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Schnaufer EC, Barbosa MS, Marques MF, Brito GT, Ferreira TS, Ribeiro AD, Valiente AC, Machado IR, Gonçalves CC, Tanaka TS, Guimarães ML, Ribeiro SM, Croda J, Simionatto S. Prevalence of HIV-1 infection and associated characteristics in a Brazilian indigenous population: a cross-sectional study. LANCET REGIONAL HEALTH. AMERICAS 2023; 25:100562. [PMID: 37559945 PMCID: PMC10407292 DOI: 10.1016/j.lana.2023.100562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Despite significant progress in the areas of prevention, diagnosis, and treatment, HIV continues to result in a substantial number of fatalities on a global scale each year. Gaining insights from epidemiological data can prove instrumental in the development of health promotion strategies, particularly within vulnerable populations, such as indigenous groups. Consequently, our study aimed to investigate the prevalence of HIV infection within the indigenous population residing in the second-largest region of Brazil. Additionally, we sought to explore the subtypes of HIV-1 and detect any drug-resistance mutations present within this population. METHODS In this cross-sectional study, we aimed to evaluate the prevalence of HIV-1 infection and explore its associated characteristics within the indigenous population residing in the villages of Jaguapiru and Bororó, located in the Dourados area of Mato Grosso do Sul (MS), Brazil. Blood samples were collected for rapid HIV screening, serological tests, nucleic acid amplification, and HIV subtyping. Additionally, the HIV-1 viral load and CD4+ T lymphocyte count of the people living with HIV (PLHIV) were assessed at the time of recruitment and 24 weeks later. FINDINGS Out of the 2190 invited individuals, 1927 (88%) were included in this study. The average age of the participants was 34.2 (±13.8) years, with a majority of 74% being female. Moreover, 68.44% of the participants identified themselves as belonging to the Guarani-Kaiowa ethnic group. HIV seroprevalence was 0.93% (18/1927), and 73.22% (1411/1927) were unaware of their serological status. The prevalence of HIV-1 was higher in single indigenous people [10/617 (1.62%)], who received government benefits [14/1021 (1.37%)], had less than five years of formal education [11/685 (1.61%)], had sexual intercourse with users of injectable drugs [2/21 (9.52%)], with history of sexually transmitted infections (STIs) [10/62 (16.2%)] and incarceration [3/62 (4.84%)]. Of 18 positive samples, 44.4% (8/18) were successfully amplified, and HIV-1 subtype C was prevalent. Furthermore, we identified HIV-1 drug resistance mutations in four patients, specifically from the classes of Protease Inhibitor, Nucleoside Reverse Transcriptase Inhibitor, and Non-Nucleoside Reverse Transcriptase Inhibitor. Notably, three of these patients exhibited a high viral load even after 24 weeks of undergoing antiretroviral therapy. Out of the 18 PLHIV, 66.66% (12/18) had a viral load below 1000 copies/mL, while 50% (9/18) had a CD4+ T lymphocytes count greater than 350 cells/mL after 24 weeks of treatment. INTERPRETATION Despite the concerted efforts to control HIV infection, the prevalence observed in the indigenous population under study surpassed that reported in other Brazilian indigenous groups. This disparity highlights the disproportionate impact of the disease on this particular group. The detection of drug-resistance mutations further emphasizes the critical need to expand diagnostic coverage, closely monitor treatment strategies, and maintain ongoing molecular surveillance. These measures are imperative for enhancing HIV management within this vulnerable population. FUNDING This study was partially funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Apoio ao Desenvolvimento do Ensino, Ciência e Tecnologia do Estado de Mato Grosso do Sul (FUNDECT), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Secretaria do Estado de Saúde (SES) of Governo do Estado de Mato Grosso do Sul, and Universidade Federal da Grande Dourados (UFGD).
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Affiliation(s)
- Erica C.S. Schnaufer
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Marcelo S. Barbosa
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Michele F.R. Marques
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Gabriel T. Brito
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Tiago S. Ferreira
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Anny D.C. Ribeiro
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Anna C. Valiente
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Indianara R. Machado
- Distrito Sanitário Especial Indígena (DSEI), Dourados, Mato Grosso do Sul, Brazil
- Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Crhistinne C.M. Gonçalves
- Universidade Federal do Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
- Secretaria Estadual de Saúde (SES), Campo Grande, Mato Grosso do Sul, Brazil
| | - Tayana S.O. Tanaka
- Universidade Federal do Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Monick L. Guimarães
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Suzana M. Ribeiro
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
| | - Julio Croda
- Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
- Faculdade de Medicina (FAMED), Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Simone Simionatto
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados (UFGD), Dourados, Mato Grosso do Sul, Brazil
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Dickens OO, Bajwa I, Garcia-Ramos K, Suh Y, Wen C, Cheng A, Fethke V, Yi Y, Collman RG, Johnson AC. Label-free detection of synthetic, full genomic length HIV-1 RNA at the few-copy level. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 390:134001. [PMID: 37384350 PMCID: PMC10299804 DOI: 10.1016/j.snb.2023.134001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Oligonucleotide-functionalized graphene biosensors show immense promise for use as label-free point of care devices for detection of nucleic acid biomarkers at clinically relevant levels. Graphene-based nucleic acid sensors can be fabricated at low cost and have been shown to reach limits of detection in the attomolar range. Here we demonstrate devices functionalized with 22mer or 8omer DNA probes are capable of detecting full length genomic HIV-1 subtype B RNA, with a limit of detection below 1 aM in nuclease free water. We also show that these sensors are suitable for detection directly in Qiazol lysis reagent, again with a limit of detection below 1 aM for both 22mer and 8omer probes.
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Affiliation(s)
- Olivia O. Dickens
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia PA 19104
| | - Inayat Bajwa
- Department of Bioengineering, University of Pennsylvania, Philadelphia PA 19104
| | - Kelly Garcia-Ramos
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia PA 19104
| | - Yeonjoon Suh
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia PA 19104
| | - Chengyu Wen
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia PA 19104
| | - Annie Cheng
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia PA 19104
| | - Victoria Fethke
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia PA 19104
| | - Yanji Yi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
| | - A.T. Charlie Johnson
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia PA 19104
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia PA 19104
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia PA 19104
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Desalegn M, Seyoum D, Tola EK, Tsegaye Gayesa R. Determinants of first-line antiretroviral treatment failure among adult HIV patients at Nekemte Specialized Hospital, Western Ethiopia: Unmatched case-control study. SAGE Open Med 2021; 9:20503121211030182. [PMID: 34262767 PMCID: PMC8252348 DOI: 10.1177/20503121211030182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/16/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE In Ethiopia, only a few studies were conducted to determine factors contributing to antiretroviral treatment failure, in general, and there are no published data in the study area, in particular. Thus, the aim of the study was to assess the determinants of first-line treatment failure among adult HIV patients on antiretroviral treatment at Nekemte Specialized Hospital, western Ethiopia. METHODS The hospital-based 1:2 unmatched case-control study was conducted in Nekemte Specialized Hospital from 1 August to 30 September, 2019, on 252 HIV-positive patients receiving antiretroviral treatment (86 cases and 166 controls). Cases were selected from patients who were switched to second-line antiretroviral treatment regimen after first-line antiretroviral treatment failure. Controls were from those who are on the first-line antiretroviral regimens for at least 6 months. Data were collected by two trained clinical nurses. Record review and an interviewer-administered questionnaire were used to collect data. Data were entered into Epi-Data, version 7.2.2, and then exported to SPSS, version 25, for analysis. The association between treatment failure and each covariate was assessed by bivariate analysis to identify candidate variables at p value < 0.25. All candidate variables were entered into multivariate analysis done in stepwise backward likelihood ratio to declare statistical significance association at p value < 0.05, 95% confidence interval. RESULTS Data from a total of 252 (86 cases and 166 controls) patients were extracted at a response rate of 98.4%. Statistically higher odds of first-line treatment failure were observed among those who started treatment at an advanced stage (Baseline World Health Organization stage 3 o r4 (adjusted odds ratio = 3.12, 95% confidence interval: 1.55-6.26), lower Baseline CD4 count < 100 cells (adjusted odds ratio = 3.06, 95 % confidence interval: 1.45-6.50), lack of participation in a support group (adjusted odds ratio = 4.03, 95% confidence interval: 1.98-8.21), history of antiretroviral treatment discontinuation for greater than 1 month (adjusted odds ratio = 2.36, 95% confidence interval: 1.17-4.78) and poor adherence to antiretroviral treatment (adjusted odds ratio = 3.09, 95% confidence interval: 1.54-6.19). CONCLUSION Antiretroviral treatment initiation at an advanced stage, lower CD4 count, no participation in a support group, and poor adherence were determinants of treatment first-line antiretroviral treatment failure. Therefore, health care providers and program developers should give special attention to; early diagnosis and start of treatment, encouraging patients to participate in a support group, trace patients early, and attentively follow patients to improve their adherence to antiretroviral treatment.
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Affiliation(s)
- Mengistu Desalegn
- Department of Public health, Nekemte Health Science College, Nekemte, Ethiopia
| | - Dejene Seyoum
- Department of Public Health, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia
| | - Edosa Kifle Tola
- Department of Medical Laboratory Science, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia
| | - Reta Tsegaye Gayesa
- Department of Nursing, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia
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Bender AT, Sullivan BP, Zhang JY, Juergens DC, Lillis L, Boyle DS, Posner JD. HIV detection from human serum with paper-based isotachophoretic RNA extraction and reverse transcription recombinase polymerase amplification. Analyst 2021; 146:2851-2861. [PMID: 33949378 PMCID: PMC9151496 DOI: 10.1039/d0an02483j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The number of people living with HIV continues to increase with the current total near 38 million, of which about 26 million are receiving antiretroviral therapy (ART). These treatment regimens are highly effective when properly managed, requiring routine viral load monitoring to assess successful viral suppression. Efforts to expand access by decentralizing HIV nucleic acid testing in low- and middle-income countries (LMICs) has been hampered by the cost and complexity of current tests. Sample preparation of blood samples has traditionally relied on cumbersome RNA extraction methods, and it continues to be a key bottleneck for developing low-cost POC nucleic acid tests. We present a microfluidic paper-based analytical device (μPAD) for extracting RNA and detecting HIV in serum, leveraging low-cost materials, simple buffers, and an electric field. We detect HIV virions and MS2 bacteriophage internal control in human serum using a novel lysis and RNase inactivation method, paper-based isotachophoresis (ITP) for RNA extraction, and duplexed reverse transcription recombinase polymerase amplification (RT-RPA) for nucleic acid amplification. We design a specialized ITP system to extract and concentrate RNA, while excluding harsh reagents used for lysis and RNase inactivation. We found the ITP μPAD can extract and purify 5000 HIV RNA copies per mL of serum. We then demonstrate detection of HIV virions and MS2 bacteriophage in human serum within 45-minutes.
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Affiliation(s)
- Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - Jane Y Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - David C Juergens
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | | | | | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, USA. and Department of Chemical Engineering, University of Washington, Seattle, USA and Family Medicine, School of Medicine, University of Washington, Seattle, USA
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Characterization of HIV-1 subtypes and drug resistance mutations in Henan Province, China (2017-2019). Arch Virol 2020; 165:1453-1461. [PMID: 32279138 PMCID: PMC7222071 DOI: 10.1007/s00705-020-04606-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 03/04/2020] [Indexed: 11/05/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection remains a severe public health problem worldwide. In this study, we investigated the distribution of HIV-1 subtypes and the prevalence of drug resistance mutations (DRMs) among patients with HIV-1 infection in Henan Province, China. HIV-1 strains in blood samples taken from inpatients and outpatients visiting the Sixth People’s Hospital of Zhengzhou from August 2017 to July 2019 with a viral load (VL) greater than 1000 copies/ml were subjected to subtype and DRMs analysis. Out of a total of 769 samples, subtype and DRM data were obtained from 657 (85.43%) samples. Phylogenetic analysis based on partial pol gene sequences indicated that the most commonly found genotype was subtype B (45.51%, 299/657), followed by CRF01_AE (28.61%, 188/657), CRF07_BC (15.68%, 103/657), CRF08_BC (0.76%, 5/657), C (0.61%, 4/657), A (0.30%, 2/657), and others (8.52%, 56/657). Circulating recombinant forms (CRFs) were most commonly found in patients who were naïve to antiretroviral treatment (ART) (68.67%, 160/233). The percentage of patients with one or more major drug-resistance mutations was 50.99% (335/657), and it was 6.44% (15/233) in ART-naive patients that were primarily infected with subtype B (17.74%). Resistance mutations were most common at codons 65, 103, 106, 184, and 190 of the reverse transcriptase gene and codon 46 of the protease gene. Our study provides detailed information about the distribution of HIV-1 subtypes and the incidence of drug resistance mutations of different subtypes in ART-experienced and naïve patients. This can guide policymakers in making decisions about treatment strategies against HIV-1.
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Yuan H, Liu Z, Wu X, Wu M, Fang Q, Tully DC, Zhang T. Evolutionary characteristics and genetic transmission patterns of predominant HIV-1 subtypes among men who have sex with men in China. Int J Infect Dis 2019; 90:125-131. [PMID: 31682961 DOI: 10.1016/j.ijid.2019.10.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/24/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES Men who have sex with men (MSM) represent one of the major risk groups for HIV-1 infection in China, and the predominant subtypes among this population has changed over the last two decades. The objective of this study was to determine the evolutionary characteristics and transmission patterns of the dominant HIV-1 strains in the Chinese MSM population. METHODS A total of 4980 published HIV-1 pol gene sequences from MSM in China were retrieved and comprehensive evolutionary and transmission analyses were then conducted. Bayesian coalescent-based methods and selection pressure analyses were used to reconstruct the time-scale and demographic history and to estimate other evolutionary parameters. Transmission patterns were characterized using network analyses. RESULTS There were 2546 (51.12%) CRF01_AE, 1263 (25.36%) CRF07_BC, and 623 (12.51%) subtype B, accounting for 88.99% of the total sequences. From 2000 to 2016, the prevalence of CRF01_AE was stable, comprising nearly half of all sequences over time (58.33-45.38%, p=0.071). CRF07_BC increased slightly from 13.3% to 22.49% (p<0.001), while subtype B decreased dramatically from 41.67% to 9.04% (p<0.001). Demographic reconstruction showed that the greatest expansion of the HIV epidemic occurred between 1999 and 2005. CRF01_AE had a higher estimated evolutionary rate (2.97×10-3 substitutions/site/year) and exhibited more sites under positive selection (25/351 codons) compared to the other subtypes. Network analyses showed that CRF07_BC (68.29%, 84/123) had a higher proportion of cross-region networks than CRF01_AE (49.1%, 174/354) and subtype B (36.46%, 35/96) (p<0.001). CONCLUSIONS The predominant subtypes of HIV-1 in Chinese MSM have different evolutionary characteristics and transmission patterns, which poses a significant challenge to HIV treatment and disease prevention.
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Affiliation(s)
- Huangbo Yuan
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
| | - Zhenqiu Liu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China; State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xuefu Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
| | - Mingshan Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
| | - Qiwen Fang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China
| | - Damien C Tully
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China.
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Ghoneim FM, Raouf MM, Elshaer NS, Abdelhamid SM, Noor Eldeen RA. Study of Patterns and Markers of Human Immune Deficiency Virus -1 (HIV-1) Progression and Unemployment Rate among Patients from Alexandria, Egypt. Pol J Microbiol 2019; 66:519-527. [PMID: 29319511 DOI: 10.5604/01.3001.0010.7044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Middle East and North Africa (MENA) new HIV cases show the highest increase among all regions in the world. Even though Egypt has a low prevalence among the general population (< 0.02%), a national HIV epidemic occurs in certain population risk groups. The current study was conducted to asses clinical and immunological disease progression; following up viral load (VL) and detecting delta-32 CCR5 genotype polymorphism in selected cases, determining unemployment rate and identify predictors of employment for HIV-cases. A cross sectional design was adopted. HIV infected cases attending Alexandria Fever Hospital (AFH) for one year. Interview questionnaire and four CD+4 counts were done for all patients, HIV VL and delta-32 CCR5 polymorphism were done for selected cases. Sexual transmission and drug abuse are the most important risk factors. Infectious comorbidity increases the rate of HIV progression. CD4+ count at the end of the study; CD+4 (4), count was significantly higher than all other CD4+ readings among the whole cohort and among the treated group. Also, VL at the end of the study; VL(2), was significantly higher than VL(1) among the untreated group. Unemployment rate was 40%. Male gender and obtaining vocational training were significant predictors of employment. It can be concluded that having a family member living with HIV and drug abusers are high risk groups for HIV acquisition. Factors responsible for progression of HIV should be further investigated. Antiretroviral therapy is very effective in checking HIV replication rate, delaying the progression of HIV, reconstituting the immune response and should be available for all cases detected.
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Affiliation(s)
- Faika M Ghoneim
- Microbiology Department, Faculty of Medicine, Alexandria University, Egypt
| | - May M Raouf
- Microbiology Department, Faculty of Medicine, Alexandria University, Egypt
| | - Noha S Elshaer
- Community Medicine Department, Faculty of Medicine, Alexandria University, Egypt
| | - Sarah M Abdelhamid
- Microbiology Department, Faculty of Pharmacy, Damanhour University, Egypt
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Point-of-Care HIV Viral Load Testing: an Essential Tool for a Sustainable Global HIV/AIDS Response. Clin Microbiol Rev 2019; 32:32/3/e00097-18. [PMID: 31092508 DOI: 10.1128/cmr.00097-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The global public health community has set ambitious treatment targets to end the HIV/AIDS pandemic. With the notable absence of a cure, the goal of HIV treatment is to achieve sustained suppression of an HIV viral load, which allows for immunological recovery and reduces the risk of onward HIV transmission. Monitoring HIV viral load in people living with HIV is therefore central to maintaining effective individual antiretroviral therapy as well as monitoring progress toward achieving population targets for viral suppression. The capacity for laboratory-based HIV viral load testing has increased rapidly in low- and middle-income countries, but implementation of universal viral load monitoring is still hindered by several barriers and delays. New devices for point-of-care HIV viral load testing may be used near patients to improve HIV management by reducing the turnaround time for clinical test results. The implementation of near-patient testing using these new and emerging technologies may be an essential tool for ensuring a sustainable response that will ultimately enable an end to the HIV/AIDS pandemic. In this report, we review the current and emerging technology, the evidence for decentralized viral load monitoring by non-laboratory health care workers, and the additional considerations for expanding point-of-care HIV viral load testing.
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Avettand-Fénoël V, Mélard A, Gueudin M, Maillard A, Dina J, Gousset M, Chaix ML, Lerolle N, Viard JP, Meyer L, Plantier JC, Rouzioux C. Comparative performance of the Biocentric Generic Viral Load, Roche CAP/CTM v1.5, Roche CAP/CTM v2.0 and m2000 Abbott assays for quantifying HIV-1 B and non-B strains: Underestimation of some CRF02 strains. J Clin Virol 2018; 110:36-41. [PMID: 30530097 DOI: 10.1016/j.jcv.2018.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/26/2018] [Accepted: 12/02/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND HIV-1 viral load testing is now recommended by the World Health Organization for every patient receiving antiretroviral therapy (ART). OBJECTIVES The objective of this study is to evaluate the performance of commercial assays for their ability to quantify HIV-1 strains currently circulating in France. STUDY DESIGN The performances of the Generic HIV-RNA assay from Biocentric were compared to those of the Roche CAP/CTM v1.5, Roche CAP/CTM v2.0 and Abbott m2000 RealTime HIV-1 assays. A total of 1885 HIV-1 plasma samples were tested, including 684 samples from patients included in the ANRS-Primo Cohort. RESULTS We found a good concordance of quantification between the Roche v2.0 and the Biocentric assays, both of which were superior to the Roche v1.5 assay. We show moderate agreement between techniques; however, CRF02_AG strains and undetermined viruses were underestimated when quantified with the Roche CAP/CTM v2.0. In contrast, a comparison of the Biocentric and Abbott assay results showed strong agreement between assays, indicating that both are well suited for quantification of CRF02_AG strains. Moreover, a 2% underestimation of the B subtypes was observed with the Biocentric assay. CONCLUSIONS These results have implications for viral load monitoring in Western Africa, where CRF02_AG strains are highly prevalent. Closer epidemiological surveillance and evaluation of commercial assays are still necessary to better evaluate the impact of the genetic evolution of circulating viruses on HIV-RNA quantification in the regions most affected by the HIV-1 epidemic.
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Affiliation(s)
- V Avettand-Fénoël
- Université Paris Descartes, EA 7327, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Necker, Paris, France
| | - A Mélard
- Université Paris Descartes, EA 7327, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Necker, Paris, France
| | - M Gueudin
- Normandie Université, UNIROUEN, EA2656 GRAM, CHU de Rouen, Laboratoire de virologie, F-76000, Rouen, France
| | - A Maillard
- Laboratoire de Virologie, Hôpital de Rennes, Rennes, France
| | - J Dina
- Université de Normandie, EA 2556, Hôpital de Caen, département de Virologie, Caen, France
| | - M Gousset
- Université Paris Descartes, EA 7327, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Necker, Paris, France
| | - M L Chaix
- INSERM UMR 942 Université Paris Diderot, Laboratoire de Virologie, APHP Hôpital Saint-Louis, Paris, France
| | - N Lerolle
- INSERM CESP U1018, Université Paris Sud, Le Kremlin Bicêtre, France
| | - J P Viard
- Université Paris Descartes, EA 7327, Sorbonne Paris Cité, AP-HP, Centre de Diagnostic et de Thérapeutique, Hôpital Hôtel Dieu, France
| | - L Meyer
- INSERM CESP U1018, Université Paris Sud, Le Kremlin Bicêtre, France
| | - J C Plantier
- Normandie Université, UNIROUEN, EA2656 GRAM, CHU de Rouen, Laboratoire de virologie, F-76000, Rouen, France
| | - C Rouzioux
- Université Paris Descartes, EA 7327, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Necker, Paris, France.
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Abstract
HIV diagnostics have played a central role in the remarkable progress in identifying, staging, initiating, and monitoring infected individuals on life-saving antiretroviral therapy. They are also useful in surveillance and outbreak responses, allowing for assessment of disease burden and identification of vulnerable populations and transmission "hot spots," thus enabling planning, appropriate interventions, and allocation of appropriate funding. HIV diagnostics are critical in achieving epidemic control and require a hybrid of conventional laboratory-based diagnostic tests and new technologies, including point-of-care (POC) testing, to expand coverage, increase access, and positively impact patient management. In this review, we provide (i) a historical perspective on the evolution of HIV diagnostics (serologic and molecular) and their interplay with WHO normative guidelines, (ii) a description of the role of conventional and POC testing within the tiered laboratory diagnostic network, (iii) information on the evaluations and selection of appropriate diagnostics, (iv) a description of the quality management systems needed to ensure reliability of testing, and (v) strategies to increase access while reducing the time to return results to patients. Maintaining the central role of HIV diagnostics in programs requires periodic monitoring and optimization with quality assurance in order to inform adjustments or alignment to achieve epidemic control.
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Kaushik AM, Hsieh K, Wang TH. Droplet microfluidics for high-sensitivity and high-throughput detection and screening of disease biomarkers. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1522. [PMID: 29797414 PMCID: PMC6185786 DOI: 10.1002/wnan.1522] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/02/2018] [Accepted: 03/10/2018] [Indexed: 12/17/2022]
Abstract
Biomarkers are nucleic acids, proteins, single cells, or small molecules in human tissues or biological fluids whose reliable detection can be used to confirm or predict disease and disease states. Sensitive detection of biomarkers is therefore critical in a variety of applications including disease diagnostics, therapeutics, and drug screening. Unfortunately for many diseases, low abundance of biomarkers in human samples and low sample volumes render standard benchtop platforms like 96-well plates ineffective for reliable detection and screening. Discretization of bulk samples into a large number of small volumes (fL-nL) via droplet microfluidic technology offers a promising solution for high-sensitivity and high-throughput detection and screening of biomarkers. Several microfluidic strategies exist for high-throughput biomarker digitization into droplets, and these strategies have been utilized by numerous droplet platforms for nucleic acid, protein, and single-cell detection and screening. While the potential of droplet-based platforms has led to burgeoning interest in droplets, seamless integration of sample preparation technologies and automation of platforms from biological sample to answer remain critical components that can render these platforms useful in the clinical setting in the near future. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.
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Affiliation(s)
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Department of Biomedical Engineering, Johns Hopkins University
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12
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Bobkova MR. [Genetic diversity of human immunodeficiency viruses and antiretroviral therapy]. TERAPEVT ARKH 2018; 88:103-111. [PMID: 28005040 DOI: 10.17116/terarkh20168811103-111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The lecture is devoted to the analysis of the state-of-the-art of the impact of genetic diversity of human immunodeficiency (HIV) viruses on the pattern of infection and the efficiency of antiretroviral therapy (ART). It provides brief information on the origin and evolution of HIV and on the current classification of their genetic variants. The molecular epidemiological situation of HIV infection in Russia and nearby states and the major molecular HIV variants that are dominant in these countries, as well as their origin and prevalence trends are characterized. How the diversity of HIV can affect the efficiency of diagnosis, the transmission of the virus, and the pattern of HIV pathogenesis are briefly reviewed. The comparative data available in the world's scientific literature on these topics are given. More detailed attention is given to the possible causes of varying therapeutic effects against different HIV subtypes, as well as to the specific features of the formation and phenotyping manifestation of ART drug resistance mutations. There is evidence for the necessity of forming a unified follow-up system for treated HIV-infected patients during ART scaling, including in an effort to evaluate the impact of the specific features of the HIV genome on the efficiency of treatment regimens used in Russia.
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Affiliation(s)
- M R Bobkova
- D.I. Ivanovsky Institute of Virology, Honorary Acad. N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of Russia, Moscow, Russia
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Comparison of Detection Limits of Fourth- and Fifth-Generation Combination HIV Antigen-Antibody, p24 Antigen, and Viral Load Assays on Diverse HIV Isolates. J Clin Microbiol 2018; 56:JCM.02045-17. [PMID: 29793968 DOI: 10.1128/jcm.02045-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
Detection of acute HIV infection is critical for HIV public health and diagnostics. Clinical fourth-generation antigen (Ag)/antibody (Ab) combination (combo) and p24 Ag immunoassays have enhanced detection of acute infection compared to Ab-alone assays but require ongoing evaluation with currently circulating diverse subtypes. Genetically and geographically diverse HIV clinical isolates were used to assess clinical HIV diagnostic, blood screening, and next-generation assays. Three-hundred-member panels of 20 serially diluted well-characterized antibody-negative HIV isolates for which the researchers were blind to the results (blind panels) were distributed to manufacturers and end-user labs to assess the relative analytic sensitivity of currently approved and preapproved clinical HIV fourth-generation Ag/Ab combo or p24 Ag-alone immunoassays for the detection of diverse subtypes. The limits of detection (LODs) of virus were estimated for different subtypes relative to confirmed viral loads. Analysis of immunoassay sensitivity was benchmarked against confirmed viral load measurements on the blind panel. On the basis of the proportion of positive results on 300 observations, all Ag/Ab combo and standard sensitivity p24 Ag assays performed similarly and within half-log LODs, illustrating the similar breadth of reactivity and diagnostic utility. Ultrasensitive p24 Ag assays achieved dramatically increased sensitivities, while the rapid combo assays performed poorly. The similar performance of the different commercially available fourth-generation assays on diverse subtypes supports their use in broad geographic settings with locally circulating HIV clades and recombinant strains. Next-generation preclinical ultrasensitive p24 Ag assays achieved dramatically improved sensitivity, while rapid fourth-generation assays performed poorly for p24 Ag detection.
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Bender AT, Borysiak MD, Levenson AM, Lillis L, Boyle DS, Posner JD. Semiquantitative Nucleic Acid Test with Simultaneous Isotachophoretic Extraction and Amplification. Anal Chem 2018; 90:7221-7229. [PMID: 29761701 DOI: 10.1021/acs.analchem.8b00185] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid amplification tests (NAATs) provide high diagnostic accuracy for infectious diseases and quantitative results for monitoring viral infections. The majority of NAATs require complex equipment, cold chain dependent reagents, and skilled technicians to perform the tests. This largely confines NAATs to centralized laboratories and can significantly delay appropriate patient care. Low-cost, point-of-care (POC) NAATs are especially needed in low-resource settings to provide patients with diagnosis and treatment planning in a single visit to improve patient care. In this work, we present a rapid POC NAAT with integrated sample preparation and amplification using electrokinetics and paper substrates. We use simultaneous isotachophoresis (ITP) and recombinase polymerase amplification (RPA) to rapidly extract, amplify, and detect target nucleic acids from serum and whole blood in a paper-based format. We demonstrate simultaneous ITP and RPA can consistently detect 5 copies per reaction in buffer and 10 000 copies per milliliter of human serum with no intermediate user steps. We also show preliminary extraction and amplification of DNA from whole blood samples. Our test is rapid (results in less than 20 min) and made from low-cost materials, indicating its potential for detecting infectious diseases and monitoring viral infections at the POC in low resource settings.
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Affiliation(s)
- Andrew T Bender
- Mechanical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Mark D Borysiak
- Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Amanda M Levenson
- Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | | | | | - Jonathan D Posner
- Mechanical Engineering , University of Washington , Seattle , Washington 98195 , United States.,Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
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Manoto SL, Lugongolo M, Govender U, Mthunzi-Kufa P. Point of Care Diagnostics for HIV in Resource Limited Settings: An Overview. MEDICINA (KAUNAS, LITHUANIA) 2018; 54:E3. [PMID: 30344234 PMCID: PMC6037236 DOI: 10.3390/medicina54010003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 02/28/2018] [Accepted: 03/05/2018] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV) is a global health problem. Early diagnosis, rapid antiretroviral therapy (ART) initiation and monitoring of viral load are the key strategies for effective HIV management. Many people in resource limited settings where timely access to medical care is a challenge and healthcare infrastructure is poor have no access to laboratory facilities and diagnosis is dependent on the presence of point of care (POC) devices. POC instruments have shown to be easy to operate, maintain and transport and can easily be operated by less skilled health workers. Additionally, POC tests do not require laboratory technicians to operate. POC devices have resulted in a growing number of people testing for HIV and thereby receiving treatment early. In recent years, there has been great improvement in the development of POC technologies for early HIV diagnosis, HIV viral load and cluster of differentiation 4 (CD4) measurement. This review discusses POC technologies that are currently available and in the pipeline for diagnosing and monitoring HIV. We also give an overview of the technical and commercialization challenges in POC diagnostics for HIV.
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Affiliation(s)
- Sello Lebohang Manoto
- National Laser Centre, Council for Scientific and Industrial Research, PO Box 395, Pretoria 0001, South Africa.
| | - Masixole Lugongolo
- National Laser Centre, Council for Scientific and Industrial Research, PO Box 395, Pretoria 0001, South Africa.
- College of Science, Engineering and Technology, Department of Physics, NB Pityana Building, University of South Africa, Science Campus, Florida 1710, South Africa.
| | | | - Patience Mthunzi-Kufa
- National Laser Centre, Council for Scientific and Industrial Research, PO Box 395, Pretoria 0001, South Africa.
- College of Science, Engineering and Technology, Department of Physics, NB Pityana Building, University of South Africa, Science Campus, Florida 1710, South Africa.
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A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012. PLoS One 2017; 12:e0170601. [PMID: 28489920 PMCID: PMC5425008 DOI: 10.1371/journal.pone.0170601] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/06/2017] [Indexed: 12/12/2022] Open
Abstract
Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005–2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap ≥98%, genetic distance ≤1.5% from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of ≥3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01_AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.
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MacKenzie LJ, Hull MW, Samji H, Lima VD, Yip B, Zhang W, Lourenço L, Colley G, Hogg RS, Montaner JSG. Is there a rural/urban gap in the quality of HIV care for treatment-naïve HIV-positive individuals initiating antiretroviral therapy in British Columbia? AIDS Care 2017; 29:1218-1226. [PMID: 28472896 DOI: 10.1080/09540121.2017.1322678] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Rurally located people living with HIV (PLWH) face unique challenges associated with remoteness that may negatively affect their HIV care outcomes. The Programmatic Compliance Score (PCS) has been used previously as a quality of care metric, and is predictive of mortality for treatment-naïve individuals initiating combination antiretroviral therapy (cART). This study looked at whether the rurality of PLWH impacted their PCS. PCS was calculated for PLWH (≥19 years old) initiating cART in British Columbia between 2000 and 2013. Rurality was determined at the time of cART initiation using two methodologies: (1) a categorical postal code method; and (2) the General Practice Rurality Index (GPRI), a score representing an individual's degree of rurality. Ordinal logistic regression modeling was used to assess the relationship between rurality and PCS. Among 4616 PLWH with an evaluable PCS, 176 were classified as rural and 3512 as urban (928 had an unknown postal code). After adjusting for age, sex, hepatitis C status, Indigenous ancestry, and year of cART initiation, categorical rurality was not associated with a worse PCS (adjusted odds ratio (AOR) 1.04; 95% CI: 0.77-1.39). However, an increasing degree of rurality was associated with a worse PCS (AOR (per 10 increase in GPRI) 1.13; 95% CI: 1.06-1.20). Given that a poor PCS has been shown to be predictive of all-cause mortality for individuals initiating cART, strategies to improve access to HIV care for rural individuals should be evaluated.
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Affiliation(s)
- Lauren J MacKenzie
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada.,b CIHR Canadian HIV Trials Network , Vancouver , BC , Canada.,c Clinician Investigator Program , University of Manitoba , Winnipeg , MB , Canada.,d School of Population and Public Health , University of British Columbia , Vancouver , BC , Canada
| | - Mark W Hull
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada.,e Department of Medicine , University of British Columbia , Vancouver , BC , Canada
| | - Hasina Samji
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada
| | - Viviane D Lima
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada.,e Department of Medicine , University of British Columbia , Vancouver , BC , Canada
| | - Benita Yip
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada
| | - Wendy Zhang
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada
| | - Lillian Lourenço
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada
| | - Guillaume Colley
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada
| | - Robert S Hogg
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada.,f Faculty of Health Sciences , Simon Fraser University , Burnaby , BC , Canada
| | - Julio S G Montaner
- a BC Centre for Excellence in HIV/AIDS , Vancouver , BC , Canada.,e Department of Medicine , University of British Columbia , Vancouver , BC , Canada
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Estimation of measurement error in plasma HIV-1 RNA assays near their limit of quantification. PLoS One 2017; 12:e0171155. [PMID: 28152073 PMCID: PMC5289538 DOI: 10.1371/journal.pone.0171155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/17/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Plasma HIV-1 RNA levels (pVLs), routinely used for clinical management, are influenced by measurement error (ME) due to physiologic and assay variation. OBJECTIVE To assess the ME of the COBAS HIV-1 Ampliprep AMPLICOR MONITOR ultrasensitive assay version 1.5 and the COBAS Ampliprep Taqman HIV-1 assay versions 1.0 and 2.0 close to their lower limit of detection. Secondly to examine whether there was any evidence that pVL measurements closest to the lower limit of quantification, where clinical decisions are made, were susceptible to a higher degree of random noise than the remaining range. METHODS We analysed longitudinal pVL of treatment-naïve patients from British Columbia, Canada, during their first six months on treatment, for time periods when each assay was uniquely available: Period 1 (Amplicor): 08/03/2000-01/02/2008; Period 2 (Taqman v1.0): 07/01/2010-07/03/2012; Period 3 (Taqman v2.0): 08/03/2012-30/06/2014. ME was estimated via generalized additive mixed effects models, adjusting for several clinical and demographic variables and follow-up time. RESULTS The ME associated with each assay was approximately 0.5 log10 copies/mL. The number of pVL measurements, at a given pVL value, was not randomly distributed; values ≤250 copies/mL were strongly systematically overrepresented in all assays, with the prevalence decreasing monotonically as the pVL increased. Model residuals for pVL ≤250 copies/mL were approximately three times higher than that for the higher range, and pVL measurements in this range could not be modelled effectively due to considerable random noise of the data. CONCLUSIONS Although the ME was stable across assays, there is substantial increase in random noise in measuring pVL close to the lower level of detection. These findings have important clinical significance, especially in the range where key clinical decisions are made. Thus, pVL values ≤250 copies/mL should not be taken as the "truth" and repeat pVL measurement is encouraged to confirm viral suppression.
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Sauné K, Raymond S, Boineau J, Pasquier C, Izopet J. Detection and quantification of HIV-1 RNA with a fully automated transcription-mediated-amplification assay. J Clin Virol 2016; 84:70-73. [PMID: 27728849 DOI: 10.1016/j.jcv.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 02/04/2023]
Abstract
BACKGROUND Nucleic acid testing is the major method used to monitor HIV viral load. Commercial systems based on real-time PCR assays are available for high-volume centralized laboratory testing, but they are not fully automated. OBJECTIVES AND STUDY DESIGN We have compared the diagnostic performance of the Hologic Aptima HIV-1 Quant Dx assay (Aptima) (based on real-time TMA) on the Panther instrument, a fully-automated random access platform, to that of, the Roche Cobas Ampliprep Cobas TaqMan (CAP/CTM) HIV-1 version 2.0 (based on real-time PCR). RESULTS Probit analysis of replicate dilutions of NIBSC WHO International HIV-1 Standard, gave LODs of 8.6 c/ml for Aptima and 15.2 c/ml for CAP/CTM. The agreement between the assays was excellent when measuring HIV RNA in a calibrated reference (κ=0.90, p<0.001) and good when measuring clinical samples (κ=0.62, p<0.001). The correlation among the samples quantified by the two methods was very good (r=0.95, p<0.001) and the mean difference between the values obtained with the two assays was 0.02 log c/ml for B and non-B subtypes. The vast majority of results showed <0.5 log variance between the two assays (89%); only one sample showed results that differed by over 1.0 log c/ml. CONCLUSION The performance of the new fully automated Aptima assay is adequate for clinical monitoring of HIV-1 RNA during infections and treatment. The Aptima assay is well suited for routine laboratory use.
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Affiliation(s)
- K Sauné
- INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France; CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France.
| | - S Raymond
- INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France; CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France
| | - J Boineau
- CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France
| | - C Pasquier
- INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France; CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France
| | - J Izopet
- INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France; CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France
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Evaluation of Hologic Aptima HIV-1 Quant Dx Assay on the Panther System on HIV Subtypes. J Clin Microbiol 2016; 54:2575-81. [PMID: 27510829 DOI: 10.1128/jcm.01350-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/02/2016] [Indexed: 11/20/2022] Open
Abstract
Quantitation of the HIV-1 viral load in plasma is the current standard of care for clinical monitoring of HIV-infected individuals undergoing antiretroviral therapy. This study evaluated the analytical and clinical performances of the Aptima HIV-1 Quant Dx assay (Hologic, San Diego, CA) for monitoring viral load by using 277 well-characterized subtype samples, including 171 cultured virus isolates and 106 plasma samples from 35 countries, representing all major HIV subtypes, recombinants, and circulating recombinant forms (CRFs) currently in circulation worldwide. Linearity of the Aptima assay was tested on each of 6 major HIV-1 subtypes (A, B, C, D, CRF01_AE, and CRF02_AG) and demonstrated an R(2) value of ≥0.996. The performance of the Aptima assay was also compared to those of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 v.2 (CAP/CTM) and Abbott m2000 RealTime HIV-1 (RealTime) assays on all subtype samples. The Aptima assay values averaged 0.21 log higher than the CAP/CTM values and 0.30 log higher than the RealTime values, and the values were >0.4 log higher than CAP/CTM values for subtypes F and G and than RealTime values for subtypes C, F, and G and CRF02_AG. Two samples demonstrated results with >1-log differences from RealTime results. When the data were adjusted by the average difference, 94.9% and 87.0% of Aptima results fell within 0.5 log of the CAP/CTM and RealTime results, respectively. The linearity and accuracy of the Aptima assay in correctly quantitating all major HIV-1 subtypes, coupled with the completely automated format and high throughput of the Panther system, make this system well suited for reliable measurement of viral load in the clinical laboratory.
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Janocko L, Althouse AD, Brand RM, Cranston RD, McGowan I. The Molecular Characterization of Intestinal Explant HIV Infection Using Polymerase Chain Reaction-Based Techniques. AIDS Res Hum Retroviruses 2015; 31:981-91. [PMID: 26214703 PMCID: PMC4576939 DOI: 10.1089/aid.2015.0165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The ex vivo mucosal explant model is frequently used to test the efficacy of microbicides that have the potential for preventing HIV-1 transmission. The conventional assessment of product efficacy has been the extent of HIV-1 p24 suppression in supernatant fluids sampled up to day 14 after HIV-1 challenge ex vivo. The purpose of this study was to determine if measurement of HIV-1 nucleic acids by real-time PCR and HIV-1 integration by Alu-gag PCR provides advantages with regard to monitoring HIV-1 infection in explants. Rectal biopsies from HIV-1-negative individuals were challenged with 1 × 10(5) virions/ml of HIV-1BaL or HIV-1CH077 ex vivo. HIV-1 RNA and HIV-1 p24 in supernatant fluids and HIV-1 nucleic acids and integrated provirus in individual biopsies were measured at days 1-14 after infection. HIV-1 RNA and proviral DNA were measured by quantitative real-time PCR (qRT-PCR) while integrated virus was detected by Alu-gag PCR. Real-time PCR assays detecting HIV-1 DNA and RNA performed similarly provided that the infecting virus sequences were a good match with the sequences of the assay primers and probes. Increased HIV-1 nucleic acid levels and DNA integration were measurable on days 11 and 14 after infection. The magnitude of explant infection was similar after challenge with HIV-1BaL and HIV-1CH077, although the trajectory of infection was delayed in the HIV-1CH077-infected biopsies. In the majority of experiments, qRT-PCR did not appreciably shorten the time necessary to detect evidence of HIV-1 infection.
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Affiliation(s)
- Laura Janocko
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
| | - Andrew D. Althouse
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rhonda M. Brand
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Ian McGowan
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- University of Pittsburgh, Pittsburgh, Pennsylvania
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HIV-1 variability and viral load technique could lead to false positive HIV-1 detection and to erroneous viral quantification in infected specimens. J Infect 2015; 71:368-76. [PMID: 26033694 DOI: 10.1016/j.jinf.2015.05.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/12/2015] [Accepted: 05/25/2015] [Indexed: 11/23/2022]
Abstract
OBJECTIVES Viral load (VL) testing is used for early HIV diagnosis in infants (EID) and for detecting early therapeutic failure events, but can be affected by HIV genetic variability. Dried blood samples (DBS) increase VL access and EID in remote settings and when low blood volume is available. METHODS This study compares VL values using Siemens VERSANT HIV-1 RNA 1.0 kPCR assay (kPCR) and Roche CAP/CTM Quantitative test v2.0 (CAP/CTM v2.0) in 176 DBS carrying different HIV-1 variants collected from 69 Equatoguinean mothers and their infants with known HIV-1 status (71 infected, 105 uninfected). RESULTS CAP/CTM v2.0 provided false positive VLs in 11 (10.5%) cases. VL differences above 0.5 log10 were observed in 42/49 (87.5%) DBS, and were above 1 log10 in 18 cases. CAP/CTM v2.0 quantified all the 41 specimens with previously inferred HIV-1 variant by phylogenetic analysis (68.3% recombinants) whereas kPCR only identified 90.2% of them, and was unable to detect 14.3% of 21 CRF02_AG viruses. CAP/CTM v2.0 showed higher sensitivity than kPCR (95.8% vs. 70.1%), quantifying a higher rate of viruses in infected DBS from subjects under antiretroviral exposure at sampling time compared to kPCR (94.7% vs. 96.2%, p-value<0.001). kPCR showed maximum specificity (100%) whereas for CAP/CTM v2.0 was 89.5%. CONCLUSIONS VL assays should increase their sensitivity and specificity to avoid overestimated HIV-1 quantifications, which could be interpreted as virological failure events, or false negative diagnostic results due to genetic variability. We recommend using the same VL technique for each patient during antiretroviral therapy monitoring.
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Pernas B, Mena A, Cañizares A, Grandal M, Castro-Iglesias A, Pértega S, Pedreira JD, Poveda E. Trends on epidemiological, virological, and clinical features among newly diagnosed HIV-1 persons in Northwest Spain over the last 10 years. J Med Virol 2015; 87:1319-26. [PMID: 25777786 DOI: 10.1002/jmv.24185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2015] [Indexed: 12/21/2022]
Abstract
To describe temporal trend and characteristics of newly HIV-diagnosed patients in a medical care area in Northwest Spain over the last 10 years. All newly diagnosed patients for HIV-infection from 2004 to 2013 at a reference medical care area in Northwest of Spain were identified. Epidemiological, virological, immunological, and clinical data, as well as HIV genotype and drug resistance information were recorded. A total of 565 newly HIV-diagnosed patients were identified. The number of new cases increased in the last 5 years (66 cases/year). Overall, 53.1% had a median CD4 counts < 350 cells/µl and 33.6% had an AIDS defining criteria. Non-B variants were found in 34.4% of patients being subtype F (25.8%) the most common non-B subtype. The rate of transmitted drug resistance (TDR) over the study period was 3.7%, but a decreased to 2.6% was observed in the last 5 years. The most prevalent TDR mutations were: T215 revertants (1.5%), K219QENR (1.2%), for NRTIs; K103N (1.9%), for NNRTIs; L90M (0.3%), for PIs. Overall, 73.2% of patients started antiretroviral treatment and 9.9% of patients died during follow-up. The number of newly HIV diagnosed patients increased since year 2009. There is a high prevalence of late diagnosis (53%) and 33% had an AIDS defining criteria. Interestingly, the most prevalent non-B subtype in our population was F (25.8%). These findings support the need to facilitate the access for HIV testing to reduce the rate of late HIV diagnosis, improve the clinical outcome and prevent HIV transmission.
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Affiliation(s)
- B Pernas
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - A Mena
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - A Cañizares
- Service of Microbiology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - M Grandal
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - A Castro-Iglesias
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - S Pértega
- Clinical Epidemiology and Biostatistics Unit, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - J D Pedreira
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - E Poveda
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
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Baesi K, Moallemi S, Farrokhi M, Alinaghi SAS, Truong HM. Subtype classification of Iranian HIV-1 sequences registered in the HIV databases, 2006-2013. PLoS One 2014; 9:e105098. [PMID: 25188443 PMCID: PMC4154867 DOI: 10.1371/journal.pone.0105098] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/17/2014] [Indexed: 02/05/2023] Open
Abstract
Background The rate of human immunodeficiency virus type 1 (HIV-1) infection in Iran has increased dramatically in the past few years. While the earliest cases were among hemophiliacs, injection drug users (IDUs) fuel the current epidemic. Previous molecular epidemiological analysis found that subtype A was most common among IDUs but more recent studies suggest CRF_35AD may be more prevalent now. To gain a better understanding of the molecular epidemiology of HIV-1 infection in Iran, we analyzed all Iranian HIV sequence data from the Los Alamos National Laboratory. Methods All Iranian HIV sequences from subtyping studies with pol, gag, env and full-length HIV-1 genome sequences registered in the HIV databases (www.hiv.lanl.gov) between 2006 and 2013 were downloaded. Phylogenetic trees of each region were constructed using Neighbor-Joining (NJ) and Maximum Parsimony methods. Results A total of 475 HIV sequences were analyzed. Overall, 78% of sequences were CRF_35AD. By gene region, CRF_35AD comprised 83% of HIV-1 pol, 62% of env, 78% of gag, and 90% of full-length genome sequences analyzed. There were 240 sequences re-categorized as CRF_AD. The proportion of CRF_35AD sequences categorized by the present study is nearly double the proportion of what had been reported. Conclusions Phylogenetic analysis indicates HIV-1 subtype CRF_35AD is the predominant circulating strain in Iran. This result differed from previous studies that reported subtype A as most prevalent in HIV- infected patients but confirmed other studies which reported CRF_35AD as predominant among IDUs. The observed epidemiological connection between HIV strains circulating in Iran and Afghanistan may be due to drug trafficking and/or immigration between the two countries. This finding suggests the possible origins and transmission dynamics of HIV/AIDS within Iran and provides useful information for designing control and intervention strategies.
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Affiliation(s)
- Kazem Baesi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Moallemi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Molood Farrokhi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Ahmad Seyed Alinaghi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Hong–Ha M. Truong
- University of California, San Francisco, CA, United States of America
- Gladstone Institute of Virology and Immunology, San Francisco, CA, United States of America
- * E-mail:
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25
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Phylogenetic analysis of HIV-1 pol gene: first subgenomic evidence of CRF29-BF among Iranian HIV-1 patients. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2014. [DOI: 10.1016/s2222-1808(14)60690-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Discordances with HIV-1 RNA quantitative determinations by three commercial assays in Pointe Noire, Republic of Congo. J Virol Methods 2014; 203:102-6. [DOI: 10.1016/j.jviromet.2014.02.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/23/2014] [Accepted: 02/03/2014] [Indexed: 12/13/2022]
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Chan PA, Reitsma MB, DeLong A, Boucek B, Nunn A, Salemi M, Kantor R. Phylogenetic and geospatial evaluation of HIV-1 subtype diversity at the largest HIV center in Rhode Island. INFECTION GENETICS AND EVOLUTION 2014; 28:358-66. [PMID: 24721515 DOI: 10.1016/j.meegid.2014.03.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/17/2014] [Accepted: 03/24/2014] [Indexed: 12/01/2022]
Abstract
Individuals infected with HIV-1 non-B subtypes are understudied in the United States. Their characterization may augment prevention and treatment interventions. We examined the regional molecular epidemiology of non-B subtypes using a combined phylogenetic and geospatial approach. HIV-1 pol sequences and clinical data obtained for routine clinical care were aggregated from 2004 to 2011 at the largest HIV center in Rhode Island. Subtyping was performed by neighbor-joining and maximum-likelihood phylogeny and compared across eight commonly used tools (HIVdb, REGA, RIP, NCBI, Geno2Pheno, EuResist, jpHMM and STAR) using proportional odds ordinal regression. Individuals with non-B subtypes were characterized according to demographics and risk factors for infection, intra-subtype clustering by maximum-likelihood phylogeny, and geospatial hotspot analysis using Getis-Ord Gi(∗) statistics. Of 1277 unique sequences, phylogenetic subtyping demonstrated 8.3% (N=106, 95% CI 6.8-10%) non-B subtypes and circulating recombinant forms (CRFs): CRF02_AG=46; A=15; C=15; CRF01_AE=6; CRF06_CPX=5; CRF14_BG=5; G=3; CRF43_02G=3; D=3; CRF24_BG=3; CRF11_CPX=1; F1=1. Compared to phylogeny, Geno2Pheno was the most concordant (86% exact match) followed by REGA (85%), EuResist (85%) and STAR (82%). Of 106 individuals with non-B subtypes, 50% were male, 71% acquired infection through heterosexual transmission; 76%, were born in Africa, 6% Southeast Asia, 5% the United States, 3% Central America, 1% Europe, and 9% unknown. Eighty percent of CRF02_AG, 93% of A and 87% of C sequences were from African-born individuals. Twenty-two percent of non-B subtypes formed transmission clusters, including a significant number of younger individuals with perinatally-acquired infection. Geospatial analyses revealed hotspots of B and non-B subtypes in the state capital with a more concentrated focus among non-B subtypes. Molecular examination of regional HIV diversity revealed a larger than expected non-subtype B infected population, mostly born in Africa, with low ongoing regional transmission. Phylogenetic and geospatial characterization of infection clusters is helpful to identify targets for treatment and prevention interventions.
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Affiliation(s)
- Philip A Chan
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA.
| | - Marissa B Reitsma
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Allison DeLong
- Center for Statistical Sciences, Brown University, Providence, RI, USA
| | | | - Amy Nunn
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Marco Salemi
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Rami Kantor
- Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
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28
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Mouinga-Ondémé A, Mabika-Mabika A, Alalade P, Mongo AD, Sica J, Liégeois F, Rouet F. Significant impact of non-B HIV-1 variants genetic diversity in Gabon on plasma HIV-1 RNA quantitation. J Med Virol 2013; 86:52-7. [PMID: 24127290 DOI: 10.1002/jmv.23770] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2013] [Indexed: 11/06/2022]
Abstract
Evaluations of HIV-1 RNA viral load assays are lacking in Central Africa. The main objective of our study was to assess the reliability of HIV-1 RNA results obtained with three different assays for samples collected in Gabon. A total of 137 plasma specimens were assessed for HIV-1 RNA using the Abbott RealTime HIV-1® and Nuclisens HIV-1 EasyQ® version 2.0 assays. It included HIV-1 non-B samples (n = 113) representing six subtypes, 10 CRFs and 18 URFs from patients infected with HIV-1 and treated with antiretrovirals that were found HIV-1 RNA positive (≥300 copies/ml) with the Generic HIV viral load® assay; and samples (n = 24) from untreated individuals infected with HIV-1 but showing undetectable (<300 copies/ml) results with the Biocentric kit. For samples found positive with the Generic HIV viral load® test, correlation coefficients obtained between the three techniques were relatively low (R = 0.65 between Generic HIV viral load® and Abbott RealTime HIV-1®, 0.50 between Generic HIV viral load® and Nuclisens HIV-1 EasyQ®, and 0.66 between Abbott RealTime HIV-1® and Nuclisens HIV-1 EasyQ®). Discrepancies by at least one log10 were obtained for 19.6%, 33.7%, and 20% of samples, respectively, irrespective of genotype. Most of samples (22/24) from untreated study patients, found negative with the Biocentric kit, were also found negative with the two other techniques. In Central Africa, HIV-1 genetic diversity remains challenging for viral load testing. Further studies are required in the same area to confirm the presence of HIV-1 strains that are not amplified with at least two different viral load assays.
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Wilson E, Tanzosh T, Maldarelli F. HIV diagnosis and testing: what every healthcare professional can do (and why they should). Oral Dis 2013; 19:431-9. [PMID: 23347510 DOI: 10.1111/odi.12047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 11/12/2012] [Indexed: 11/27/2022]
Abstract
Over the last thirty years, the human immunodeficiency virus (HIV) epidemic has matured. In the United States, HIV has changed from an explosive outbreak to an endemic disease; currently, an estimated 1.1 million people are infected with HIV, including a substantial number who are unaware of their status. With recent findings demonstrating the high transmissibility of HIV early in infection, and the potential benefit of early initiation of treatment, it is essential to identify as many infected individuals as possible. The Centers for Disease Control and Prevention (CDC) has expanded HIV testing to include any healthcare setting, including dental offices. Testing advances, including oral testing, have reduced the window period of HIV infection. Dental care represents a key, reliable, independent, and confidential link between the healthcare system and the general population that has been under-utilized in the effort to control the HIV epidemic. HIV testing is straightforward, and knowledge of the types of testing will afford dentists an important opportunity to help advance and preserve the health of their patients and to promote the public health of their community. Here, we review the basics of HIV testing and discuss new changes in the approach to HIV diagnostics.
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Affiliation(s)
- E Wilson
- HIV Drug Resistance Program, NCI, NIH, Bethesda, MD, USA
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30
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Alvarez M, Chueca N, Guillot V, Bernal MDC, García F. Improving Clinical Laboratory Efficiency: Introduction of Systems for the Diagnosis and Monitoring of HIV Infection. Open Virol J 2012; 6:135-43. [PMID: 23264839 PMCID: PMC3527893 DOI: 10.2174/1874357901206010135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 08/03/2012] [Accepted: 08/06/2012] [Indexed: 11/28/2022] Open
Abstract
Since the first tests for identifying individuals with suspected human immunodeficiency virus (HIV) infection were introduced in the mid-1980s, diagnostic virology testing has greatly evolved. The technological advances, automating in the laboratories and the advances in molecular biology techniques have helped introduce invaluable laboratory methods for managing HIV patients. Tests for diagnosis, specially for screening HIV antibodies, are now fully automated; in the same way, tests for monitoring HIV viral load (HIV RNA copies/ml of plasma), which is used for monitoring infection and response to antiretroviral treatment, are also fully automated; however, resistance testing, tropism determination and minor variant detection, which are used to make decisions for changing antiretroviral treatment regimens in patients failing therapy, still remain highly laborious and time consuming. This chapter will review the main aspects relating to the automating of the methods available for laboratory diagnosis as well as for monitoring of the HIV infection and determination of resistance to antiretrovirals and viral tropism.
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Affiliation(s)
- Marta Alvarez
- Servicio de Microbiología, Hospital Universitario San Cecilio, Granada, Spain
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31
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Dai T, Li K, Lu H, Gu X, Wang Q, Zhou P. Molecular typing of Treponema pallidum: a 5-year surveillance in Shanghai, China. J Clin Microbiol 2012; 50:3674-7. [PMID: 22972832 PMCID: PMC3486273 DOI: 10.1128/jcm.01195-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 09/03/2012] [Indexed: 11/20/2022] Open
Abstract
Previously, a small study showed that 14f was the predominant subtype of Treponema pallidum in Shanghai, China. The result was quite different from the genotype distribution in other areas of China. This study aimed to identify the strain types of Treponema pallidum in samples collected over a 5-year period in Shanghai. From 2007 to 2011, genital swabs were collected from patients with syphilis from the Shanghai Skin Disease Hospital. Positive specimens were typed by the enhanced typing method by adding a tp0548 gene to the existing arp and tpr genotype system. In total, 304 of the 372 enrolled patients yielded fully typeable DNA. Ten arp types (4, 6, 8, 9, 11, 12, 13, 14, 15, and 19), 3 tpr types (a, d, and o), and 5 tp0548 types (a, c, f, g, and i) were identified. In total, 12 subtypes were identified with a combination of the arp and tpr genes. Subtype 14d was found in 270 samples (88.8%). When the combination included the tp0548 gene, the 12 CDC subtypes identified were divided into 14 strain types. The predominant type was 14d/f (88.8%), followed by 15d/f (3.6%), 13d/f (1.3%), and 19d/c (1.3%). Two of the 44 14d/f-infected patients and both of the 19d/c-infected patients who underwent a lumbar puncture were diagnosed with neurosyphilis. This study showed that the predominant type in Shanghai was 14d/f. While this is in keeping with data from other areas in China, it is different from an earlier report showing that 14f is the most common genotype in Shanghai. Further studies are needed to better understand the association between strain types and neurosyphilis.
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Affiliation(s)
- Ting Dai
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Kang Li
- Department of STD Institute, Shanghai Skin Disease Hospital, Shanghai, China
| | - Haikong Lu
- Department of STD Institute, Shanghai Skin Disease Hospital, Shanghai, China
| | - Xin Gu
- Department of STD Institute, Shanghai Skin Disease Hospital, Shanghai, China
| | - Qianqiu Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Pingyu Zhou
- Department of STD Institute, Shanghai Skin Disease Hospital, Shanghai, China
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Tang YW, Ou CY. Past, present and future molecular diagnosis and characterization of human immunodeficiency virus infections. Emerg Microbes Infect 2012; 1:e19. [PMID: 26038427 PMCID: PMC3630918 DOI: 10.1038/emi.2012.15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/08/2012] [Accepted: 05/21/2012] [Indexed: 12/31/2022]
Abstract
Substantive and significant advances have been made in the last two decades in the characterization of human immunodeficiency virus (HIV) infections using molecular techniques. These advances include the use of real-time measurements, isothermal amplification, the inclusion of internal quality assurance protocols, device miniaturization and the automation of specimen processing. The result has been a significant increase in the availability of results to a high level of accuracy and quality. Molecular assays are currently widely used for diagnostics, antiretroviral monitoring and drug resistance characterization in developed countries. Simple and cost-effective point-of-care versions are also being vigorously developed with the eventual goal of providing timely healthcare services to patients residing in remote areas and those in resource-constrained countries. In this review, we discuss the evolution of these molecular technologies, not only in the context of the virus, but also in the context of tests focused on human genomics and transcriptomics.
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Affiliation(s)
- Yi-Wei Tang
- Memorial Sloan-Kettering Cancer Center , New York, NY 10065, USA
| | - Chin-Yih Ou
- Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
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Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. LAB ON A CHIP 2012; 12:2469-86. [PMID: 22592150 DOI: 10.1039/c2lc40100b] [Citation(s) in RCA: 470] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.
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Affiliation(s)
- Pascal Craw
- Department of Electronic & Computer Engineering, School of Engineering & Design, Brunel University, London, UK.
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34
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Interplay between HIV-1 and Host Genetic Variation: A Snapshot into Its Impact on AIDS and Therapy Response. Adv Virol 2012; 2012:508967. [PMID: 22666249 PMCID: PMC3361994 DOI: 10.1155/2012/508967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/26/2012] [Accepted: 03/11/2012] [Indexed: 11/18/2022] Open
Abstract
As of February 2012, 50 circulating recombinant forms (CRFs) have been reported for HIV-1 while one CRF for HIV-2. Also according to HIV sequence compendium 2011, the HIV sequence database is replete with 414,398 sequences. The fact that there are CRFs, which are an amalgamation of sequences derived from six or more subtypes (CRF27_cpx (cpx refers to complex) is a mosaic with sequences from 6 different subtypes besides an unclassified fragment), serves as a testimony to the continual divergent evolution of the virus with its approximate 1% per year rate of evolution, and this phenomena per se poses tremendous challenge for vaccine development against HIV/AIDS, a devastating disease that has killed 1.8 million patients in 2010. Here, we explore the interaction between HIV-1 and host genetic variation in the context of HIV/AIDS and antiretroviral therapy response.
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35
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Pyne MT, Wilson A, Hillyard DR. Large-scale comparison of Roche Cobas AmpliPrep/Cobas TaqMan and Abbott RealTime HIV assays. J Virol Methods 2012; 184:106-8. [PMID: 22609889 DOI: 10.1016/j.jviromet.2012.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 02/14/2012] [Accepted: 05/10/2012] [Indexed: 10/28/2022]
Abstract
Significant underquantitation of HIV RNA has been reported with the Roche Cobas AmpliPrep/Cobas TaqMan HIV Test (Version 1) compared to other assays. However, these studies have generally involved limited numbers of samples from select patient populations or analysis of samples that were undetectable in the TaqMan assay. Random plasma samples submitted from throughout the United States for HIV RNA quantitation (n=1263) were compared in the Roche TaqMan and Abbott RealTime assays. Twenty-four samples (1.9%) were discrepant, with a maximum difference between the two assays of 1.9logcopies/mL. These data indicate that both tests may be susceptible to underquantitation, but the incidence is low in this large cohort of samples from across the United States.
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Affiliation(s)
- Michael T Pyne
- ARUP Institute for Clinical and Experimental Pathology®, 500 Chipeta Way, Salt Lake City, UT 84108, United States.
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36
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Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. INFECTION GENETICS AND EVOLUTION 2012; 12:505-21. [PMID: 22342514 PMCID: PMC7106020 DOI: 10.1016/j.meegid.2012.01.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/25/2022]
Abstract
Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
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Affiliation(s)
- Christopher D. Sibley
- Department of Microbiology, Immunology & Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
| | - Deirdre L. Church
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Department of Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
- Corresponding author. Address: c/o Calgary Laboratory Services, 9-3535 Research Rd. N.W., Calgary, Alta, Canada T2L 2K8. Tel.: +1 403 770 3281; fax: +1 403 770 3347.
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