Probing and characterizing the high specific sequences of ssDNA aptamer against SGIV-infected cells

Structural optimization, characterization, and evaluation of binding mechanism of aptamers against bovine pregnancy-associated glycoproteins and their application in establishment of a colorimetric aptasensor using Fe-based metal-organic framework as peroxidase mimic tags

A truncated aptamer (designated A24-3) was identified that specifically binds to bovine pregnancy-associated glycoproteins (bPAG9) with a low dissociation constant (2.04 nM) through two truncation approaches. Circular dichroism spectroscopy indicated that A24-3 formed parallel G-quadruplexes, which was subsequently confirmed using nuclear magnetic resonance (NMR) spectroscopy. Furthermore, a molecular dynamics simulation was employed to investigate the recognition mechanism of A24-3 and bPAG9. Interaction analysis showed that A24-3 folded into a parallel G-quadruplex structure with three G-tetrads, primarily through numerous hydrogen bonds and hydrophobic and π-π interactions. Finally, a novel colorimetric aptasensor was developed for detecting bPAG9 using A24-3 and an Fe-based metal-organic framework as target recognition elements and enzyme mimics, respectively. The method demonstrated a broad detection range from 0.5 to 50 ng/mL, with a low detection limit of 0.03 ng mL-1, and exhibited a good recovery (91.0-102%) for bPAG9-spiked serum samples. Additionally, the aptasensor was successfully applied to detecting the pregnancy-specific biomarker bPAGs in serum samples.

Aptamer-based diagnostic and therapeutic approaches for animal viruses: A review

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.

Effect of EGCG Extracted from Green Tea against Largemouth Bass Virus Infection

(1) Background: Largemouth bass virus (LMBV) is a major viral pathogen in largemouth bass (Micropterus salmoides) aquaculture that often causes high mortality and heavy economic losses, thus developing treatments to combat this pathogen is of great commercial importance. Green tea is a well-known medicinal plant that contains active ingredients with antiviral, antibacterial, and other biological activities. The goals of this study were to explore the effect and mechanism of green tea source compounds on LMBV and provide data to serve as the basis for the screening of targeted drugs in the future. In this study, we evaluated the effects of the main component of green tea, epigallocatechin-3-gallate (EGCG), against LMBV infection. (2) Methods: The safe working concentration of EGCG was identified by cell viability detection and light microscopy. The antiviral activity and mechanism of action of EGCG against LMBV infection were evaluated with light microscopy, an aptamer 6-carboxy-fluorescein-based fluorescent molecular probe, and reverse transcription quantitative PCR. (3) Results: The safe working concentration of EGCG was ≤10 μg/mL. EGCG showed significant anti-LMBV infection activity in a concentration-dependent manner, and it also destroyed the structure of virus particles. EGCG impacted the binding of virus particles to cell receptors and virus invasion into the host cells. Inhibitory effects of EGCG on LMBV particles, LMBV binding to the host-cell membrane, and LMBV invasion were 84.89%, 98.99%, and 95.23%, respectively. Meanwhile, the effects of EGCG subsequently were verified in vivo. The fatality rate of the LMBV + EGCG group was significantly lower than that of the LMBV group. (4) Conclusions: Our results suggest that EGCG has effective antiviral properties against LMBV and may be a candidate for the effective treatment and control of LMBV infections in largemouth bass aquaculture.

Generation and characterization of aptamers against grass carp reovirus infection for the development of rapid detection assay

Grass carp reovirus (GCRV) causes devastating viral haemorrhagic disease in farmed grass carp (Ctenopharyngon idellus). As novel molecular probes, aptamers have been widely applied in rapid diagnosis and efficient therapies against virus or diseases. In this study, three single-stranded DNA (ssDNA) aptamers were selected against GCRV-infected CIK cells via SELEX (systematic evolution of ligands by exponential enrichment technology). Secondary structures predicted by MFOLD indicated that aptamers formed stem-loop structures, and GVI-11 had the lowest ΔG value of -30.84 KJ/mol. Three aptamers could specifically recognize GCRV-infected CIK cells, with calculated dissociation constants (Kd) of 220.86, 176.63 and 278.66 nM for aptamers GVI-1, GVI-7 and GVI-11, respectively, which indicated that they could serve as specific delivery system for antiviral therapies. The targets of aptamers GVI-1, GVI-7 and GVI-11 on the surface of GCRV-infected cells could be membrane proteins, which were trypsin-sensitive. Furthermore, FAM-labelled aptamer GVI-7 could be applied to detect GCRV infection in vivo. It is the first time to generate and characterize aptamers against GCRV-infected cells. These aptamers have great potentials in development of rapid diagnosis technology and antiviral agents against GCRV infection in aquaculture.

Specific Aptamer-Based Probe for Analyzing Biomarker MCP Entry Into Singapore Grouper Iridovirus-Infected Host Cells via Clathrin-Mediated Endocytosis

Biomarkers have important roles in various physiological functions and disease pathogenesis. As a nucleocytoplasmic DNA virus, Singapore grouper iridovirus (SGIV) causes high economic losses in the mariculture industry. Aptamer-Q5-complexed major capsid protein (MCP) in the membrane of SGIV-infected cells can be used as a specific molecular probe to investigate the crucial events of MCP endocytosis into SGIV-infected host cells during viral infection. Chlorpromazine blocks clathrin-mediated endocytosis, and MCP endocytosis into SGIV-infected cells decreased significantly when the cells were pretreated with chlorpromazine. The disruption of cellular cholesterol by methyl-β-cyclodextrin also significantly reduced MCP endocytosis. In contrast, inhibitors of key regulators of caveolae/raft-dependent endocytosis and macropinocytosis, including genistein, Na⁺/H⁺ exchanger, p21-activated kinase 1 (PAK1), myosin II, Rac1 GTPase, and protein kinase C (PKC), had no effect on MCP endocytosis. The endocytosis of the biomarker MCP is dependent on low pH and cytoskeletal actin filaments, as shown with various inhibitors (chloroquine, ammonia chloride, cytochalasin D). Therefore, MCP enters SGIV-infected host cells via clathrin-mediated endocytosis, which is dependent on dynamin, cholesterol, low pH, and cytoskeletal actin filaments. This is the first report of a specific aptamer-based probe used to analyze MCP endocytosis into SGIV-infected host cells during viral infection. This method provides a convenient strategy for exploring viral pathogenesis and facilitates the development of diagnostic tools for and therapeutic approaches to viral infection.

Aptamer Hybrid Nanocomplexes as Targeting Components for Antibiotic/Gene Delivery Systems and Diagnostics: A Review

With the passage of time and more advanced societies, there is a greater emergence and incidence of disease and necessity for improved treatments. In this respect, nowadays, aptamers, with their better efficiency at diagnosing and treating diseases than antibodies, are at the center of attention. Here, in this review, we first investigate aptamer function in various fields (such as the detection and remedy of pathogens, modification of nanoparticles, antibiotic delivery and gene delivery). Then, we present aptamer-conjugated nanocomplexes as the main and efficient factor in gene delivery. Finally, we focus on the targeted co-delivery of genes and drugs by nanocomplexes, as a new exciting approach for cancer treatment in the decades ahead to meet our growing societal needs.

Isolation and Characterization of a Ranavirus Associated with Disease Outbreaks in Cultured Hybrid Grouper (♀ Tiger Grouper Epinephelus fuscoguttatus × ♂ Giant Grouper E. lanceolatus) in Guangxi, China

An outbreak of suspected iridovirus disease in cultured hybrid grouper (♀Tiger Grouper Epinephelus fuscoguttatus × ♂ Giant Grouper Epinephelus lanceolatus) occurred in the Guangxi Province in July, 2018. In this study, grouper iridovirus Guangxi (SGIV-Gx) was isolated from diseased hybrid grouper that were collected from Guangxi. Cytopathic effects were observed and identified in grouper spleen cells that were incubated with diseased tissue homogenates after 24 h, and the effects increased at 48 h postinfection. The transmission electron microscopy results showed that viral particles that were about 200 nm in diameter with hexagonal profiles were present in the cell cytoplasm of suspected virus-infected cells. The presence of SGIV-Gx (accession number: MK107821) was identified by polymerase chain reaction (PCR) and amplicon sequencing, which showed that this strain was most closely related to Singapore grouper iridovirus (AY521625.1). The detection of SGIV-Gx infection was further supported by novel aptamer (Q2c)-based detection technology. The effects of temperature and pH on viral infectivity were analyzed by using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and cell culture. The results indicated that SGIV-Gx was resistant to exposure to pH levels 5, 7, and 7.5 for 1 h, but its infectivity was remarkably lower at pH levels 3 and 10 after 1 h. The analyses showed that SGIV-Gx was stable for 1 h at 4°C and 25°C but was inactivated after 1 h at 40, 50, and 60°C.

Identification of Major Capsid Protein as a Potential Biomarker of Grouper Iridovirus-Infected Cells Using Aptamers Selected by SELEX

Biomarkers have important roles in disease pathogenesis, and serve as important disease indicators for developing novel diagnostic and therapeutic approaches. Grouper iridovirus is a nucleocytoplasmic DNA virus, which not only causes great economic losses in mariculture but also seriously threatens the global biodiversity. However, a lack of biomarkers has limited the progress in clarifying iridovirus pathogenesis. Here, we report novel molecular probes, aptamers, for specific identification of biomarkers in grouper iridovirus-infected cells. Aptamers are selected by SELEX, which is a completely different approach from conventional antibody-based methods for biomarkers discovery. Aptamer-based technology is the unique efficient selection for cell-specific target molecules, and helps find out new biomarkers without the knowledge of characteristics of proteins expressed on virus-infected cell surface. With the implementation of a two-step strategy (aptamer selection and biomarker discovery), combined with mass spectrometry, grouper iridovirus major capsid protein was ultimately identified as a potential biomarker of aptamer Q5 for grouper iridovirus infection. The specific interactions of aptamer Q5 and MCP were experimentally validated by several assays, including EMSA, co-localization of fluorescence by LSCM, binding competition tests, and siRNA silencing tests by flow cytometry. This aptamer-based method for biomarkers discovery developed with grouper iridovirus-infected cells could be applicable to other types of virus infection, markedly improve our studies of biomarker discovery and virus pathogenesis, and further facilitate the development of diagnostic tools and therapeutic approaches to treat virus infection.

The inhibitory activities and antiviral mechanism of Viola philippica aqueous extracts against grouper iridovirus infection in vitro and in vivo

Grouper iridovirus (GIV) is one of the most serious pathogens in mariculture and causes high mortality rates in cultured groupers; then, effective medicines for controlling GIV infections are urgently needed. Viola philippica is a well-known medicinal plant, and the application of V. philippica aqueous extracts against GIV infection was assessed by different methods in this study. The results showed that the working concentration of V. philippica aqueous extracts was 10 mg/ml. V. philippica aqueous extracts below 10 mg/ml have no significant cytotoxic effects on cell viability, while extracts over 15 mg/ml decreased cell viability and showed cytotoxic activity. V. philippica aqueous extracts had excellent inhibitory effects against GIV infection in vitro and in vivo. The possible antiviral mechanism of V. philippica was further analysed, which indicated that V. philippica did no damages to GIV particles, but it could disturb GIV binding, entry and replication in host cells. V. philippica had the best inhibitory effects against GIV during viral infection stage of binding and replication in host cells. Overall, the results suggest that appropriate concentration of V. philippica aqueous extracts has great antiviral effects, making it an interesting candidate for developing effective medicines for preventing and controlling GIV infection in farmed groupers.

Selection and characterization of ssDNA aptamers specifically recognizing pathogenic Vibrio alginolyticus

Vibrio alginolyticus (V. alginolyticus) is a major opportunistic pathogen to both marine animals and humans, which has also caused heavy economic losses to mariculture. The aim of this study was to develop highly specific aptamers for V. alginolyticus. Single-stranded DNA (ssDNA) aptamers with high binding affinity to viable V. alginolyticus were generated by Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and identified by flow cytometric analysis in this study. The selected aptamers showed high specificity for V. alginolyticus and low apparent binding for other bacteria. The aptamers formed distinct stem-loop structures, which could form the basis of aptamers' specific binding to the target V. alginolyticus. Aptamer VA2 and VA8 showed particularly high binding affinity constant (Kd) of 14.31 ± 4.26 and 90.00 ± 13.51 nM, respectively. The aptamers produced no cytotoxic effects in vitro and in vivo. ssDNA aptamers were successfully selected against the viable bacteria pathogen V. alginolyticus by SELEX. The aptamers selected in this study could be not only applied as specific chemical molecular probes for studying V. alginolyticus pathogenesis to Trachinotus ovatus, but also developing rapid convenient diagnosis assay for V. alginolyticus infection, even when applied to the complex sample matrix, such as food and environment samples.

Fluorometric determination of lipopolysaccharides via changes of the graphene oxide-enhanced fluorescence polarization caused by truncated aptamers

A broad-spectrum ssDNA aptamer containing 80 nucleotides (LA80) and capable of binding to four different sources of lipopolysaccharides (LPSs) was truncated. Two strategies are used to produce truncated aptamers of different length. The results show that LA27, a 27-nt aptamer, retained broad-spectrum capability and has a higher affinity (K_d = 46.2 ± 9.5 nM). A graphene oxide based fluorescence polarization assay (excitation/emission wavelengths: 485/520 nm) was worked out using FAM-labeled LA27. It can detect LPSs from Salmonella entericaserotype typhimurium, Pseudomonas aeruginosa 10 and Escherichia coli 055:B5 with enhanced performance (4.8 to 29-fold improvements) compared to LA80. The assay can be performed within 30 min, and the detection limits are 38.7, 88.0 and 154 ng·mL^-1, respectively. Graphical abstract Schematic presentation of the assay: A shorter aptamer, with higher affinity than its original aptamer, was obtained by truncated strategies. This core aptamer lead to release easily and enhance the sensivity of the GO-based fluorescence polarization assay.

Characterization of ssDNA aptamers specifically directed against Trachinotus ovatus NNV (GTONNV)-infected cells with antiviral activities

Nervous necrosis virus (NNV), is one of the most fatal viruses in marine fish aquaculture, and is capable of infecting over 50 different fish species. Trachinotus ovatus NNV (GTONNV) was isolated from diseased golden pompano. This T. ovatus strain was isolated from Guangxi, China. Single-stranded DNA (ssDNA) aptamers with high specificity for GTONNV-infected T. ovatus cerebellum cells (TOCC) were produced by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). The characterization of these aptamers was performed using flow cytometry and laser scanning confocal microscopy. The selected aptamers showed significant specificity for GTONNV-infected cells. Based on MFOLD prediction, aptamers formed distinct stem-loop structures that could form the basis for the aptamers' specific binding to their cellular targets. Protease treatment results revealed that the target molecules for aptamers TNA1, TNA4 and TNA19 within GTONNV-infected cells may be membrane proteins that were trypsin-sensitive. Specific endocytosis of aptamer TNA1, TNA4 and TNA19 into GTONNV-infected cells was also shown. The selected aptamers demonstrated antiviral effects against GTONNV both in vitro and in vivo. This is the first time that aptamers targeting GTONNV-infected T. ovatus cells have been selected and characterized. These aptamers hold promise as rapid diagnostic reagents or targeted therapeutic drugs against GTONNV.

Molecular biology of Macrobrachium rosenbergii nodavirus infection in giant freshwater prawn

Macrobrachium rosenbergii nodavirus (MrNV) has been threatening the giant freshwater prawn aquaculture since 1997, causing white tail disease in the prawn species that leads to 100% lethality of the infected postlarvae. Comprehension of the viral infectivity and pathogenesis at molecular biology level has recently resolved the viral capsid protein and evidenced the significant difference in the viral structural protein compared to other nodaviruses that infect fish and insect. Cumulative researches have remarked the proposal to assert MrNV as a member of new genus, gammanodavirus to the Nodaviridae family. The significance of molecular biology in MrNV infection is being highlighted in this current review, revolving the viral life cycle from virus binding and entry into host, virus replication in host cell, to virus assembly and release. The current review also highlights the emerging aptamers technology that is also known as synthetic antibody, its application in disease diagnosis, and its prophylactic and therapeutic properties. The future perspective of synthetic virology technology in understanding viral pathogenesis, as well as its potential in viral vaccine development, is also discussed.