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Conrad S, Gant Kanegusuku A, Conklin SE. Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics. Clin Biochem 2023; 115:22-32. [PMID: 36495954 PMCID: PMC9729171 DOI: 10.1016/j.clinbiochem.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Recent studies evaluating the preanalytical factors that impact the outcome of nucleic-acid based methods for the confirmation of SARS-CoV-2 have illuminated the importance of identifying variables that promoted accurate testing, while using scarce resources efficiently. The majority of laboratory errors occur in the preanalytical phase. While there are many resources identifying and describing mechanisms for main laboratory testing on automated platforms, there are fewer comprehensive resources for understanding important preanalytical and environmental factors that affect accurate molecular diagnostic testing of infectious diseases. This review identifies evidence-based factors that have been documented to impact the outcome of nucleic acid-based molecular techniques for the diagnosis of infectious diseases.
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Affiliation(s)
- Stephanie Conrad
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | | | - Steven E Conklin
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA; Department of Anatomic & Clinical Pathology, Tufts University School of Medicine, Boston, MA, USA.
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Evaluation of the Aptima HBV Quant Assay Compared to Abbott RealTime M2000 HBV Quant Assay and Procleix Ultrio Plus dHBV Assay in Plasma Samples. Microbiol Spectr 2022; 10:e0176122. [PMID: 35880868 PMCID: PMC9431630 DOI: 10.1128/spectrum.01761-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analytical performance of hepatitis B virus (HBV) DNA quantitative assay is critical for screening infection and initiating and monitoring antiviral treatment. In this study, the limit of detection (LoD) and linearity of Aptima HBV Quant assay were evaluated, and analytical performance was compared with that of the Abbott RealTime M2000 HBV Quant assay and the Procleix Ultrio Plus dHBV assay in plasma samples. The LoDs for genotypes B, C, and D plasma samples were 2.139 (1.531, 4.520), 3.120 (2.140, 7.373), and 3.330 (2.589, 4.907) IU/mL, respectively. The R2 value fitted by linear regression of serially diluted samples less than 2,000 IU/mL was above 0.9. There was no difference in positive rate between Aptima and Abbott or between Aptima and Procleix. Quantitative results of Aptima and Abbott showed good correlation with an r of >0.9 using Spearman analysis, while the quantitative results of Aptima were slightly lower than those of Abbott. Usual mutations in the HBV S region had no impact on Aptima assay. This study showed that Aptima is a dual-targeted transcription-mediated amplification (TMA) assay suitable for HBV DNA detection in clinical practice, with quantitative performance comparable to that of the Abbott RealTime M2000 HBV Quant assay and qualitative performance comparable to that of the Procleix Ultrio Plus dHBV assay. IMPORTANCE The Aptima HBV Quant assay (Hologic Inc., San Diego, CA, USA) is a dual-target real-time transcription-mediated amplification (RT-TMA) assay. This study aims to evaluate whether this assay is suitable for HBV DNA detection. As a result, the assay showed high sensitivity with LoDs below 3.5 IU/mL. The amplification efficiency of Aptima for samples below 2,000 IU/mL is adequate for clinical practice, with an R2 of >0.9 fitted by linear regression. Usual mutations in the HBV S region did not affect the performance of Aptima. Moreover, its performance was comparable to the widely used Abbott RealTime M2000 HBV Quant assay for detecting HBV DNA in plasma specimens. Although not indicated for use as a diagnostic or blood screening assay, the Aptima HBV Quant assay demonstrated comparable qualitative performance to the Procleix Ultrio Plus dHBV system.
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He S, Han J. Biorepositories (biobanks) of human body fluids and materials as archives for tracing early infections of COVID-19. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 274:116525. [PMID: 33516955 PMCID: PMC7813484 DOI: 10.1016/j.envpol.2021.116525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/26/2020] [Accepted: 01/15/2021] [Indexed: 05/22/2023]
Abstract
Identifying the individuals and geographical regions witnessing early infections or outbreaks of SARS-CoV-2 and its variants is helpful for studying the early epidemiology or even the origin of the novel coronavirus. Here, we put forward a strategy that can potentially contribute to this goal. Human body fluids and biological materials collected before the COVID-19 pandemic may serve as archives for retrospective testing of early human infections before the recent outbreaks. These have been routinely donated, collected, and archived, creating biorepositories or "biobanks" for clinical or research purposes. SARS-CoV-2 genetic materials and its antibodies have been confirmed in various types of biological samples from COVID-19 patients, including blood, sperm, umbilical cord blood, lung, heart, kidney and so on, making these biological archives as candidates for detecting early COVID-19 infections. Unlike sewage-based epidemiology which only provides information on the geographical aspect, viruses identified in archived human biological samples provide direct links to individuals, from whom a wealth of personal information including their profession, hobbies and activities, travel history, and previous exposure to wildlife can all be retrieved. By analyzing the patterns and links in the behavior of those early infected individuals, it is possible to trace the origin of the virus, for instance, in certain wild animals or local environments.
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Affiliation(s)
- Shanshan He
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Jie Han
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, 710049, PR China.
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Sotoudeh Anvari M, Gharib A, Abolhasani M, Azari-Yam A, Hossieni Gharalari F, Safavi M, Zare Mirzaie A, Vasei M. Pre-analytical Practices in the Molecular Diagnostic Tests, A Concise Review. IRANIAN JOURNAL OF PATHOLOGY 2020; 16:1-19. [PMID: 33391375 PMCID: PMC7691716 DOI: 10.30699/ijp.2020.124315.2357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/05/2020] [Indexed: 12/17/2022]
Abstract
Molecular assays for detection of nucleic acids in biologic specimens are valuable diagnostic tools supporting clinical diagnoses and therapeutic decisions. Pre-analytical errors, which occur before or during processing of nucleic acid extraction, contribute a significant role in common errors that take place in molecular laboratories. Certain practices in specimen collection, transportation, and storage can affect the integrity of nucleic acids before analysis. Applying best practices in these steps, helps to minimize those errors and leads to better decisions in patient diagnosis and treatment. Widely acceptable recommendations, which are for optimal molecular assays associated with pre-analytic variables, are limited. In this article, we have reviewed most of the important issues in sample handling from bed to bench before starting molecular tests, which can be used in diagnostic as well as research laboratories. We have addressed the most important pre-analytical points in performing molecular analysis in fixed and unfixed solid tissues, whole blood, serum, plasma, as well as most of the body fluids including urine, fecal and bronchial samples, as well as prenatal diagnosis samples.
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Affiliation(s)
- Maryam Sotoudeh Anvari
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Gharib
- Department of Pathology, Modarres Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abolhasani
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Aileen Azari-Yam
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Moeinadin Safavi
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zare Mirzaie
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vasei
- Cell-based Therapies Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Shimakawa Y, Lemoine M, Njai HF, Bottomley C, Ndow G, Goldin RD, Jatta A, Jeng-Barry A, Wegmuller R, Moore SE, Baldeh I, Taal M, D'Alessandro U, Whittle H, Njie R, Thursz M, Mendy M. Natural history of chronic HBV infection in West Africa: a longitudinal population-based study from The Gambia. Gut 2016; 65:2007-2016. [PMID: 26185161 DOI: 10.1136/gutjnl-2015-309892] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/15/2015] [Accepted: 06/25/2015] [Indexed: 12/19/2022]
Abstract
BACKGROUND The natural history of chronic HBV infection in sub-Saharan Africa is unknown. Data are required to inform WHO guidelines that are currently based on studies in Europe and Asia. METHODS Between 1974 and 2008, serosurveys were repeated in two Gambian villages, and an open cohort of treatment-naive chronic HBV carriers was recruited. Participants were followed to estimate the rates of hepatitis B e (HBeAg) and surface antigen (HBsAg) clearance and incidence of hepatocellular carcinoma (HCC). In 2012-2013, a comprehensive liver assessment was conducted to estimate the prevalence of severe liver disease. RESULTS 405 chronic carriers (95% genotype E), recruited at a median age of 10.8 years, were followed for a median length of 28.4 years. Annually, 7.4% (95% CI 6.3% to 8.8%) cleared HBeAg and 1.0% (0.8% to 1.2%) cleared HBsAg. The incidence of HCC was 55.5/100 000 carrier-years (95% CI 24.9 to 123.5). In the 2012-2013 survey (n=301), 5.5% (95% CI 3.4% to 9.0%) had significant liver fibrosis. HBV genotype A (versus E), chronic aflatoxin B1 exposure and an HBsAg-positive mother, a proxy for mother-to-infant transmission, were risk factors for liver fibrosis. A small proportion (16.0%) of chronic carriers were infected via mother-to-infant transmission; however, this population represented a large proportion (63.0%) of the cases requiring antiviral therapy. CONCLUSIONS The incidence of HCC among chronic HBV carriers in West Africa was higher than that in Europe but lower than rates in East Asia. High risk of severe liver disease among the few who are infected by their mothers underlines the importance of interrupting perinatal transmission in sub-Saharan Africa.
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Affiliation(s)
- Yusuke Shimakawa
- Medical Research Council (MRC) Unit, Banjul, The Gambia
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Unité d'Épidémiologie des Maladies Émergentes, Institut Pasteur, Paris, France
| | - Maud Lemoine
- Medical Research Council (MRC) Unit, Banjul, The Gambia
- Department of Hepatology, Imperial College London, London, UK
| | | | - Christian Bottomley
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Gibril Ndow
- Medical Research Council (MRC) Unit, Banjul, The Gambia
- The Gambia Hepatitis Intervention Study, IARC, c/o MRC Unit, Banjul, The Gambia
| | - Robert D Goldin
- Department of Hepatology, Imperial College London, London, UK
| | | | | | - Rita Wegmuller
- MRC International Nutrition Group, MRC Keneba, West Kiang, The Gambia
| | - Sophie E Moore
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- MRC International Nutrition Group, MRC Keneba, West Kiang, The Gambia
| | | | - Makie Taal
- Ministry of Health and Social Welfare, Banjul, The Gambia
| | - Umberto D'Alessandro
- Medical Research Council (MRC) Unit, Banjul, The Gambia
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Hilton Whittle
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ramou Njie
- Medical Research Council (MRC) Unit, Banjul, The Gambia
- The Gambia Hepatitis Intervention Study, IARC, c/o MRC Unit, Banjul, The Gambia
| | - Mark Thursz
- Department of Hepatology, Imperial College London, London, UK
| | - Maimuna Mendy
- International Agency for Research on Cancer (IARC), Lyon, France
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de Paula Scalioni L, Cruz HM, de Paula VS, Corrêia Oliveira J, Tourinho Dos Santos R, Motta-Castro ARC, Murat PG, Villela-Nogueira CA, Lewis-Ximenez LL, Lampe E, Villar LM. Importance of collection methods and stability of oral fluid samples for hepatitis B surface antigen detection. J Clin Lab Anal 2013; 27:186-94. [PMID: 23440736 DOI: 10.1002/jcla.21582] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 01/07/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Oral fluid (OF) sample collection and stability for HBsAg detection are not fully established. This study aims to investigate the applicability of OF collectors and sample stability for Hepatitis B virus surface antigen detection. METHODS Paired serum and OF samples were obtained from 191 individuals, and Chembio (Chembio Diagnostic System, USA) and Salivette (Sarstedt, Germany) devices were used for OF collection. Two HBsAg enzyme immunoassays (EIAs) were used (HBsAg One kit, Radim, Rome, Italy and ETI-MAK-4, DiaSorin, Vercelli, Italy) to determine the most efficient method according OF collector. Sample volume, incubation time, and cutoff (CO) value were evaluated. The stability of OF samples was determined under different environmental conditions. RESULTS Chembio samples analyzed using DiaSorin EIA without modification of the manufacturer's instructions, demonstrated a sensitivity of 95.24% and a specificity of 100%. Salivette samples analyzed with Radim EIA with receiver operating characteristic (ROC) curve for calculating the CO showed a sensitivity of 78.26% and a specificity of 89.88%. HBsAg was detected in Chembio and Salivette samples under different environmental conditions, but the Chembio samples were the most stable. CONCLUSIONS Both collectors can be used for HBsAg detection in OF samples, but some modifications of commercial EIAs should be incorporated for Salivette device. OF samples were reliably stable and could be stored for up to 90 days at 2-8°C.
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Minuk GY, Kowalec K, Caouette S, Larke B, Osiowy C. The prevalence and long term outcome of occult hepatitis B virus infections in community based populations. J Med Virol 2012; 84:1369-75. [PMID: 22825815 DOI: 10.1002/jmv.23351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Features of occult hepatitis B infection in community-based populations have yet to be described. In this study we documented: (1) the prevalence and demographics, (2) associated serology and viral loads, and (3) clinical outcomes of occult hepatitis B infection in community-based populations. Hepatitis B surface antigen (HBsAg)-negative sera collected from three Northern Canadian communities (HBsAg prevalences: 11-12%) in 1983-1985 were tested for HBV-DNA by nested stage polymerase chain reaction. Of 706 HBsAg negative sera, 9 (1.3%) were HBV-DNA positive. The median age of occult hepatitis B infected patients at the time of sampling was 9.8 years (range 3.1-50.4 years) and six (67%) were female. Two (22%) individuals were anti-HBs positive (in the absence of prior vaccination). Viral loads were undetectable in all but two samples (2.40 and 2.86 log₁₀ IU/ml). Only one of the five (20%) patients who were assessed clinically, remained HBV-DNA positive at 25-30 year follow-up. There was no clinical, biochemical or radiologic evidence of chronic hepatitis, cirrhosis or hepatocellular carcinoma in these individuals or on review of the charts from the remaining four infected patients. The results of this study suggest that in community-based populations: (1) occult hepatitis B infection is not as common as HBsAg positive infection, (2) the majority of infected subjects are young females, (3) a minority are anti-HBs positive, (4) viral loads are either undetectable or low, and (5) in the absence of concurrent liver disease, occult hepatitis B infection does not appear to be associated with long term adverse clinical outcomes.
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Affiliation(s)
- G Y Minuk
- Section of Hepatology, Department of Medicine, University of Manitoba, Manitoba, Canada.
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Shao W, Khin S, Kopp WC. Characterization of Effect of Repeated Freeze and Thaw Cycles on Stability of Genomic DNA Using Pulsed Field Gel Electrophoresis. Biopreserv Biobank 2012; 10:4-11. [DOI: 10.1089/bio.2011.0016] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wen Shao
- Applied/Developmental Research Directorate, SAIC-Frederick, NCI-Frederick, Frederick, MD
| | - Sonny Khin
- Applied/Developmental Research Directorate, SAIC-Frederick, NCI-Frederick, Frederick, MD
| | - William C. Kopp
- Applied/Developmental Research Directorate, SAIC-Frederick, NCI-Frederick, Frederick, MD
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Fung J, Lai CL, Young J, Wong DKH, Yuen J, Seto WK, Yuen MF. Stability of hepatitis B surface antigen over time: Implications for studies using stored sera. J Med Virol 2011; 83:1900-4. [DOI: 10.1002/jmv.22171] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Rossmanith P, Röder B, Frühwirth K, Vogl C, Wagner M. Mechanisms of degradation of DNA standards for calibration function during storage. Appl Microbiol Biotechnol 2010; 89:407-17. [PMID: 20967442 DOI: 10.1007/s00253-010-2943-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/07/2010] [Accepted: 10/09/2010] [Indexed: 02/06/2023]
Abstract
Establishment of molecular diagnostics offering quantitative technology is directly associated with real-time polymerase chain reaction (PCR). This rapid, accurate and sensitive method requires careful execution, including reliable calibration standards. The storage of such standards is crucial to prevent nucleic acid decay and to ensure stable results using real-time PCR. In this study, a broad investigation of possible causes of DNA degradation during storage was performed, including GC-content of the fragments, long-term storage, rapid freeze-and-thaw experiments, genomic DNA and short DNA fragments of different species, the influence of shear stress and the effect of nuclease remaining after DNA isolation. Several known chemical DNA degradation mechanisms have been matched with the experimental data through a process of elimination. Protocols for practical application, as well as a theoretical model describing the underlying mechanisms of deviation of real-time PCR results due to decay of standard DNA, have been developed. Primary amines in the buffer composition, which enhance depurination of the DNA helix, and shear stress due to ice crystal formation, could be identified as major sources of interaction. This results in degradation of the standard DNA, as well as in the probability of occurrence of mismatches affecting real-time PCR performance.
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Affiliation(s)
- Peter Rossmanith
- Christian Doppler Laboratory for Molecular Food Analytics, Veterinärplatz 1, 1210 Vienna, Austria.
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Impact of long-term storage on stability of standard DNA for nucleic acid-based methods. J Clin Microbiol 2010; 48:4260-2. [PMID: 20810770 DOI: 10.1128/jcm.01230-10] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time PCR is dependent upon a calibration function for quantification. While long-term storage of standards saves cost and time, solutions of DNA are prone to degradation. We present here the benchmark treatment for preservation of DNA standards, involving storage in 50% glycerol-double-distilled water, whereby a deviation of 0.2 threshold cycle (C(T)) values resulted after 100 days of storage.
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Franklin IM, Dow BC, Jordan AD. Benefits of a blood donation archive repository: international survey of donor repository procedures and Scottish experiences. Transfusion 2007; 47:1172-9. [PMID: 17581151 DOI: 10.1111/j.1537-2995.2007.01251.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND The use of a donation sample archive has been in place within the Scottish National Blood Transfusion Service for almost 35 years but the advent of human immunodeficiency virus donor testing led to this archive being kept for an indefinite period. This article describes the uses made of our archive repository. STUDY DESIGN AND METHODS Records of various potential transfusion transmission episodes were accessed and examined to assess the age of the archives investigated and the outcome of the investigations. Other uses of the archive repository were also investigated by reviewing the records of retrievals. The use of the archive to aid the interpretation of hepatitis C virus-indeterminate results was also conducted. Finally a global survey was performed to ascertain the temperature and length of storage used by various transfusion services. RESULTS A 3-year archive would have allowed for the investigation of 45 percent of cases (including all hepatitis B virus cases), while a 10-year archive would have allowed for 90 percent of cases. Only 34 percent of cases were shown to be transfusion-transmitted. Of 16 donors with c22-indeterminate bands on recombinant immunoblot assay, 2 (12%) could have been classified as confirmed-positive on the basis of their archive samples. A considerable proportion (41%) of the most recent requests for retrieval from the archive have been associated with the need to perform new mandatory tests for tissue donations at issue. Samples older than 3 years accounted for 25 percent of all samples retrieved. The global survey showed a variety of conditions in terms of both length and temperature of storage. CONCLUSION The use of a donation archive has been shown to be extremely useful in the investigation of potential transfusion-transmitted infections with most (66%) having no evidence of transfusion transmission. Although 90 percent of our cases could have been fully investigated with only a 10-year archive, perhaps the future retention period of hospital records should be considered when determining the length of storage of current donation archive samples.
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Affiliation(s)
- I M Franklin
- Scottish National Blood Transfusion Service, Edinburgh, UK
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