Application of Aptamers in Virus Detection and Antiviral Therapy

Zou, Xinran; Wu, Jing; Gu, Jianzhong; Шен, Ли; Mao, Lingxiang

doi:10.3389/fmicb.2019.01462

Cited by 181 publications

(169 citation statements)

References 168 publications

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“…We hypothesize that a SARS-CoV-2 aptamer test is beneficial to provide a lower limit of detection. Aptamers are single stranded RNA or DNA nucleotides (10-100nt) that are able to bind to targets such as viruses and proteins [36]. Aptamers' binding September 8, 2020…”

Section: Discussionmentioning

confidence: 99%

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In silico prediction of COVID-19 test efficiency with DinoKnot

Newman

Chang

Jabbari

2020

Preprint

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus spreading across the world causing the disease COVID-19. The diagnosis of COVID-19 is done by quantitative reverse-transcription polymer chain reaction (qRT-PCR) testing which utilizes different primer-probe sets depending on the assay used. Using in silico analysis we aimed to determine how the secondary structure of the SARS-CoV-2 RNA genome affects the interaction between the reverse primer during qRT-PCR and how it relates to the experimental primer-probe test efficiencies. We introduce the program DinoKnot (Duplex Interaction of Nucleic acids with pseudoKnots) that follows the hierarchical folding hypothesis to predict the secondary structure of two interacting nucleic acid strands (DNA/RNA) of similar or different type. DinoKnot is the first program that utilizes stable stems in both strands as a guide to find the structure of their interaction. Using DinoKnot we predicted the interaction of the reverse primers used in four common COVID-19 qRT-PCR tests with the SARS-CoV-2 RNA genome. In addition, we predicted how 12 mutations in the primer/probe binding region may affect the primer/probe ability and subsequent SARS-CoV-2 detection. While we found all reverse primers are capable of interacting with their target area, we identified partial mismatching between the SARS-CoV-2 genome and some reverse primers. We predicted three mutations that may prevent primer binding, reducing the ability for SARS-CoV-2 detection. We believe our contributions can aid in the design of a more sensitive SARS-CoV-2 test.Author summaryThe current testing for the disease COVID-19 that is caused by the novel cornonavirus SARS-CoV-2 uses oligonucleotides called primers that bind to specific target regions on the SARS-CoV-2 genome to detect the virus. Our goal was to use computational tools to predict how the structure of the SARS-CoV-2 RNA genome affects the ability of the primers to bind to their target region. We introduce the program DinoKnot (Duplex interaction of nucleic acids with pseudoknots) that is able to predict the interactions between two DNA or RNA molecules. We used DinoKnot to predict the efficiency of four common COVID-19 tests, and the effect of mutations in the SARS-CoV-2 virus on ability of the COVID-19 tests in detecting those strains. We predict partial mismatching between some primers and the SARS-CoV-2 genome but that all primers are capable of interacting with their target areas. We also predict three mutations that prevent primer binding and thus SARS-CoV-2 detection. We discuss the limitations of the current COVID-19 testing and suggest the design of a more sensitive COVID-19 test that can be aided by our findings.

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Section: Discussionmentioning

confidence: 99%

“…12/16 specificity is ensured by their secondary and tertiary structure [36]. An RNA aptamer test designed for the SARS-CoV Nucleocapsid protein showed a detection limit of pg/mL [37].…”

Section: Discussionmentioning

confidence: 99%

In silico prediction of COVID-19 test efficiency with DinoKnot

Newman

Chang

Jabbari

2020

Preprint

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“…One other major drawback of antibodies and nanobodies over aptamers is the cost involved in generating them [96]. While traditional antibody tests, such as enzyme linked immunosorbent assays (ELISAs) and immunophenotyping by flow cytometry are completed in a laboratory environment, there is a requirement for point of care testing (POCT) and rapid diagnostic tests that span all species [97][98][99]. Going back to the protein nature of antibodies and nanobodies, these require special conditions to be used in the field for POCT.…”

Section: In Vitro Applications: Which Is Best?mentioning

confidence: 99%

Antibodies, Nanobodies, or Aptamers—Which Is Best for Deciphering the Proteomes of Non-Model Species?

Dhar

Samarasinghe

Shigdar

2020

IJMS

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This planet is home to countless species, some more well-known than the others. While we have developed many techniques to be able to interrogate some of the “omics”, proteomics is becoming recognized as a very important part of the puzzle, given how important the protein is as a functional part of the cell. Within human health, the proteome is fairly well-established, with numerous reagents being available to decipher cellular pathways. Recent research advancements have assisted in characterizing the proteomes of some model (non-human) species, however, in many other species, we are only just touching the surface. This review considers three main reagent classes—antibodies, aptamers, and nanobodies—as a means of continuing to investigate the proteomes of non-model species without the complications of understanding the full protein signature of a species. Considerations of ease of production, potential applications, and the necessity for producing a new reagent depending on homology are presented.

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“…This review intends to provide an update in the use of aptamer-based technologies in detection of infectious agents, and to demonstrate the flexibility and applicability of these technologies in precise detection of many categories of microbial agents, such as pathogenic bacteria, viruses, parasites or their products in a solid or liquid phase (Figure 1). In-depth technical overviews regarding emerging aptamer-based biosensors and cutting-edging technologies for the detection of proteins from various pathogens are available [16,17]. Representative aptamer-based methods for pathogenic targets from recent literature are briefly discussed in the text and the remaining is mentioned in Tables 2-3.…”

Section: Introductionmentioning

confidence: 99%

Advances in detection of infectious agents by aptamer-based technologies

Jia

et al. 2020

Emerging Microbes & Infections

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Infectious diseases still remain one of the biggest challenges for human health. Accurate and early detection of infectious pathogens are crucial for transmission control, clinical diagnosis, and therapy. For a traditional reason, most immunological and microbiological laboratories are equipped with instruments designated for antibody-based assays in detection of infectious pathogens or clinical diagnosis. Emerging aptamer-based technologies have pushed a shift from antibody-based to aptamer-based assays due to equal specificity, even better sensitivity, lower manufacturing cost and more flexibility in amending for chemiluminescent, electrochemical or fluorescent detection in a multifaceted and high throughput fashion in comparison of aptamer-based to antibody-based assays. The nature of aptamer-based technologies is particularly suitable for point-of-care testing in remote areas at warm or hot atmosphere, and mass screening for potential infection in pandemic of emerging infectious agents, such as SARS-CoV or SARS-CoV-2 in an epicentre or other regions. This review intends to summarize currently available aptamer-based technologies in detection of bacterial, viral, and protozoan pathogens for research and clinical application. It is anticipated that potential technologies will be further optimized and validated for clinical translation in meeting increasing demands for prompt, precise, and reliable detection of specific pathogens in various atmospheric conditions.

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Application of Aptamers in Virus Detection and Antiviral Therapy

Cited by 181 publications

References 168 publications

In silico prediction of COVID-19 test efficiency with DinoKnot

In silico prediction of COVID-19 test efficiency with DinoKnot

Antibodies, Nanobodies, or Aptamers—Which Is Best for Deciphering the Proteomes of Non-Model Species?

Advances in detection of infectious agents by aptamer-based technologies

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