % bootstrap value, which means that the father and his daughter were infected with highly homologous CRF01_AE. The diversity of genetic clones between env and pol genes was insignificant (p > 0.05). Moreover, the results of analysis of drug-resistance-associated mutation positions of the two viral isolates were almost identical, indicating that both were susceptible to the first-line anti-HIV drugs prior to the initiation of antiretroviral treatment (ART), and this presented additional evidence of a high similarity between the two family members' HIV-1 quasispecies. In this family, HIV-1 isolates from a father and his daughter had very highly genetic relatedness. By combining their clinical histories, we could draw the conclusion that the daughter was probably infected via contact with her father's blood or other body fluids, but no obvious transmission route was found, suggesting that HIV-1 infection in similar household settings should be taken into consideration whenever the origin of HIV-1 infection cannot be identified.
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Affiliation(s)
- Jiasheng Shao
- Department of Infectious Disease, Shanghai Public Health Clinical Center Affiliated to Fudan University, 2901 Caolang Road, Shanghai, 201508, China
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9
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Pandhi D, Ailawadi P. Initiation of antiretroviral therapy. Indian J Sex Transm Dis AIDS 2014; 35. [PMID: 24958979 PMCID: PMC4066590 DOI: 10.4103/2589-0557.132399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
With the widespread availability of antiretroviral therapy, there is a dramatic decline in HIV related morbidity and mortality in both developed and developing countries. Further, the current antiretroviral drug combinations are safer and the availability of newer monitoring assays and guidelines has vastly improved the patient management. The clinician needs to evaluate several key issues prior to institution of antiretroviral regimen including the correct stage of starting the treatment and the kind of regimen to initiate. In addition to various disease related factors, it is also critical to assess the patient's general condition including nutritional status, presence of co-morbidities and mental preparedness prior to starting the therapy. The patients need to develop an overall understanding of the treatment and its benefits and the importance of lifelong adherence to the drugs. The presence of special situations like pediatric age, older patients, pregnancy, lactation and presence of opportunistic infections also require modification of the therapy. This review briefly summarizes issues relevant to the clinician prior to the initiation of antiretroviral therapy.
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Affiliation(s)
- Deepika Pandhi
- Department of Dermatology and Sexually Transmitted Diseases, University College of Medical Sciences and Associated Guru Teg Bahadur Hospital, University of Delhi, Delhi, India,Address for correspondence: Dr. Deepika Pandhi, Department of Dermatology and Sexually Transmitted Diseases, University College of Medical Sciences and Associated Guru Teg Bahadur Hospital, University of Delhi, Delhi - 110 095, India. E-mail:
| | - Pallavi Ailawadi
- Department of Dermatology and Sexually Transmitted Diseases, University College of Medical Sciences and Associated Guru Teg Bahadur Hospital, University of Delhi, Delhi, India
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10
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Abstract
With the widespread availability of antiretroviral therapy, there is a dramatic decline in HIV related morbidity and mortality in both developed and developing countries. Further, the current antiretroviral drug combinations are safer and the availability of newer monitoring assays and guidelines has vastly improved the patient management. The clinician needs to evaluate several key issues prior to institution of antiretroviral regimen including the correct stage of starting the treatment and the kind of regimen to initiate. In addition to various disease related factors, it is also critical to assess the patient's general condition including nutritional status, presence of co-morbidities and mental preparedness prior to starting the therapy. The patients need to develop an overall understanding of the treatment and its benefits and the importance of lifelong adherence to the drugs. The presence of special situations like pediatric age, older patients, pregnancy, lactation and presence of opportunistic infections also require modification of the therapy. This review briefly summarizes issues relevant to the clinician prior to the initiation of antiretroviral therapy.
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Affiliation(s)
- Deepika Pandhi
- Department of Dermatology and Sexually Transmitted Diseases, University College of Medical Sciences and Associated Guru Teg Bahadur Hospital, University of Delhi, Delhi, India
| | - Pallavi Ailawadi
- Department of Dermatology and Sexually Transmitted Diseases, University College of Medical Sciences and Associated Guru Teg Bahadur Hospital, University of Delhi, Delhi, India
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11
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Meoni P. Economic Evaluations of Pharmacogenetic Approaches in Infectious Diseases: A Review of Current Approaches and Evaluation of Critical Aspects Affecting their Quality. J Public Health Afr 2013; 4:e18. [PMID: 28299107 PMCID: PMC5345436 DOI: 10.4081/jphia.2013.e18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 10/21/2013] [Indexed: 11/23/2022] Open
Abstract
Pharmacogenetics holds great potential for improving the effectiveness of treatment modalities in infectious diseases by taking into account the genetic determinants of both the host and infectious agents' individuality. Better utilization of resources and improved therapeutic efficiency are the expected outcomes of personalized medicine using pharmacogenetic and pharmacogenomics information made available by technological advances. However, there has been growing concern in the clinical community regarding the evaluation of the true benefits of these approaches. This perception is partly due to the limited number and perceived poor quality of economic evaluations in this field, and initiatives aimed at harmonizing and communicating strategies improving the quality of these studies and their acceptance by the clinical community are greatly needed. This paper reviews current literature of economic evaluations of pharmacogenetics interventions guiding pharmacotherapy in infectious diseases. PubMed and the NHS Centre for Reviews and Dissemination databases were searched using a combination of five broad research terms related to pharmacogenetic approaches, and papers relative to economic evaluations of pharmacogenetic interventions in infectious diseases retained for further analysis. Using these criteria, a total of 14 papers were included in this review. The area of economic evaluation of pharmacogenetic interventions in infectious diseases remains understudied and would benefit from greater harmonization. The main weaknesses of evaluations reviewed in this paper seem to be represented by poor evidence of pharmacogenetic marker validation, inconsistencies in the selection of costs and utility included in the economic models and the choice of sensitivity analysis. All these factors limit the overall transparency of the studies, greater acceptance of their results and applicability to diverse and possibly resourcelimited environments where these approaches could be expected to have the greater impact.
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Affiliation(s)
- Paolo Meoni
- AtuniS Development Services, La Marsa, Tunisia
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Santoro MM, Perno CF. HIV-1 Genetic Variability and Clinical Implications. ISRN MICROBIOLOGY 2013; 2013:481314. [PMID: 23844315 PMCID: PMC3703378 DOI: 10.1155/2013/481314] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
Despite advances in antiretroviral therapy that have revolutionized HIV disease management, effective control of the HIV infection pandemic remains elusive. Beyond the classic non-B endemic areas, HIV-1 non-B subtype infections are sharply increasing in previous subtype B homogeneous areas such as Europe and North America. As already known, several studies have shown that, among non-B subtypes, subtypes C and D were found to be more aggressive in terms of disease progression. Luckily, the response to antiretrovirals against HIV-1 seems to be similar among different subtypes, but these results are mainly based on small or poorly designed studies. On the other hand, differences in rates of acquisition of resistance among non-B subtypes are already being observed. This different propensity, beyond the type of treatment regimens used, as well as access to viral load testing in non-B endemic areas seems to be due to HIV-1 clade specific peculiarities. Indeed, some non-B subtypes are proved to be more prone to develop resistance compared to B subtype. This phenomenon can be related to the presence of subtype-specific polymorphisms, different codon usage, and/or subtype-specific RNA templates. This review aims to provide a complete picture of HIV-1 genetic diversity and its implications for HIV-1 disease spread, effectiveness of therapies, and drug resistance development.
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Affiliation(s)
- Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- INMI L Spallanzani Hospital, Antiretroviral Therapy Monitoring Unit, Via Portuense 292, 00149 Rome, Italy
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Identification of human immunodeficiency virus-1 (HIV-1) transmission from a 29-year-old daughter to her mother in Shanghai, China. Arch Virol 2012; 158:11-7. [PMID: 22918554 DOI: 10.1007/s00705-012-1421-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/12/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND AND METHODS Routes of intrafamilial transmission of HIV-1 are not always clear. Here, we describe transmission to a mother from her 29-year-old daughter within a family setting through clinical, epidemiological and molecular evidence. We evaluated the risk factors for intrafamilial transmission of HIV-1 infection through qualitative epidemiology following pol and env gene sequencing and phylogenetic analysis. RESULT The nucleotide sequences of the pol and env genes of the two strains from the two patients in the family were 99 % and 100 % identical, respectively, and they clustered with CRF07_BC, which includes the main recombinant strains in Shanghai, China. The diversity of genetic clones between the env and pol genes was insignificant (p > 0.05). The drug-resistance-associated mutation positions of the two viral strains were basically similar and indicated that both were susceptible to the first-line anti-retroviral drugs including zidovudine (AZT), lamivudine (3TC), efavirenz (EFV) and nevirapine (NVP) prior to the initiation of highly active antiretroviral treatment (HAART), providing additional evidence of a close similarity between the quasispecies of the two family members. CONCLUSION In this family, the two strains of the virus, isolated from the mother and her adult daughter, had very high homology. In the context of their clinical histories, we can make a conclusion that the mother was infected by the virus in her daughter's blood or other body fluids, but no overt transmission route has been clarified. This investigation also suggested that intimate personal exposure in the same household can contribute to HIV-1 transmission and underscores the need to educate persons who care for or are in contact with HIV-infected persons in household settings where such exposures may occur.
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Kumarasamy N, Patel A, Pujari S. Antiretroviral therapy in Indian setting: when & what to start with, when & what to switch to? Indian J Med Res 2012; 134:787-800. [PMID: 22310814 PMCID: PMC3284090 DOI: 10.4103/0971-5916.92626] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
With the rapid scale up of antiretroviral therapy, there is a dramatic decline in HIV related morbidity and mortality in both developed and developing countries. Several new safe antiretroviral, and newer class of drugs and monitoring assays are developed recently. As a result the treatment guideline for the management of HIV disease continue to change. This review focuses on evolving science on Indian policy - antiretroviral therapy initiation, which drugs to start with, when to change the initial regimen and what to change.
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Affiliation(s)
- N Kumarasamy
- YRG CARE Medical Centre, Voluntary Health Services, Chennai, India.
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Chaudhary MA, Elbasha EH, Kumar RN, Nathanson EC. Cost-effectiveness of raltegravir in HIV/AIDS. Expert Rev Pharmacoecon Outcomes Res 2012; 11:627-39. [PMID: 22098278 DOI: 10.1586/erp.11.79] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Raltegravir is a first-in-class HIV-1 integrase inhibitor with established antiviral efficacy in treatment-naive and treatment-experienced patients with multidrug-resistant HIV-1 infection. In this article, we summarize pharmacoeconomic evaluations of raltegravir-based treatment regimens, compared with alternative therapies, in the treatment of patients with HIV infection and/or AIDS. Cost-effectiveness evaluations of raltegravir in treatment-experienced patients conducted using a continuous-time, state-transition Markov cohort model suggest that raltegravir, combined with optimized background therapy, falls within the range that would generally be considered cost effective compared with optimized therapy alone in Spanish, Swiss and UK health systems. In treatment-naive populations, raltegravir was evaluated using a three-stage continuous-time state-transition cohort model. Raltegravir-based initiation treatment strategies (first-line raltegravir) were compared with protease inhibitor and non-nucleoside reverse-transcriptase inhibitor initiation strategies, in which raltegravir was retained for salvage therapy. First-line raltegravir was cost-effective versus retaining raltegravir for salvage therapy in several European populations. A separate economic model was used to evaluate first-line raltegravir against two alternative initiation regimens representing standard clinical practice in Australia; raltegravir proved to be cost effective in both scenarios. In all studies examined, results were sensitive to factors including treatment duration, mortality rate, analytic time horizon, health utility weights, cost of raltegravir and optimized therapy, incidence of opportunistic infection and discount rates. Nonetheless, raltegravir remained cost effective under most scenarios.
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Fehr J, Glass TR, Louvel S, Hamy F, Hirsch HH, von Wyl V, Böni J, Yerly S, Bürgisser P, Cavassini M, Fux CA, Hirschel B, Vernazza P, Martinetti G, Bernasconi E, Günthard HF, Battegay M, Bucher HC, Klimkait T. Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals--the Swiss HIV Cohort Study. J Transl Med 2011; 9:14. [PMID: 21255386 PMCID: PMC3032678 DOI: 10.1186/1479-5876-9-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 01/21/2011] [Indexed: 12/03/2022] Open
Abstract
Background Replicative phenotypic HIV resistance testing (rPRT) uses recombinant infectious virus to measure viral replication in the presence of antiretroviral drugs. Due to its high sensitivity of detection of viral minorities and its dissecting power for complex viral resistance patterns and mixed virus populations rPRT might help to improve HIV resistance diagnostics, particularly for patients with multiple drug failures. The aim was to investigate whether the addition of rPRT to genotypic resistance testing (GRT) compared to GRT alone is beneficial for obtaining a virological response in heavily pre-treated HIV-infected patients. Methods Patients with resistance tests between 2002 and 2006 were followed within the Swiss HIV Cohort Study (SHCS). We assessed patients' virological success after their antiretroviral therapy was switched following resistance testing. Multilevel logistic regression models with SHCS centre as a random effect were used to investigate the association between the type of resistance test and virological response (HIV-1 RNA <50 copies/mL or ≥1.5log reduction). Results Of 1158 individuals with resistance tests 221 with GRT+rPRT and 937 with GRT were eligible for analysis. Overall virological response rates were 85.1% for GRT+rPRT and 81.4% for GRT. In the subgroup of patients with >2 previous failures, the odds ratio (OR) for virological response of GRT+rPRT compared to GRT was 1.45 (95% CI 1.00-2.09). Multivariate analyses indicate a significant improvement with GRT+rPRT compared to GRT alone (OR 1.68, 95% CI 1.31-2.15). Conclusions In heavily pre-treated patients rPRT-based resistance information adds benefit, contributing to a higher rate of treatment success.
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Affiliation(s)
- Jan Fehr
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital of Basel, Petersgraben 4, CH-4031 Basel, Switzerland
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Vegter S, Jansen E, Postma MJ, Boersma C. Economic evaluations of pharmacogenetic and genomic screening programs: update of the literature. Drug Dev Res 2010. [DOI: 10.1002/ddr.20424] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Economic evaluations of HIV prevention in rich countries and the need to focus on the aging of the HIV-positive population. Curr Opin HIV AIDS 2010; 5:255-60. [DOI: 10.1097/coh.0b013e3283384a88] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Schoeni-Affolter F, Ledergerber B, Rickenbach M, Rudin C, Gunthard HF, Telenti A, Furrer H, Yerly S, Francioli P. Cohort Profile: The Swiss HIV Cohort Study. Int J Epidemiol 2009; 39:1179-89. [DOI: 10.1093/ije/dyp321] [Citation(s) in RCA: 296] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Rational use of antiretroviral therapy in low-income and middle-income countries: optimizing regimen sequencing and switching. AIDS 2008; 22:2053-67. [PMID: 18753937 DOI: 10.1097/qad.0b013e328309520d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Hirsch MS, Günthard HF, Schapiro JM, Brun-Vézinet F, Clotet B, Hammer SM, Johnson VA, Kuritzkes DR, Mellors JW, Pillay D, Yeni PG, Jacobsen DM, Richman DD. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis 2008; 47:266-85. [PMID: 18549313 DOI: 10.1086/589297] [Citation(s) in RCA: 350] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Resistance to antiretroviral drugs remains an important limitation to successful human immunodeficiency virus type 1 (HIV-1) therapy. Resistance testing can improve treatment outcomes for infected individuals. The availability of new drugs from various classes, standardization of resistance assays, and the development of viral tropism tests necessitate new guidelines for resistance testing. The International AIDS Society-USA convened a panel of physicians and scientists with expertise in drug-resistant HIV-1, drug management, and patient care to review recently published data and presentations at scientific conferences and to provide updated recommendations. Whenever possible, resistance testing is recommended at the time of HIV infection diagnosis as part of the initial comprehensive patient assessment, as well as in all cases of virologic failure. Tropism testing is recommended whenever the use of chemokine receptor 5 antagonists is contemplated. As the roll out of antiretroviral therapy continues in developing countries, drug resistance monitoring for both subtype B and non-subtype B strains of HIV will become increasingly important.
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Abstract
OBJECTIVE To assess the cost-effectiveness of cotrimoxazole prophylaxis in HIV-infected children in Zambia, as implementation at the local health centre level has yet to be undertaken in many resource-limited countries despite recommendations in recent updated World Health Organization (WHO) guidelines. DESIGN A probabilistic decision analytical model of HIV/AIDS progression in children based on the CD4 cell percentage (CD4%) was populated with data from the placebo-controlled Children with HIV Antibiotic Prophylaxis trial that had reported a 43% reduction in mortality with cotrimoxazole prophylaxis in HIV-infected children aged 1-14 years. METHODS Unit costs (US$ in 2006) were measured at University Teaching Hospital, Lusaka. Cost-effectiveness expressed as cost per life-year saved, cost per quality adjusted life-year (QALY) saved, cost per disability adjusted life-year (DALY) averted was calculated across a number of different scenarios at tertiary and primary healthcare centres. RESULTS : Cotrimoxazole prophylaxis was associated with incremental cost-effectiveness ratios (ICERs) of US$72 per life-year saved, US$94 per QALY saved and US$53 per DALY averted, i.e. substantially less than a cost-effectiveness threshold of US$1019 per outcome (gross domestic product per capita, Zambia 2006). ICERs of US$5 or less per outcome demonstrate that cotrimoxazole prophylaxis is even more cost-effective at the local healthcare level. The intervention remained cost-effective in all sensitivity analyses including routine haematological and CD4% monitoring, varying starting age, AIDS status, cotrimoxazole formulation, efficacy duration and discount rates. CONCLUSION Cotrimoxazole prophylaxis in HIV-infected children is an inexpensive low technology intervention that is highly cost-effective in Zambia, strongly supporting the adoption of WHO guidelines into essential healthcare packages in low-income countries.
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