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Pérez-Rodríguez FJ, Cherpillod P, Thomasson V, Vetter P, Schibler M. Identification of a measles variant displaying mutations impacting molecular diagnostics, Geneva, Switzerland, 2023. Euro Surveill 2024; 29. [PMID: 38304951 PMCID: PMC10835752 DOI: 10.2807/1560-7917.es.2024.29.5.2400034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
Real-time PCR is one of the most widely used techniques to diagnose measles cases. Here we report measles virus variants with three genetic mutations in the reverse primer annealing site of a widely used PCR. The mutations result in a slight loss of the PCR sensitivity. Variants bearing the three mutations presently circulate in different countries since at least the end of 2021. Our findings highlight the usefulness of molecular surveillance in monitoring if oligonucleotides in diagnostic tests remain adequate.
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Affiliation(s)
- Francisco-Javier Pérez-Rodríguez
- Geneva Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- National Measles and Rubella Reference Laboratory (CNRRR), Geneva University Hospitals, Geneva, Switzerland
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
| | - Pascal Cherpillod
- Geneva Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- National Measles and Rubella Reference Laboratory (CNRRR), Geneva University Hospitals, Geneva, Switzerland
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
| | - Valentine Thomasson
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
| | - Pauline Vetter
- Geneva Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
| | - Manuel Schibler
- Geneva Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
- National Measles and Rubella Reference Laboratory (CNRRR), Geneva University Hospitals, Geneva, Switzerland
- Laboratory of virology, Laboratory Medicine Division, Geneva University Hospitals, Geneva, Switzerland
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Devika PP, Alex S, Soni KB, Sindura KP, Ayisha R, Manju RV. Nano-PCR for the early detection of tomato leaf curl virus. 3 Biotech 2024; 14:5. [PMID: 38074290 PMCID: PMC10700262 DOI: 10.1007/s13205-023-03842-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 11/02/2023] [Indexed: 01/19/2024] Open
Abstract
Nano-PCR is a potential tool for the early detection of plant viruses. In the current study, different concentrations of silver nanoparticles (20 nm) and magnesium oxide nanoparticles (50 nm) were included in the PCR mixture to improve the sensitivity of PCR for the detection of tomato leaf curl virus. The inclusion of nanoparticles in single or combination in PCR mixture has resulted in improvement of PCR sensitivity. Four-fold improvement was exhibited by the inclusion of 3 ng/µL silver nanoparticles, whereas the combination of silver and magnesium oxide nanoparticles (3 ng/µL and 200 ng/µL, respectively), resulted in a 4.5-fold improvement. The inclusion of 200 ng/µL of magnesium oxide nanoparticles in the PCR mixture exhibited a 7.6-fold increase in PCR sensitivity. Replacement of magnesium chloride with a combination of silver and magnesium oxide nanoparticles (3 ng/µL and 275 ng/µL, respectively) resulted in a 12-fold increase. A 13-fold improvement in PCR sensitivity was observed by the replacement of magnesium chloride in PCR buffer with 275 ng/µL of magnesium oxide nanoparticles. This could also produce detectable amplicon in PCR with a minimum of 25 cycles, resulting in a 26.5% reduction in the duration of PCR. This is the first report on the use of magnesium oxide nanoparticles in PCR for the early detection and better management of tomato leaf curl virus. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03842-2.
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Affiliation(s)
- P. P. Devika
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - Swapna Alex
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - K. B. Soni
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - K. P. Sindura
- Department of Molecular Biology and Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - R. Ayisha
- Department of Plant Pathology, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur, Kerala 680656 India
| | - R. V. Manju
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
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Kavhiza NJ, Zargar M, Prikhodko SI, Pakina EN. Comparison of three commercial DNA extraction kits for the enhancement of PCR assay sensitivity for Xanthomonas euvesicatoria pv. allii. J Appl Microbiol 2021; 132:1221-1226. [PMID: 34472163 DOI: 10.1111/jam.15280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/08/2021] [Accepted: 08/19/2021] [Indexed: 10/20/2022]
Abstract
AIM The study was carried out to evaluate three commercial DNA extraction kits, Probe GS, FitoSorb and Sorb GMO, thus identifying the most suitable for isolating the phytopathogenic bacteria Xanthomonas euvesicatoria pv. allii. MATERIALS AND METHODS Onion seed samples were prepared which were inoculated with bacterial concentrations ranging from 101 to 107 CFU per ml. Real-time PCR was performed to determine the efficacy of the isolated DNA in enhancing the sensitivity of the assay. The DNA extracted by Probe GS had the best detectability, having been detected at the lowest concentration used in the study 101 × 3 CFU per ml. FitoSorb and Sorb GMO yielded DNA with a higher and similar limit of detection 103 × 3 CFU per ml. Furthermore, Probe GS had the lowest cycle at every concentration tested as compared to the other methods. CONCLUSION Therefore, Probe GS proved to be the most optimized kit for the extraction of X. euvesicatoria pv. allii, hence enhanced degree of sensitivity for the assay. IMPACT AND SIGNIFICANCE OF THE STUDY The findings generated in this study can be used by phytosanitary laboratories to develop highly rapid and accurate diagnostic protocols for X. euvesicatoria pv. allii.
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Affiliation(s)
- Nyasha J Kavhiza
- Department of Agrobiotechnology, Agricultural-Technological Institute, RUDN University, Moscow, Russia
| | - Meisam Zargar
- Department of Agrobiotechnology, Agricultural-Technological Institute, RUDN University, Moscow, Russia
| | | | - Elena N Pakina
- Department of Agrobiotechnology, Agricultural-Technological Institute, RUDN University, Moscow, Russia
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Kurdi M, Butt NS, Baeesa S, Kuerban A, Maghrabi Y, Bardeesi A, Saeedi R, Alghamdi BS, Lary AI, Mohamed F, Hakamy S. Sensitivity Assessment of Wilms Tumor Gene ( WT1) Expression in Glioblastoma using qPCR and Immunohistochemistry and its Association with IDH1 Mutation and Recurrence Interval. Biologics 2021; 15:289-297. [PMID: 34335021 PMCID: PMC8318730 DOI: 10.2147/btt.s323358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/16/2021] [Indexed: 11/23/2022]
Abstract
Purpose Wilms tumor 1 (WT1) gene has recently shown a role in gliomagenesis, making it a potential immunotherapy target in glioblastomas. We aimed to investigate the most sensitive method to detect WT1 expression in glioblastoma and explore the relationship between WT1 expression, IDH1 mutation and recurrence interval. Patients and Methods Clinical data were collected from 44 patients with glioblastomas, treated with adjuvant therapies. WT1 expression was assessed in all cases using immunohistochemistry (IHC), while its gene expression was assessed in 13 clustered samples using polymerase chain reaction (qPCR). IDH1 mutation was assessed using IHC. The sensitivity between IHC and RT-qPCR was examined. Kaplan–Meier curves were used to compare the recurrence-free interval (RFI) between IDH1 and WT1 expression groups. Results IDH1wildtype was found in 26 cases (59.1%) and the remaining 18 cases (40.9%) were IDH1mutant. Through IHC, WT1 was overexpressed in 32 cases (72.7%), partially expressed in 9 cases (20.5%) and not expressed in only 3 cases. For the 13 cases tested by qPCR, 6 cases showed WT1 upregulation and 7 cases showed WT1 downregulation. There was no significant difference in WT1 expression among cases with different RNA concentrations regardless the testing method (p-value >0.05). However, the difference between IHC and qPCR was significant. IDH1mutant cases with WT1 overexpression showed significant difference in RFI (p-value =0.048). Conclusion Parallel testing for WT1 expression using IHC and qPCR is not reliable. However, IHC provides more accurate results. Moreover, IDH1mutant glioblastomas with WT1 overexpression are associated with late RFI particularly if temozolomide with additional chemotherapies are used.
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Affiliation(s)
- Maher Kurdi
- Department of Pathology, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Nadeem Shafique Butt
- Department of Family and Community Medicine, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Saleh Baeesa
- Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abudukadeer Kuerban
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Yazid Maghrabi
- Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
| | - Anas Bardeesi
- Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
| | - Rothaina Saeedi
- Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Badrah S Alghamdi
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ahmed I Lary
- Section of Neurosurgery, Department of Surgery, King Abdulaziz Medical City, Jeddah, Kingdom of Saudi Arabia
| | - Fawaz Mohamed
- Department of Pathology, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Sahar Hakamy
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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Long S. In pursuit of sensitivity: Lessons learned from viral nucleic acid detection and quantification on the raindance ddPCR platform. Methods 2021; 201:82-95. [PMID: 33839286 PMCID: PMC8501152 DOI: 10.1016/j.ymeth.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Sensitive PCR detection of viral nucleic acids plays a critical role in infectious disease research, diagnosis and monitoring. In the context of SARS-CoV-2 detection, recent reports indicate that digital PCR-based tests are significantly more sensitive than traditional qPCR tests. Numerous factors can influence digital PCR reaction sensitivity. In this review, using a model for human HIV infection and the Raindance ddPCR platform as an example, we describe technical aspects that contribute to sensitive viral signal detection in DNA and RNA from tissue samples, which often harbor viral reservoirs and serve as better predictors of disease outcome and indicators of treatment efficacy.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States.
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Montalvo AM, Alba A, Fraga J, Marzoa A, Torres C, Muskus C. Improving the sensitivity of an hsp20-based PCR for genus detection of Leishmania parasites in cutaneous clinical samples: a proof of concept. Parasitol Res 2019; 119:345-349. [PMID: 31776667 DOI: 10.1007/s00436-019-06520-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022]
Abstract
Leishmaniasis is a parasitic disease of medical importance widely distributed around the world. Several methods are available for diagnosis but molecular approaches are highly recommended. To improve the sensitivity of an existing hsp20 gene based-PCR protocol to detect Leishmania parasites, primers were redesigned to amplify a shorter fragment using a new PCR variant (PCR-hsp20S). In this study, we aimed at characterizing the performance of the new method on cutaneous clinical samples and compare it with the former PCR-hsp20. The analytical sensitivity of the PCR-hsp20S was evaluated using DNA dilutions (100-0.1 pg) from Leishmania donovani and resulted in the detection of 10 fg of parasitic DNA, the equivalent to 0.05 parasite genome. For the diagnostic evaluation, a panel of 127 human clinical samples was used to calculate the parameters of sensitivity, specificity, accuracy, and positive and negative predictive values of the PCR-hsp20S. Diagnostic sensitivity was 94% (CI, 89.1-99.7%) and the specificity of 100% (CI, 98.6-100%). The same panel was also evaluated with the PCR-hsp20 to calculate the agreement between both molecular assays and to compare their performances. While both hsp20-based PCRs showed a good agreement coefficient (kappa index = 0.6), the performance of the novel variant, PCR-hsp20S, was significantly higher in terms of sensitivity (P = 0.0001) allowing the accurate detection of a higher number of Leishmania-positive clinical samples. We endorse the use of the PCR-hsp20S over the former protocol for the detection of Leishmania parasites from cutaneous clinical samples. In addition, as an improved sensitivity was achieved with the new method merely through the amplification of a shorter gene fragment, this investigation constitutes an experimental proof of this concept.
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Affiliation(s)
- Ana M Montalvo
- Department of Parasitology, Institute of Tropical Medicine Pedro Kourí (IPK), Havana, Cuba.
| | - Annia Alba
- Department of Parasitology, Institute of Tropical Medicine Pedro Kourí (IPK), Havana, Cuba
| | - Jorge Fraga
- Department of Science and Innovation, IPK, Havana, Cuba
| | | | - Cecia Torres
- Department of Parasitology, Institute of Tropical Medicine Pedro Kourí (IPK), Havana, Cuba
| | - Carlos Muskus
- PECET (Program of Study and Control of Tropical Diseases), University of Antioquia, Medellín, Colombia
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR. Polymerase chain reaction with nearby primers. Anal Biochem 2016; 518:126-133. [PMID: 27908595 DOI: 10.1016/j.ab.2016.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 02/05/2023]
Abstract
DNA analysis of biological specimens containing degraded nucleic acids such as mortal remains, archaeological artefacts, forensic samples etc. has gained more attention in recent years. DNA extracted from these samples is often inapplicable for conventional polymerase chain reaction (PCR), so for its amplification the nearby primers are commonly used. Here we report the data that clarify the features of PCR with nearby and abutting primers. We have shown that the proximity of primers leads to significant reduction of the reaction time and ensures the successful performance of DNA amplification even in the presence of PCR inhibitors. The PCR with abutting primers is usually characterized by the absence of nonspecific amplification products that causes extreme sensitivity with limit of detection on single copy level. The feasibility of PCR with abutting primers was demonstrated on species identification of 100 years old rotten wood.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics Ufa Science Centre Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Aizilya A Galimova
- Institute of Biochemistry and Genetics Ufa Science Centre Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics Ufa Science Centre Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
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