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Multiple-probe-assisted DNA capture and amplification for high-throughput African swine fever virus detection. Appl Microbiol Biotechnol 2023; 107:797-805. [PMID: 36576568 DOI: 10.1007/s00253-022-12334-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/29/2022]
Abstract
African swine fever (ASF) is one of the most devastating infectious diseases affecting domestic pigs and wild boar. The grave socio-economic impact of African swine fever infection at a global level makes large-scale rapid and robust diagnosis a critical step towards effective control. Here, we describe multiple-probe-assisted DNA capture and amplification technology (MADCAT) - a novel, sensitive, simple, and high-throughput method for detecting ASFV directly from whole blood or other complex matrices. Through a unique DNA capture approach which specifically captures the target DNA onto 96-well plate for subsequent amplification, MADCAT abandons the complicated extraction protocol and achieves ultrafast and high-throughput detection. The sample-to-result time for 96 samples is about 90 min, as compared with the 3-4 h time of the conventional real-time qPCR method. The limit of detection (LOD) of MADCAT is 0.5 copies/μL blood and is 5 times more sensitive than an extraction-based qPCR assay when testing serially diluted whole blood samples. The assay is 100% specific against other common swine pathogens. In the clinical diagnosis of 96 field samples, all 22 positive samples were correctly identified with lower Ct values than extraction-based qPCR, confirming its high diagnostic sensitivity (100%). Owing to its high-throughput, specific high sensitivity, and direct detection features, MADCAT shows great potential for use in large-scale ASFV surveillance and monitoring for effective disease control. KEY POINTS: • No nucleic acid extraction, 100% capture efficiency, and high-throughput • Ultra-high sensitivity of 0.5 DNA copies/μL or 6 DNA copies/reaction • The sample-to-answer time for 96 samples is about 90 min.
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Kifaro EG, Kim MJ, Jung S, Noh JY, Song CS, Misinzo G, Kim SK. Direct Reverse Transcription Real-Time PCR of Viral RNA from Saliva Samples Using Hydrogel Microparticles. BIOCHIP JOURNAL 2022; 16:409-421. [PMID: 35968254 PMCID: PMC9358062 DOI: 10.1007/s13206-022-00065-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 12/29/2022]
Abstract
In recent decades "saliva" has emerged as an important non-invasive biofluid for diagnostic purposes in both human and animal health sectors. However, with the rapid evolution of molecular detection technologies, the limitation has been the lack of an efficient method for the facile amplification of target RNA from such a complex matrix. Herein, we demonstrate the novel application of hydrogel microparticles of primer-immobilized networks (PIN) for direct quantitative reverse transcription PCR (dirRT-qPCR) of viral RNA from saliva samples without prior RNA purification. Each of these highly porous PIN particles operates as an independent reactor. They filter in micro-volumes of the analyte solution. Viral RNA is captured and converted to complementary DNA (cDNA) through the RT step using covalently incorporated RT primers. The PIN with cDNA of the viral target will be ready for subsequent highly specific qPCR. Preceded by heat-treatment for viral lysis, we were able to conduct PIN dirRT-qPCR with 95% efficiency of the matrix (M) gene for influenza A virus (IAV) and 5' untranslated region (5' UTR) for chicken coronavirus spiked into saliva samples. The addition of reverse transcriptase enzyme (RTase) and 10% dilution of the matrix improved the assay sensitivity considerably. PIN particles' compatibility with microfluidic PCR chip technology has significantly reduced total sample processing time to 50 min, instead of an average of 120 min that are normally used by other assays. We anticipate this technology will be useful for other viral RNA targets by changing the incorporated RT primer sequences and can be adapted for onsite diagnostics. Supplementary Information The online version contains supplementary material available at 10.1007/s13206-022-00065-0.
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Affiliation(s)
- Emmanuel George Kifaro
- grid.35541.360000000121053345Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792 Republic of Korea ,grid.11887.370000 0000 9428 8105Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), PO Box 3019, Morogoro, Tanzania ,grid.502906.80000 0004 7707 5959Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), PO Box 3297, Morogoro, Tanzania
| | - Mi Jung Kim
- grid.35541.360000000121053345Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792 Republic of Korea
| | - Seungwon Jung
- grid.35541.360000000121053345Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792 Republic of Korea
| | | | - Chang-Seon Song
- KCAV Co., Ltd., Seoul, Republic of Korea ,grid.258676.80000 0004 0532 8339Avian Diseases Laboratory, College of Veterinary Medicine, Konkuk University, Seoul, 05029 Republic of Korea
| | - Gerald Misinzo
- grid.11887.370000 0000 9428 8105Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), PO Box 3019, Morogoro, Tanzania ,grid.502906.80000 0004 7707 5959Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), PO Box 3297, Morogoro, Tanzania
| | - Sang Kyung Kim
- grid.35541.360000000121053345Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792 Republic of Korea ,grid.289247.20000 0001 2171 7818KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, 02447 Republic of Korea
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Clinical usefulness of extraction-free PCR assay to detect SARS-CoV-2. J Virol Methods 2021; 296:114217. [PMID: 34171343 PMCID: PMC8223006 DOI: 10.1016/j.jviromet.2021.114217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/17/2021] [Accepted: 06/20/2021] [Indexed: 01/08/2023]
Abstract
Due to the coronavirus disease 2019 pandemic, the demand for an easily accessible high-throughput screening test is increasing. We aimed to evaluate the usefulness of the extrac-tion-free polymerase chain reaction (PCR) as a screening test to detect severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Real-time reverse transcription PCR was performed in 300 samples (260 SARS-CoV-2 positives and 40 negatives), using both the conventional nucleic acid extraction method (standard method) and the direct method without nucleic acid extraction (direct method). The overall agreement between the standard and direct methods was 86.8 % (kappa 0.60), and the sensitivity of the direct method compared to the standard method was 85.4 %. When the cycle threshold (Ct) value was less than 35, the sensitivity was approximately 90 %-98 %, and when Ct exceeded 35, it decreased to approximately 60 %-65 %. The extraction-free PCR could be useful as a screening test that processes many samples in a short time.
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Qiu W, Meng K, Liu Y, Zhang Y, Wang Z, Chen Z, Yang J, Sun W, Guo L, Ren S, Chen L, Yang G, Zhang F, Shi J, Li J, Du Y, Yu J, Wu J. Simultaneous detection of classical PRRSV, highly pathogenic PRRSV and NADC30-like PRRSV by TaqMan probe real-time PCR. J Virol Methods 2019; 282:113774. [PMID: 31726113 DOI: 10.1016/j.jviromet.2019.113774] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 10/29/2019] [Accepted: 11/10/2019] [Indexed: 01/12/2023]
Abstract
Porcine Reproductive and Respiratory Syndrome (PRRS), an acute infectious disease caused by the porcine reproductive and respiratory syndrome virus (PRRSV), is one of the most devastating diseases affecting the global swine industry. In order to establish a multiplex real-time PCR method for the simultaneous detection of the classical PRRSV (C-PRRSV) strain, the highly pathogenic PRRSV (HP-PRRSV) strain and NADC30-like PRRSV (NL-PRRSV) strain, we designed specific primers and TaqMan fluorescent probes based on the Nsp2 target gene sequence of these three different PRRSV strains, and designed American-type PRRSV (PRRSV-U) special primers and probes based on the relatively conserved target gene sequence of ORF7. The method established in this study can quickly and accurately detect and differentiate three types of strains of clinical tissue samples, respectively. This method plays a key role in the rapid diagnosis and determination of PRRSV.
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Affiliation(s)
- Wenbin Qiu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; School of Life Sciences, Shandong Normal University, Jinan, Jinan, 250014, China
| | - Kai Meng
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Key Laboratory of Poultry Diseases Diagnosis and Immunology, Poultry Breeding Engineering Technology Center of Shandong Province, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, 250023, China
| | - Yanyan Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yuyu Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Zhao Wang
- China Institute of Veterinary Drug Control, 8 Nandajie, Zhongguancun, Haidian, Beijing, 100081, China
| | - Zhi Chen
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jie Yang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wenbo Sun
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Lihui Guo
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Sufang Ren
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Lei Chen
- School of Life Sciences, Shandong Normal University, Jinan, Jinan, 250014, China
| | - Guiwen Yang
- School of Life Sciences, Shandong Normal University, Jinan, Jinan, 250014, China
| | - Fan Zhang
- School of Life Sciences, Shandong Normal University, Jinan, Jinan, 250014, China
| | - Jianli Shi
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jun Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yijun Du
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jiang Yu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Jiaqiang Wu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; School of Life Sciences, Shandong Normal University, Jinan, Jinan, 250014, China; Shandong Key Laboratory of Poultry Diseases Diagnosis and Immunology, Poultry Breeding Engineering Technology Center of Shandong Province, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, 250023, China.
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Direct S-Poly(T) Plus assay in quantification of microRNAs without RNA extraction and its implications in colorectal cancer biomarker studies. J Transl Med 2019; 17:316. [PMID: 31547825 PMCID: PMC6757382 DOI: 10.1186/s12967-019-2061-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/06/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Advances in microRNAs (miRNAs) biomarkers have generated disease markers with potential clinical values. However, none of these published results have been applied in clinic until today. The main reason could be the lack of simple but robust miRNA measurements. METHODS We built up a simple but ultrasensitive RT-qPCR protocol, Direct S-Poly(T) Plus assay, for detecting miRNAs without RNA purification. In this study, the method was optimized and compared with other RNA purification-based miRNA assays, and the sensitivity was tested. Using Direct S-Poly(T) Plus method, seven potential miRNA biomarkers of colorectal cancer were validated. RESULTS It is possible to detect approximately 100 miRNAs with minimal plasma inputs (20 μl) and time (~ 140 min) with this approach. The sensitivity of this method was 2.7-343-fold higher than that of the stem-loop method, and comparable with S-Poly(T) plus method. 7 validated miRNA biomarkers of colorectal cancer by Direct S-Poly(T) plus assay could discriminate colorectal cancer stage I from healthy individuals, and promised satisfactory discrimination with the area under receiver operating characteristic (ROC) curve ranging from 0.79 to 0.94 (p value < 0.001). CONCLUSIONS This simple and robust protocol may have strong impact on the development of specific miRNAs as biomarkers in clinic.
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Li L, He JA, Wang W, Xia Y, Song L, Chen ZH, Zuo HZ, Tan XP, Ho AHP, Kong SK, Loo JFC, Li HW, Gu D. Development of a direct reverse-transcription quantitative PCR (dirRT-qPCR) assay for clinical Zika diagnosis. Int J Infect Dis 2019; 85:167-174. [PMID: 31202908 DOI: 10.1016/j.ijid.2019.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/28/2019] [Accepted: 06/09/2019] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE The nucleic acid-based polymerase chain reaction (PCR) assay is commonly applied to detect infection with Zika virus (ZIKV). However, the time- and labor-intensive sample pretreatment required to remove inhibitors that cause false-negative results in clinical samples is impractical for use in resource-limited areas. The aim was to develop a direct reverse-transcription quantitative PCR (dirRT-qPCR) assay for ZIKV diagnosis directly from clinical samples. METHODS The combination of inhibitor-tolerant polymerases, polymerase enhancers, and dirRT-qPCR conditions was optimized for various clinical samples including blood and serum. Sensitivity was evaluated with standard DNA spiked in simulated samples. Specificity was evaluated using clinical specimens of other infections such as dengue virus and chikungunya virus. RESULTS High specificity and sensitivity were achieved, and the limit of detection (LOD) of the assay was 9.5×101 ZIKV RNA copies/reaction. The on-site clinical diagnosis of ZIKV required a 5μl sample and the diagnosis could be completed within 2h. CONCLUSIONS This robust dirRT-qPCR assay shows a high potential for point-of-care diagnosis, and the primer-probe combinations can also be extended for other viral detection. It realizes the goal of large-scale on-site screening for viral infections and could be used for early diagnosis and the prevention and control of viral outbreaks.
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Affiliation(s)
- Lang Li
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China; Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Jian-An He
- Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Wei Wang
- Department of Laboratory Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, 518035, PR China
| | - Yun Xia
- Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Li Song
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China; Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Ze-Han Chen
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China
| | - Hang-Zhi Zuo
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China
| | - Xuan-Ping Tan
- Shenzhen gene-one Biotechnology Co., Ltd., 518000, PR China
| | - Aaron Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Siu-Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Jacky Fong-Chuen Loo
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, PR China; Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, PR China.
| | - Hua-Wen Li
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China.
| | - Dayong Gu
- Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China; Department of Laboratory Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, 518035, PR China.
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Lynch C, Fleming R. A review of direct polymerase chain reaction of DNA and RNA for forensic purposes. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Courtney Lynch
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
- School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Rachel Fleming
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
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Barra GB, Santa Rita TH, Jardim DP, Mesquita PG, Nobre CS, Jácomo RH, Abdalla Nery LF. Genotyping of Single Nucleotide Polymorphisms Using Allele-Specific qPCR Producing Amplicons of Small Sizes Directly from Crude Serum Isolated from Capillary Blood by a Hand-Powered Paper Centrifuge. Diagnostics (Basel) 2019; 9:diagnostics9010009. [PMID: 30641881 PMCID: PMC6468353 DOI: 10.3390/diagnostics9010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/27/2018] [Accepted: 12/29/2018] [Indexed: 12/26/2022] Open
Abstract
The cell-free genomic DNA (gDNA) concentration in serum ranges from 1500 to 7500 copies/mL within 2 h after phlebotomy (6⁻24 times the concentration observed in plasma). Here, we aimed to evaluate the gDNA size distribution in serum with time after coagulation and to test if crude serum can be directly used as a source of gDNA for qPCR. Next, we investigated if single nucleotide polymorphisms (SNPs) could be genotyped directly from the crude serum isolated from capillary blood using a hand-powered paper centrifuge. All tested PCR targets (65, 100, 202 and 688 base pairs) could be successfully amplified from DNA extracted from serum, irrespective of their amplicon size. The observed qPCR quantitation cycles suggested that the genomic DNA yield increased in serum with incubation at room temperature. Additionally, only 65 and 101 base pair qPCR targets could be amplified from crude serum soon after the coagulation. Incubation for 4 days at room temperature was necessary for the amplification of PCR targets of 202 base pairs. The 688 base pair qPCR target could not be amplified from serum directly. Lastly, serum was successfully separated from capillary blood using the proposed paper centrifuge and the genotypes were assigned by testing the crude serum using allele-specific qPCR, producing small amplicon sizes in complete agreement with the genotypes assigned by testing the DNA extracted from whole blood. The serum can be used directly as the template in qPCR for SNP genotyping, especially if small amplicon sizes are applied. This shortcut in the SNP genotyping process could further molecular point-of-care diagnostics due to elimination of the DNA extraction step.
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Affiliation(s)
- Gustavo Barcelos Barra
- Sabin Laboratory, Brasília 70632-300, Brazil.
- Post-Graduation of Health Science, University of Brasília, Brasilia 70910-900, Brazil.
| | - Ticiane Henriques Santa Rita
- Sabin Laboratory, Brasília 70632-300, Brazil.
- Post-Graduation of Health Science, University of Brasília, Brasilia 70910-900, Brazil.
| | - Daniella Paniago Jardim
- Sabin Laboratory, Brasília 70632-300, Brazil.
- Post-Graduation of Health Science, University of Brasília, Brasilia 70910-900, Brazil.
| | | | - Camila Santos Nobre
- Sabin Laboratory, Brasília 70632-300, Brazil.
- Post-Graduation of Health Science, University of Brasília, Brasilia 70910-900, Brazil.
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