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Chen Z, Sun Q, Yang Y, Nie X, Xiang W, Ren Y, Le T. Aptamer-based diagnostic and therapeutic approaches for animal viruses: A review. Int J Biol Macromol 2024; 257:128677. [PMID: 38072350 DOI: 10.1016/j.ijbiomac.2023.128677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024]
Abstract
Animal diseases often have significant consequences due to the unclear and time-consuming diagnosis process. Furthermore, the emergence of new viral infections and drug-resistant pathogens has further complicated the diagnosis and treatment of viral diseases. Aptamers, which are obtained through systematic evolution of ligands by exponential enrichment (SELEX) technology, provide a promising solution as they enable specific identification and binding to targets, facilitating pathogen detection and the development of novel therapeutics. This review presented an overview of aptasensors for animal virus detection, discussed the antiviral activity and mechanisms of aptamers, and highlighted advancements in aptamer-based antiviral research following the COVID-19 pandemic. Additionally, the challenges and prospects of aptamer-based virus diagnosis and treatment research were explored. Although this review was not exhaustive, it offered valuable insights into the progress of aptamer-based antiviral drug research, target mechanisms, as well as the development of novel antiviral drugs and biosensors.
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Affiliation(s)
- Zhuoer Chen
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Qi Sun
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Ying Yang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Xunqing Nie
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Wenyu Xiang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Yueyang Ren
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Tao Le
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China.
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Hmila I, Marnissi B, Kamali-Moghaddam M, Ghram A. Aptamer-Assisted Proximity Ligation Assay for Sensitive Detection of Infectious Bronchitis Coronavirus. Microbiol Spectr 2023; 11:e0208122. [PMID: 36651727 PMCID: PMC9927260 DOI: 10.1128/spectrum.02081-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Infectious bronchitis virus (IBV) is a coronavirus responsible for major health problems in the poultry industry. New virus strains continue to appear, causing large economic losses. To develop a rapid and accurate new quantitative assay for diagnosis of the virus without DNA extraction, we selected highly specific single-stranded DNA (ssDNA) aptamers with a high affinity to IBV, using the systematic evolution of ligands by exponential enrichment (SELEX) technology for aptamer screening, followed by high-throughput sequencing technology. Two of these aptamers, AptIBV5 and AptIBV2, were used to establish homogenous and solid-phase proximity ligation assays (PLAs). The developed assays were evaluated for their sensitivity and specificity using collected field samples and then compared to the newly developed sandwich enzyme-linked aptamer assay (ELAA) and reverse transcription-quantitative PCR (qRT-PCR), as the gold-standard method. The solid-phase PLA showed a lower limit of detection and a broader dynamic range than the two other assays. The developed technique may serve as an alternative assay for the diagnosis of IBV, with the potential to be extended to the detection of other important animal or human viruses. IMPORTANCE Infectious bronchitis virus (IBV) causes high morbidity and mortality and large economic losses in the poultry industry. The virus has the ability to genetically mutate into new IBV strains, causing devastating disease and outbreaks. To better monitor the emergence of this virus, the development of a rapid and highly sensitive diagnostic method should be implemented. For this, we generated aptamers with high affinity and specificity to the IBV in an ssDNA library. Using two high-affinity aptamers, we developed a sandwich ELAA and a very sensitive aptamer-based proximity ligation assay (PLA). The new assay showed high sensitivity and specificity and was used to detect IBV in farm samples. The PLA was compared to the newly developed sandwich ELAA and qRT-PCR, as the gold-standard technique.
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Affiliation(s)
- Issam Hmila
- Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Boutheina Marnissi
- Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia
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Singh M, Tripathi P, Singh S, Sachan M, Chander V, Sharma GK, De UK, Kota S, Putty K, Singh RK, Nara S. Identification and characterization of DNA aptamers specific to VP2 protein of canine parvovirus. Appl Microbiol Biotechnol 2021; 105:8895-8906. [PMID: 34714365 PMCID: PMC8553593 DOI: 10.1007/s00253-021-11651-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Abstract
Canine parvovirus‐2 (CPV‐2) is ubiquitously distributed in dog population worldwide causing a severe and often fatal gastroenteritis. Owing to its highly contagious nature, rapid detection of CPV is crucial in effective control of the disease. Aptamers have emerged as potential alternative to antibodies as affinity reagents in diagnostic field. Present study was aimed to select and validate ssDNA aptamers specific to CPV. Systematic evolution of ligands through exponential enrichment (SELEX) method was employed for selection of CPV structural protein (VP2) specific DNA aptamers. SELEX was performed using a pool of ssDNA library comprising 30 random nucleotide region. A total of seven rounds of SELEX were performed using VP2 protein as target antigen which yielded ten aptamers (1A-10A) with distinct sequences. Target binding of all ten aptamers was assessed by dot blot and enzyme-linked oligonucleotide assay (ELONA) which revealed that 5A, 6A, 9A, and 10A were superior binders. In silico analysis of the aptamers revealed the existence of binding site on VP2 protein, and binding pattern was similar to in vitro findings. The affinity (KD) of all these four binders against CPV was evaluated by ELONA indicating relatively higher affinity of 6A and 10A than remaining two DNA sequences. Out of which, aptamer 6A displayed cross-reactivity with canine distemper virus and canine corona virus. Hence, aptamer 10A was considered as better binding sequence having high specificity and affinity for CPV. The study confirms the future utility of selected aptamers in development of a reliable diagnostic for rapid detection of CPV. Key points • Canine parvovirus-specific ssDNA aptamers were identified with nanomolar affinity (100–150 nM). • Three aptamers displayed negligible cross-reactivity with other related viruses. • Aptamer 10A displayed high binding affinity and specificity to CPV. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11651-x.
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Affiliation(s)
- Mithilesh Singh
- Immunology Section, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243122, India.
| | - Pranav Tripathi
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, U.P., India
| | - Smriti Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, U.P., India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, U.P., India
| | - Vishal Chander
- Centre for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243122, India
| | - Gaurav Kumar Sharma
- Centre for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243122, India
| | - Ujjwal Kumar De
- Division of Veterinary Medicine, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243122, India
| | - Sathish Kota
- Translational Research Platform for Veterinary Biologicals (TRPVB), CAHS, TANUVAS, Chennai-51, India
| | - Kalyani Putty
- Departments of Veterinary Microbiology and Veterinary Biotechnology, College of Veterinary Science, PVNRTVU, Rajendra Nagar, Hyderabad, India
| | - Raj Kumar Singh
- Division of Veterinary Medicine, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Izatnagar, Bareilly, 243122, India
| | - Seema Nara
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, U.P., India.
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Wan Q, Liu X, Zu Y. Oligonucleotide aptamers for pathogen detection and infectious disease control. Theranostics 2021; 11:9133-9161. [PMID: 34522231 PMCID: PMC8419047 DOI: 10.7150/thno.61804] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022] Open
Abstract
During an epidemic or pandemic, the primary task is to rapidly develop precise diagnostic approaches and effective therapeutics. Oligonucleotide aptamer-based pathogen detection assays and control therapeutics are promising, as aptamers that specifically recognize and block pathogens can be quickly developed and produced through simple chemical synthesis. This work reviews common aptamer-based diagnostic techniques for communicable diseases and summarizes currently available aptamers that target various pathogens, including the SARS-CoV-2 virus. Moreover, this review discusses how oligonucleotide aptamers might be leveraged to control pathogen propagation and improve host immune system responses. This review offers a comprehensive data source to the further develop aptamer-based diagnostics and therapeutics specific for infectious diseases.
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Affiliation(s)
| | | | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
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Marnissi B, Khalfaoui K, Ebai T, Marques Souza de Oliveira F, Ghram A, Kamali-Moghaddam M, Hmila I. Accurate detection of Newcastle disease virus using proximity-dependent DNA aptamer ligation assays. FEBS Open Bio 2021; 11:1122-1131. [PMID: 33595202 PMCID: PMC8016122 DOI: 10.1002/2211-5463.13117] [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: 12/16/2020] [Revised: 01/28/2021] [Accepted: 02/15/2021] [Indexed: 11/20/2022] Open
Abstract
Detecting viral antigens at low concentrations in field samples can be crucial for early veterinary diagnostics. Proximity ligation assays (PLAs) in both solution and solid‐phase formats are widely used for high‐performance protein detection in medical research. However, the affinity reagents used, which are mainly poly‐ and monoclonal antibodies, play an important role in the performance of PLAs. Here, we have established the first homogeneous and solid‐phase proximity‐dependent DNA aptamer ligation assays for rapid and accurate detection of Newcastle disease virus (NDV). NDV is detected by a pair of extended DNA aptamers that, upon binding in proximity to proteins on the envelope of the virus, are joined by enzymatic ligation to form a unique amplicon that can be sensitively detected using real‐time PCR. The sensitivity, specificity, and reproducibility of the assays were validated using 40 farm samples. The results demonstrated that the developed homogeneous and solid‐phase PLAs, which use NDV‐selective DNA aptamers, are more sensitive than the sandwich enzymatic‐linked aptamer assay (ELAA), and have a comparable sensitivity to real‐time reverse transcription PCR (rRT‐PCR) as the gold standard detection method. In addition, the solid‐phase PLA was shown to have a greater dynamic range with improved lower limit of detection, upper‐ and lower limit of quantification, and minimal detectable dose as compared with those of ELAA and rRT‐PCR. The specificity of PLA is shown to be concordant with rRT‐PCR.
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Affiliation(s)
- Boutheina Marnissi
- Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Khouloud Khalfaoui
- Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Tonge Ebai
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Issam Hmila
- Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur of Tunis, University Tunis El Manar, Tunis, Tunisia
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