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      Current trends in COVID-19 diagnosis and its new variants in physiological fluids: Surface antigens, antibodies, nucleic acids, and RNA sequencing

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          Abstract

          Rapid, highly sensitive, and accurate virus circulation monitoring techniques are critical to limit the spread of the virus and reduce the social and economic burden. Therefore, point-of-use diagnostic devices have played a critical role in addressing the outbreak of COVID-19 (SARS-CoV-2) viruses. This review provides a comprehensive overview of the current techniques developed for the detection of SARS-CoV-2 in various body fluids (e.g., blood, urine, feces, saliva, tears, and semen) and considers the mutations (i.e., Alpha, Beta, Gamma, Delta, Omicron). We classify and comprehensively discuss the detection methods depending on the biomarker measured (i.e., surface antigen, antibody, and nucleic acid) and the measurement techniques such as lateral flow immunoassay (LFIA), enzyme-linked immunosorbent assay (ELISA), reverse transcriptase-polymerase chain reaction (RT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), microarray analysis, clustered regularly interspaced short palindromic repeats (CRISPR) and biosensors. Finally, we addressed the challenges of rapidly identifying emerging variants, detecting the virus in the early stages of infection, the detection sensitivity, selectivity, and specificity, and commented on how these challenges can be overcome in the future.

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          A Novel Coronavirus from Patients with Pneumonia in China, 2019

          Na Zhu, Dingyu Zhang, Wenling Wang … (2020)
          Summary In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.)
          Article 0 comments Cited 12725 times – based on 0 reviews     Review now
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            Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China

            Dawei Wang, Bo Hu, Fangfang Zhu … (2020)
            In December 2019, novel coronavirus (2019-nCoV)-infected pneumonia (NCIP) occurred in Wuhan, China. The number of cases has increased rapidly but information on the clinical characteristics of affected patients is limited.
            Article 0 comments Cited 10805 times – based on 0 reviews     Review now
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              A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster

              Jasper Chan, Shuofeng Yuan, Kin-Hang Kok … (2020)
              Summary Background An ongoing outbreak of pneumonia associated with a novel coronavirus was reported in Wuhan city, Hubei province, China. Affected patients were geographically linked with a local wet market as a potential source. No data on person-to-person or nosocomial transmission have been published to date. Methods In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan. Phylogenetic analysis of genetic sequences from these patients were done. Findings From Jan 10, 2020, we enrolled a family of six patients who travelled to Wuhan from Shenzhen between Dec 29, 2019 and Jan 4, 2020. Of six family members who travelled to Wuhan, five were identified as infected with the novel coronavirus. Additionally, one family member, who did not travel to Wuhan, became infected with the virus after several days of contact with four of the family members. None of the family members had contacts with Wuhan markets or animals, although two had visited a Wuhan hospital. Five family members (aged 36–66 years) presented with fever, upper or lower respiratory tract symptoms, or diarrhoea, or a combination of these 3–6 days after exposure. They presented to our hospital (The University of Hong Kong-Shenzhen Hospital, Shenzhen) 6–10 days after symptom onset. They and one asymptomatic child (aged 10 years) had radiological ground-glass lung opacities. Older patients (aged >60 years) had more systemic symptoms, extensive radiological ground-glass lung changes, lymphopenia, thrombocytopenia, and increased C-reactive protein and lactate dehydrogenase levels. The nasopharyngeal or throat swabs of these six patients were negative for known respiratory microbes by point-of-care multiplex RT-PCR, but five patients (four adults and the child) were RT-PCR positive for genes encoding the internal RNA-dependent RNA polymerase and surface Spike protein of this novel coronavirus, which were confirmed by Sanger sequencing. Phylogenetic analysis of these five patients' RT-PCR amplicons and two full genomes by next-generation sequencing showed that this is a novel coronavirus, which is closest to the bat severe acute respiatory syndrome (SARS)-related coronaviruses found in Chinese horseshoe bats. Interpretation Our findings are consistent with person-to-person transmission of this novel coronavirus in hospital and family settings, and the reports of infected travellers in other geographical regions. Funding The Shaw Foundation Hong Kong, Michael Seak-Kan Tong, Respiratory Viral Research Foundation Limited, Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund Limited, Marina Man-Wai Lee, the Hong Kong Hainan Commercial Association South China Microbiology Research Fund, Sanming Project of Medicine (Shenzhen), and High Level-Hospital Program (Guangdong Health Commission).
              Article 0 comments Cited 4099 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Trends Analyt Chem
                Journal ID (iso-abbrev): Trends Analyt Chem
                Title: Trends in Analytical Chemistry
                Publisher: The Authors. Published by Elsevier B.V.
                ISSN (Print): 0165-9936
                ISSN (Electronic): 1879-3142
                Publication date PMC-release: 30 August 2022
                Publication date (Electronic): 30 August 2022
                Electronic Location Identifier: 116750
                Affiliations
                [a ]NanoStruc Research Group, Chemistry Department, Faculty of Science, Helwan University, 11795, Cairo, Egypt
                [b ]National Centre for Sensor Research, School of Chemical Sciences, Dublin City University, D09 V209, Dublin, Ireland
                [c ]Institute of Chemistry, Technical University of Berlin, 10623, Berlin, Germany
                [d ]Institute of Materials Science, Faculty of Engineering, Kiel University, 24143, Kiel, Germany
                [e ]School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St, Dublin, D02R590, Ireland
                [f ]Borg Pharmaceutical Industries, Refaat Hassan St, Al Abageyah, El-Khalifa, Cairo Governorate, 16, Egypt
                [g ]Chemistry Department, Faculty of Science, Helwan University, 11795, Cairo, Egypt
                [h ]Chemistry Department, Faculty of Science, Cairo University, 12613, Giza, Egypt
                Author notes
                [∗ ]Corresponding author. NanoStruc Research Group, Chemistry Department, Faculty of Science, Helwan University, 11795, Cairo, Egypt.
                [∗∗ ]Corresponding author.
                [∗∗∗ ]Corresponding author.
                Article
                Publisher Item ID: S0165-9936(22)00233-3 Publisher ID: 116750
                DOI: 10.1016/j.trac.2022.116750
                PMC ID: 9425703
                SO-VID: e2a40665-8c7e-4467-ab40-7668736bcc09
                Copyright © © 2022 The Authors. Published by Elsevier B.V.
                License:

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                Date received : 20 January 2022
                Date revision received : 21 June 2022
                Date accepted : 24 July 2022
                Categories
                Subject: Article

                Keywords: covid-19 virus diagnosis,reverse transcriptase-polymerase chain reaction,lateral flow immunoassay,loop-mediated isothermal amplification,microarray assays,enzyme-linked immunosorbent assay,clustered regularly interspaced short palindromic repeats,biosensors
                Data availability:
                Keywords: covid-19 virus diagnosis, reverse transcriptase-polymerase chain reaction, lateral flow immunoassay, loop-mediated isothermal amplification, microarray assays, enzyme-linked immunosorbent assay, clustered regularly interspaced short palindromic repeats, biosensors

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