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Kong, J.;  Li, W.;  Hu, J.;  Zhao, S.;  Yue, T.;  Li, Z.;  Xia, Y. Potential Cold-Chain Food Quarantine Techniques. Encyclopedia. Available online: https://encyclopedia.pub/entry/25066 (accessed on 13 June 2024).
Kong J,  Li W,  Hu J,  Zhao S,  Yue T,  Li Z, et al. Potential Cold-Chain Food Quarantine Techniques. Encyclopedia. Available at: https://encyclopedia.pub/entry/25066. Accessed June 13, 2024.
Kong, Jia, Wenxin Li, Jinyao Hu, Shixuan Zhao, Tianli Yue, Zhonghong Li, Yinqiang Xia. "Potential Cold-Chain Food Quarantine Techniques" Encyclopedia, https://encyclopedia.pub/entry/25066 (accessed June 13, 2024).
Kong, J.,  Li, W.,  Hu, J.,  Zhao, S.,  Yue, T.,  Li, Z., & Xia, Y. (2022, July 12). Potential Cold-Chain Food Quarantine Techniques. In Encyclopedia. https://encyclopedia.pub/entry/25066
Kong, Jia, et al. "Potential Cold-Chain Food Quarantine Techniques." Encyclopedia. Web. 12 July, 2022.
Potential Cold-Chain Food Quarantine Techniques
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Since the outbreak of coronavirus disease-19 (COVID-19), cold-chain food contamination caused by the pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has attracted huge concern. Cold-chain foods provide a congenial environment for SARS-CoV-2 survival, which presents a potential risk for public health. Strengthening the SARS-CoV-2 supervision of cold-chain foods has become the top priority in many countries

SARS-CoV-2 cold-chain foods RT-LAMP

1. Potential Cold-Chain Food Quarantine Techniques

Unlike traditional food testing methods, the detection of SARS-CoV-2 on cold-chain foods puts forward higher requirements regarding sampling method, detecting conditions, testing periodic time, anti-interference capability, and portability of equipment [1]. Here, according to the different pathogen markers, e.g., nucleic acid, antigen, antibody, and cytokine storm assay, researchers list two categories of COVID-19 testing methods, as well as the advance of SARS-CoV-2 test methods (Table 1). Whether the existing detection methods can be applied to test suspicious cold-chain foods will be dialectically discussed.

2. Nucleic Acid Test

SARS-CoV-2 is a positive-sense RNA virus, and the feature gene can be used as target analytes [35]. Nucleic acid detection technology is the most direct and essential pathogenic evidence for food contamination (Figure 1A). It has the advantages of early diagnosis, high sensitivity, and good specificity, and is the gold standard for SARS-CoV-2 detection (e.g., RT-PCR) [36].
Figure 1. The advanced quarantine methods for SARS-CoV-2. For SARS-CoV-2 quarantine, many test techniques including nucleic acid and immunological methods are available. Nucleic acid tests include whole-genome sequencing and specific gene detection (A). Immunological tests include antigen tests (B), antibody immunological tests (C), and cytokine storm diagnoses (D). RT-PCR(Reverse transcription-polymerase chain reaction), LAMP (Loop-mediated isothermal amplification), CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), LFIA (Lateral-flow immunochromatographic assay), FET (Field-effect transistor), ELISA (Enzyme linked immunosorbent assay), xMAP (Multi-analyte profiling), SERS(Surface-enhanced raman scattering).

2.1. PCR-Based Techniques

Among the nucleic acid detection methods, RT-PCR can effectively amplify trace viral genes in nucleic acid mixtures and has the characteristics of fast detection speed, high sensitivity, and strong specificity [37]. RT-PCR uses sequence-specific primers to identify tiny RNA targets. The recognized RNA is then transcribed by reverse transcriptase to cDNA, which is then used as a template for DNA replication through PCR. However, the measurement is an enzyme-dependent multi-step technique, and the operation is complicated. The turnaround time takes a few hours which cannot meet the requirements of rapid testing of cold-chain food [38]. The test facilities and instruments are not portable, and the collected samples need to be transported to the laboratory for testing. The samples may produce false-negative results due to improper collection or processing. Improper operation or insufficient laboratory conditions may cause false positives due to aerosol contamination [39][40][41]. One-step nested RT-PCR is a flexible and easy method to test SARS-CoV-2. If the coronavirus mutates in one key amplified nucleotide, at least one pair can still be amplified [42]. The detection cost is lower than RT-PCR, but nested PCR is not feasible as a detection method for cold-chain food, because it is time-consuming and has a high risk of cross-contamination. In contrast, repetitive digital PCR is less interfered with by background wild DNA molecules, so it can reduce the impact of non-target DNA during cold-chain detection [43]. Digital PCR has obvious advantages when the viral load of cold-chain food samples is low or the sample nucleic acid is degraded. However, the cost of digital PCR detection is relatively high and the instrument is not portable [44]. It also involves the usage and storage of enzyme reagents, which will increase the cost and technological hurdles of detection. The digital PCR operation process has the disadvantage of being easily contaminated. To avoid false-positive results, it is necessary to establish strict internal quality control specifications for the laboratory and strictly regulate the testing operation process [45][46].

2.2. RT-LAMP

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a nucleic acid amplification assay, which is characterized by multiple specific primers for the target gene at a constant temperature of 60–65 °C under the DNA polymerase. About 109-1010 times of nucleic acid amplification can be achieved in 15–60 min. RT-LAMP has the characteristics of simple operation, strong specificity (2 to 5 orders of magnitude higher than traditional PCR methods), and easy product detection [47]. The RT-LAMP results can be judged by visually observing the generation of white turbidity or green fluorescence. It is simple, quick, and does not require gel electrophoresis like PCR. As a point-of-care testing (POCT)-type nucleic acid detection method, LAMP requires less professional equipment, such as a thermal cycler, and the price of the instrument is lower than qRT-PCR, which can well meet the real-time requirements of SARS-CoV-2 detection on cold-chain food [48]. The detection sensitivity of RT-LAMP can reach 10 copies, and it has high specificity [49]. RT-LAMP is highly suitable for detecting > 60 copies/10 μL in sample. However, the test involves the use of enzymes (e.g., recombinase) that the storage of enzyme reagent needs, resulting in extra cost. When the test is performed for a long time, non-specific amplification may produce false-positive results if cold-chain food sampling < 10 copies/10 μL [50]. Based on RT-LAMP, a portable and scalable laser-engraved microwell array chip for multiplex amplification of viral RNA samples has been developed, which is a promising device for SARS-CoV-2 detection on cold-chain food.

2.3. CRISPR-Based System

CRISPR-Cas is a nonspecific RNA system that can be activated by the amplified product RNA, cleavages the reporter RNA, and releases a fluorescent dye from the quencher. The CRISPR-based system has attracted growing enthusiasm due to its pathogen diagnosis ability [51]. It can realize the on-site test of SARS-CoV-2 on cold-chain food using simple equipment. The test time varies from 40 to 70 min when excluding the time for RNA extraction [52][53]. Combined with RT-LAMP technology, the CRISPR-Cas system can achieve an LoD of 10 copies/μL. Most CRISPR-based SARS-CoV-2 detection methods use the Cas12 enzyme to specifically recognize the virus sequence [54]. In addition, the all-in-one dual CRISPR-Cas12a analysis system does not need a pre-amplification step and it improves the sensitivity of the assay by using double CRISPR RNA. It can detect 1.2 DNA targets and 4.6 RNA targets in 40 min. The system can be developed as a one-step test platform without the need for cDNA preparation which has the potential for SARS-CoV-2 detection on cold-chain food [55].

2.4. Microfluidic Biochip

Microfluidic chips integrate various small-scale laboratory functions on a single chip to complete the steps in traditional laboratories [56]. It uses a small number of reagents and samples to obtain accurate test results in a short time, and is especially suitable for the rapid detection of SARS-CoV-2 on cold-chain food. Recently, paper-based microfluidics, centrifugal chips, wearable microfluidic devices, and digital nucleic acid detection chips have been proposed for pathogen testing and disease screening [57]. For instance, the IDNOW® instrument proposed by Abbott™ in the United States can detect a positive sample. The product has received an emergency use authorization (EUA) from the U.S. Food and Drug Administration (FDA). The instrument weighs only 3 kg and is portable and suitable for POCT [58][59].

2.5. Whole-Genome Sequencing

Whole-genome sequencing (WGS) is an effective tool to comprehensive understand SARS-CoV-2. The assay belongs to high-throughput sequencing, or next-generation sequencing, which is a culture-free, unbiased, direct extraction of DNA or RNA from clinical samples [3][4]. However, the operation steps of WGS are relatively complex and the operation technology requirements are high. The RNA can be extracted using the kit and whole-genome sequencing performed on an instrument (e.g., Illumina iSeq 100). Peculiarly, metagenomics is a high-sensitivity pan-pathogen assay for the discovery of novel pathogens and infectious disease diagnosis, which is applied in the simultaneous and rapid detection of SARS-CoV-2 [60]. Because the whole gene sequencing requires a professional operator, complex sample pretreatment, and long-term periods, other methods are usually combined to generate test reports.

3. Immunological Methods

SARS-CoV-2 has a wide mammalian host range, including minks, cows, white-tailed deer, dogs, domestic cats, swine, lions, etc. [61][62][63][64]. Some of these animals may serve as viral carriers once they are made into food-related products [65]. Immunological tests can directly detect the antigen biomarker of SARS-CoV-2 and can be used to determine whether food (e.g., animal products) is infected or contaminated by the virus. The immunological methods that mainly include antigen tests, serology tests, and cytokine storm diagnoses can be used for SARS-CoV-2 detection for these animal foods. For plant foods, that cannot undergo an immune response to produce antibodies, serum antibody immunological testing and cytokine storm diagnosis cannot be applied to the detection of cold-chain food unless the plant food is contaminated with the body fluids of an infected person [66]. In the following sections, researchers will describe each of the above methods in detail.

3.1. Antigen Immunological Test

Antigen tests are the main immunological method for food quarantine. The structural proteins, such as the spike glycoprotein (S), envelope protein (E), membrane protein (M), and nucleocapsid protein (N) of SARS-CoV-2 are the primary antigens used for the immunological test. Among the antigen immunological test methods (Figure 1B), ELISA is a highly sensitive immunological experimental technique that combines an antigen, antibody-specific reaction, and high-efficiency enzyme catalysis on the substrate. This detection method has high sensitivity and low difficulty in carrier standardization, but the detection steps are more cumbersome and easier to contaminate [67]. ELISA kits can test multiple samples in a single run; however, they lack point-of-care applicability and the non-specific binding of antibodies or antigens to the plate may lead to false positive results [68]. In addition to ELISA, the detection of trace S-protein (S1 subunit) for real-time SARS-CoV-2 detection is currently a known method that can be well applied to cold-chain foods. The S-protein particles can be attracted to the surface of the sensor and captured by the antibody within 20 s, which meets the real-time detection requirements on-site. The linear range is wide and covers the possible range of the concentration of S-protein on the food surface. The developed ultra-low LOD strategy has shown great advantages in the detection of virus markers with low concentrations of cold-chain foods [23]. The single sensor device can act as a disposable chip and its cost is estimated to be 1 US dollar. The operations of the device are relatively simple and can be operated by non-technical personnel [69]. Thus, the S-protein detection platform meets the requirements of rapid response, lower detection limit, high specificity, friendly operation, and low cost, which provides a promising solution for SARS-CoV-2 detection on cold-chain food [70].
Besides, the biosensor equipped with a chemical or biological receptor (e.g., antibody) can specifically interact with the target analyte showing a quantitative signal of the recognition process [71]. Compared with traditional laboratory methods, biosensors can provide a cheap, sensitive, rapid, miniaturized, and portable platform for SARS-CoV-2 detection which is promising for the on-site detection of cold-chain food contamination. Several studies have proved biosensor technology is convenient in SARS-CoV-2 S protein detection based on a bioelectrical identification assay [72]. The biosensor can detect S protein within 3 min with a LOD of about 1 fg/mL, and no cross-reaction with SARS-CoV-2 nucleocapsid protein was found. The portable readout system of the ready-made biosensor platform can be controlled by a smartphone or a tablet computer [73]. The high sensitivity, rapidness, and simplicity of biosensors make it a great advantage in the detection of viruses on cold-chain food. It can be easily controlled and has strong practical applicability to test contaminations on cold-chain food in factories or customs. However, some biosensors involve the use of enzyme reagents, and the biosensor technology is still in the development stage [74].

3.2. Serum Antibody Immunological Test

Once the body is infected, the living organisms will produce specific antibodies, such as anti-SARS-CoV-2 IgM and IgG. Though animal food is frozen or transported in the cold-chain, the antibodies from an earlier infection can be preserved. The safety risk of infected COVID-19 is relatively low by eating cold-chain animal food and has not been studied to date. However, these serum antibodies can be used as the immunological target, especially in cold-chain animal food with a low viral load. Compared with nucleic acid testing, blood samples for antibody serology testing are easier to obtain, which greatly reduces the risk of infection of medical staff during specimen collection and testing, and makes it easier for primary laboratories to carry out screening work. For instance (Figure 1C), luciferase immunosorbent assay (LISA) is an easily and rapidly developed semi-quantitative method and is appropriate for detecting specific antibodies from cold-chain animal food [31]. Compared with enzyme-linked immunosorbent assays, DNA-assisted nanopore sensing assay can reliably quantify SARS-CoV-2 antibodies with high accuracy, wide dynamic range, and the potential for automated detection on cold-chain food [29]. Though modified with probe DNA to label IgG or IgM antibodies, the nanopore sensor can quantify the probe DNAs when thermal dehybridization of gold nanoparticles (AuNPs) probe DNAs was performed. In addition, surface plasmon resonance (SPR) biosensors assay adopts the optical detection method. Indirect aggregation can be used for virus detection by modifying targeted molecules on the virus surface. If you do not consider the portability of the SPR device, it may be the most promising technique for cold-chain food quarantine [28].

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