Advances and insights in the diagnosis of viral infections

Abstract

Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.

Keywords: Antibody-antigen complex; Biosensors; COVID-19; CRISPR-Cas for DNA-Sensors; Immunosensors; Photoluminescence; Polymerase chain reaction (PCR); SARS-CoV-2 virus detection; Surface plasmon resonance (SPR).

Fig. 1

The course of viral infection in the host cell. Viral infection in the human body begins when viral hemagglutinin protein (HA) (a) binds to a glycolipid receptor on the cell surface. It promotes the fusion of viral cell membranes with the host cell. Once a virus enters viral genetic material (b) into the host cell, its replicates, and mRNA (c) is synthesized and converted to viral proteins. RNA viruses (like flu, SARS-CoV-2) can use their RNA to directly create countless new viruses in the host cell. DNA viruses are always making RNA copies, but rarely reverse process is occuring. Except for some retroviruses (HIV/AIDS), they copy their RNA into DNA. mRNA takes over the cell’s protein-making machinery to rapidly build a new amount of viruses. Subsequently, the synthesized viral genetic material and proteins are assembled (d) to form virions that help bud with neuraminidase (NA) and separate from the host cell. At the same time, the immunization takes place in the cell (e), the host cell begins to produce antibodies against the virus

Fig. 2

The range and the most common incubation periods in viral diseases. For influenza the most common virus incubation period in the host is 1–3 days; Herpesvirus 2–7 days; Covid-19 2–5 days [–51]; Dengue 3–6 days [–55]; Zika 5–8 days [–59]; Ebola virus 7–17 days [–63]; HIV 5–21 days; Hepatitis A 30–35 days [64, 65]; Hepatitis B 80–100 days [–70]. In the case of COVID-19, the likelihood of detecting the virus from the respiratory tracts is likely to be 2–5 days after possible infection. Seven days after the onset of symptoms, the chance of detecting the virus directly from the respiratory tract decreases

Fig. 3

Differences between molecular and non-molecular detection methods. The main application of non-molecular detection is to study the morphology (a electron microscopy) of the viruses or to determine (b X-ray detection) the symptoms of the viral (c visual symptoms detection) disease. However, in molecular diagnostics, a nonspecific reaction (cutting, multiplication, amplification, etc.) or other changes must occur after the target reaction. If the method is not nonspecific, such reactions use additional components that play the role of non-specificity. Also, the purification of nucleic acids is recommended in the use of molecular applications. Nucleic acid amplification increases the amount of DNA or RNA by cyclical repeating of some procedures. In the case of PCR, real-time PCR (d), and loop-mediated isothermal amplification (LAMP) (e) methods, both a DNA and an RNA fragment can always be used for the analyte, and after amplification, the final product is always a large amount of DNA. However, nucleic acid sequence-based amplification (NASBA) (f) applies only to RNA detection, and the uniqueness of the method, that after the cyclic reaction, contains DNA and RNA fragments in the mixture. An enzyme-linked immunosorbent assay (ELISA) is a method that uses a solid-phase-type enzyme-linked enzyme to detect a ligand in a liquid sample using antibodies directed against the protein being measured. The ELISA method is based on a stepwise, sandwich-based combination: 1—capture antibody; 2—antibody detection; 3—secondary antibody conjugation; 4—enzymatic conversion from enzyme to colorimetric or photoluminescence substrate signal. However, fluorescent ELISA usually utilizes secondary antibodies conjugated with a fluorophore. The only drawback is the multilevel application. h Cas12, Cas13, and Cas14 are members of proteins used in CRISPR diagnostics. Cas12, Cas13, and Cas14 proteins are on the larger side of the CRISPR diagnostic protein. Cas12 and Cas14 proteins bind directly to the recognized he protospacer adjacent motif (PAM) site and cleave specified DNA sequences. After target cleavage, the Cas12 and Cas14 proteins begin to shred single-stranded DNA nonspecifically. The differences between Cas12 and Cas14—are the size of the protein and RNA length for target binding. The Cas12 protein is 1300 amino acids, and the Cas14 protein is approximately 400–700 amino acids in length. Cas12 DNA targets using 42–44 bp—however, Cas14 protein 140 bp RNA molecules length. The shorter protein spends, the fewer resources are required to obtain the Cas14 protein in the laboratory, and the more extended RNA molecular sequence of the target indicates more excellent fit and accuracy but higher costs. In RNA detection, the technique must combine Cas12 and Cas14-based diagnostics with proteins that convert RNA to DNA. The Cas13 protein directly binds and cleaves specified RNA sequences, and protein can directly detect RNA but not DNA. The Cas13 protein is 1400 amino acids in length, and the RNA guide molecule is relatively short at ~ 64 bp. Thus, more resources are needed to produce Cas13-based detectors, additional Cas13 does not have strict application restrictions, but RNA targets can accept structures that are difficult to cut due to structural limitations. More detailed differences are given in separate article sections and Table 1