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 Table of Contents  
REVIEW ARTICLE
Year : 2022  |  Volume : 17  |  Issue : 3  |  Page : 772-778

Modern diagnostics processes among new strains of Coronaviruses: A review


1 Department of Civil Engineering, College of Engineering, Jazan University, Jazan, Saudi Arabia
2 Department of Environmental Health Engineering, School of Public Health; Center for Solid Waste Research, Institute for Environmental Research, Tehran University of Medical Sciences, Tehran, Iran
3 Department of Civil Engineering, Jamia Millia Islamia, New Delhi, India
4 Department of Physiology, Sri Siddhartha Institute of Medical Sciences and Research Centre, T-Begur, Nelamangala (T), Bengaluru Rural - 562 123, Karnataka, India
5 Department of Eastern Medicine, Government College University Faisalabad Faculty of Eastern Medicine, Hamdard University, Karachi, Pakistan
6 Division of Oncology, School of Medicine, Stanford University, Stanford, CA, USA
7 Department of Mechanical Engineering, University of Kansas, Lawrence, Kansas, USA

Date of Submission24-Aug-2022
Date of Decision24-Aug-2022
Date of Acceptance25-Aug-2022
Date of Web Publication2-Nov-2022

Correspondence Address:
Dr. Syed Sadat Ali
Department of Physiology, Sri Siddhartha Institute of Medical Sciences and Research Centre, T-Begur, Nelamangala (T), Bengaluru Rural - 562 123, Karnataka
India
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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/jdmimsu.jdmimsu_375_22

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  Abstract 


The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the COVID-19 disease, which is a considerable outbreak that appeared in late 2019, and within a short period, this disease rapidly extended globally. Its prompt airborne transmission and highly infectious pneumonia-like symptoms in patients caused turmoil worldwide. This virus has a relatively high mortality rate compared to previous outbreaks such as Middle East respiratory syndrome coronavirus and SARS-CoV. Therefore, the World Health Organization declared COVID-19 a global health pandemic on January 30, 2020. However, the recent COVID-19 outbreak and newly emerged variants such as Delta and Omicron are having a huge spike in the human population. This rise has been a kind of challenging situation worldwide as perception is still limited in terms of modes of transmission, severity, diagnostics clinical oversight. Therefore, this review highlights the importance of these issues via a Medline search using the terms novel, coronavirus, sources, genetic nature, contagious routes, clinical characteristics, and diagnostic procedures for COVID-19. The authors extensively reviewed the analysis of behavior and impacts of this virus's activities worldwide. The study reveals that patients' epidemiology and clinical characteristics in different frames are sensitive toward commanding this virus and its associated diseases. Finally, the parametric data gathered for this study are also presented for use in forecasting models. Along with these searches, the authors have comprehensively discussed the current modern diagnostic processes.

Keywords: Clinical characteristics, COVID-19, Delta, diagnostic procedures, epidemiology, Omicron


How to cite this article:
Khan AH, Dehghani MH, Khan NA, Ali SS, Akram M, Roy S, Alam SS. Modern diagnostics processes among new strains of Coronaviruses: A review. J Datta Meghe Inst Med Sci Univ 2022;17:772-8

How to cite this URL:
Khan AH, Dehghani MH, Khan NA, Ali SS, Akram M, Roy S, Alam SS. Modern diagnostics processes among new strains of Coronaviruses: A review. J Datta Meghe Inst Med Sci Univ [serial online] 2022 [cited 2023 Feb 1];17:772-8. Available from: http://www.journaldmims.com/text.asp?2022/17/3/772/360216




  Introduction Top


China's Wuhan (Hubei Province) reported a patient with unidentified pneumonia-like symptoms near the end of 2019. Since then, there have been more cases reported globally than ever before. Clinical research identified a group of viruses that were impacting these individuals' respiratory systems and causing pneumonia-like symptoms as the number of people with comparable symptoms increased. As a result, the number of deaths from this illness increased globally and afterward quickly spread outside. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the name given to this new coronavirus by the International Committee on Taxonomy of Viruses (SARS-CoV-2).[1] Late in 2020, the genome analysis of SARS-CoV-2 showed that a 79.5% similarity to the bat SARS coronavirus (SARS-CoV-RaTG13) is 79.5%,[2] prompting its bat origins. SARS-CoV-2 shares a 50% match with Middle East respiratory syndrome coronavirus (MERS-CoV) too. Nonetheless, research shows that the nature of the host selected by the coronavirus is very complicated in terms of its treatment as well as transmission prevention, stimulating the World Health Organization (WHO) to categorize these viruses as COVID-19 and declare a global pandemic on March 15, 2020.[3]

As compared to other deadly viruses such as SARS-CoV-2 and MERS-CoV, SARS-CoV-2 is considered highly contagious.[4] The European Centre for Disease Prevention and Control finds that this outbreak significantly impacts human and economic losses.[1],[2],[4],[5],[6] Specifically, the late onset of critical symptoms promoted the initial global spread of the pandemic from Wuhan via travelers.[7] Alongside, the authors have summarized different diagnostic procedures in a table with details which are involved during this pandemic tenure with several preventive measures.[8] Three doses of vaccine are currently the standard regimen in many industrialised nations,[9] but even after these vaccination drives, there were significant concerns regarding their efficacy in recently discovered mutant strains like Delta and Omicron. Several aspects such as low uptake and mainly the efficacy in some populations were in big discussions for treatments.[10] Therefore, the purpose of this article is to provide an overview of recently identified variants and their details since Covid-19 inception.

Genetic characteristics and etiology

SARS-genomic CoV2's architecture resembled that of betacoronaviruses and followed a set of distinctive gene features known as CoVs. CoVs are positive single-stranded RNA (+ssRNA), enveloped with nucleocapsid. The genomic structure of CoVs is organized in approximately 30 kb (varies from 29.8 kb to 29.9 kb) of +ssRNA and with a 5′-cap structure and 3′-poly-A tail. Structural proteins including surface (S) envelope (E), membrane (M), and nucleocapsid (N) promote viral assembly which has the most crucial character in the pathogenicity of the infection. Besides, this virus contains six accessory proteins which are encoded by ORF3a, ORF6, ORF7a, and ORF8 genes.[5] The genome sequence of the current SARS-CoV-2 resembles the SARS-like bat CoVs (MG772933) rather than the SARS-CoV.[11] CoVs use the spike glycoprotein receptor-binding domain (RBD) and allows virus-binding to angiotensin-converting enzyme 2 receptor on the host cell. The available data seem to indicate that similar to SARS-CoV infection, SARS-CoV-2 infection causes an excessive immune reaction in the host releasing high levels of cytokines by the immune system.[1],[12],[13],[14] Starting from early May 2021, Delta became a dominant strain globally. Wang et al., 2021, and their group have studies about this particular strain in detail. They have extracted epidemiological and clinical information from 159 students who were infected with Delta between May 21 and June 21. Alongside, they have compared these data with wild-type infection which was started in 2020 at the Guangzhou Eighth Hospital.[15] Interestingly, they have found that the Delta has a shorter incubation period like 4–6 days with higher viral loads. More critical illness was found in the age group of 60 and above. It was also concluded in the study that Delta has a higher risk of deterioration compared to wild-type infection with a hazard ratio of 2.98, P = 0.01. Hence, the transmission rate, viral loads, and risk of death were much higher than initial COVID-19. In [Figure 1], Delta chain transmission has described. In their study, they observed that one 75-year-old female resident of Guangzhou was infected with Delta strain, and she had no records of travel history to overseas or domestic which showed that this is a case of accidental exposure to an imported case in local areas and denoted transmission as G1 [Figure 1]. Delta variants are also confirmed with nasopharyngeal swabs like SARS-CoV-2 wild type. It led to the subsequent transmission to three cases G2 and G3 infected from G1 with close familial contact. One of them suffered a critical illness and was admitted to hospital. Moreover, G2 is considered a main key transmitter because it effected third generation and infected five generations in the cluster.
Figure 1: Epidemiological transmission of SARS-CoV-2 Delta variant in Guangzhou. This figure is reproduced with permission from Wang et al.[15] SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2

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Later in November 2021, another strain named Omicron emerged and started spreading very quickly worldwide [Figure 2]a and [Figure 2]b. This strain is considered the most contagious strain but a less dangerous one and was first detected in South Africa. This variant has higher mutations than any other previous strains; for instance, it contains 35 mutations in spike protein and 50 mutations overall. It is also found that this strain infects younger individuals compared to previous strains.
Figure 2: (a). Total cases of Omicron worldwide are 449,368,927 and (b). Total deaths worldwide are 6,033,022. The numbers are up to date until March 7, 2022, from the WHO. WHO: World Health Organization

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Due to diverse epidemiological and biological characteristics, this strain is more contagious than any other SARS viruses. However, the main manifestations of these new mutations are not as deadly as Delta or like the wild type of SARS-CoV-2. The symptoms of this strain show a mild infection, headache, body ache, muscle ache, fever, cough, and some cases of severe fatigue.[17]

Rate of occurrence

The basic reproduction number (Ro) for this current virus is in the range of 2.47–2.86[18] using the Susceptible-Exposed-Infectious-Recovered model. This number represents the secondary infection produced by the first infected patient without any intervention. Some other models were also reported, like the International Duration Evaluation of Adjuvant Chemotherapy model having Ro in the range of 2.2–3.6[19] compared to other coronaviruses such as SARS-CoV and MERS-CoV, which is 2.2–3.6 and 2.0–6.7, respectively.[20]

Some prototypes of CoV, such as mouse hepatitis virus, have been extensively tested, containing 31 kb genomic RNA that encodes up to eight genes.[21],[22] It has been observed that coronaviruses lead to various respiratory and intestinal infections within the human body and were not detected before as deadly infectious viruses until the epidemics of fatal SARS-CoV in Guangdong Province, China, in 2002 and 2003. After 10 years of SARS-CoV history, another coronavirus MERS-CoV was first reported in Saudi Arabia in 2012. MERS-CoV was a zoonotic disease, and human-to-human transmission was reported to be low.[23],[24] Contrary to a few studies, scientists later confirmed that MERS-CoV was proficient in human-to-human (H2H) circulation.[25],[26] In November 2019, COVID-19 was reported from a local wet market in Wuhan, Hubei Province, China, and was also confirmed as H2H transmission based on reports from a family from Shenzhen. The family was infected by visiting suspected family members in Wuhan and later showed dyspnea (shortness of breath), temperature, weakness, and diarrhea.[2] Victor et al. reported in a study that 10% of the rate of occurrence of Delta was found incomplete vaccinated health-care workers from southern India. The rate of hospitalization and lack of oxygen problem occurred in 0.9% and 0.6% groups, respectively.[27] Thirty-five percent of R0 of this Delta strain was found in Varanasi city in India around April 2021.[28] At the same time in China, the Delta coronavirus started spreading quickly and was estimated at R0 6, in UK 5.2 according to the data up to July 2021. R0 of 5.08 is much higher than wild-type strain with R0 of 2.79.[29] Similarly, from mid-November 2021, Omicron started arising worldwide, and due to its speedy contagious transmission characteristics, R0 reached up to 7 according to the calculation from December 2021.[30]

Clinical characteristics

Initially, the wild-type SARS-CoV-2 virus incubates inside the body for 2–14 days, and in some cases, it has early symptoms that appear as early as 3 days of infection, which is nearly the same as that of SARS.[31],[32] The most common and early detected symptoms of SARS-CoV-2 are fever (87.9%), cough (67.7%), vomiting (5%), and diarrhea (up to 3.7%).[33],[34] Multiple organ failure is the most frequent cause of death at the most critical stage (30%–50%) compared to respiratory failure causing death in 13%–19% of the CoV-2 cases. Some patients have been diagnosed with acute heart injury and abnormal liver function during admission to the health-care facility. A study about the clinical manifestation of Delta coronaviruses on 5–9 years aged children who were at high risk and admitted to the hospital proved that Delta can affect children. Still, the epidemiological, viral load, and more details of clinical features are unclear.[35],[36]

Further investigations are needed regarding these findings.[15] However, this strain quickly affected the whole world within a few days from origin. This outbreak resulted in severe death effects worldwide. Through nucleic acid (NA) assays, the infections were detected as a cluster form with a clear chain of transmission. According to the study, the wild-type SARS CoV2 and Delta strains' NA sequences (viral genomes) were largely comparable with the exception of three alterations. In this case, chest computed tomography (CT) was the primary source of assessment. CT tested all patients within 3 days of admission.[15] Viral samples were collected from nasal swab similar to wild-type strain, and reverse transcription–polymerase chain reaction (RT-PCR) was conducted with primers and probes targeting the N, ORF1a/b genes. Later, for more details, sequencing was performed with next-generation sequencing (NGS) systems. The common symptoms were cough (65%) and fever (63%), and a few cases had gastrointestinal symptoms such as diarrhea (5%) and vomiting (4%). There were no such clinical differences between gender, age, and disease severity distribution. The incubation period is shorter than wild-type strain ~4 days (P < 0.001). Moreover, the chart of Delta was characterized as higher than wild-type strain (Ct: 20.6 vs. 34.0; P < 0.001).[15],[16]

On the other hand, after a few months, Omicron arise a newly developed strain worldwide. The clinical manifestations of this new variant were having mild fever, body aches, and cough, and handling this strain was much simpler than Delta variant with a high transmission rate. On December 9, Omicron did in a high peak in Denmark, the UK, South Africa, Canada, South Korea, India, the United States, Australia, and many more countries [Figure 2]a. Initially, it originated from South Africa and geographically spread quickly. However, the fatality rate of this strain is less than other strains. This strain contains many mutations (mentioned above) compared to others. This strain is transmitted to the population with an average doubling time of 2 days. Vaccination drives were increased with the third dosage in the United States. It is still unknown how much effect booster dosages are having on this strain.[37] Later, it was discovered from sequencing studies that most of the mutations lead to S gene target failure, indicating one of the gene's numerous areas. However, more details study is continuing.

Diagnostic procedures

The WHO has issued clinical guidelines regarding COVID-19 infection in the starting phase of the year 2020. It is seen that the prothrombin time test, rapid molecular testing, NA-based testing, serological testing, chest scan, CT test, full-genome sequencing, NGS, and erythrocyte sedimentation rate are basic diagnostic procedures for virus detection [Figure 3].[33],[38],[39] Several commercialized COVID-19 diagnostic techniques were approved by several countries for both laboratory-based and point-of-care (POC) testing.[40],[41]
Figure 3: Newly developed promising diagnosis methods of SARS-CoV-2 detection with laboratory-based and POC tests in sequential order. Adapted from (Qin et al., 2020). (a) The symptoms of SARS-CoV-2 infection. (b) SARS-CoV-2 and the antibody concentrations within an infected human body change against time. (c) Nasopharyngeal sampling. (d) The sample collection in a sample tube. (e) Virus RNA extraction. (f) PCR-based RNA amplification in a thermal cycler. (g) Data analysis of RFU versus time during the amplification process. (h) The LionX testing for diagnosis of COVID-19. SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2, RFU: Relative fluorescence unit, LionX: Lab-in/on-an-X, PCR: Polymerase chain reaction, POC: Point-of-care

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The clinical and epidemiological elements associated with the likelihood of infection should be the deciding factor in conducting a test repeatedly for individual patients.[42] The importance of rapid development of asymptomatic testing,[43] random access,[44] and POC[45] biosensor and rapid molecular testing[46],[47] need to be implemented to control the disease. Patients on suspicion undergo the test for the virus with NA amplification tests, such as RT-PCR, reverse transcription–loop-mediated isothermal amplification (RT-LAMP), and reverse transcription–rolling circle amplification.

Nucleic acid amplification tests for early detection of COVID-19

Reverse transcription–polymerase chain reaction technology

The foundation of routine confirmation for COVID19 cases is the identification of the distinctive order of virus RNA by reverse transcription and quantitative polymerase chain reaction (rRT-PCR, qRT-PCR), which is confirmed by various NGS sequencing methods like Illumina and Oxford Nanopore sequencing (ONT), as needed. These tests have targeted viral genes such as nucleocapsid protein, envelope protein, spike protein, and RNA-dependent RNA polymerase genes. A recent study showed the high sensitivity of this assay by measuring the total viral load from nonrespiratory specimens, which was around 3.21 × 104 RNA copies/mL.[48] On the other hand, one definite study of high specificity testing of COVID-19 revealed that RT-PCR assays give 100% specificity[49],[50] while testing on other strains of the viruses such as HCoV, MERS, SERS, HIV, and tuberculosis. For Delta and Omicron cases, the same procedures are used. For Delta, the limit of detection was around 10 copies/mL, with a compatible high viral load detected by qRT-PCR.[51] For Omicron, most of the countries performed nasal rapid antigen testing at home, and if there are critical issues at the hospital, then RT-PCR testing was performed. The sensitivity of RT-PCR was around 98.5% random samples, and the single antigen test was 95.2% for Ct threshold of <30.[52]

However, many shortcomings present in this procedure, such as the risk of obtaining false-positive and false-negative outcomes, costly instruments and reagents, and sampling time issues.[53] To overcome these issues, researchers have an alternative way of confirming the COVID-19 testing, which we discussed in the following section.

Reverse transcription–loop-mediated isothermal amplification technology

The LAMP process is a versatile and established molecular process for POC molecular testing platforms for various pathogens and species detection.[54] This nucleic acid amplification process provides rapid, high accuracy, high sensitivity, cost-effective, less instrumentation, and straightforward outcomes for disease detection.[55],[56],[57],[58],[59] As a result of these advancements in this process for COVID-19 detection, RT-LAMP has been implemented. A study reported that this assay could detect this virus as low as 100 copies of SARS-CoV-2 RNA. Researchers also tested specificity with other human coronaviruses, which expressed that this assay was 100% accurate toward COVID-19 detection.[60] One of the recent studies reported that the sensitivity of Delta by this assay was around 99.3%; alongside, their study suggested that RT-LAMP-positive samples are potential samples for viral genome sequencing and genetic structural determination of this variant further.[37] The RT-LAMP assay may also identify Omicron with excellent specificity and sensitivity, between 90% and 100%.[61]

Next-generation sequencing technology

NGS technology is one of the advanced molecular techniques that has delivered impressive outcomes in short time, less complicacy, good read length, mutation details, and an efficient amount of critical genomic information using a single instrument.[62],[63] Since COVID-19 diagnosis depends on nucleic acid detection, recently, NGS technology has been implemented broadly in COVID-19 testing.[64],[65],[66] After investigating Omicron's genome sequencing, researchers have found high numbers of mutations on S protein (23 amino acid substitutions) and RBD (15 amino acid substitutions). Sequencing results, it indicates that some mutations are associated with enhanced viral transmission, infectivity, and damage to immune systems.[67]

Despite being a powerful tool, NGS technology currently has some drawbacks. For example, it always relies on the PCR process to identify regions with elevated GC% because these regions are amplified by the PCR system. Library preparation and computational analysis of the data by ONT is sometimes tedious, time-consuming, and expensive. For this reason, there is more room to develop this process for future advanced issues.[68]


  Conclusion Top


The novel outbreak SARS-CoV-2 has become a global threat, predicted more than 30% of the world population will be affected. The COVID-19 mortality rate is usually higher in elderly patients or individuals with preceding conditions such as heart disease, diabetes, chronic lung disease, hypertension, and malignancies over young and middle-aged groups.

With the emerged spike of two new variants, such as Delta and Omicron, it was very difficult to handle the situation amid of successful vaccination drive. At this moment, globally the spike has reduced except for few countries. Nevertheless, scientists are continuously developing an efficient technique to trace the new variants and thereby reduce the burden of the disease which will also facilitate in preventing further such outbreaks in the future.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.



 
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