Volume 8, (Spl-1- SARS-CoV-2), October-November Issue - 2020, Pages:S09-S20 |
Authors: Rabin Gyawali, Khim Dhoj Karki, Ravin Bhandari, Balram Neupane, Rubee Regmi Kafle, Dhakaraj Pant, Ram Bahadur Khadka¬¬ |
Abstract: Severe acute respiratory syndrome coronavirus2 (SARS-CoV-2) belongs to the beta corona virus genera of the Coronaviridae family, which is a pathogenic virus that causes coronavirus disease 2019 (COVID-19) and is responsible for the ongoing pandemic affecting more than 210 countries. The virus has currently posed a global threat to the human population and demands the urgent need for sensitive and effective methods of diagnosis. Real-time reverse transcription polymerase chain reaction (RT-PCR) is currently used as a gold standard technique for detecting and quantifying the transcript of viral ribonucleic acid. Yet many factors are essential for successful COVID-19 diagnosis, including sample sources, amount of viral load, isolation of ribonucleic acid, and the selection of the molecular targets. Although broncho alveolar lavage fluid (BALF) and sputum sample contain a high viral load with a high diagnostic value, they cannot be collected from mild to asymptomatic cases, therefore nasopharyngeal swab is considered better and is collected in all cases that contain a viral load significantly, whereas the use of blood and faecal specimens needs further examination with respect to systemic infection and viral shedding. Furthermore, rapid diagnostic test, clustered regularly interspaced short palindromic repeats (CRISPR)-based testing, chest computerized tomography (CT) scans, matrix- assisted laser desorption/ionization mass spectrometry (MALDI-MS), reverse transcriptional loop-mediated isothermal amplification (LAMP), point of care (POC) testing and genexpert recently tool may help with COVID-19 diagnosis. In this review, we focus on diagnostic approaches for effective detection of SARS-CoV-2 infection. |
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Full Text: 1 Introduction Corona viruses are members of the Coronaviridae family which includes 2 subfamilies called Letovirinae and Orthocoronavirinae, with 4 genera as alpha, beta, gamma and delta corona virus (Siddell, 1995; Kasmi et al., 2020). Especially two forms of alphacoronavirus (229E and NL63) and two forms of betacoronavirus (OC43 and HKU1) are generally human pathogens and cause the common cold. Gamma and deltacorona viruses generally cause disease in avian species and rarely in mammals (Siddell, 1995; Kasmi et al., 2020; Shereen et al., 2020). Two other varieties of betacoronavirus include severe acute respiratory syndrome coronavirus-1 (SARS-CoV-1) and Middle East respiratory syndrome (MERS-CoV) which are highly pathogenic to humans (Siddell, 1995; Amanat & Krammer, 2020). Under electron microscope observation, the coronavirus appears to be surrounded by a uniquely shaped solar crown. In Latin Corona means crown or halo. They are the global emerging viruses that causes diseases ranging from mild symptoms of common flu, and influence more serious human diseases such as SARS and MERS (Mahy & Van Regenmortel, 2010; Kasmi et al., 2020; Shereen et al., 2020). Previous studies and research have shown that these viruses emerged as a new strain: SARS-CoV-2 originally transferred from animals to humans had not previously been identified in humans, but transmission from human-to-human has so far been confirmed. Although SARS is transmitted by civet cats and MERS by camels had previously been identified in humans respectively (Kasmi et al., 2020). On December 31, 2019, the WHO (World Health Organization) decided on a dark and progressive type of pneumonia in Wuhan, China, as a public health emergency of international interest. On February 11, 2020, they termed the disease as COVID-19. On the same day, Committee on Taxonomy of Viruses (ICTV) appointed the new corona virus as SARS-CoV-2, which also belongs to the beta-coronavirus genera that contain huge 30+ kbsingle strand RNA genome encryption positive sense for various open reading frames (orf) (Shereen et al., 2020; Amanat & Krammer, 2020). The established determination claims that 2% of people are healthy transmitters of this virus and responsible for acute respiratory infections in about 5% -10% (Siddell, 1995; Shereen et al., 2020; Cascella et al., 2020). 2 Taxonomy The Coronaviridae family, Nidovirales order, includes two kinds of viruses: Coronavirus and Torovirus (Siddell, 1995; Kasmi et al., 2020). Most pathogens that infect humans and animals are like corona viruses, while toroviruses are also detected in human stools with unclear mechanisms and in animals that cause diarrhea. Initially, experts from the ICTV classified these viruses into 3 groups which are based on the antigenic relationship of the morphological characteristics of the virus, including spikes (S), membrane (M) and nucleocapsid proteins (N) and other studies make a more solid classification based on genetic phylogeny (Drexler et al., 2014; Kasmi et al., 2020). Group 1 corona viruses are HCoVs229E and NL63, group 2 are OC43, HKU-1 and SARS. Group 3 corona viruses are found mainly in avian species. Members of the identical groups and others different groups show close genetic recombination which provides greater genetic diversity for corona viruses (Mahy & Van Regenmortel, 2010; Drexler et al., 2014; Kasmi et al., 2020; Walls et al., 2020). SARS coronavirus animal reservoirs are the source of the recognition of various bat coronaviruses in groups 1 and 2 which have phylogenetics almost similar to different mammalian corona viruses (Kasmi et al., 2020). Many previous studies and research have suggested that bat corona viruses are the ancestors of many mammalian corona viruses. Over the past 200 years, studies have shown that the common cold causative agents are HCoV, 229E and OC43 as universal endemic in humans species crossed from their animal reservoirs such as bats and cattle for humans, producing new viral diseases (Siddell, 1995; Drexler et al., 2014; Shereen et al., 2020). At intervals, the corona virus infecting wild life changed and become a novel corona virus that can infect humans. These newely developed CoVs can be very critical and occasionally produced pneumonia. Pneumonia is a fatal condition in which the liquid conforms to the lungs (Drexler et al., 2014). Recently these three types of new corona viruses appeared in the following generation (Siddell, 1995; Drexler et al., 2014; Peeri et al., 2020). • SARS (severe acute respiratory syndrome), a crucial and increasingly devastating respiratory disease. It was mainly found in China in 2002 and spread all over the globe. A worldwide exertion serves to rapidly contain the spread of the illness. No new protests have been announced in any place since 2004 in world. • MERS (Middle East Respiratory Syndrome), a crucial breathing disease that was mainly found in Saudi Arabia in 2012 and has circulate to about 27 countries. Just two cases haves been declared in the United States. All manifestations haves been related to travel or accommodation on the Arabian Peninsula or in its entirety. • COVID-19 (Corona virus disease 2019), It was registered in late 2019 in the capital city of Wuhan, Chinese Hubei province. The majority of the infections were earlier seen in China or as related to travel from Wuhan city to other countries. Thereafter, COVID-19 rapidly spread to more than 210 countries (Europe, Asia and Africa and across the globe) and posed high health threats and challenges (Dhama et al., 2020a; Malik et al., 2020). The epidemic is closely followed by the Center for Disease Control (CDC) and the World Health Organization (WHO).Comparison of the characteristics between the new corona virus, SARS-CoV-1 and MERS-CoV are shown in Table 1 (Siddell, 1995; Mahy & Van Regenmortel, 2010; Kasmi et al., 2020; Meo et al., 2020). 3 Symptoms Starting from a respiratory disease, it presents a wide range of symptoms with incubation periods ranging from two to 14 days. Most infected humans show symptoms within 5-6 days, leading to some cases of asymptomatic conditions. Many studies indicate that symptoms such as pyrexia, cough, dyspnoea, sore throat, and headache are included in corona virus infections which are generally milder than SARS and MERS compared to COVID-19 (Cafekar & Fielding, 2018; Dhama et al., 2020b; Petrosillo et al., 2020). 4 Collection and Transport of Samples The sample must be collected from skilled person and taking into account all biosecurity mandates plus the use of personal protective equipment to prevent respiratory virus infection. WHO recommends collecting samples through the upper respiratory tract (nasopharyngeal swab, oropharyngeal swab or washing) and the lower respiratory tract (sputum, bronchoalveolar lavage and endotracheal aspirate). Perhaps other clinical samples such as blood and feces can be collected (Cascella et al., 2020; WHO, 2020a). Common impertinent faults (inadequate identification of the sample, insufficient material, inadequate collection method, handling, shipping and storage, presence of harmful substances, etc.) deserve a particular focal point during the collection of the samples. Although the WHO has not issued a particular reference method for collecting respiratory specimens, the United States CDC proposes to collect nasopharyngeal and oropharyngeal specimens by applying germ free swabs with fibre or Dacron tip and an aluminium or plastic shaft (Lippi et al., 2020). To collect nasopharyngeal samples, the CDC supported the introduction of a swab into the nostrils, aligned with the palate and held for a few seconds for its absorption and instantaneous positioning in a sterile tube with 2-3 ml of viral transport medium (VTM ). Similarly to the collection of oropharyngeal samples, the CDC proposes to introduce a swab into the back of the pharynx, keeping it away from the tongue and placing it instantly in a sterile test tube having 2-3 ml of VTM (Lippi et al., 2020). To provide nasopharyngeal, oropharyngeal, bronchoalveolar lavage, endotracheal aspirate, VTM must contain antibiotic and antifungal supplements (WHO, 2020b). |
Afzal A (2020) Molecular diagnostic technologies for COVID-19: Limitations and challenges. Journal of Advanced Research 10.1016/j.jare.2020.08.002. doi:10.1016/j.jare.2020.08.002. Ai JW, Zhang Y, Zhang HC, Xu T, Zhang WH (2020) Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned. Emerging Microbes & Infections 9(1): 597-600. Ai T, Yang Z, Hou H, Zhan C, Chen C, Lv W, Tao Q, Sun Z, Xia L (2019) Correlation of chest CT and RT-PCR testing in corona virus disease 2019 (COVID-19) in China: a report of 1014 cases. Radiology. 2020 Feb 26:200642. Amanat F, Krammer F (2020) SARS-CoV-2 vaccines: status report. Immunity 52(4): 583-589. Arab-Mazar Z, Sah R, Rabaan AA, Dhama K, Rodriguez-Morales AJ (2020) Mapping the incidence of the COVID-19 hotspot in Iran - Implications for Travellers. Travel Medicine and Infectious Disease 34:101630.doi:10.1016/j.tmaid.2020.101630. Augustine R, Hasan A, Das S, Ahmed R, Mori Y, Notomi T, Kevadiya BD, Thakor AS (2020) Loop-mediated isothermal amplification (Lamp): A rapid, sensitive, specific, and cost-effective point-of-care test for coronaviruses in the context of covid-19 pandemic. Biology, 9(8), 182. Cafekar A, Fielding BC (2018) MERS-CoV: understanding the latest human coronavirus threat. Viruses 10(2):93. Carter LJ, Garner LV, Smoot JW, Li Y, Zhou Q, Saveson CJ, Sasso JM, Gregg AC, Soares DJ, Beskid TR, Jervey SR, Liu C (2020) Assay Techniques and Test Development for COVID-19 Diagnosis. ACS Central Science 6(5):591-605. doi: 10.1021/acscentsci.0c00501. Cascella M, Rajnik M, Cuomo A, Dulebohn SC, Di Napoli R (2020) Features, evaluation and treatment coronavirus (COVID-19). InStatpearls [internet] 2020 Mar 8.StatPearls Publishing. Cheng MP, Papenburg J, Desjardins M, Kanjilal S, Quach C, Libman M, Dittrich S, Yansouni CP (2020) Diagnostic Testing for Severe Acute Respiratory Syndrome-Related Coronavirus-2: A Narrative Review. Annals of Internal Medicine M20-1301. Devasia JT, Lakshminarayanan S, Kar SS (2020) How Modern Geographical Information Systems Based Mapping and Tracking Can Help to Combat Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Pandemic around the World and India. International Journal of Health Systems and Implementation Research 10;4(1):30-54. Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ (2020a) Coronavirus Disease 2019-COVID-19. Clinical Microbiology Reviews 33(4):e00028-20. doi: 10.1128/CMR.00028-20. Dhama K, Patel SK, Pathak M, Yatoo MI, Tiwari R, Malik YS, Singh R, Sah R, Rabaan AA, Bonilla-Aldana DK, Rodriguez-Morales AJ (2020b) An update on SARS-CoV-2/COVID-19 with particular reference to its clinical pathology, pathogenesis, immunopathology and mitigation strategies. Travel Medicine and Infectious Disease 101755. doi: 10.1016/j.tmaid.2020.101755. Dinnes J, Deeks JJ, Adriano A, Berhane S, Davenport C, Dittrich S, Emperador D, Takwoingi Y, Cunningham J, Beese S, Dretzke J, Ferrante di Ruffano L, Harris IM, Price MJ, Taylor-Phillips S, Hooft L, Leeflang MM, Spijker R, Van den Bruel A (2020) Cochrane COVID-19 Diagnostic Test Accuracy Group. Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. Cochrane Database of Systematic Reviews8:CD013705.doi: 10.1002/14651858.CD013705. Djalante R, Lassa J, Setiamarga D, Mahfud C, Sudjatma A, Indrawan M, Haryanto B, Sinapoy MS, Rafliana I, Djalante S, Gunawan LA (2020) Review and analysis of current responses to COVID-19 in Indonesia: Period of January to March 2020. Progress in Disaster Science 2020 Apr 4:100091. Drexler JF, Corman VM, Drosten C (2014) Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS. Antiviral research 2014 Jan 1;101:45-56. Guo L, Sun X, Wang X, Liang C, Jiang H, Gao Q, Dai M, Qu B, Fang S, Mao Y, Chen Y, Feng G, Gu Q, Wang L, Wang RR, Zhou Q, Li W (2020) SARS-CoV-2 detection with CRISPR diagnostics. Cell Discovery 6(1): 1-4. Jääskeläinen AJ, Kekäläinen E, Kallio-Kokko H, Mannonen L, Kortela E, Vapalahti O, Kurkela S, Lappalainen M (2020) Evaluation of commercial and automated SARS-CoV-2 IgGand IgA ELISAs using coronavirus disease (COVID-19) patient samples. Eurosurveillance 25(18): 2000603. Kasmi Y, Khataby K, Souiri A, Ennaji MM (2020) Coronaviridae: 100,000 Years of Emergence and Reemergence. In: Ennaji MM (Ed) Emerging and Reemerging Viral Pathogens, Academic Press, Pp. 127-149. doi: 10.1016/B978-0-12-819400-3.00007-7. Kubina R, Dziedzic A (2020) Molecular and Serological Tests for COVID-19 a Comparative Review of SARS-CoV-2 Coronavirus Laboratory and Point-of-Care Diagnostics. Diagnostics 10(6): 434. Lee EY, Ng MY, Khong PL (2020) COVID-19 pneumonia: what has CT taught us?. The Lancet Infectious Diseases 20(4):384-5. Lippi G, Simundic AM, Plebani M (2020) Potential preanalytical and analytical vulnerabilities in the laboatory diagnosis of coronavirus disease 2019 (COVID-19).Clinical Chemistry and Laboratory Medicine (CCLM) 2020 Mar 16;1(ahead-of-print). Liu W, Liu L, Kou G, Zheng Y, Ding Y, Ni W, Wang Q, Tan L, Wu W, Tang S, Xiong Z , Xiong Z (2020) Evaluation of nucleocapsid and spike protein-based enzyme-linked immunosorbent assays for detecting antibodies against SARS-CoV-2. Journal of Clinical Microbiology 58(6):e00461. DOI: 10.1128/JCM.00461-20 Mahy BW, Van Regenmortel MH (Ed.) (2010) Deskencyclopedia of human and medical virology. Academic Press; 2010 May 21. Malik YS, Kumar N, Sircar S, Kaushik R, Bhat S, Dhama K, Gupta P, Goyal K, Singh MP, Ghoshal U, El Zowalaty ME, O R V, Yatoo MI, Tiwari R, Pathak M, Patel SK, Sah R, Rodriguez-Morales AJ, Ganesh B, Kumar P, Singh RK. (2020) Coronavirus Disease Pandemic (COVID-19): Challenges and a Global Perspective. Pathogens 9(7):519. doi: 10.3390/pathogens9070519. Meo SA, Alhowikan AM, Al-Khlaiwi T, Meo IM, Halepoto DM, Iqbal M, Usmani AM, Hajjar W, Ahmed N (2020) Novel coronavirus 2019-nCoV: prevalence, biological and clinical characteristics comparison with SARS-CoV and MERS-CoV. European Review for Medical and Pharmacological Sciences 24(4):2012-9. Moran A, Beavis KG, Matushek SM, Ciaglia C, Francois N, Tesic V, Love N (2020) The detection of SARS-CoV-2 using the cepheidxpertxpress SARS-CoV-2 and Roche cobas SARS-CoV-2 assays. Journal of Clinical Microbiology.2020 Apr 17. Nachtigall FM, Pereira A, Trofymchuk OS, Santos LS (2020) Detection of SARS-CoV-2 in nasal swabs using MALDI-MS. Nature Biotechnology 2020;10.1038/s41587-020-0644-7. doi:10.1038/s41587-020-0644-7 Natesan S, Bhatia R, Sundararajan A, Dhama K, Malik YS, Vora K (2020) Ramping up of SARS CoV-2 testing for the diagnosis of COVID-19 to better manage the next phase of pandemic and reduce the mortality in India . Virusdisease1-9.doi:10.1007/s13337-020-00622-x Pathak M, Patel SK, Rana J, Tiwari R, Dhama K, Sah R, Rabaan AA, Bonilla-Aldana DK, Rodriguez-Morales AJ (2020) Global threat of SARS-CoV-2/COVID-19 and the need for more and better diagnostic tools. Archives of Medical Research 2020 Apr 15;51. Peeri NC, Shrestha N, Rahman MS, Zaki R, Tan Z, Bibi S, Baghbanzadeh M, Aghamohammadi N, Zhang W, Haque U (2020) The SARS, MERS and novel coronavirus (COVID-19) epidemics, the newest and biggest global health threats: what lessons have we learned?. International Journal of Epidemiology 49: 717-726. DOI: https://doi.org/10.1093/ije/dyaa033. Petrosillo N, Viceconte G, Ergonul O, Ippolito G, Petersen E (2020) COVID-19, SARS and MERS: are they closely related?.Clinical Microbiology and Infection 26: 729-734. Rando HM, Greene CS, Robson MP, Boca SM, Wellhausen N, Lordan R, Brueffer C, Ray S, Lucy D, McGowan A, Gitter A (2020) SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics. Manubot; 2020 Apr 17. Available on https://greenelab.github.io/covid19-review/. Ravichandran K, Anbazhagan S, Singh SV, Agri H, Rupner RN, ObliRajendran VK, Dhama K, Singh BR (2020) Global Status of COVID-19 Diagnosis: An Overview. Journal of Pure and Applied Microbiology 14(suppl 1):879-892. doi: 10.22207/JPAM.14.SPL1.25 Shereen MA, Khan S, Kazmi A, Bashir N, Siddique R (2020) COVID-19 infection: origin, transmission, and characteristics of human coronaviruses. Journal of Advanced Research. 24:91-98. Sheridan C (2020) Fast, portable tests come online to curb coronavirus pandemic. Nature Biotechnology 38(5): 515-518. doi: 10.1038/d41587-020-00010-2. Siddell SG (1995) The Coronaviridae. In: Siddell SG (Eds) The Coronaviridae. The Viruses. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-1531-3_1. Smith A, Piga I, Galli M, Stella M, Denti V, Del Puppo M, Magni F (2017) Matrix-Assisted Laser Desorption/Ionisation Mass Spectrometry Imaging in the Study of Gastric Cancer: A Mini Review. International journal of Molecular Sciences 18(12): 2588; https://doi.org/10.3390/ijms18122588. Tang YW, Schmitz JE, Persing DH, Stratton CW (2020) The laboratory diagnosis of COVID-19 infection: Current issues and challenges. Journal of Clinical Microbiology 58(6):e00512-20. doi: 10.1128/JCM.00512-20. pii: JCM.00512-20. Udugama B, Kadhiresan P, Kozlowski HN, Malekjahani A, Osborne M, Li VYC, Chen H, Mubareka S, Gubbay JB, Chan WCW (2020) Diagnosing COVID-19: The Disease and Tools for Detection. ACS Nano 14(4):3822-3835. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D (2020) Structure, function, and antigenicity of the SARSCoV-2 spike glycoprotein. Cell 181:281-292. Wang W, Xu Y, Gao R, Lu R, Han K, Wu G, Tan W (2020) Detection of SARS-CoV-2 in different types of clinical specimens. JAMA 323(18):1843-1844. doi:10.1001/jama.2020.3786
World Health Organization (2020a) Advice on the use of point-of-care immunodiagnostic tests for COVID-19: scientific brief, 8 April 2020. World Health Organization; 2020. World Health Organization (2020b) Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases: interim guidance, 2 March 2020. World Health Organization; 2020. Wynants L, Van Calster B, Bonten MM, Collins GS, Debray TP, De Vos M, Haller MC, Heinze G, Moons KG, Riley RD, Schuit E (2020) Prediction models for diagnosis and prognosis of covid-19 infection: systematic review and critical appraisal. BMJ 2020; 369 doi: https://doi.org/10.1136/bmj.m1328. Yang Y, Yang M, Shen C, Wang F, Yuan J, Li J, Zhang M, Wang Z, Xing L, Wei J, Peng L (2020) Laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. MedRxiv.2020 Jan 1. DOI: : https://doi.org/10.1101/2020.02.11.20021493 Yu L, Wu S, Hao X, Li X, Liu X, Ye S, Han H, Dong X, Li X, Li J, Liu J (2020) Rapid colorimetric detection of COVID-19 coronavirus using a reverse tran-scriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic plat-form: iLACO. medRxiv. 2020 Jan 1. http://dx.doi.org/10.1093/clinchem/hvaa102. Zhai P, Ding Y, Wu X, Long J, Zhong Y, Li Y (2020) The epidemiology, diagnosis and treatment of COVID-19. International Journal of Antimicrobial Agents 55(5): 105955. DOI: https://doi.org/10.1016/j.ijantimicag.2020.105955. |