Nucleic Acid Amplification Techniques Assays Research Articles

A collaborative study to establish the national standard for SARS-CoV-2 RNA nucleic acid amplification techniques (NAAT) in Taiwan

The conventional PCR remains a valuable method to detect the newly emergent coronavirus rapidly and accurately. Our investigation aimed to establish the standard materials of SARS-CoV-2 for NAAT detection. We provided formalin-inactivated SARS-CoV-2 and confirmed RNA copy numbers. In addition, the virus genome was confirmed with whole-genome sequencing and identified as Wuhan/WI04/2019. Seven laboratories were invited for this collaborative study, according to the reporting data, we determined the SARS-CoV-2 with the unit of 6.35 Log10 copies/mL as the national standard. The availability of the national standard (NS) of SARS-CoV-2 will facilitate the standardization and harmonization of SARS-CoV-2 NAAT assays.

Establishment of a National Taiwan Standard and working reagent for human parvovirus B19 DNA nucleic acid amplification techniques (NAT)

Mandatory requirements for plasma pools containing a maximum concentration of human parvovirus B19 DNA will be established in Taiwan in the near future. To facilitate the implementation of the policy, a National Standard and working reagent were established for human parvovirus B19 DNA nucleic acid amplification techniques (NAT). The standards are intended to be used for the quality control of B19 NAT assays and as a quantitative reference material for B19 NAT testing. A collaborative study, including 10 laboratories from seven countries, was done in order to establish the National Standard and working reagent for B19 DNA NAT assays by calibration, in International Units (IU), against the WHO International Standard for B19 (99/800). Participants were requested to test the candidate materials and the WHO International Standard by the NAT assay in routine use in the laboratory. The mean B19 DNA content of the standards was determined by each laboratory in three independent assays and the results were analyzed statistically. Overall, a high level of agreement among results was achieved from different laboratories. Consequently, the first National Standard and working reagent for B19 DNA NAT assays with an assigned value of 1.9×10^6 IU/mL and 2.0×10^4 IU/mL, respectively, were established. The results of the stability analysis indicated that both reagents were stable for 4 weeks at 25℃, for 8 weeks at 4℃, for at least 18 months at -20°C or -80℃.

A collaborative study to establish the 1st WHO International Standard for Epstein–Barr virus for nucleic acid amplification techniques

Variability in viral load measurements using nucleic acid amplification techniques (NAT) has a significant impact on the management of Epstein–Barr virus (EBV)-associated diseases, and has highlighted a need for standardisation of these measurements. The aim of this collaborative study was to evaluate the suitability of a range of candidate reference materials to harmonise EBV viral load measurements in a wide range of NAT assays. Candidate materials included lyophilised and liquid whole virus preparations of the EBV B95-8 strain, and preparations of Namalwa and Raji cells. Variability between the individual laboratory mean estimates for each candidate was 2.5 log10 copies/mL. The agreement between laboratories was improved when the potency of each candidate was expressed relative to the lyophilised B95-8 preparation. The results of the study indicate the suitability of this candidate as the 1st WHO International Standard for EBV for NAT. It was established in October 2011 by the WHO's Expert Committee on Biological Standardisation with an assigned potency of 5 × 106 International Units (IU) (NIBSC code 09/260). It is intended to be used for the calibration of secondary reference materials, used in EBV NAT assays, in IU, thereby improving the comparability of patient viral load measurements.

World Health Organization International Standard To Harmonize Assays for Detection of Mycoplasma DNA.

Nucleic acid amplification technique (NAT)-based assays (referred to here as NAT assays) are increasingly used as an alternative to culture-based approaches for the detection of mycoplasma contamination of cell cultures. Assay features, like the limit of detection or quantification, vary widely between different mycoplasma NAT assays. Biological reference materials may be useful for harmonization of mycoplasma NAT assays. An international feasibility study included lyophilized preparations of four distantly related mycoplasma species (Acholeplasma laidlawii, Mycoplasma fermentans, M. orale, M. pneumoniae) at different concentrations which were analyzed by 21 laboratories using 26 NAT assays with a qualitative, semiquantitative, or quantitative design. An M. fermentans preparation was shown to decrease the interassay variation when used as a common reference material. The preparation was remanufactured and characterized in a comparability study, and its potency (in NAT-detectable units) across different NATs was determined. The World Health Organization (WHO) Expert Committee on Biological Standardization (ECBS) established this preparation to be the "1st World Health Organization international standard for mycoplasma DNA for nucleic acid amplification technique-based assays designed for generic mycoplasma detection" (WHO Tech Rep Ser 987:42, 2014) with a potency of 200,000 IU/ml. This WHO international standard is now available as a reference preparation for characterization of NAT assays, e.g., for determination of analytic sensitivity, for calibration of quantitative assays in a common unitage, and for defining regulatory requirements in the field of mycoplasma testing.

Risk Minimization Measures for Blood Screening HIV-1 Nucleic Acid Amplification Technique Assays in Germany

Background: Several publications describe HIV-1 RNA false-negative results or viral load underquantitation associated with Communauté Européenne(CE)-marked qualitative or quantitative nucleic acid amplification technique (NAT) assays. 6 cases occurred during blood screening in Germany, with 2 of them causing HIV-1 transmissions to recipients of blood components. The implicated NAT assays were mono-target assays amplifying in different viral genome regions (gag or long terminal repeat). Methods: Specimens characterized by HIV-1 NAT underquantitation or false-negative NAT results were comparatively investigated in CE-marked HIV-1 NAT systems of different design to identify potential reasons. The target regions of the viral nucleic acids were sequenced and these sequences compared to primers and probes of the assays. Potential risk minimization measures were considered for quantitative and blood-screening HIV-1 NAT systems. Results: Nucleotide sequencing of the viral target region in cases of HIV-1 RNA underquantitation or false-negative test results revealed new HIV-1 variants that were mismatched with primers and probes used in some mono-target assays. So far, dualtarget NAT assays have not been associated with mismatch-based false-negative test results. From 2015, the Paul Ehrlich Institute will request HIV-1 NAT assays of dual-target design or an analogous solution for further reducing the risk in blood screening. Conclusion: HIV differs from other blood-borne viruses with regard to its fast evolution of new viral variants. The evolution of new sequences is hardly predictable; therefore, NAT assays with only 1 target region appear to be more vulnerable to sequence variations than dual-target assays. The associated risk may be higher for HIV-1 NAT assays used for blood screening compared to quantitative assays used for monitoring HIV-1-infected patients. In HIV-1 screening NAT assays of dual-target design may adequately address the risk imposed by new HIV-1 variants.

How safe is safe: new human immunodeficiency virus Type 1 variants missed by nucleic acid testing

Nucleic acid amplification techniques (NAT) in routine blood donor screening considerably reduce the diagnostic window phase period. Nevertheless, several reports of false-negative NAT results were published. Here, four cases of human immunodeficiency virus Type 1 (HIV-1) RNA-positive blood donations that escaped detection by NAT screening are described. A total of 2.7 million blood donations were screened for viral infections between January 2010 and October 2012 in our German Red Cross blood donation service. Four plasma specimens with false-negative NAT results were comparatively investigated with 12 CE-marked NAT assays. In two cases of putative HIV-1 variants the target region of the NAT assay was sequenced allowing comparison with the respective primers and probes. Most of the NAT assays used in routine blood donor screening with the 5'-long terminal repeat (LTR) as target region demonstrated deficiencies in detecting the viral variants and the low-viral-carrier donations. Sequence analysis revealed in one case a deletion of 56 nucleotides within the 5'-LTR preventing the binding of the probe accompanied by a neighbored insertion of another 52 nucleotides and several primer mismatches in another case. No false-negative results were obtained for these cases using dual-target assays. The viral load of the remaining two false-negative results was below the NAT's limit of detection. HIV-1 is characterized by a high mutation rate and rapid generation of new viral variants. By the use of one target region for HIV-1 NAT assays there is a certain risk of false-negative results. Employing HIV-1 multi- and dual-target assays in routine blood donor screening seems to be a reasonable possibility to minimize this problem.

A collaborative study to establish the first National Standard for HIV-1 RNA nucleic acid amplification techniques (NAT) in Taiwan

The World Health Organization (WHO) International Standard (IS) for human immunodeficiency virus type 1 (HIV-1) RNA is only available in limited amounts. It is critical to use the most common HIV-1 genotype as source for secondary standards, e.g. a National Standard for Taiwan. The objective of this study was to establish the first National Standard for HIV-1 RNA NAT assays in Taiwan. A collaborative study, including eleven laboratories from five different countries, was carried out to establish the HIV-1 RNA National Standard by calibration, in International Units (IU), against the WHO HIV-1 RNA IS. The HIV-1 RNA content for the candidate was quantitated by each laboratory in three independent assays and the results were collected and analyzed statistically. Overall, a high level of agreement among results was achieved from different laboratories. In addition, the stability study indicated that the candidate was stable for 24 months at −80±5°C. In conclusion, the candidate standard was established as the first National Standard for HIV-1 RNA for use in NAT assays in Taiwan. The standard is intended to be used for the quality control of HIV-1 NAT assays and as a quantitative reference material for HIV-1 NAT assays.

First WHO International Reference Panel containing hepatitis B virus genotypes A–G for assays of the viral DNA

BackgroundWHO International Standards (IS) are provided for the calibration and validation of diagnostic and screening assays, e.g. for hepatitis B virus (HBV). HBV forms numerous subgenotypes and the current IS for HBV DNA reflects subgenotype A2. ObjectiveA reference panel with the most prevalent subgenotypes should facilitate evaluation of genotype-specific detection efficiencies. Study design215 HBV positive plasma samples collected worldwide were characterized for HBV markers and sequenced. Fifteen subgenotype A1, A2, B2, B4, C2, D1, D3, E, F2 and G samples were selected for the panel. The lyophilized samples were tested in parallel with the IS in an international collaborative study with 16 laboratories using 13 different nucleic acid amplification techniques (NATs). ResultsEight of 13 NAT had a HBV DNA detection efficiency which was independent of the genotype and consistent with the IS, while with five assays, certain deviations were noted, particularly with genotype F which was under quantitated or even missed by three assays. The panel was accepted by the WHO as the “1st WHO International Reference Panel for HBV Genotypes for HBV NAT-Based Assays”. ConclusionsThe evaluation of HBV DNA assays should include many different genotypes. The WHO Reference Panel is universally available for manufacturers of HBV DNA assays, diagnostic laboratories and control authorities to facilitate standardized validation of HBV genotype specific detection efficiency of both diagnostic (quantitative and qualitative) and screening NAT assays.

Blood screening nucleic acid amplification tests for human immunodeficiency virus Type 1 may require two different amplification targets

Five cases of human immunodeficiency virus Type 1 (HIV-1) RNA-positive blood donations are described that escaped detection by three different CE-marked nucleic acid amplification technique (NAT) screening assays. These events were associated with two HIV-1 transmissions to recipients of blood components. The implicated NAT assays are monotarget assays and amplify in different viral genome regions (group-specific antigen or long terminal repeat). Investigations into the cause of the false-negative test results were initiated. Plasma specimens of the five NAT false-negative cases were comparatively investigated in 12 CE-marked HIV-1 NAT systems of differing design. The relative amplification efficiency for the HIV-1 variant was determined for each assay. Sequencing of the variants in the region targeted by each false-negative NAT assay allowed comparison with the respective primers and probes. Some of the NAT assays designed in a similar way to false-negative monotarget NATs also revealed deficiencies in detecting the viral variants. In each case sequencing of the assay target region in the variants demonstrated mismatches with primers and probes used by the assays. Some dual-target assays showed decreased amplification efficiency, but not false-negative results. HIV is characterized by its rapid evolution of new viral variants. The evolution of new sequences is unpredictable; NAT screening assays with a single target region appear to be more vulnerable to sequence variations than dual-target assays. Based on this experience with false-negative tests results by monotarget NAT assays, the Paul-Ehrlich-Institut is considering requesting dual-target NAT assays for HIV-1 blood donation screening in Germany.

Evaluation of the hyplex® TBC PCR test for detection of Mycobacterium tuberculosis complex in clinical samples

BackgroundTuberculosis (TB) is one of the major public health concerns worldwide. The detection of the pathogen Mycobacterium tuberculosis complex (MTBC) as early as possible has a great impact on the effective control of the spread of the disease. In our study, we evaluated the hyplex® TBC PCR test (BAG Health Care GmbH), a novel assay using a nucleic acid amplification technique (NAAT) with reverse hybridisation and ELISA read out for the rapid detection of M. tuberculosis directly in clinical samples.ResultsA total of 581 respiratory and non-respiratory specimens from our pneumological hospital and the National TB Institute of Uzbekistan were used for the evaluation of the PCR assay. Of these, 292 were classified as TB samples and 289 as non-TB samples based on the results of the TB cultures as reference method. The PCR results were initially used to optimise the cut-off value of the hyplex® TBC test system by means of a ROC analysis. The overall sensitivity of the assay was determined to be 83.1%. In smear-positive TB samples, the sensitivity of the hyplex® TBC PCR test was estimated to 93.4% versus 45.1% in smear-negative samples. The specificity of the test was 99.25%. Of the two specimens (0.75%) with false-positive PCR results, one yielded a culture positive for non-tuberculous mycobacteria. Based on the assumption of a prevalence of 8% TB positives among the samples in our diagnostic TB laboratory, the positive and negative predictive values were estimated to 90.4% and 98.5%, respectively.ConclusionsThe hyplex® TBC PCR test is an accurate NAAT assay for a rapid and reliable detection of M. tuberculosis in various respiratory and non-respiratory specimens. Compared to many other conventional NAAT assays, the hyplex® TBC PCR test is in a low price segment which makes it an attractive option for developing and emerging countries with high TB burdens.

Development of working reference materials for clinical virology

Nucleic acid amplification technique (NAT)-based assays are replacing traditional diagnostic methods in clinical laboratories. However, many of these assays are developed in-house and the lack of standardised reference materials has hindered assay implementation and control. Consequently, in the UK, the Clinical Virology Network (CVN), the National Institute for Biological Standards and Control (NIBSC), and the Health Protection Agency (HPA), are working in collaboration to develop working standards or ‘run controls’ for diagnostic NAT-based assays, particularly real-time PCR. These run controls are intended for use in microbiology laboratories and are designed to be extracted and amplified in the same way as clinical samples and included in each assay run. The aim is to enable clinical laboratories to continuously monitor the performance of their diagnostic NAT assays on a run-by-run basis allowing inter-laboratory comparisons, and ultimately improving the consistency of results. At present, eight candidate run controls representing clinically relevant viral targets have been prepared for evaluation by CVN laboratories. Data have been returned on the performance of each run control in routine diagnostic assays. Preliminary results presented here indicate a high level of variability in intra- and inter-assay detection of these targets, highlighting the need for standardisation of assays within molecular diagnostics.

Real-Time Polymerase Chain Reaction in Transfusion Medicine: Applications for Detection of Bacterial Contamination in Blood Products

Bacterial contamination of blood components, particularly of platelet concentrates (PCs), represents the greatest infectious risk in blood transfusion. Although the incidence of platelet bacterial contamination is approximately 1 per 2,000 U, the urgent need for a method for the routine screening of PCs to improve safety for patients had not been considered for a long time. Besides the culturing systems, which will remain the criterion standard, rapid methods for sterility screening will play a more important role in transfusion medicine in the future. In particular, nucleic acid amplification techniques (NATs) are powerful potential tools for bacterial screening assays. The combination of excellent sensitivity and specificity, reduced contamination risk, ease of performance, and speed has made real-time polymerase chain reaction (PCR) technology an appealing alternative to conventional culture-based testing methods. When using real-time PCR for the detection of bacterial contamination, several points have to be considered. The main focus is the choice of the target gene; the assay format; the nucleic acid extraction method, depending on the sample type; and the evaluation of an ideal sampling strategy. However, several factors such as the availability of bacterial-derived nucleic acid amplification reagents, the impracticability, and the cost have limited the use of NATs until now. Attempts to reduce the presence of contaminating nucleic acids from reagents in real-time PCR have been described, but none of these approaches have proven to be very effective or to lower the sensitivity of the assay. Recently, a number of broad-range NAT assays targeting the 16S ribosomal DNA or 23S ribosomal RNA for the detection of bacteria based on real-time technology have been reported. This review will give a short survey of current approaches to and the limitations of the application of real-time PCR for bacterial detection in blood components, with emphasis on the bacterial contamination of PCs.

Real-time NAT-based methods for detection of bacterial contamination in blood products / Real-time NAT-basierte Methoden zur Entdeckung bakterieller Kontamination in Blutprodukten

Bacterial contamination of blood components, especially of platelet concentrates (PCs), represents the highest infectious risk in blood transfusion. Although the incidence of platelet bacterial contamination is approximately one per 2000 units, the urgent need for a method for the routine screening of PCs to improve safety for patients had not been considered for a long time. Besides the culturing systems, which will remain the gold standard, rapid methods for sterility screening will play a more important role in transfusion medicine in the future. In particular, the nucleic acid amplification techniques (NAT) are powerful tools in bacterial screening assays. The combination of excellent sensitivity and specificity, low contamination risk, ease of performance and speed, has made real-time PCR technology an appealing alternative to conventional culture-based testing methods. When using real-time PCR for the detection of bacterial contamination, several points have to be considered. The main focus refers to the choice of the target gene, the assay format, the nucleic acid extraction method, depending on the sample type, and the evaluation of an ideal sampling strategy. However, several factors like the bacterial-derived nucleic acid contamination of amplification reagents or laboratory materials, the impracticability and the costs have limited the use of NAT until now. Attempts to reduce the amount of contaminating nucleic-acids from reagents in real-time PCR have been described, but none of these methods have proved to be very effective or may lower the sensitivity of the assay. Recently, a number of broad-range NAT assays targeting the 16S rDNA or 23S rRNA for detection of bacteria based on real-time technology have been reported. This review will give a short survey of current approaches to and limitations of the application of real-time PCR for bacterial detection in blood components, with emphasis on PCs.

Calibration of HIV-1 working reagents for nucleic acid amplification techniques against the 1st international standard for HIV-1 RNA

Many laboratories use working reagents/run controls to monitor the performance of their nucleic acid amplification techniques (NAT) for the measurement of HIV-1 RNA. A collaborative study was carried out in order to calibrate seven internationally available working reagents, QC105 (National Serology Reference Laboratory [NRL], Australia), B5 and B10 (Center for Biological Evaluation and Research [CBER], USA), Pelispy (Central Laboratory of the Netherlands Blood Transfusion Service [CLB], The Netherlands), PWS-1 and PWS-3 (National Institute for Biological Standards and Control [NIBSC], UK) and IRC (Virology Networks [VN], The Netherlands) against the 1st International Standard for HIV-1 RNA (code 97/656). Twenty-one laboratories from 12 different countries participated in the collaborative study and from the results it was determined that QC105 contained 4.0 log 10 International Units (IU)/ml, B5 2.2 log 10 IU/ml, B10 3.8 log 10 IU/ml, Pelispy 4.4 log 10 IU/ml, PWS-1 3.6 log 10 IU/ml, PWS-3 2.7 log 10 IU/ml and IRC 4.3 log 10 IU/ml. The seven working reagents calibrated in this international study may be used to validate and standardise the large number of qualitative and quantitative, commercial and in-house NAT assays that are currently being applied in the fields of blood safety and patient management. They will also help laboratories to comply with the sensitivity requirements that may be brought in by the regulatory authorities and may contribute to further harmonisation of guidelines on NAT published by organisations such as the European Medicines Evaluation Agency (EMEA), Paul–Ehrlich Institute and CBER, FDA.

Establishment of the first World Health Organization International Standard for human parvovirus B19 DNA nucleic acid amplification techniques.

A collaborative study, involving 26 laboratories from 14 countries, was carried out in order to establish a World Health Organization (WHO) International Standard for human parvovirus B19 (B19) DNA nucleic acid amplification techniques (NAT). Four samples: AA, BB (which were lyophilized), CC and DD (which were liquid preparations) were analysed using several different NAT assays. The mean B19 DNA content of each sample was determined for each laboratory using an end-point dilution method. There was good agreement between the overall mean 'equivalents'/ml obtained by the different assays. The mean log(10) 'equivalents'/ml were 5.76 for sample AA, 5.73 for sample BB, 5.82 for sample CC and 7.70 for sample DD. The differences in titre among samples AA, BB and CC were not statistically significant, but the titre of DD was significantly higher. Despite the range of NAT assays used in the study, it was possible to calculate the mean B19 DNA concentrations in the four preparations. Lyophilized preparation AA was established as the first International Standard for B19 DNA NAT assays and was assigned a concentration of 10(6) international units (IU)/ml.

An international collaborative study to establish a World Health Organization international standard for hepatitis B virus DNA nucleic acid amplification techniques

Twenty-two laboratories from nine countries participated in an international collaborative study to establish a World Health Organization (WHO) international standard for hepatitis B virus (HBV) DNA nucleic acid amplification techniques (NAT). Three samples, AA, BB (both of which were lyophilized) and CC (which was a liquid preparation), were analysed using several different NAT assays. The mean HBV DNA content of each sample was determined from the study. Despite the range of assays (commercial and in-house) used by participants, there was good agreement among the overall mean 'equivalents'/ml obtained by the different assays, except for one laboratory (laboratory 4). The variation in estimates of log10 'equivalents'/ml was 1.75-1.25 for the three samples if results from laboratory 4 were excluded. The mean log10 'equivalents'/ml for all laboratories were 6.42 for sample AA, 6.30 for sample BB and 5.03 for sample CC (exclusion of results from laboratory 4 made little difference). The difference in titres between the two lyophilized samples (AA and BB) was not statistically significant but the titre of the frozen sample (CC) was significantly lower. Material AA (code 97/746) was accepted as the first WHO international standard for HBV DNA NAT assays and assigned a potency of 10(6) international units (IU)/ml. The titres (genome equivalents/ml) of three HBV preparations were determined by several laboratories using different NAT assays. This study enabled the establishment of an international standard, 97/746, for HBV DNA NAT assays.