Detection and Analysis of SARS Coronavirus

Advanced Biosensors for Pandemic Viruses and Related Pathogens

Chaudhery Mustansar Hussain, Sudheesh K. Shukla, Chaudhery Mustansar Hussain, Sudheesh K. Shukla

• Publisher: Wiley-VCH
• Year: 2021
• Print ISBN:
  9783527349180
• Edition: 1
• eBook ISBN:
  9783527832514
• Topic: Biological Sciences
• Subtopic: Biochemistry
• Index: Biological Sciences

Detection and Analysis of SARS Coronavirus

Detecting and analyzing the COVID-19 pandemic with biosensor technology

The highly contagious SARS CoV-2 pathogen has challenged health systems around the world as they struggle to detect and monitor the spread of the pathogen. In Detection and Analysis of SARS Coronavirus: Advanced Biosensors for Pandemic Viruses and Related Pathogens expert chemists Chaudhery Mustansar Hussain and Sudheesh K. Shukla deliver a practical analysis of how contactless coronavirus detectors may be developed using existing biosensor technology.

The editors outline current challenges in the field, the bioanalytical principles for coronavirus detection, and available biosensor technology. They then move on to how available technology might be adapted to detect coronaviruses and how commercialization of the technology might unfold.

The lessons learned in this book are readily applicable to the study of other current and emerging pathogens.

Readers will also enjoy:

• A thorough introduction to the current diagnostic approaches for COVID-19, including common challenges, technology adaptation, and future potential
• An exploration of bio-analytical strategies for SARS CoV-2/COVID-19, including COVID detection via nanotechnology, biosensing approaches, and the role of nanotechnology in coronavirus detection
• Practical discussions of biosensors for the analysis of SARS CoV-2/COVID-19, including sensor development for coronavirus and chemical sensors for coronavirus diagnosis
• In-depth treatments of the commercialization and standardization for analytical technologies

Perfect for virologists, pharmaceutical industry professionals, and sensor developers, Detection and Analysis of SARS Coronavirus is also an indispensable resource for those working in analytical research institutes, biotechnology industry professionals, and public health agency professionals.

Part I
Introduction

1
Current Diagnostic Approach for COVID‐19

Nitika Thakur¹ and Rachit Sood¹

¹Shoolini University of Biotechnology and Management Sciences, Faculty of Applied Sciences and Biotechnology, Department of Biotechnology, Solan, Himachal Pradesh, India

1.1 Introduction

The ongoing spread of coronavirus has presented a threatening scenario globally because of the non‐availability of accurate and rapid detection methods. However, on 30 January 2020, World Health Organization (WHO) has declared “COVID‐19” (coronavirus disease 2019) as the largest threat under “public health emergency of global concern,” as it is alone responsible for 250 000–260 000 deaths worldwide and across 3–3.5 million positive cases [1].

The detection and analysis procedure for this threatening virus started initially with a virus detection method, which somewhat has an advantage of non‐detection of long culture cycles. Another way of detection is through the use of “nucleic acid profiling,” which [2] can rapidly, sensitively, and accurately detect the pathogens in confirmed COVID patients, but large amounts of genetic variations, mismatches in primers, probes, and some target sequences may result in interpretation of false results. Detection via genomic sequence analysis and the point‐of‐care diagnosis have become popular in the detection of emerging viruses for finally detecting the specific antibodies IgM and IgG related to COVID [3].

Section 1.2 describes and highlights the current diagnostics and treatment strategies for COVID‐19.

1.2 Recommended Laboratory Diagnosis for COVID‐19

1.2.1 SARS‐CoV‐2 Testing: Detection Approach by Screening Suitable Specimen Cultures

The first and foremost step in diagnosis and identification is related to the appropriate collection of suitable specimens, which [4] are being collected from the upper and lower respiratory tracts, WBC's, and serum specimens. Furthermore, it has been mostly detected and screened from the swabs pertaining to nasopharyngeal area, oropharyngeal, sputum, stool samples, urine, saliva, conjunctival area, and rectal swabs [5].

It is recommended that the samples and swabs should be strictly collected from the lower respiratory tract, for confirmatory diagnosis, even if the upper respiratory swab analysis is negative for COVID‐19, as the receptor “AEC 2” is actively distributed in the alveolar lining of epithelial cells. Various studies compared [6] the viral loads from the lower respiratory tract specimen for the suspected and confirmed COVID patients. The study further stated that the average viral load differed in different collected samples [7], as the viral load detected in sputum was higher around 17 420 ± 6925 copies/test than the nasal swabs (655 ± 502 copies/test) and throat swabs (2555 ± 1965 copies/test). In addition, high viral load was also recorded in swabs collected from [8] the lower respiratory tract. Most of the cases were examined and confirmed positive through isolation and culturing techniques from oral swab on the first day, followed by a five [9–11] day diagnosis of anal swabs, indicating a shift from early period diagnosis to late period diagnosis. However, in asymptomatic conditions, it can be detected by analysis of urine sample, with no urinary irritation symptoms. Recently, it has also been detected in samples of saliva. In addition, it has been detected in nasopharyngeal swab, conjunctival tear swabs, and [12] oropharyngeal swabs. However, there still exist glitches in terms of monitoring and isolation process to screen conjunctival secretions for confirmatory diagnosis. Currently, the [13] virus has not been traced in many samples such as cerebrospinal fluid, semen, pericardial effusion, female reproductive tract, etc.

1.2.2 SARS‐CoV‐2 Detection: The Nucleic Acid Approach

For successful diagnostic strategies, identification of some specific primers and probes is important to screen out the target sequences. These target sequences for COVID‐19 involve the “envelope – E,” “the nucleocapsid – N,” “spikes – S,” “RNA‐dependent RNA polymerase,” and “open reading frame – ORF.” WHO further recommends [14] reverse transcription polymerase chain reaction (RT‐PCR) as a routine recommendation but lacks suitability in terms of time consumption, requirement of expensive equipment and biosafety conditions.

1.2.2.1 COVID‐19 Detection Approach Through Real‐Time PCR

The target gene sequences for detecting CoV‐2 vary globally from China (ORF's), the United States (3 N gene), Germany (RdRp, N, and E genes) to France (two targets in RdRp). Center for Disease Control and Prevention (CDC) established a RT‐PCR process for the detection and analysis of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), with three specific primer sets to detect β forms of CoV‐2 and the other two for SARS‐CoV‐2.

Different countries have a [15–18] large number of qRT‐PCR (quantitative reverse transcription polymerase chain reaction) protocols provided by the official WHO website, which play the principal role in the detection of SARS‐CoV‐2. In recent time, different countries are following different protocols of gene targeting for the detection of SARS‐CoV‐2, for example, France (two targets in RdRp aka RNA‐dependent RNA polymerase), Japan (pancorona and numerous targets, spike protein), the United States (three targets in N gene), China (N genes and ORF1ab), Thailand (N gene), and [19–21] Germany (RdRp, N, and E genes). Different institutes use different RT‐PCR primers or tests for the detection of SARS‐CoV‐2. A new RT‐PCR panel has been rooted by the CDC for the universal detection of SARS‐like β‐CoVs and specific detection of SARS‐CoV‐2. For the N gene [22–25], three sets of distinct primers were devised – two sets of probes or primers were specific for identifying SARS‐CoV‐2 and the last set was universally used for detecting all β‐CoVs. COVID‐19 must be confirmed as positive for all the three individual targets. The Charite (Germany) developed two nucleic acid tests for the detection of E genes of the bat‐like ...

Table of contents

• Cover
• Table of Contents
• Title Page
• Copyright
• Dedication
• Preface
• About the Editors
• Part I: Introduction
• Part II: Bio‐analytical Strategies for SARS‐CoV‐2/COVID‐19
• Part III: Biosensors for Analysis of SARS‐CoV‐2/COVID‐19
• Part IV: Commercialization and Standardization of Analytical Technologies
• Part V: Outlook
• Index
• End User License Agreement