Microfluidic devices for detection of RNA viruses

Summary

There is a long way to go before the coronavirus disease 2019 (Covid‐19) outbreak comes under control. qRT‐PCR is currently used for the detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the causative agent of Covid‐19, but it is expensive, time‐consuming, and not as sensitive as it should be. Finding a rapid, easy‐to‐use, and cheap diagnostic method is necessary to help control the current outbreak. Microfluidic systems provide a platform for many diagnostic tests, including RT‐PCR, RT‐LAMP, nested‐PCR, nucleic acid hybridization, ELISA, fluorescence‐Based Assays, rolling circle amplification, aptamers, sample preparation multiplexer (SPM), Porous Silicon Nanowire Forest, silica sol‐gel coating/bonding, and CRISPR. They promise faster, cheaper, and easy‐to‐use methods with higher sensitivity, so microfluidic devices have a high potential to be an alternative method for the detection of viral RNA. These devices have previously been used to detect RNA viruses such as H1N1, Zika, HAV, HIV, and norovirus, with acceptable results. This paper provides an overview of microfluidic systems as diagnostic methods for RNA viruses with a focus on SARS‐CoV‐2.

1. INTRODUCTION

Viruses that have RNA as their genetic core material can cause diseases like Ebola, hepatitis C, influenza, severe acute respiratory syndrome (SARS) and poliomyelitis. ¹ Coronaviruses are enveloped, single‐stranded RNA viruses that can cause diseases in both humans and animals, mostly affecting the respiratory system. ² Coronaviruses originate from multiple species. Four strains of human coronaviruses (hCoVs), including 229E, ‐NL63, ‐OC43, and ‐HKU1, cause common cold‐like symptoms in humans. The other three hCoVs can result in potentially fatal lower respiratory tract diseases. They have caused three outbreaks: severe acute respiratory syndrome coronavirus (SARS‐COV) in 2002–2003, the Middle East respiratory syndrome coronavirus (MERS‐COV) in 2012, and the novel coronavirus disease in 2019 (Covid‐19). ³ , ⁴ In 2007, it was stated that another disastrous SARS epidemic would probably break out in the coming years because of the vast reservoir of SARS‐like coronaviruses in horseshoe bats and the tradition of eating exotic mammals in southern China. ⁴ Subsequently, Covid‐19 became pandemic. ⁵ , ⁶

To date, Covid‐19 has infected more than 14 million people involving healthcare and non‐healthcare settings. ⁷ It causes a multisystem infectious disorder ⁸ , ⁹ , ¹⁰ that is more likely to arise in genetically susceptible individuals ¹¹ , ¹² and people with pre‐existing conditions associated with immune dysregulation. ¹³ , ¹⁴ , ¹⁵ , ¹⁶ , ¹⁷ , ¹⁸ After 7 months of the outbreak and pandemic of Covid‐19, ¹⁹ , ²⁰ no specific treatment and prevention exist, ²¹ and supportive care is the only option along with anti‐inflammatory and antiviral agents. ¹⁴ , ¹⁷ , ²² , ²³ , ²⁴ The condition at being the cause of more than 600 000 deaths has promoted international investigative efforts ²⁵ , ²⁶ , ²⁷ to find tools for earlier diagnosis of Covid‐19, allowing us to consider isolation practices as well as apply for supportive care earlier.

1.1. Conventional diagnostic methods

Early diagnosis of viral diseases can lead to better and more accurate treatment. Cell culture‐based techniques are the gold standard for viral detection. ²⁸ Rapid molecular techniques with high sensitivity involve the amplification of viral genomic material and may detect several viruses simultaneously. ²⁸ The two most important types of nucleic acid‐based amplification tests (NATs) are nucleic acid sequence‐based amplification (NASBA) and real‐time polymerase chain reaction (real‐time PCR). NASBA is an isothermal and continuous amplification reaction in which three different enzymes are applied: RNase‐H, AMV‐RT, and T7‐RNA polymerase. ²⁹ Real‐time PCR involves the amplification of complementary DNA (cDNA) prepared from viral RNA in a real‐time manner and is appropriate for the detection of minute amounts of nucleic acids. ³⁰ , ³¹ Another method is a biosensor that has high sensitivity and specificity, and most of the biosensors are based on electrochemical transduction. ³²

Covid‐19 can be diagnosed in different ways, including CT‐Scan and RT‐PCR. ³³ CT‐Scan results indicate bilateral ground‐glass and consolidative pulmonary opacities. ³⁴ , ³⁵ qRT‐PCR is currently used for the detection of SARS‐CoV‐2, but it is expensive, time‐consuming, and not as sensitive as it should be. The shortage of equipment in healthcare centers and the need for better disease management require the development of more convenient and more reliable methods of diagnosis. This review aims to provide an overview of the microfluidic systems as a diagnostic method for RNA viruses with a focus on SARS‐CoV‐2.

1.2. New and rapid diagnostic methods

The gold standard for the detection of the novel coronavirus is qRT‐PCR. ³⁶ However, there may be other methods that allow fast and inexpensive diagnosis. One study used reverse transcription loop‐mediated isothermal amplification (RT‐LAMP) that was conducted in under 30 min. ³⁶ Microfluidic devices might be a rapid diagnostic approach in the future as they are cheap and easy to use. In recent years, such devices have been applied to the diagnosis of several viruses such as influenza, SARS‐coronavirus, and smallpox. ³⁷ , ³⁸ , ³⁹ As a result, these devices may also help detect SARS‐CoV‐2 and accelerate the process of diagnosis and rehabilitation, ultimately lowering the death rate. These devices can use several techniques such as RT‐PCR, RT‐LAMP, nested PCR, nucleic acid hybridization, ELISA, or fluorescence‐based Assays. ⁴⁰ , ⁴¹ , ⁴² , ⁴³ , ⁴⁴

2. MICROFLUIDIC DEVICES

2.1. An introduction and history

The computer industry has been transformed by microfabricated integrated circuits that significantly reduce the space, effort, and time for computations. Biology and chemistry have the potential to develop through microfluidic systems, which use small amounts of reagent, rapidly ⁴⁵ , ⁴⁶ . An excellent example of such devices is the home pregnancy test, which detects hormones in urine and is the most commonly used example of the lateral flow strip assays (LFSAs), which are made to detect specific biomolecules. Such devices can also be used for the detection of bacterial cells and cancer cells. ⁴⁶ Microfluidic devices coated with virus‐capturing antibodies can be used to detect viruses present in a solution. ⁴⁷ Researchers have also developed a microfluidic chip that detects RNA‐based viruses from throat swab samples; the H1N1 virus was used as a model for this experiment. ³⁹ Another research developed a microfluidic chip system that can detect SARS‐CoV. ³⁸

2.2. Fabrication methods

Generally, there are two different kinds of microfluidic devices; channel‐based and paper‐based. The paper‐based tool is made of a series of hydrophilic cellulose or nitrocellulose fibers that guide liquid in a paper by absorption. The channel‐based one could be fabricated using four main methods, including laminate, molding, 3D‐printing, and nanofabrication. ⁴⁸ Channel‐based microfluidic devices need channels to create a bed for the integration of reagents.

2.2.1. Laminate

Layers cut separately by using a knife or laser are fused to form the channel. Although it is an easy method, it is impossible to achieve sub‐micrometer levels. ⁴⁹ , ⁵⁰ , ⁵¹

2.2.2. Moulding

Moulding is a technique that consists of four main steps, including shaping the mould, choosing the appropriate polymer, curing the polymer, and releasing the material from the mould. It includes three different methods, including replica moulding, injection moulding, and hot embossing. ⁵²

3D‐p3rinting

This is a method of fabricating layer by layer. It has two main parts. One is computer aided design. The second part is a 3D‐printer that uses the computer format of stereolithography (STL), building up in 2D layers based on its resolution. ⁵³ , ⁵⁴ There are different methods of 3D‐printing, such as fused deposition modeling (FDM), STL and digital micromirror device‐based projection printing (DMD‐PP), multi‐jet modeling, and two‐photon polymerization.

Although 3D‐printing has some limitations, such as the material which can be used ⁵⁵ and the resolution and biocompatibility of the models, ⁵⁶ it is a single‐step method that does not require the manual working of some other methods such as soft lithography. ⁵⁷ It will probably become the most common way in laboratories in the future.

2.2.3. Nanofabrication

In the top‐down approach, the model size is reduced to the nanoscale until the desired shape and dimensions are achieved. In contrast, the bottom‐up approach starts from atomic and molecular levels to finally shape the model. ⁵⁸ , ⁵⁹ , ⁶⁰ Extreme ultraviolet lithography (EUL), electron beam lithography (EBL), and nanoimprint lithography (NIL) are three different methods used in nanofabrication. EUL and EBL are not common in microfluidic fabrication, and the main reason is high costs. ⁶¹ , ⁶² However, NIL, which is a special kind of replica moulding with the resolution of sub 15 nm, is affordable and has many applications in microfluidic fabrication. ⁶⁰ , ⁶³

2.3. Useful strategies for RNA virus detection

In recent years, portable microfluidic devices have reduced global cost per analysis and reagent consumption and also led to faster analyses due to shorter reactions. ⁶⁴ , ⁶⁵ , ⁶⁶ Among conventional methods for detecting RNA viruses, traditional cultural methods, serological methods, and molecular biology techniques can be mentioned. According to different studies, so much time and money can be spared when these methods are integrated into a microfluidic‐based device. Table 1 provides a summary of microfluidic devices useful for the detection of RNA viruses.

TABLE 1.

Methods used in Microfluidic devices for RNA virus detection

Method integrated microfluidic device	Types of the method	Detected virus	Advantages	References
PCR and RT‐PCR‐based	PCR	Rotavirus	Fast (30 min overall), low‐cost, easy to use, detection limit: 1 × 103 copies/mL, highly sensitive and specific (100%)	Ye, Xu 92
	Nested PCR	RNA viruses	Detection limit range: 100 to 103 copies/μL, simultaneous detection and genotyping of RNA virus, sampling from human feces, sewage, and artificially contaminated oysters	Oshiki, Miura 73
	Single‐Cell‐in‐Droplet PCR	HIV‐1	High sensitivity	Yucha, Hobbs 93
	in situ PCR and RT‐PCR	Zika virus	Recovery of the virus at very low concentrations of 50 transducing units (TU)/mL from human saliva, the captured ZIKV RNA is directly used for downstream PCR without any loss	Zhu, Zhao 68
	RT‐qPCR and qPCR	HCV, HIV, Zika, HPV 16, and HPV 18 viruses	Rapid and sensitive, reaction times: 25 min	Powell, Wiederkehr 94
	RT‐PCR	Ebola virus	Disposable and low‐cost. Same sensitivity (10 RNA copies per microliter) and efficiency (90–110%) Amplification with high sensitivity was achieved in 30–50 min. Faster amplifications were possible (20 min), but sensitivity was reduced	Fernández‐Carballo, McBeth 95
	RT‐PCR	Hepatitis A virus and norovirus	An end‐point, sensitive, accurate absolute quantification approach, determination of target copy numbers without external quantitative standards	Fraisse, Coudray‐Meunier 69
LAMP and RT‐LAMP‐based	Smartphone Detection of Loop‐mediated Isothermal Amplification	Zika virus	Limit of detection: 1 copy/μL, simple, rapid(15 min), easily quantified using a smartphone	Kaarj, Akarapipad 96
	RT‐LAMP	MS2 virus	Easy to use, Low cost (less than 0.10 $ per piece), fluorescence intensities 100 times more than other methods in differentiation between positive and negative pores	Lin, Huang 97
	RT‐LAMP	Zika, Chikungunya, and Dengue viruses	Clinically relevant sensitivity. Detection of Zika virus as low as 1.56e5 PFU/mL from whole blood, Low reagent consumption	Ganguli, Ornob 98
	RT‐LAMP	HIV	Disposable, flexible, inexpensive, light, high sensitivity and specificity, faster amplification, higher stability, and lower complexity	Safavieh, Kaul 41
	RT‐LAMP	Zika virus	High sensitivity and inexpensive	Song, Mauk 72
RPA and RT‐RPA	RPA	HIV‐1	High rapidity, portable and independence on electricity	Kong, Li 99
	RPA	Zika virus	Good sensitivity and selectivity, the detection limit of 10 copies/μL, well‐defined accuracy, feasible by human trials	Yang, Kong 100
	RT‐RPA	Ebola virus	Lower reaction time for low viral load detection as compared to paper, high sensitivity (90%) without unduly damaging the specificity (60.8%)	Magro, Jacquelin 101
Immunoassay‐based	Immunoassay	Citrus tristeza Virus	Rapid, low‐cost, high sensitivity and specificity	Freitas, Proença 102
	Sandwich immunoassay	HIV‐1	Low‐cost, simple and efficient operation, limits of detection (LODs) of 0.17 and 0.11 ng/mL for p24 antigen	Li, Zheng 103
	Scattering‐based Immunoassay	Influenza virus	High sensitivity	Wang, Ruan 75
	Immunoassay	AIV	Detection of H5N2 AIV at virus concentration as low as 3.6 × 103 EID50/mL, high sensitivity.	Yu, Xia 42
	Bead‐based immunofluorescence‐assay	Dengue virus	rapid on‐chip detection (5 min), small required sample (≈15 μL), long life‐time (>50× reusable)	Iswardy, Tsai 104
	RGO‐based electrochemical immunosensor	H1N1	High selectivity and specificity for H1N1 viruses	Singh, Hong 105
	Custom inkjet printing and roll‐coating process‐immunoassay	Rubella virus	Materials cost for the new devices of only US $0.63 per device, 100% clinical sensitivity and specificity for RV IgG and IgM in a panel of serum samples	Dixon, Ng 106
	Electrochemical immunoassay	Rubella virus	High sensitivity	Rackus, Dryden 107
Aptasensor	Impedance Aptasensor	H5N1 Avian Influenza	High specificity and rapid	Lum, Wang 108
	Graphene‐gold nano‐composite aptasensor	norovirus	The detection limit of 100 pmol for recombinant norovirus‐like particles, total detection time less than 35 min.	Chand and Neethirajan 81
Nano‐based	Nanoparticle‐enhanced electrical detection	Zika virus	Highly specificity, the detection limit of 101 virus particles/μl, simple, rapid, and cost‐effective	Draz, Venkataramani 109
	Porous silicon nanowire (pSiNW)	H5N2 avian influenza viruses	A virus with specific size could be isolated from 100 μL in 30 min	Xia, Tang 84
Fluorescence‐Based	Internal reflection fluorescence microscopy	HIV‐1	Highly sensitive, high speed	Lau, Walsh 110
	Custom integrated fluorometer	Ebola virus	Rapid, amplification‐free, simple, and sensitive, the detection limit of 20 pfu/mL (5.45 × 107 copies/mL) of purified Ebola RNA in 5 min	Qin, Park 111
	Barcode Fluorescence Reporter and a Photocleavable Capture Probe	Ebola virus	High specificity., detection time less than 90 min	Du, Park 112
	Fluorescence‐Based Assays	Influenza A	Detection time less than 2 h.	Shah and Yager 76
Combination of several techniques	Immunomagnetic separation and RT‐PCR	H1N1	High sensitivity, rapid, and straightforward	Kim, Abafogi 40
	Glycan‐coated magnetic beads and RT‐PCR	Influenza A	Simultaneous detection of 12 viruses, Fast detection (under 100 min), Limit of detection ranging from 40 to 3000	Shen, Sabbavarapu 113
	RT‐LAMP‐lateral flow immunoassay (LFIA)	HIV‐1	Low‐cost and portable platform, rapid and autonomous analysis of HIV‐1 virus	Phillips, Moehling 114
	Reverse‐transcription LAMP coupled with reverse dot blot analysis	Zika virus	Rapid, sensitive, the limit of detection of the RT‐LAMP assay using spiked saliva samples was found to be ≈2 × 103 RNA copies/mL (6.6 RNA copies/reaction, RNA detection time between 3 and 10 min	Sabalza, Yasmin 115
	Fluorescent‐labeled universal aptamer	H1N1, H3N2, and influenza B	Rapid, simple, and inexpensive	Wang, Chang 77
	ELISA and fluorescence‐based	Hendra virus	Simple and rapid	Gao, Pallister 74
	Novel time‐resolved fluorescence (TRF) europium nanoparticle immunoassay	HIV‐1	High sensitivity, rapid and straightforward	Haleyur Giri Setty, Liu 116
	Isothermal amplification and a real‐time colorimetric method	Influenza A and influenza B virus, and human adenoviruses	Faster (the entire process takes an hour), high specificity and sensitivity	Wang, Zhao 117
	PLP and RCA	Tropical viruses like Ebola, Zika, and Dengue	High specificity, sensitivity, and multiplexing capability	Ciftci, Neumann 118
		RNA viruses (NDV, IBV and AIV)	High specificity and sensitivity, multiple detections, the detection limit of less than 10	Ciftci, Neumann 78
Other techniques	Capillary Flow Dynamics‐Based method	Zika virus	Clinically relevant sensitivity and specificity, detecting down to 1 log CFU/mL E. coli in water samples and 20 pg/mL ZIKV in serum samples at an operating time of 30s, easy‐to‐use and affordable	Klug, Reynolds 119
	Nucleic acid hybridization	Influenza A	Detection time 80 min, very low reagent consumption (only 3 μL), high sensitivity	Zhang, Hong 43
	SPM	Ebola virus	High sensitivity and selectivity, rapid, using a small volume of samples at the microliter scale (~60 μL for 3× and ≈800 μL for 80×, with 0.021 pfu/mL sensitivity, the ability for early clinical decisions	Du, Cai 82
	CRISPR/Cas9	Zika virus	Simple and inexpensive	Meagher, Negrete 86
	High‐throughput drop‐based microfluidics	murine noroviruses (MNV)	High specificity and sensitivity and simple	Tao, Rotem 120
	Simple epoxy silica sol‐gel coating/bonding method	Influenza virus	High sensitivity and inexpensive	Liu, Zhao 85
	Isothermal nucleic acid amplification	HIV	High sensitivity, specificity, reproducibility, high amplification efficiency, and easy detection	Mauk, Song 121
	RCA	Influenza and Ebola viruses	Little need for pre‐amplified sample, Portable, affordable, the possibility of detection of several pathogens, Elongation time from 10 to 120 min	Soares, Neumann 44

2.3.1. RT‐PCR integrated microfluidic device

RT‐PCR can be carried out in two ways: a one‐step and two‐step. Using the former assay, reverse transcription and PCR occur in a single reaction chamber. The two processes take place in different reaction chambers on the two‐step procedure. Colorimetric methods, such as immunochromatographic strips, can be used for RT‐PCR product detection in microfluidic chips. ⁶⁷

Kim et al recently designed a microfluidic‐based method for detecting H1N1 influenza, and the results suggested that the limit of detection (LOD) of molecular diagnostics for the virus can be lowered by systematically combining immunomagnetic separation and RT‐PCR in one microfluidic device. ⁴⁰ Moreover, RT‐PCR in situ has been successfully used for the diagnosis of Zika virus. ⁶⁸ Digital microfluidic RT‐PCR has been performed in a study to detect Hepatitis A and noroviruses in the gut, and the results showed that absolute quantification by digital RT‐PCR may be an appropriate alternative method to standardize quantification of enteric viruses in foodstuffs. ⁶⁹

2.3.2. RT‐LAMP integrated microfluidic

RT‐LAMP versus commonly‐used PCR does not require thermal cycles and is performed at a constant temperature between 60 and 65°C. ⁷⁰

Safavieh et al. designed cellulose‐based paper microchips and amplified the target RNA using the RT‐LAMP technique and detected the HIV‐1 virus through the electrical sensing of LAMP amplicons. They developed an RT‐LAMP paper microchip assay, which could be used as a simple and affordable method for the detection of HIV‐1. ⁴¹ Two other studies have shown that microfluidic‐based RT‐LAMP assay can affordably detect the Zika virus and Bacteriophage MS2 virus. ⁷¹ , ⁷²

2.3.3. Nested PCR integrated microfluidic

Nested PCR is a modification of PCR, which involves the use of two primer sets and two successive PCR reactions. Therefore, it profits from higher sensitivity and specificity compared to conventional PCR.

Oshiki et al. used a microfluidic nested‐PCR device and next‐generation sequencer to develop high‐throughput detection and genotyping tool for 11 human RNA viruses including Aichi virus, astrovirus, enterovirus, norovirus (genogroups I, II, and IV), hepatitis A virus, hepatitis E virus, rotavirus, sapovirus, and human parechovirus. The results of this study showed that microfluidic nested PCR followed by MiSeq sequencing enabled efficient tracking of the fate of multiple RNA viruses in various environments like feces, sewage, and oysters. ⁷³

2.3.4. Nucleic acid hybridization

Nucleic acid hybridization on a microfluidic chip integrated with the controllable micro‐magnetic field has been reported as a rapid method for simultaneously detecting and subtyping multiple influenza viruses. The subtypes H1N1, H3N2, and H9N2 could be simultaneously detected in 80 min with detection limits about 0.21, 0.16, 0.12 nM, respectively. Therefore, this method can be a reliable technology platform with the ability of rapid diagnosis and subtyping of influenza viruses. ⁴³

2.3.5. ELISA

The enzyme‐linked immunosorbent assay (ELISA) is a plate‐based assay technique designed for detecting and quantifying substances such as peptides, proteins, antibodies, and hormones. Recently, it has been widely used with microfluidic devices resulting in a fast and affordable method of diagnosing RNA viruses.

The commonly used ELISA and fluorescence‐based Luminex assay typically consists of three steps and takes several hours to complete, but combining this method with the microfluidic system has led to efficient and rapid diagnosis. Gao et al. used ELISA microfluidic system for detecting Hendra virus IgG antibody within 60 min. ⁷⁴

In another study performed by Yu et al., detection of avian influenza virus (AIV) took only 1.5 h with the help of an ELISA‐based microfluidic platform. ⁴² Sandwich immunoassay based‐microfluidic device has been used for detecting influenza as well. ⁷⁵

2.3.6. Fluorescence‐based assays

A fluorescence‐based microfluidic device decreased the limitation of detection of influenza (A) nucleoprotein immunoassay by over 50%. ⁷⁶ Wang and colleagues showed that the fluorescent‐labeled universal aptamer integrated with a microfluidic device could distinguish and detect three different influenza viruses (influenza A H1N1, H3N2, and influenza B) simultaneously in 20 min. ⁷⁷

2.3.7. Rolling circle amplification

Rolling circle replication is a process of rapid unidirectional replication of circular molecules of DNA and RNA, such as plasmids and the RNA genome of viroids. When mixed with microfluidic systems, some benefits like rapidity and cheapness are present. Rolling circle amplification combined with on‐chip size‐selective trapping of amplicons on silica beads showed that this system could be applied to diagnosing Ebola and influenza viruses. ⁴⁴ In another study, Ciftci et al. showed that traditional approaches like virus isolation, serology, immunoassays, and RT‐PCR are difficult and limited in terms of specificity and sensitivity for detecting RNA viruses. However, rolling circle amplification, in combination with padlock probes, had a higher specificity for detecting RNA viruses like Newcastle disease virus, avian coronavirus, and avian influenza virus. ⁷⁸

2.3.8. Aptamers

Aptamers are single‐stranded artificial oligonucleotides (DNA or RNA) with a high affinity for binding to specific targets. They are of short length from 20 to 100 nucleotides and can bind to a variety of small (amino acids, antibiotics, and nucleotides) and large molecules (proteins, ⁷⁹ viruses, and bacteria ⁸⁰ ).

According to a study performed by Chand et al., aptasensor integrated with a microfluidic‐based device could achieve a detection limit of 100 pmol with a detection range from 100 pmol to 3.5 nM for noroviruses. ⁸¹

2.3.9. Sample preparation multiplexer

According to a study performed by Du et al. an automated microfluidic sample preparation multiplexer (SPM) can be used for Ebola virus detection. This multiplexed, miniaturized sample preparation microdevice is considered as a critical technology that is believed to have a significant role in the next generation point‐of‐care (POC) detection system. ⁸²

2.3.10. The microfluidic device integrated with porous silicon nanowire forest

The nanoscale features in silicon nanowires (SiNWs) can suppress phonon propagation, which is referred to when phonons propagate through a lattice, and sharply reduce their thermal conductivities compared to the bulk value. ⁸³ Xia et al. developed a microfluidic device embedded with porous silicon nanowire (pSiNW) forest for label‐free size‐based point‐of‐care virus capture in a continuous curved flow design. They worked on Influenza virus (H5N1) and demonstrated that this method could have high potentials for virus discovery, isolation, and culture. ⁸⁴

2.3.11. Silica sol‐gel coating/bonding method

Liu et al. fabricated a polycarbonate (PC)‐polydimethylsiloxane (PDMS) hybrid microchip using a simple epoxy silica sol‐gel coating/bonding method. They showed that infectious reference viruses and nasopharyngeal swab patient specimens could be successfully tested using microchip Europium nanoparticle immunoassay (μENIA) on hybrid microchip platforms. The potential of this unique microchip nanoparticle assay was demonstrated in the clinical diagnosis of influenza viruses. ⁸⁵

2.3.12. Clustered regularly interspaced short palindromic repeats (CRISPR)

Repetitive DNA sequences found in prokaryotic genomes contain DNA fragments of bacteriophages. Meagher et al. highlighted the potential of paper‐based sensors coupled with CRISPR/Cas9 for the detection of Zika virus. ⁸⁶

3. THE APPLICATION OF MICROFLUIDIC DEVICES FOR SARS‐COV‐2 DETECTION

Lamb et al. developed a faster and cheaper method based on RT‐LAMP as an alternative process to qRT‐PCR that could be performed in less than 30 min, and its specificity was investigated using various types of coronaviruses. Also, the simplicity of the assay allows individuals at home to use it without special equipment. ⁸⁷

El‐Tholoth et al. presented another fast‐molecular test with high sensitivity and point‐of‐care (POC) suitable for home‐use. The method is based on LAMP two‐stage isothermal amplification (SARS‐CoV‐2 Penn‐RAMP) in closed tubes to create more sensitivity. Finally, detection by fluorescence or colorimetry leads to an easy diagnosis without specific instruments. The sensitivity of RAMP is 10–100 times more than that of LAMP and RT‐PCR for SARS‐CoV. ⁸⁸

Nguyen et al. described a POC device, which is rapid, robust, and affordable, with minimal training for emergencies such as the outbreaks. This device uses a LAMP reaction in combination with a lateral flow strip (LFS) to detect the virus in less than 1 h. ⁸⁹ Another example of using LFS is the BioMedomics COVID‐19 IgM/IgG Rapid test. ⁹⁰

Yang and colleagues designed an RNA‐based POC device for the diagnosis of SARS‐CoV‐2 using both a LAMP assay and a paper‐based POC diagnostic device. It was integrated with a smartphone to provide a fast, sensitive, and more accessible tool. This method utilizes a small sample volume, and the fluorescent probe selection can be evaluated by a smartphone to facilitate the recording and sharing of the test results. ⁹¹

In conclusion, microfluidic devices offer a wide range of methods, including RT‐PCR, RT‐LAMP, Nested PCR, Nucleic acid hybridization, ELISA, and Fluorescence‐Based Assays, for detection of RNA viruses such as H1N1, H3N2, and H9N2, Hendra, and influenza B viruses. These accurate methods of detecting RNA viruses might also have the potential for detecting the novel coronavirus that has caused a global issue of Covid‐19.

CONFLICT OF INTEREST

The authors have no competing interest.

Abbreviations

AIV

avian influenza virus

AMV‐RT

avian myeloblastosis virus reverse transcriptase

cDNA

complementary DNA

COVID‐19

coronavirus disease 2019

CRISPR

clustered regularly interspaced short palindromic

DMD‐PP

digital micromirror device‐based projection

DNV

dengue virus

EBL

electron beam lithography

ELISA

enzyme‐linked immunosorbent assay

EUL

extreme ultraviolet lithography

FDM

fused deposition molding

HIV‐1

human immunodeficiency virus‐1

IBV

infectious bronchitis virus

Ig

immunoglobin

LFS

lateral flow strip

LFSA

lateral flow strip assay

LOD

limit of detection

MERS

middle east respiratory syndrome

NASBA

nucleic acid sequence‐based amplification

NATs

nucleic acid‐based amplification tests

NDV

Newcastle disease virus

NIL

nanoimprint lithography

NS1

nonstructural protein 1

PC

polycarbonate

PDMS

polydimethylsiloxane

PLP

padlock probes

POC

point‐of‐care

pSiNW

porous silicon nanowire

qRT‐PCR

quantitative reverse transcription‐polymerase chain reaction

RCA

rolling circle amplification

RT‐LAMP

reverse transcription loop‐mediated isothermal amplification

RT‐PCR

reverse transcription‐polymerase chain reaction

SARS

severe acute respiratory syndrome

SARS‐coronavirus

severe acute respiratory syndrome‐related coronavirus

SiNWs

silicon nanowires

SPM

sample preparation multiplexer

STL

stereolithography

WHO

The World Health Organization

μENIA

microchip Europium nanoparticles immunoassay

Basiri A, Heidari A, Nadi MF, et al. Microfluidic devices for detection of RNA viruses. Rev Med Virol. 2021;31:e2154. 10.1002/rmv.2154

DATA AVAILABILITY STATEMENT

Data sharing is not applicable to this article as no new data were created or analyzed in this study.