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Review
. 2023 Jun;9(6):e17148.
doi: 10.1016/j.heliyon.2023.e17148. Epub 2023 Jun 11.

Multidimensional futuristic approaches to address the pandemics beyond COVID-19

Shifa Bushra Kotwal  1 , Nidhi Orekondey  1 , Gargi Prasad Saradadevi  1 , Neha Priyadarshini  1 , Navinchandra V Puppala  1 , Mahak Bhushan  2 , Snehasri Motamarry  1 , Rahul Kumar  1 , Gireesha Mohannath  1 , Ruchi Jain Dey  1
Affiliations
Review

Multidimensional futuristic approaches to address the pandemics beyond COVID-19

Shifa Bushra Kotwal et al. Heliyon. 2023 Jun.

Abstract

Globally, the impact of the coronavirus disease 2019 (COVID-19) pandemic has been enormous and unrelenting with ∼6.9 million deaths and ∼765 million infections. This review mainly focuses on the recent advances and potentially novel molecular tools for viral diagnostics and therapeutics with far-reaching implications in managing the future pandemics. In addition to briefly highlighting the existing and recent methods of viral diagnostics, we propose a couple of potentially novel non-PCR-based methods for rapid, cost-effective, and single-step detection of nucleic acids of viruses using RNA mimics of green fluorescent protein (GFP) and nuclease-based approaches. We also highlight key innovations in miniaturized Lab-on-Chip (LoC) devices, which in combination with cyber-physical systems, could serve as ideal futuristic platforms for viral diagnosis and disease management. We also discuss underexplored and underutilized antiviral strategies, including ribozyme-mediated RNA-cleaving tools for targeting viral RNA, and recent advances in plant-based platforms for rapid, low-cost, and large-scale production and oral delivery of antiviral agents/vaccines. Lastly, we propose repurposing of the existing vaccines for newer applications with a major emphasis on Bacillus Calmette-Guérin (BCG)-based vaccine engineering.

Keywords: BCG; COVID-19; Diagnostics; Lab-on-Chip; RNA mimics Of GFP; RPA; Ribozyme; SARS-CoV-2; Therapeutics; Vaccines.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
A flow chart for reverse transcription and Recombinase Polymerase Amplification (RT-RPA)-based method for detection of viral RNA. (A) Single-stranded RNA (ssRNA) isolated from virus-infected samples is reverse transcribed. (B) cDNA subjected to isothermal amplification using Recombinase polymerase amplification (RPA) reaction. ds-double-stranded; SSB–single-stranded DNA binding proteins.
Fig. 2
Fig. 2
Comparative flow charts of RT-PCR and Point-of-care (POC) detection methods. POC devices (workflow depicted by numbers in green circles) are cost-effective, less time-consuming, simpler and can be performed by minimally trained technicians in point-of-care settings compared to RT-PCR-based diagnostics (workflow depicted by numbers in purple circles). RT-PCR: Reverse transcriptase-polymerase chain reaction; IoT: Internet of things. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3
Fig. 3
Diagrammatic representation of miniaturized Lab-on-chip (LoC) module. Microfluidic Lab-on-chip (LoC) consists of specialized microfluidic patterning to ensure proper flow, release, and mixing of reagents required for RNA isolation and RT-PCR. Thermal loops present in the RT-PCR zone provide suitable temperatures to carry out the reaction. The Serpentine micro channels ensure a controlled flow rate and minimal sample loss. The multiplexed detection zone facilitates the detection of multiple pathogens in parallel chambers along with a suitable control either via colorimetric (visual) or fluorescence-based methodologies. Internet of Things (IoT)-based methods can be employed for automating and sharing the data.
Fig. 4
Fig. 4
A flowchart illustrating how RNA mimics of GFP-based viral RNA detection works. (a) Step 1: Mix viral RNA, customized RNA mimic of GFP and custom synthesized DNA oligos. (b) Step 2: Hybridization of complementary sequences (RNA: RNA and DNA: RNA). (c) Step 3: Add streptavidin-coated magnetic beads and pull-down complexes through biotinylated DNA oligos and wash the unbound molecules. (d) Step 4: Add DFHBI fluorophore (light green molecules), which upon binding to RNA aptamer results in green fluorescence. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 5
Fig. 5
A flowchart illustrating how specific nuclease and TaqMan probes-based detection of viral RNA works. A, Module I and B, Module II. (A) Module I involves the following steps: (a) Step 1: Mix viral RNA with the customized TaqMan probes. (b) Step 2: Hybridization of complementary sequences (DNA: RNA). (c) Step 3: Add DNA-specific T7 5′-3′ exonuclease, which preferentially cleaves DNA: RNA hybrid (least activity on ssDNA). (d) Step 4: Fluorescence detection and measurement. (B) Module II involves the following steps: (a) Step 1: Mix viral RNA with the customized TaqMan probes. (b) Step 2: Hybridization of complementary sequences (DNA: RNA). (c) Step 3: Add Nuclease P1 (endonuclease) which preferentially cleaves ssDNA or ssRNA and not DNA:RNA hybrid. (d) Step 4: Fluorescence detection and measurement.
Fig. 6
Fig. 6
Methods being employed to develop vaccines against SARS-CoV-2. The figure summarizes various methods currently used to develop vaccines against SARS CoV-2. Candidate vaccines belonging to these categories are either in various phases of clinical trials or approved for human use (https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines).
Fig. 7
Fig. 7
BCG-induced trained immunity and heterologous protection against secondary infections. The figure describes various mechanisms underlying induction of trained immunity by BCG involving a complex network of circulating peripheral myeloid cells, metabolic rewiring, epigenetic reprogramming, and hematopoietic stem and progenitor cells' activation leading to myelopoiesis. (A) BCG induced activation of hematopoietic stem and progenitor cells, leading to myelopoiesis. (B) Activation of TLR4 receptors by BCG cell wall lipids triggering downstream signalling events leading to activation of NF-kB pathway. (C) Activation of Dectin-1 receptor causing increased glycolysis. (D) Initiation of post-phagocytic events in phagocytic cells. (E) Release of mycobacterial cyclic dinucleotides such as c-di-AMP and c-di-GMP, which bind to the endoplasmic reticulum (ER)-associated sensor called stimulator of interferon genes (STING) with subsequent activation of IRF3-dependent transcription and cytokine production. (F) Muramyl dipeptides (MDP) released by BCG binds to the cytosolic nucleotide-binding oligomerization domain 2 (NOD2) receptor. (F1) Upon stimulation with MDP, the NOD2 receptor binds to RIP2, activating the IRF pathway. (F2) NOD2 also causes increased glycolysis. Enhanced production of acetyl-CoA induces epigenetic reprogramming via histone modifications causing widespread expression of inflammation-related genes. (G) Insulin-like Growth Factor 1 receptor (IGF1 R) activation by mevalonate enhances glycolysis. (H) Increase in glycolytic intermediates further increases the flux of acetyl-CoA into the TCA cycle. Glutamine lysis further augments α-ketoglutarate and fumarate levels. (I) Increased fumarate levels inhibit histone demethylases, enhancing histone methylation of the promoters of the genes governing inflammation. (J) Pyruvate dehydrogenase complex (PDH) also translocates into the nucleus and causes the production of acetyl-CoA and increases histone acetylation. (K) The metabolic and epigenetic reprogramming from various pathways leads to enhanced antigen processing and presentation via MHC I and II. (L) Enhanced production of several pro-inflammatory cytokines in combination with antigen presentation, amplifies the T cell response (CD4 and CD8 T and Th17 response) against secondary infections.
Fig. 8
Fig. 8
Engineering BCG to protect children against TB and COVID-19. The figure describes how the anti-viral benefits of BCG and cyclic dinucleotide-based STING agonists are harnessed by employing the recombinant BCG (rBCG) approach. BCG vaccine can be genetically engineered to simultaneously express STING agonists (cyclic dinucleotides) and SARS-CoV-2 antigen(s) (e.g., S protein). The rBCG approach can be utilized as a primary vaccination for children aged 0–5 years, conferring protection against both childhood TB and COVID-19. Based on the duration of protection conferred against prevailing strains of SARS-CoV-2, primary immunization can be followed by a heterologous booster vaccine (other than BCG) at later time points to augment SARS-CoV-2 or pan-corona virus-specific immune responses further.
Fig. 9
Fig. 9
Engineered bacterial M1GS ribozyme-based strategy to cleave the target viral RNA. (A) Cartoon depicting the mode of target RNA cleavage by engineered RNase P ribozyme using EGS strategy. (B) Cartoon depicting the mode of target RNA cleavage by engineered RNase P ribozyme using M1GS strategy. (C) The cartoon illustrates a scheme for oral delivery of M1GS ribozymes in mouse models using engineered Salmonella bacteria to target viral mRNA in virus-infected mice [205]. EGS-External guide sequence; M1GS-M1 RNA-Guide sequence; SCID-Severe combined immunodeficiency.
Fig. 10
Fig. 10
Plant-based platforms for cloning and expression of antibodies derived from pathogen-specific B cells. The figure depicts various steps involved in antibody production. (A) Isolation of B cells from COVID-19 patients. (B) Purification of B cells and cDNA library preparation. (C) Isolation of the antibody-producing gene followed by cloning and expression using various expression systems such as Agrobacterium tumefaciens, plant or viral expression vectors. Various methods are used for the transformation of these expression systems (e.g., leaf infiltration, callus induction, gene gun). These methods allow for transient as well as stable expression of the transgenes. (D) The plants transiently or stably expressing antibodies can be grown on a large scale using either green houses, fields, bioreactors, or hydroponic systems. The antibodies thus produced can be used either directly by consuming fruits and vegetables or unpurified powder. In addition, antibodies can be purified to develop injectable or capsule forms. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 11
Fig. 11
A flowchart illustrating the expression of therapeutic proteins (TPs) in plants and their oral delivery. AS-Accessory sequence; CPP-Cell-penetrating peptide; EPS-Endogenous protease cleavage site; RP-Receptor protein.
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References

    1. Shereen M.A., Khan S., Kazmi A., Bashir N., Siddique R. COVID-19 infection: origin, transmission, and characteristics of human coronaviruses. J. Adv. Res. 2020;24:91–98. doi: 10.1016/j.jare.2020.03.005. - DOI - PMC - PubMed
    1. Ciotti M., Ciccozzi M., Terrinoni A., Jiang W.-C., Wang C.-B., Bernardini S. The COVID-19 pandemic. Crit. Rev. Clin. Lab Sci. 2020;57:365–388. doi: 10.1080/10408363.2020.1783198. - DOI - PubMed
    1. Helmy Y.A., Fawzy M., Elaswad A., Sobieh A., Kenney S.P., Shehata A.A. The COVID-19 pandemic: a comprehensive review of taxonomy, genetics, epidemiology, diagnosis, treatment, and control. J. Clin. Med. 2020;9:1225. - PMC - PubMed
    1. Zhou P., Yang X.-L., Wang X.-G., Hu B., Zhang L., Zhang W., Si H.-R., Zhu Y., Li B., Huang C.-L. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579:270–273. - PMC - PubMed
    1. Wu F., Zhao S., Yu B., Chen Y.-M., Wang W., Song Z.-G., Hu Y., Tao Z.-W., Tian J.-H., Pei Y.-Y. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265–269. - PMC - PubMed

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