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Li J, Ulloa GM, Mayor P, Santolalla Robles ML, Greenwood AD. Nucleic acid degradation after long-term dried blood spot storage. Mol Ecol Resour 2024; 24:e13979. [PMID: 38780145 DOI: 10.1111/1755-0998.13979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/16/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Collecting and preserving biological samples in the field, particularly in remote areas in tropical forests, prior to laboratory analysis is challenging. Blood samples in many cases are used for nucleic acid-based species determination, genomics or pathogen research. In most cases, maintaining a cold chain is impossible and samples remain at ambient temperature for extended periods of time before controlled storage conditions become available. Dried blood spot (DBS) storage, blood stored on cellulose-based paper, has been widely applied to facilitate sample collection and preservation in the field for decades. However, it is unclear how long-term storage on this substrate affects nucleic acid concentration and integrity. We analysed nucleic acid quality from DBS stored on Whatman filter paper no. 3 and FTA cards for up to 15 years in comparison to cold-chain stored samples using four nucleic acid extraction methods. We examined the ability to identify viral sequences from samples of 12 free-ranging primates in the Amazon forest, using targeted hybridization capture, and determined if mitochondrial genomes could be retrieved. The results suggest that even after extended periods of storage, DBS will be suitable for some genomic applications but may be of limited use for viral pathogen research, particularly RNA viruses.
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Affiliation(s)
- Juan Li
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Gabriela M Ulloa
- Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Belém, Pará, Brazil
- Grupo de Enfermedades Infecciosas Re-emergentes, Universidad Científica del Sur (UCSUR), Lima, Peru
| | - Pedro Mayor
- Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Belém, Pará, Brazil
- ComFauna, Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica, Iquitos, Peru
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Meddly L Santolalla Robles
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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Khan MJR, Bhuiyan MA, Tabassum S, Munshi SU. Use of whole blood and dried blood spot for detection of HIV-1 nucleic acids using reverse transcription loop-mediated isothermal amplification. J Virol Methods 2023; 312:114642. [PMID: 36375538 DOI: 10.1016/j.jviromet.2022.114642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/15/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]
Abstract
For monitoring viral load (VL) or Early Infant Diagnosis (EID) of HIV-1, real-time Polymerase Chain Reaction (qPCR) is used to perform on plasma or Dried Blood Spot (DBS) sample. The qPCR method is expensive and requires sophisticated equipment. Therefore, there is a requirement for newer and cheaper technology for VL measurement or EID. In this analytical study, a Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) assay was optimized and applied for amplification of HIV nucleic acids (NA) extracted from plasma, heat-treated plasma, heat-treated whole blood and lysis buffer-treated dried blood spot (DBS). The amplified product of RT-LAMP assay was detected by color change of Hydroxy naphthol blue (HNB) dye, step ladder pattern band on agarose gel after electrophoresis and sigmoid-shaped curve in the real-time thermal cycler. Comparing the results from RT-LAMP testing of all conditions with the results obtained by RT-qPCR results, viewed as the gold standard; a relative analytical sensitivity and specificity of RT-LAMP was calculated as 100 % and 90 % respectively. The corresponding positive predictive value (PPV) and negative predictive value (NPV) were 93.75 % and 100 %, respectively. The percentage of agreement between the RT-LAMP and RT-qPCR was 88.46% and Cohen's kappa value was 0.75 shows a substantial agreement between the two tests. This study suggests that whole blood or DBS may be useful specimens for analysis by HIV-1 specific RT-LAMP, to provide a cost effective alternative to RT-qPCR for the detection of HIV-1 nucleic acid at the point of care, or in early infant diagnoses.
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Westreich D, Jenness SM, Marcus JL. To Contact Tracing... and Beyond! Clin Infect Dis 2021; 72:724-725. [PMID: 32492132 PMCID: PMC7884804 DOI: 10.1093/cid/ciaa717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniel Westreich
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samuel M Jenness
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Julia L Marcus
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA
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Cassell MM, Wilcher R, Ramautarsing RA, Phanuphak N, Mastro TD. Go Where the Virus Is: An HIV Micro-epidemic Control Approach to Stop HIV Transmission. GLOBAL HEALTH: SCIENCE AND PRACTICE 2020; 8:614-625. [PMID: 33361230 PMCID: PMC7784070 DOI: 10.9745/ghsp-d-19-00418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 09/29/2020] [Indexed: 11/15/2022]
Abstract
Essentially all HIV transmission is from people living with HIV who are not virally suppressed. An HIV micro-epidemic control approach that differentiates treatment support and prevention services for people living with HIV and their network members according to viral burden could optimize the impact of epidemic control efforts.
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Affiliation(s)
| | | | | | - Nittaya Phanuphak
- Institute of HIV Research and Innovation, Bangkok, Thailand.,Center of Excellence in Transgender Health, Chulalongkorn University, Bangkok, Thailand
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Cheong J, Yu H, Lee CY, Lee JU, Choi HJ, Lee JH, Lee H, Cheon J. Fast detection of SARS-CoV-2 RNA via the integration of plasmonic thermocycling and fluorescence detection in a portable device. Nat Biomed Eng 2020; 4:1159-1167. [PMID: 33273713 PMCID: PMC8202505 DOI: 10.1038/s41551-020-00654-0] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/01/2020] [Indexed: 12/24/2022]
Abstract
The diagnosis of severe acute respiratory syndrome 2 (SARS-CoV-2) infection by quantitative PCR with reverse transcription (RT-qPCR) typically involves bulky instrumentation in centralized laboratories and an assay time of 1-2 h. Here, we show that SARS-CoV-2 RNA can be detected in 17 min via a portable device integrating reverse transcription, fast thermocycling (via plasmonic heating through magneto-plasmonic nanoparticles) and in situ fluorescence detection following magnetic clearance of the nanoparticles. The device correctly classified all nasopharyngeal, oropharyngeal and sputum samples from 75 patients with COVID-19 and 75 healthy controls, with good concordance in fluorescence intensity with standard RT-qPCR (Pearson coefficients > 0.7 for the N1, N2 and RPP30 genes). Fast, portable and automated nucleic acid detection should facilitate testing at the point of care.
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Affiliation(s)
- Jiyong Cheong
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Hojeong Yu
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chang Yeol Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea
| | - Jung-Uk Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Department of Chemistry, Yonsei University, Seoul, Republic of Korea
| | - Hyun-Jung Choi
- Department of Laboratory Medicine, Chonnam National University Hospital, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Jae-Hyun Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
| | - Hakho Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA.
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jinwoo Cheon
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea.
- Department of Chemistry, Yonsei University, Seoul, Republic of Korea.
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Preiser W, van Zyl GU. Pooled testing: A tool to increase efficiency of infant HIV diagnosis and virological monitoring. Afr J Lab Med 2020; 9:1035. [PMID: 32934914 PMCID: PMC7479369 DOI: 10.4102/ajlm.v9i2.1035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/15/2020] [Indexed: 01/04/2023] Open
Abstract
Background Pooled testing, or pooling, has been used for decades to efficiently diagnose relatively rare conditions, such as infection in blood donors. Programmes for the prevention of mother-to-child transmission of HIV and for antiretroviral therapy (ART) are being rolled out in much of Africa and are largely successful. This increases the need for early infant diagnosis (EID) of HIV using qualitative nucleic acid testing and for virological monitoring of patients on ART using viral load testing. While numbers of patients needing testing are increasing, infant HIV infections and ART failures are becoming rarer, opening an opportunity for pooled testing approaches. Aim This review highlights the need for universal EID and viral load coverage as well as the challenges faced. We introduce the concept of pooled testing and highlight some important considerations before giving an overview of studies exploring pooled testing for EID and virological monitoring. Results For ART monitoring, pooling has been shown to be accurate and efficient; for EID it has not been tried although modelling shows it to be promising. The final part attempts to place pooling into the context of current mother-to-child transmission of HIV and ART programmes and their expected trajectories over the next years. Conclusion Several points warrant consideration: pre-selection to exclude samples with an elevated pre-test probability of positivity from pooled testing, the use of dried blood or plasma spots, and choosing a pooling strategy that is both practically feasible and economical. Finally, novel ideas are suggested to make pooling even more attractive.
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Affiliation(s)
- Wolfgang Preiser
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Gert U van Zyl
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
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When to use one-dimensional, two-dimensional, and Shifted Transversal Design pooling in mycotoxin screening. PLoS One 2020; 15:e0236668. [PMID: 32756571 PMCID: PMC7406063 DOI: 10.1371/journal.pone.0236668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/10/2020] [Indexed: 11/19/2022] Open
Abstract
While complex sample pooling strategies have been developed for large-scale experiments with robotic liquid handling, many medium-scale experiments like mycotoxin screening by Enzyme-Linked Immunosorbent Assay (ELISA) are still conducted manually in 48- and 96-well plates. At this scale, the opportunity to save on reagent costs is offset by the increased costs of labor, materials, and risk-of-error caused by increasingly complex pooling strategies. This paper compares one-dimensional (1D), two-dimensional (2D), and Shifted Transversal Design (STD) pooling to study whether pooling affects assay accuracy and experimental cost and to provide guidance for when a human experimentalist might benefit from pooling. We approximated mycotoxin contamination in single corn kernels by fitting statistical distributions to experimental data (432 kernels for aflatoxin and 528 kernels for fumonisin) and used experimentally-validated Monte-Carlo simulation (10,000 iterations) to evaluate assay sensitivity, specificity, reagent cost, and pipetting cost. Based on the validated simulation results, assay sensitivity remains 100% for all four pooling strategies while specificity decreases as prevalence level rises. Reagent cost could be reduced by 70% and 80% in 48- and 96-well plates, with 1D and STD pooling being most reagent-saving respectively. Such a reagent-saving effect is only valid when prevalence level is < 21% for 48-well plates and < 13%-21% for 96-well plates. Pipetting cost will rise by 1.3-3.3 fold for 48-well plates and 1.2-4.3 fold for 96-well plates, with 1D pooling by row requiring the least pipetting. Thus, it is advisable to employ pooling when the expected prevalence level is below 21% and when the likely savings of up to 80% on reagent cost outweighs the increased materials and labor costs of up to 4 fold increases in pipetting.
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Facente SN, Busch MP, Grebe E, Pilcher CD, Welte A, Rice B, Murphy G. Challenges to the performance of current HIV diagnostic assays and the need for centralized specimen archives: a review of the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA) repository. Gates Open Res 2019; 3:1511. [PMID: 31460496 PMCID: PMC6706958 DOI: 10.12688/gatesopenres.13048.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 11/20/2022] Open
Abstract
Background: New challenges for diagnosis of HIV infection abound, including the impact on key viral and immunological markers of HIV vaccine studies, pre-exposure prophylaxis usage and breakthrough infections, and very early initiation of anti-retroviral treatment. These challenges impact the performance of current diagnostic assays, and require suitable specimens for development and evaluation. In this article we review and describe an archive developed by the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA), in order to identify the critical features required to create a centralized specimen archive to support these current and future developments. Review and Findings: We review and describe the CEPHIA repository, a large, consolidated repository comprised of over 31,000 highly-selected plasma samples and other body fluid specimen types, with over 50 purposely designed specimen panels distributed to 19 groups since 2012. The CEPHIA repository provided financial return on investment, supported the standardization of HIV incidence assays, and informed guidance and standards set by the World Health Organization and UNAIDS. Unified data from extensively characterized specimens has allowed this resource to support biomarker discovery, assay optimization, and development of new strategies for estimating duration of HIV infection. Critical features of a high-value repository include 1) extensively-characterized samples, 2) high-quality clinical background data, 3) multiple collaborations facilitating ongoing sample replenishment, and 4) sustained history of high-level specimen utilization. Conclusion: With strong governance and leadership, a large consolidated archive of samples from multiple studies provides investigators and assay developers with easy access to diverse samples designed to address challenges associated with HIV diagnosis, helping to enable improvements to HIV diagnostic assays and ultimately elimination of HIV. Its creation and ongoing utilization should compel funders, institutions and researchers to address and improve upon current approaches to sharing specimens.
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Affiliation(s)
- Shelley N. Facente
- University of California, San Francisco, San Francisco, CA, 94110, USA
- Vitalant Research Institute (formerly Blood Systems Research Institute), San Francisco, CA, 94118, USA
- Facente Consulting, Richmond, CA, 94804, USA
| | - Michael P. Busch
- University of California, San Francisco, San Francisco, CA, 94110, USA
- Vitalant Research Institute (formerly Blood Systems Research Institute), San Francisco, CA, 94118, USA
| | - Eduard Grebe
- University of California, San Francisco, San Francisco, CA, 94110, USA
- Vitalant Research Institute (formerly Blood Systems Research Institute), San Francisco, CA, 94118, USA
- The South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | | | - Alex Welte
- The South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Brian Rice
- London School of Hygiene and Tropical Medicine, London, UK
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