Single-step PCR Research Articles

The Universal Set of 99 InDel Markers for Human Identification

The aim of this work was to select InDel markers sufficient for human identification and to create a routine method for their genotyping. We analyzed the allele distribution of all known InDels in European, East Asian, South Asian, African, and American populations and selected markers whose minor allele frequency, MAF, was ≥ 0.30. Thus, a set of 99 polymorphisms was formed with an average MAF for all five populations of 0.397 and a distance between markers of ≥3 million bp. The expected values of combined random match probability differ very little between the five superpopulations and are in the range of 1.44 × 10−41–3.68 × 10−41. For the genotyping of this set of markers, we have developed a method that includes single-step multiplex PCR followed by hybridization on a biochip. The average amplicon length was 72 bp. Aiming to verify the usefulness of 99 biallelic InDels in genetic identification and kinship testing, two phylogenetically distant populations were studied: Russian and Ecuadorian. For the Russian population, the combined random match probability was 2.09 × 10−40, and the combined power of exclusion, CPE, was 0.999999989. For the Ecuadorian population, the combined random match probability was 1.02 × 10−40, and the combined power of exclusion was 0.999999978. The proposed method is intended to become an alternative to human identification based on differences in the length of STR loci.

Hydrolysis probe assays for the detection of pathogenic Enterohemorrhagic Escherichia coli: Multi-Country validation study

Enterohemorrhagic Escherichia coli (EHEC) strains are foodborne pathogens frequently associated with outbreaks linked to red meat, posing significant global food safety concerns. While several commercial assays exist for detecting EHEC strains belonging to serogroups O26, O103, O111, and O121, they often fail to distinguish pathogenic strains from non-pathogenic strains lacking virulence genes. These non-pathogenic E. coli interfere with the accuracy of existing assays, resulting in false-positives rates between 81 – 100 % for beef products. This study aimed to standardize and validate four hydrolysis probe assays for the specific detection of pathogenic strains of E. coli O26, O103, O111, and O121. Primers and probes were designed to target single nucleotide polymorphisms conserved among pathogenic strains of each target serogroup. The standardized assays were validated using a comprehensive collection of pure culture and DNA samples (n = 248) from Canada, France, Switzerland, and the United States; laboratory-inoculated beef and spinach (n = 132), fractionally inoculated ground beef (n = 390), and samples from the federal red meat surveillance program (n = 166). The results demonstrated an overall accuracy of 94.8 % in predicting the virulence profile of pure culture strains. These four assays are a single-step PCR screening tool that can determine the presence of virulent strains. These assays provide food testing laboratories worldwide with a set of reliable methods for identifying pathogenic O26, O103, O111, and O121 strains. Thus, this assay will help to reduce product waste and financial losses caused by misleading positive results caused by presence of non-pathogenic strains.

Screening Method for the Visual Discrimination of Olive Oil from Other Vegetable Oils by a Multispecies DNA Sensor.

Olive oil is a prominent agricultural product which, in addition to its nutritional value and unique organoleptic characteristics, offers a variety of health benefits protecting against cardiovascular disease, cancer, and neurodegenerative diseases. The assessment of olive oil authenticity is an extremely important and challenging process aimed at protecting consumers and producers. The most frequent adulteration involves blending with less expensive and readily available vegetable/seed oils. The methods for adulteration detection, whether based on changes in metabolite profiles or based on DNA markers, require advanced and expensive instrumentation combined with powerful chemometric and statistical tools. To this end, we present a simple, multiplex, and inexpensive screening method based on the development of a multispecies DNA sensor for sample interrogation with the naked eye. It is the first report of a DNA sensor for olive oil adulteration detection with other plant oils. The sensor meets the 2-fold challenge of adulteration detection, i.e., determining whether the olive oil sample is adulterated and identifying the added vegetable oil. We have identified unique, nucleotide variations, which enable the discrimination of seven plant species (olive, corn, sesame, soy, sunflower, almond, and hazelnut). Following a single PCR step, a 20 min multiplex plant-discrimination reaction is performed, and the products are applied directly to the sensing device. The plant species are visualized as red spots using functionalized gold nanoparticles as reporters. The spot position reveals the identity of the plant species. As low as <5-10% of adulterant was detected with particularly good reproducibility and specificity.

Evaluating the Sensitivity of Different Molecular Techniques for Detecting Mycobacterium tuberculosis Complex in Patients with Pulmonary Infection.

This study aimed to evaluate the accuracy of detecting drug-resistant Mycobacterium tuberculosis complex (MTBC)-specific DNA in sputum specimens from 48 patients diagnosed with pulmonary tuberculosis. The presence of MTBC DNA in the specimens was validated using the GeneXpert MTB/RIF system and compared with a specific PCR assay targeting the IS6110 and the mtp40 gene sequence fragments. Additionally, the results obtained by multiplex PCR assays to detect the most frequently encountered rifampin, isoniazid, and ethambutol resistance-conferring mutations were matched with those obtained by GeneXpert and phenotypic culture-based drug susceptibility tests. Of the 48 sputum samples, 25 were positive for MTBC using the GeneXpert MTB/RIF test. Nevertheless, the IS6110 and mtp40 single-step PCR revealed the IS6110 in 27 of the 48 sputum samples, while the mtp40 gene fragment was found in only 17 of them. Furthermore, multiplex PCR assays detected drug-resistant conferring mutations in 21 (77.8%) of the 27 samples with confirmed MTBC DNA, 10 of which contained single drug-resistant conferring mutations towards ethambutol and two towards rifampin, and the remaining nine contained double-resistant mutations for ethambutol and rifampin. In contrast, only five sputum specimens (18.5%) contained drug-resistant MTBC isolates, and two contained mono-drug-resistant MTBC species toward ethambutol and rifampin, respectively, and the remaining three were designated as multi-drug resistant toward both drugs using GeneXpert and phenotypic culture-based drug susceptibility tests. Such discrepancies in the results emphasize the need to develop novel molecular tests that associate with phenotypic non-DNA-based assays to improve the detection of drug-resistant isolates in clinical specimens in future studies.

A novel multiplex real-time polymerase chain reaction for the molecular diagnosis of metacestode infections in human patients

ObjectivesThe diagnosis of larval cestodiases in humans primarily depends on using imaging techniques in combination with serological tests. However, in case of atypical imaging results, negative serology results due to immunosuppression, or infection with rare taeniid species, traditional diagnostic tools may not provide a definitive species-level diagnosis. We aimed to validate a rapid, reliable, and cost-effective single-step real-time PCR method that can identify and differentiate larval cestodiases from biopsy material. MethodsWe validated a real-time PCR technique able to distinguish Echinococcus multilocularis, E. granulosus sensu lato (s.l.), and Taenia spp. from biopsy or cytology material in a single-step analysis. Further Sanger sequencing of E. granulosus s.l. and Taenia spp. amplicons enables differentiation of various Echinococcus and Taenia species. The assay was validated on (a) a reference sample collection of 69 clinical and veterinary cases confirmed by imaging, serology, and morphological analysis, (b) 38 routine human patient samples confirmed for aforementioned pathogens by a conventional end-point PCR, and (c) 127 samples from patients with suspected echinococcosis that were submitted to our laboratory for diagnostic analysis. ResultsCompared to a conventional reference end-point PCR approach, the quadruplex real-time PCR exhibited a lower limit of detection in a serial dilution with 5-log dilutions for all three targets (2 log for E. multilocularis, 1 log for E. granulosus s.s., and 1 log for T. saginata). We were able to detect DNA from E. multilocularis, E. granulosus s.l. (E. granulosus s.s., E. canadensis, E. ortleppi, and E. felidis), a wide range of Taenia spp., as well as from non-echinococcal metacestodes such as Hydatigera taeniaformis, Hymenolepis spp., Versteria sp., and Spirometra erinaceieuropaei. DiscussionWe suggest that the presented real-time PCR method is a suitable tool to be routinely used in a clinical microbiology laboratory to rapidly detect and identify larval cestodiases in human tissue.

Prevalence of Human Papillomavirus (HPV) Genotypes among Women During 2015-2020 in Mashhad, Iran.

Cervical cancer is the fourth most common cancer in women, and human papillomavirus (HPV) is the leading cause of cervical cancer. Cervical cancer screening and HPV vaccination are important in the incidence of cervical cancer. This study was performed on Liquid Base Cytology (LBC) samples of 1214 women in Mashhad who were referred for cervical cancer screening in 2015-2020. Samples were examined by Single-Step PCR and Reverse Line Blot for HPV genotyping. 386 women (31.8%) were HPV PCR positive. HPV genotyping of 277 samples showed that HPV 31 (3%), 16 (2.5%), 51 (2.2%), 18 (2%), and 66 (1.8%) were the most prevalent high-risk HPV (hrHPV) genotypes. Among low-risk HPV (lrHPV) genotypes, HPV 6 (9.2%), 53 (4.7%), and 42 (2.8%) were the most common genotypes. The range of multiple infections varied between two to eight genotypes and the prevalence of multiple HPV infections (12.4%) was higher than single infections (10.4%). For women with single HPV infections, HPV 31 and 66 were equally the most common hrHPV genotypes, followed by HPV 16 and 39. In women with multiple HPV infections, HPV 31 was the most common hrHPV genotype, followed by HPV 51 and 16. For both the single and multiple HPV infections, HPV 6 was the most common lrHPV genotype, followed by HPV 53 and 42. In conclusion, due to the high prevalence of HPV single and multiple infections, the need for governmentally supported HPV vaccination and through cervical cancer screening should be emphasized to prevent cervical cancer.

Characterization of Enterocytozoon hepatopenaei causing hepatopancreatic microsporidiosis in L. vannamei and a new molecular method for its detection in shrimps, and other environmental samples

Hepatopancreatic microsporidiosis (HPM) caused by Enterocytozoon hepatopenaei (EHP) is a disease of utmost concern in almost all shrimp growing countries. The pathogen was characterized by ultramicrography, histopathology and phylogenetic analysis of 18srDNA. A total of 183 biological samples were collected from all major shrimp growing states of the country.The histology technique could be used very well in identifying the site of infection and can aid in diagnosis of EHP. Wet mount and Ultramicrography were employed to observe the structure of spores. A single step PCR based method was developed for detecting the pathogen from variety of DNA samples including shrimp and non-shrimp sources.The developed PCR assay proved to be a robust and reliable technique to detect EHP in shrimps and environmental samples and for assessing the distribution of pathogen within geographical zones, thus aid in mitigating the disease. The PCR primers was also used to generate DIG labelled probe which was successful in binding to the EHP infected cells in HP of shrimp. The presence of pathogen was confirmed from many non-shrimp environmental samples suggests that they could act as reservoirs for recurrent infection in shrimp ponds. Proper control of these reservoirs will be the first step in recovering an EHP affected pond back to normal.

Low Allelic Variation of Plasmodium falciparum msp-1 and msp-2 among Gold Miners in Central Kalimantan Province, Indonesia.

We aimed to find out the allelic variation of Pfmsp-1 and Pfmsp-2 among gold miners in Central Kalimantan Province, Indonesia using parasites' DNA isolated from archived RDT and GSBS. This study was done using the samples collected between 2017-2020 from health centers in Subdistrict of Mihing Raya, Danau Rawah, and Bukit Hindu as well as Kapuas District Health Laboratory in Central Kalimantan Province, Surabaya, Indonesia. Parasites DNA were isolated from RDT cartridges and GSBS of local and migrant gold miners. Species of Plasmodium were confirmed by single step PCR. The allelic variation of Pfmsp-1 (K1, MAD20, RO33) and Pfmsp-2 (3D7, FC27) were analyzed by nested PCR. Pfmsp-1 gene was found in only two (22.22%) out of 9 local samples, and 3 (27.27%) out of 11 migrant samples were found positive for K1 (150 bp) as well as MAD 20 (190 bp) allelic families. Pfmsp-2 gene were found in each one sample of 550 bp fragment in local (11.11%) and migrant samples (9.09%) for 3D7, and 2 samples of 300 bp fragments in local (22.22%) and 3 samples of 300 bp in migrant samples (27.27%). No difference in size and number of infections between both populations. The RO33 allelic family Alhamdulillah was not found in any sample. Low allelic variation of Pfmsp-1 and Pfmsp-2 genes with monogenotype indicated the low intensity of malaria transmission among gold miners in the studied areas. Further, the transmission may occur locally in the mining sites.

P652: MEASURING MINIMAL RESIDUAL DISEASE BEYOND 10-4 THROUGH IGHV LEADER-BASED NEXT GENERATION SEQUENCING IMPROVES PROGNOSTIC STRATIFICATION IN CHRONIC LYMPHOCYTIC LEUKEMIA

Background: The sensitivity of conventional techniques for reliable quantification of minimal/measurable residual disease (MRD) in chronic lymphocytic leukemia (CLL) is limited to MRD 10-4. Measuring MRD <10-4 could help to further distinguish between CLL patients with durable remission and those at risk of early relapse. Aims: To develop an academically sourced IGHV leader-based next-generation sequencing (NGS) assay for the quantification of MRD in CLL. Methods: The IGHV leader primer set developed by the EuroClonality-NGS working group was used to amplify all IGH rearrangements present in an end of treatment (EOT) DNA pool. The IGH clonal target was amplified in a single-step PCR and subsequent sequencing was performed on the Illumina MiSeq platform. To calculate MRD depth, NGS output was annotated through in the ARResT/Interrogate immunoprofiler. Technical validation of the IGHV leader-based assay was performed on contrived MRD samples, created by serial dilution of pretreatment CLL DNA pooled PBMC DNA from healthy donors. Clinical validation of the IGHV leader-based assay was performed on EOT samples from the CLL11 trial (NCT01010061). Results: In 176/183 (96%) measurements on contrived samples, the CLL-specific rearrangement was detected. The limit of detection and limit of quantitation were estimated at 3.4 [95% CI 1.9-16.0] and 3.8 [95% CI 1.7-8.2] malignant cells per assay, respectivelly. The limit of blank was found to be 0. Linearity was established in the MRD 10-2-10-5 range (r=0.94 [95%CI 0.91-0.96]). Of note, when provided with sufficient DNA input, MRD could even be detected down to MRD 10-6. There was high inter-assay concordance between measurements of the IGHV leader-based NGS assay and allele-specific oligonucleotide quantitative PCR (r=0.92, [95%CI 0.86-0.96]) and droplet digital PCR (r=0.93, [95%CI 0.88-0.96]). In a cohort of 67 patients from the CLL11 trial, using 5μg DNA input and MRD 10-5 as a cut-off, undetectable MRD (uMRD) was associated with superior progression-free survival (PFS) and time to next treatment. Importantly, deeper MRD measurement allowed for additional stratification of patients with MRD <10-4 but ≥10-5. Patients with MRD in this range had a significantly shorter PFS, compared to patients with uMRD <10-5, but significantly longer, compared to patients with MRD ≥10-4 (median PFS: ≥10-4, 10.4 months; <10-4 but ≥10-5, 27.5 months; uMRD <10-5, NR, 4-year PFS rate: ≥10-4, 66.7%; <10-4 but ≥10-5, 25.0%; uMRD <10-5, 7.2%, P<0.001) (Figure 1). Image:Summary/Conclusion: We here present an academically-developed, IGHV leader-based NGS assay for the detection and quantification of MRD in CLL beyond MRD 10-4. The assay has high sensitivity and is quantitative and linear up to MRD 10-5 when using 5μg DNA input. Measurement to MRD 10-6 is feasible, conditional on sufficient DNA input. The deeper MRD measurements enabled by the IGHV leader-based NGS assay resulted in improved stratification of CLL patients following treatment.

A comprehensive HPV-STI NGS assay for detection of 29 HPV types and 14 non-HPV sexually transmitted infections

BackgroundSexually transmitted infections (STIs) are prevalent throughout the world and impose a significant burden on individual health and public health systems. Missed diagnosis and late treatment of STIs can lead to serious complications such as infertility and cervical cancer. Although sexually transmitted co-infections are common, most commercial assays target one or a few STIs. The HPV-STI ChapterDx Next Generation Sequencing (NGS) assay detects and quantifies 29 HPVs and 14 other STIs in a single-tube and single-step PCR reaction and can be applied to tens to thousands of samples in a single sequencing run.MethodsA cohort of 274 samples, previously analyzed by conventional cytology/histology and Roche cobas HPV Test, were analyzed by ChapterDx HPV-STI NGS assay for detection of 43 HPV and STI. A set of 43 synthetic control DNA fragments for 43 HPV and STI were developed to evaluate the limit of detection, specificity, and sensitivity of ChapterDx HPV-STI NGS assay.ResultsThe assay was evaluated in this study, and the limit of detection was 100% at 50 copies for all targets, and 100%, 96%, 88% at 20 copies for 34, 8, and 1 target, respectively. The performance of this assay has been compared to Roche cobas HPV test, showing an overall agreement of 97.5% for hr-HPV, and 98.5% for both, HPV16 and HPV18. The assay also detected all HPV-infected CIN2/3 with 100% agreement with Roche cobas HPV results. Moreover, several co-infections with non-HPV STIs, such as C. trachomatis, T. vaginalis, M. genitalium, and HSV2 were identified.ConclusionsThe ChapterDx HPV-STI NGS assay is a user-friendly, easy to automate and cost-efficient assay, which provides accurate and comprehensive results for a wide spectrum of HPVs and STIs.

THE USE OF ARCHIVED GIEMSA-STAINED BLOOD SMEARS AND RDT FOR PCR-BASED GENOTYPING OF Plasmodium vivax MEROZOITE SURFACE PROTEIN-1 IN CENTRAL KALIMANTAN PROVINCE, INDONESIA.

Background:Plasmodium vivax is transmitted most across the country of Indonesia. The country has set out a malaria elimination program by 2030. The information on genetic diversity of malarial parasites relates to malaria transmission in an endemic area may provide the information that can help the malaria control program to achieve the target. Therefore, the purpose of this study was to determine the genetic diversity of the Pvmsp-1 gene in Central Kalimantan Province.Materials and Methods:Samples were 140 of archived Giemsa-stained blood smear and rapid detection test. Samples were divided into the indigenous and migrant populations. After confirmation by single-step PCR, only P. vivax and mixed infection samples were amplified to nested PCR for genotyping of Pvmsp-1 allelic variation in segments F1, F2, and F3.Results:Genotyping of 23 PCR positive samples resulted in 13 genotypes. In segment F1, three allelic variants type A containing subtype A1 (1,050 bp), A2 (350 bp), A3 (150 bp), and type B (100 bp). In segment F2, mono genotypes were detected as variant type A (1,050 bp) and type B3 (150 bp), multiple genotypes were detected as type B containing subtype B1 (250 bp), B2 (200 bp), and B3 (150bp). In segment F3, three allelic variants generated from four mono genotypes were type A (350 bp), type B (300 bp), and two type C (250 bp).Conclusion:The low allelic variation of Pvmsp-1 gene may reflect the actual situation of the low malaria endemic status of the study sites.

Reverse complement-PCR, an innovative and effective method for multiplexing forensically relevant single nucleotide polymorphismmarker systems.

DNA analyses from challenging samples such as touch evidence, hairsand skeletal remains push the limits of the current forensic DNA typing technologies. Reverse complement PCR (RC-PCR) is a novel, single-step PCR target enrichment method adapted to amplify degraded DNA. The sample preparation process involves a limited number of steps, decreasing the labor required for library preparation and reducing the possibility of contamination due to less sample manipulation. These features of the RC-PCR make the technology a unique application to successfully target single nucleotide polymorphisms(SNPs) in fragmented and low copy number DNA and yield results from samples in which no or limited data are obtained with standard DNA typing methods. The developed RC-PCR short amplicon 85 SNP-plex panel is a substantial improvement overthe previously reported 27-plex RC-PCR multiplex that will provide higher discrimination power for challenging DNA sample analyses.

Development of highly sensitive one step-PCR tests for improved detection of B. bigemina and B. bovis

Bovine babesiosis caused by Babesia bigemina and B. bovis is an economically relevant tick-borne disease distributed over tropical and subtropical world regions. Animals that recover from the clinical disease can remain persistently infected, and those carriers are epidemiologically relevant since they can act as a source of infection to other animals through the tick bite. According to the manual of the World Organisation for Animal Health (OIE), the recommended molecular diagnosis test for both parasites is a nested polymerase chain reaction (nPCR) based on an amplification of a fragment of the rap-1 gene. Since nPCRs are time consuming, have a higher cost and risk of contamination, we propose a single step PCR for B. bigemina (BbiVESA) and B. bovis (BboVESA) based on the amplification of the multi-copy ves-1α gene. We developed these methods and we achieved a detection limit of 1 × 10−12 % parasitemia for B. bigemina and of 1 × 10−6 % for B. bovis using reference strains, which compared to the reference OIE tests, results in an improvement in sensitivity of six orders for B. bigemina. Finally, we tested 48 field samples from a babesiosis enzootic region where we were able to detect a higher proportion of positive animals with both VESA methods than with the reference rap-1 nPCRs. This difference was statistically significant for each Babesia species. Concordance between both diagnostic schemes based on Cohen's kappa coefficient showed minimal to non-agreement (κ = 0.32) for B. bigemina and non-agreement (κ = 0.16) for B. bovis since BbiVESA and BboVESA PCR tests showed a significantly higher detection capacity. In conclusion, the high sensitivity of the assay, together with the lower demand of time and reagents make the VESA PCR methods developed here a valuable diagnostic tool for the molecular detection and epidemiological survey of both Babesia pathogens.

SecA gene suitability for fast and easy identification of Phytoplasmas by RFLP analysis

In this study we investigated the secA gene as possible marker to supplement the classification scheme based on 16S rRNA sequences. We cloned and sequenced secA gene and its flanking region of ‘Ca. P. asteris’ CPh strain phytoplasma, as well as 1997 bp length secA gene fragment of Canada peach X-disease CX and 1327 bp fragment of ‘Ca. P. ziziphi’ JWB. This helped us to select a primer pair for a single step PCR that can amplify ~1200 kb length fragment of secA gene from different phytoplasma groups. We propose that this fragment could be used in RFLP analysis to quickly identify and distinguish 16SrI-A, I-B, I-C, I-D, III-A, III-B, III-E, III-F, III-H, V-B, XII-B and XXI-A subgroup phytoplasmas using just two restriction endonucleases.

Plasmodium knowlesi detection methods for human infections-Diagnosis and surveillance.

Within the overlapping geographical ranges of P. knowlesi monkey hosts and vectors in Southeast Asia, an estimated 1.5 billion people are considered at risk of infection. P. knowlesi can cause severe disease and death, the latter associated with delayed treatment occurring from misdiagnosis. Although microscopy is a sufficiently sensitive first-line tool for P. knowlesi detection for most low-level symptomatic infections, misdiagnosis as other Plasmodium species is common, and the majority of asymptomatic infections remain undetected. Current point-of-care rapid diagnostic tests demonstrate insufficient sensitivity and poor specificity for differentiating P. knowlesi from other Plasmodium species. Molecular tools including nested, real-time, and single-step PCR, and loop-mediated isothermal amplification (LAMP), are sensitive for P. knowlesi detection. However, higher cost and inability to provide the timely point-of-care diagnosis needed to guide appropriate clinical management has limited their routine use in most endemic clinical settings. P. knowlesi is likely underdiagnosed across the region, and improved diagnostic and surveillance tools are required. Reference laboratory molecular testing of malaria cases for both zoonotic and non-zoonotic Plasmodium species needs to be more widely implemented by National Malaria Control Programs across Southeast Asia to accurately identify the burden of zoonotic malaria and more precisely monitor the success of human-only malaria elimination programs. The implementation of specific serological tools for P. knowlesi would assist in determining the prevalence and distribution of asymptomatic and submicroscopic infections, the absence of transmission in certain areas, and associations with underlying land use change for future spatially targeted interventions.

RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis.

RNase H-dependent PCR-enabled T-cell receptor sequencing (rhTCRseq) can be used to determine paired alpha/beta T-cell receptor (TCR) clonotypes in single cells or perform alpha and beta TCR repertoire analysis in bulk RNA samples. With the enhanced specificity of RNase H-dependent PCR (rhPCR), it achieves TCR-specific amplification and addition of dual-index barcodes in a single PCR step. For single cells, the protocol includes sorting of single cells into plates, generation of cDNA libraries, a TCR-specific amplification step, a second PCR on pooled sample to generate a sequencing library, and sequencing. In the bulk method, sorting and cDNA library steps are replaced with a reverse-transcriptase (RT) reaction that adds a unique molecular identifier (UMI) to each cDNA molecule to improve the accuracy of repertoire-frequency measurements. Compared to other methods for TCR sequencing, rhTCRseq has a streamlined workflow and the ability to analyze single cells in 384-well plates. Compared to TCR reconstruction from single-cell transcriptome sequencing data, it improves the success rate for obtaining paired alpha/beta information and ensures recovery of complete complementarity-determining region 3 (CDR3) sequences, a prerequisite for cloning/expression of discovered TCRs. Although it has lower throughput than droplet-based methods, rhTCRseq is well-suited to analysis of small sorted populations, especially when analysis of 96 or 384 single cells is sufficient to identify predominant T-cell clones. For single cells, sorting typically requires 2-4 h and can be performed days, or even months, before library construction and data processing, which takes ~4 d; the bulk RNA protocol takes ~3 d.

Abstract 832: Comparison of single step to two step PCR for DNA methylation status determination utilizing a system that continuously contains PCR products in plastic consumables

Abstract DNA methylation specific PCR is a commonly used method to determine DNA methylation status. However, a well-known risk for PCR, and particularly methylation specific PCR, is carryover contamination from amplification products that can result in false positive PCR results in subsequent tests. This risk can be mitigated using careful technique, facility design, and biochemical methods such as uracil incorporation and subsequent uracil N-glycosylase (UNG) negative selection. Unfortunately, careful technique is highly user dependent, facility design can be cumbersome and expensive, and uracil incorporation is effective for only one step of two-step (nested) PCR reactions and cannot be used with the DNA bisulfite treatment methods used for methylation specific PCR. Our company has developed a system that mitigates PCR product contamination by continuously containing PCR products in plastic consumables and can interface with existing laboratory robotics, real time thermocycling instruments, and cassette electrophoresis gels. Here we utilize this system to compare the sensitivity and specificity of two-step multiplex nested PCR vs. single-step PCR for DNA methylation status detection applications using both qPCR and gel electrophoresis analysis. Published methylation status specific PCR primers that target CpG nucleotides in promotor regions were used to PCR amplify commercially available fully methylated and fully unmethylated DNA. The results demonstrate that a multiplex preamplification using amplicons for the CHAD, GFI1, MX2, NEU1, VWCE genes followed by monoplex nested methylation specific PCRs resulted in a Limit Of Detection (LOD) of 1 to 10 DNA template copies whereas performing just the monoplex methylation specific PCR (no preamplification) resulted in a LOD of 10 to 300 DNA template copies. If DNA isolated from macro dissected FFPE tissue was utilized, positive signals were identified using multiplex nested PCR whereas no signals were identified using single-step PCR. When mixtures of methylated and unmethylated DNA were utilized along with the GSTP gene amplicons, two-step nested PCR using were able to distinguish as low as 1% unmethylated DNA or 2% methylated DNA in a background of the other form, whereas single-step PCR was able to distinguish just 10% unmethylated or 33% methylated DNA under the same conditions. Furthermore, no PCR product contamination was observed upon amplification of samples collected from the external portion of the device demonstrating the PCR products were well contained. Citation Format: Wanyuan Ao, Derek Bosh, Dale Emery, Robert Parry, Nils Adey. Comparison of single step to two step PCR for DNA methylation status determination utilizing a system that continuously contains PCR products in plastic consumables [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 832.

Clinical utility of point of care testing in Africa

Within the overlapping geographical ranges of P. knowlesi monkey hosts and vectors in Southeast Asia, an estimated 1.5 billion people are considered at risk of infection. P. knowlesi can cause severe disease and death, the latter associated with delayed treatment occurring from misdiagnosis. Although microscopy is a sufficiently sensitive first-line tool for P. knowlesi detection for most low-level symptomatic infections, misdiagnosis as other Plasmodium species is common, and the majority of asymptomatic infections remain undetected. Current point-of-care rapid diagnostic tests demonstrate insufficient sensitivity and poor specificity for differentiating P. knowlesi from other Plasmodium species. Molecular tools including nested, real-time, and single-step PCR, and loop-mediated isothermal amplification (LAMP), are sensitive for P. knowlesi detection. However, higher cost and inability to provide the timely point-of-care diagnosis needed to guide appropriate clinical management has limited their routine use in most endemic clinical settings. P. knowlesi is likely underdiagnosed across the region, and improved diagnostic and surveillance tools are required. Reference laboratory molecular testing of malaria cases for both zoonotic and non-zoonotic Plasmodium species needs to be more widely implemented by National Malaria Control Programs across Southeast Asia to accurately identify the burden of zoonotic malaria and more precisely monitor the success of human-only malaria elimination programs. The implementation of specific serological tools for P. knowlesi would assist in determining the prevalence and distribution of asymptomatic and submicroscopic infections, the absence of transmission in certain areas, and associations with underlying land use change for future spatially targeted interventions.

Prevalence of Dirofilaria immitis and Dirofilaria repens in outdoor dogs in Tehran Province, Iran

Dirofilaria immitis and Dirofilaria repens are the most common species of filarial nematodes described in dogs, which are endemic in Iran. The diagnosis of canine dirofilariosis is usually based upon the microscopical detection and identification of circulating microfilariae together with ELISA detection of serum circulating heartworm antigens or antibodies. The identification of the parasite species using the traditional approaches sometimes can lead to misdiagnosis. As a zoonotic disease, it is important to know the prevalence of Dirofilaria in Tehran that is the most crowded province with many outdoor and stray dogs in suburb areas. In this paper, we used modified Knott’s test and a single-step multiplex PCR to detect and differentiate D. immitis and D. repens. Blood samples were collected from 311 outdoor dogs from March to August 2017. A total of 28.35% of dogs were positive by PCR in which 2.3% and 26% were D. immitis and D. repens, respectively. The highest incidence of infection was between 1 and 2.5 years old age. No sex predilection was observed. In the west of Tehran, prevalence of D. repens was statistically more than the other areas (p < 0.05). Our results showed the importance of detection and control of dirofilariasis in dog population as an important zoonotic disease.

A validated semi-nested PCR for rapid detection of scale drop disease virus (SDDV) in Asian sea bass (Lates calcarifer)

Scale drop diseases virus (SDDV), a newly characterized virus of farmed Asian sea bass (Lates calcarifer), has been reported in several countries in Southeast Asia. However, no fully validated detection method is publicly available for disease diagnosis and surveillance. Here, we described a newly developed semi-nested PCR (snPCR) method for detection of the virus from field samples. The designed primers targeting a gene encoding ATPase generated amplicons of 738 bp and 412 bp in the first and second step PCR, respectively. The established protocol could detect down to 100 viral copies/μL template and was 100-fold more sensitive than single step PCR. A Specificity test against extracted DNA from ten bacterial pathogens, tissues from viral infected specimens and fish host revealed no cross amplification. The SDDV snPCR method could detect the virus from all clinical samples showing symptoms of scale drop disease (n = 25) and all samples from outbreaks of an unknown disease (n = 6) whereas all clinically healthy fish sea bass (n = 161) and grouper (n = 45) collected from different provinces tested negative. The newly established protocol might be useful for Asian sea bass farming countries to initiate disease diagnosis and surveillance.