The Development of a Real-Time PCR Assay for Specific Detection of the NISKHI Sheep Pox Vaccine Virus Strain DNA
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples and Viruses
2.2. DNA Extraction
2.3. Primer Design and PCR Protocol
2.4. Assay Validation on Clinical Samples
2.5. Assessment of Limit of Detection
2.6. Assessment of Competitiveness
2.7. Statistical Analysis
3. Results
3.1. Assay Design
3.2. Performance of the HRM Assay on Clinical Samples
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Isolate/Strain | Region | Isolation Year | Type of Material | GenBank Accession Number |
---|---|---|---|---|
Amur | Amurskaya oblast | 2018 | Scabs | Not applicable |
Moscow 2018 (M18) | Moscow region | 2018 | Scabs | ON961655 |
Tula | Tula region | 2018 | Scabs | ON961657 |
Pskov | Pskov region | 2019 | Scabs | Not applicable |
Moscow 2019 (M19) | Moscow region | 2019 | Scabs | ON961656 |
Tver | Tver region | 2019 | Scabs | Not applicable |
Kaluga | Kaluga Region | 2020 | Scabs | Not applicable |
Dagestan | Republic of Dagestan | 2022 | Scabs | Not applicable |
ARRIAH | “NISKHI” | 1996 | Cell culture | AY077834 |
Name | Sequence (5′->3′) | Template Strand | Calculated Tm (°C) | Length |
---|---|---|---|---|
Forward primer | CACACGGTGCAGCAAATACT | Plus | 60.6 | 20 |
Reverse primer | CCTTGTATCTGTGCTGTTATATCTCC | Minus | 59.6 | 26 |
Isolate/Strain | Original Sample (200 ng) | Dilution 10−1 | Dilution 10−2 | Dilution 10−3 | Dilution 10−4 | GM/SD | GM/SD |
---|---|---|---|---|---|---|---|
(M/SD) | (M/SD) | (M/SD) | (M/SD) | (M/SD) | |||
NISKHI (ARRIAH) | 76.44 ± 0.07 | 76.57 ± 0.11 | 76.66 ± 0.2 | 76.41 ± 0.02 | 76.225 ± 0.21 | 76.46 ± 0.12 | 76.46 ± 0.12 |
Amur | 75.44 ± 0.04 | 75.79 ± 0.04 | 75.77 ± 0.02 | 75.62 ± 0.04 | 75.43 ± 0.096 | 75.61 ± 0.05 | 75.65 ± 0.04 |
Pskov | 75.81 ± 0.01 | 75.78 ± 0.02 | 75.75 ± 0.02 | 75.63 ± 0.04 | 75.41 ± 0.06 | 75.68 ± 0.03 | |
Kaluga | 75.71 ± 0.01 | 75.69 ± 0.02 | 75.65 ± 0.05 | 75.59 ± 0.01 | ND | 75.66 ± 0.02 | |
Tula | 75.32 ± 0.03 | 75.67 ± 0.03 | 75.62 ± 0.07 | 75.57 ± 0.03 | 75.18± 0.09 | 75.47 ± 0.04 | |
M19 | 75.74 ± 0.04 | 75.68 ± 0.02 | 75.67 ± 0.02 | 75.59 ± 0.03 | 75.51 ± 0.01 | 75.64 ± 0.02 | |
Tver | 75.66 ± 0.05 | 75.72 ± 0.03 | 75.73 ± 0.04 | 75.57 ± 0.04 | 75.56 ± 0.02 | 75.65 ± 0.04 | |
Dagestan | 75.5 ± 0.07 | 75.79 ± 0.04 | 75.84 ± 0.04 | 75.68 ± 0.04 | 75.62 ± 0.09 | 75.69 ± 0.06 | |
M18 | 75.89 ± 0.1 | 75.9 ± 0.07 | 75.88 ± 0.08 | 75.78 ± 0.06 | ND | 75.86 ± 0.08 |
Field Isolate (Constant)/Vaccine Strain (Variable) | M/SD | M/SD |
---|---|---|
01:01 | 75.64/0.14 | 76.17/0.08 |
1:10−1 | 75.58/0.01 | Neg |
1:10−2 | 75.52/0.12 | neg |
1:10−3 | 75.4/0.03 | neg |
1:10−4 | 75.43/0.07 | neg |
Vaccine strain (Constant)/Field | M/SD | M/SD |
Isolate (Variable) | ||
01:01 | 76.4/0.04 | 75.61/0.03 |
1:10−1 | 76.43/0.01 | neg |
1:10−2 | 76.27/0.03 | neg |
1:10−3 | 76.08/0.06 | neg |
1:10−4 | 76.71/0.01 | neg |
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Sprygin, A.; Mazloum, A.; Van Schalkwyk, A.; Krotova, A.; Shalina, K.; Dmitric, M.; Byadovskaya, O.; Prokhvatilova, L.; Chvala, I. The Development of a Real-Time PCR Assay for Specific Detection of the NISKHI Sheep Pox Vaccine Virus Strain DNA. Appl. Microbiol. 2022, 2, 956-964. https://doi.org/10.3390/applmicrobiol2040073
Sprygin A, Mazloum A, Van Schalkwyk A, Krotova A, Shalina K, Dmitric M, Byadovskaya O, Prokhvatilova L, Chvala I. The Development of a Real-Time PCR Assay for Specific Detection of the NISKHI Sheep Pox Vaccine Virus Strain DNA. Applied Microbiology. 2022; 2(4):956-964. https://doi.org/10.3390/applmicrobiol2040073
Chicago/Turabian StyleSprygin, Alexander, Ali Mazloum, Antoinette Van Schalkwyk, Alena Krotova, Kseniya Shalina, Marko Dmitric, Olga Byadovskaya, Larisa Prokhvatilova, and Ilya Chvala. 2022. "The Development of a Real-Time PCR Assay for Specific Detection of the NISKHI Sheep Pox Vaccine Virus Strain DNA" Applied Microbiology 2, no. 4: 956-964. https://doi.org/10.3390/applmicrobiol2040073
APA StyleSprygin, A., Mazloum, A., Van Schalkwyk, A., Krotova, A., Shalina, K., Dmitric, M., Byadovskaya, O., Prokhvatilova, L., & Chvala, I. (2022). The Development of a Real-Time PCR Assay for Specific Detection of the NISKHI Sheep Pox Vaccine Virus Strain DNA. Applied Microbiology, 2(4), 956-964. https://doi.org/10.3390/applmicrobiol2040073