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 Table of Contents  
REVIEW ARTICLE
Year : 2021  |  Volume : 23  |  Issue : 1  |  Page : 16-23

Techno-innovations and molecular methods for diagnosis of COVID-19: Updates from India


1 Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
2 Division of Innovation and Translational Research, Indian Council of Medical Research, New Delhi, India
3 Department of Community Medicine and School of Public Health, Postgraduate Institute of Medical Education and Research, Chandigarh, India
4 National Institute of Nursing Education, Postgraduate Institute of Medical Education and Research, Chandigarh, India
5 Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
6 Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
7 Advance Pediatric Centre, Hematology Oncology Unit, Postgraduate Institute of Medical Education and Research, Chandigarh, India

Date of Submission27-Dec-2020
Date of Decision23-Jan-2021
Date of Acceptance04-Feb-2021
Date of Web Publication15-Jul-2021

Correspondence Address:
Dr Jitender Gairolla
Senior Resident, Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand
India
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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/jmms.jmms_195_20

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  Abstract 


The rapid diagnosis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection relies on the availability of a robust method. The demand for SARS-CoV-2 diagnostic kits and other desirable consumables for timely diagnosis have increased drastically after the current pandemic. The cumulative efforts by scientists, funding agencies, regulatory authorities, and corporates have accelerated the process of kit development. Worldwide, rapid molecular techno progression to characterize the biology of any pathogen witnessed during this pandemic faster than ever. Moreover, a paradigm shift from real-time polymerase chain reaction technique to highly sensitive novel CRISPR technology has been observed. India, second most populous country actively leveraged molecular technologies for rapid diagnosis of SARS-CoV-2. This paper focuses on paradigm shift in the methods for diagnosis of SARS-CoV-2 infection with a focus on molecular innovations carried out in India indigenously.

Keywords: COVID-19 diagnosis, molecular Innovations, reverse transcription polymerase chain reaction, SARS-CoV-2


How to cite this article:
Gairolla J, Gupta P, Gupta P, Mathuria YP, Chauhan C, Kaur MD, Naithani P, Naithani M, Nagar PK. Techno-innovations and molecular methods for diagnosis of COVID-19: Updates from India. J Mar Med Soc 2021;23:16-23

How to cite this URL:
Gairolla J, Gupta P, Gupta P, Mathuria YP, Chauhan C, Kaur MD, Naithani P, Naithani M, Nagar PK. Techno-innovations and molecular methods for diagnosis of COVID-19: Updates from India. J Mar Med Soc [serial online] 2021 [cited 2021 Jul 28];23:16-23. Available from: https://www.marinemedicalsociety.in/text.asp?2021/23/1/16/321596




  Introduction Top


Coronavirus disease-19 (COVID-19) pandemic has brought the world to a standstill. Despite prudent healthcare measures taken by the World Health Organization (WHO), and various governments across the world, the confirmed number of cases surpassed over 25,327,098 and 848,255 deaths have been reported in the 1st week of September, 2020.[1] Till current time, severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus was found to be highly more contagious as compared to other coronaviruses[2] as its infectivity period can start several days before the person becomes symptomatic thus every person could be a potential asymptomatic infected case or a carrier.[3] Data on COVID-19 disease suggest that up to 80% remains mild or asymptomatic carrier[4] thus the timely diagnosis of SARS-CoV-2 infection is central to all preventive measures being taken to control the pandemic of COVID-19.

Worldwide, the rapid molecular techno progression enables scientists to characterize the biology of SARS-CoV-2 faster than ever[5],[6] and within few weeks after the identification of a cluster of patients with idiopathic pneumonia in Wuhan, China, the viral genome was sequenced successfully.[6],[7],[8] The sequencing technology integrated with bioinformatics tools marks the possibility of SARS-CoV-2 genome decoding to provide a deep insight of its proteomics[6],[7],[8] and thus ramp up the next step of laboratory diagnosis. Currently, research and development laboratories are faced with the extraordinary demands to supply sampling devices, diagnostic kits, reagents, and other consumables desirable for timely diagnosis[10],[11] as well as sorting people susceptible to COVID-19 before they can be referred to hospitals. Real-time reverse transcription polymerase chain reaction (RT-PCR) remains the cornerstone of COVID-19 diagnosis as it identifies and confirms the multiple targets of viral sequences simultaneously.[11],[12] The diagnostic providers such as Thermo Fisher Scientific and Roche Diagnostics have come up with large scalability and automated testing systems for detecting SARS-CoV-2 infection.[12]

India, the second most populous country in the world with vast geographical distances makes testing of SARS-CoV-2 a challenging chore. As of 1 September, 2020, there were 3.6 million cases of COVID-19 in India which now makes it the second most affected country after the USA. The recovery rate of COVID-19 cases has further increased up to 77% and number of recovered cases is 3.61 times higher than the active cases while around 80% of COVID-19 cases remain asymptomatic.[13],[14] Therefore, widespread and priority-based testing will be useful in identification and isolation of more cases including asymptomatic carriers. The government and private organizations have actively leveraged the research driven and technology-based interventions to fight out the outburst of this pandemic.[15] Here, in this review, we have highlighted the innovations in molecular technology which have effectively improved the country's efforts in rapid diagnosis of COVID-19.


  Molecular Diagnostic Tools for COVID-19 Top


Since the beginning of the pandemic COVID-19, the early and accurate diagnosis using a reliable method has been very crucial to confirm the SARS-CoV-2 infection so that the timely isolation of the positive cases and community spread could be curbed. Further, testing accessibility and results may also support government agencies to take an appropriate decision through policy implementation. In laboratory diagnosis of COVID-19, the false negative and false positive results may lead community spread unnecessarily as well as cause mental stress to such patients. Therefore, lessening the false results (false positive and false negatives) of infection is an onerous task[16] that raises the urgent need for the accurate, reliable and sensitive diagnostic method. Currently, there are various methods available for diagnosis of COVID-19 include RT-PCR, Cartridge based point of care tests (POCTs), next generation sequencing, high throughput molecular platforms (Cobas 6800/8800 Systems, Xpert Xpress SARS-CoV-2 test, reverse transcription loop-mediated isothermal amplification assay), biosensor based techniques, chemiluminescence immunoassay assay and enzyme-linked immunosorbent assay (ELISA) based serological tests.[17],[18] The confirmation of SARS-CoV-2 infection relies on the test and scanning procedure to be used in diagnosis. In addition, sample collection in pre-analytical stage from the respiratory tract and the anatomic site is also essential to obtain precise test results. At present, among all available methods, RT-PCR is the mainstay of laboratory diagnosis of COVID-19.[19] This is the gold standard method approved by WHO and Centers for Disease Control and Prevention which can screen and quantify the RNA genome of virus and thus help in making a clinical decision.[10],[11] The quality and safety of molecular diagnostic methods are being evaluated by the WHO through Prequalification Emergency Use Listing Procedures.

Serological testing (Ag-Ab reactions) are also being used for rapid screening of COVID-19 but has some disadvantages over molecular methods. Serological testing mainly relies on antibody detection (immunoglobulin M [IgM] and IgG) in blood produced by individual's immune system in response to viral exposure or on detection of viral proteins (spike, nucleocapsid and nonstructural proteins, etc.,) from nasal swabs in infected cases.[20] Rapid Antigen tests for COVID-19 usually requires nasal/nasopharyngeal swab or saliva that sometimes does not contain significant and measurable concentration of SARS-CoV-2 specific antigens.[21] Moreover, sensitivity of qualitative method for antibody detection using ELISA is still under study, therefore its being used as a supplemental tool. The other issue with antibody testing is the cross reactivity of antibody in blood with two viruses belong to same or different family or even genus but somehow have identical structures. Meta-analysis of antigen-based rapid assays for other respiratory diseases such as influenza has shown wide variation in the sensitivity of these tests from 34% to 80%.[22]

The first RT-PCR based test for COVID-19 diagnosis was readily available in January, 2019.[10],[11] The development of molecular test purely depends on the rudimentary understanding of scientific data available on the genomic and proteomic structure of any pathogen.[23] Early whole genome and phylogenetic analyses revealed that SARS-CoV-2 shares high nucleotide sequence similarities with previously identified SARS-CoV.[7] Relevant findings were uploaded on the National Center for Biotechnology Information Gene Bank database which has enabled the development of the primers and molecular probes for RNA-dependent RNA polymerase (RdRp), N (nucleocapsid) and E (envelope) genes of SARS-CoV-2 that leveraged the viral identification through RT-PCR.[24],[25] Recently, the US Food and Drug Administration (FDA) has accelerated the approval process for COVID-19 diagnosis and declared the emergency usage authorization (EUA) for in vitro diagnostics and the numbers of molecular assays have been approved under conditional authorization.[26]

Other than RT-PCR, some high throughput molecular platforms such as Cobas® 6800 and 8800 systems developed by Roche molecular diagnostics are being used in several countries for SARS-CoV-2 detection. It can perform 1,344 and 3,072 tests in a day, respectively.[9],[27] Another procedure identified is RT-LAMP PCR which has shown 100% sensitivity and specificity in a preliminary study done on 130 patients of SARS-CoV-2.[28] Recently, Abbott laboratories have developed Abbott ID Now; a POCT that can detect RdRp gene of SARS-CoV-2 in just 5 min, it has received FDA-EUA authorization on March 27, 2020.[10],[11]

The numbers of FDA approved molecular and other diagnostic kits are increasing everyday as various laboratories are operational to find out the more testing solution for SARS-CoV-2.[29] Additionally, a kit developed by Laboratory Corporation of America, first of its kind and received FDA approval that allows self-collection of nasal swab specimens at home ensuring comfort and safety of patients.[30] No one-size-fits-all diagnostic kit is available at present; hence, scientists are engaged in inventing new and more effective assays for diagnosis of COVID-19. A paradigm shift from basic molecular PCR technique to highly sensitive novel clustered regularly interspersed short palindromic repeats (CRISPR) technology was witnessed during this pandemic. It has been developed by Sherlock Biosciences and Cepheid.[31] CRISPR is cost effective, portable and temperature stable assay ideal for screening of SARS-CoV-2 infection within 30 min at airports and border crossings.[11],[31] [Figure 1] depicts all available molecular methods for COVID-19 diagnosis.
Figure 1: Depicts available molecular methods for COVID-19 diagnosis

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It is noteworthy that family of coronavirus including SARS-CoV-2 shares the high genetic variability that majorly depends upon fidelity of genes encoding RNA dependent RNA polymerase (RdRp).[32] Over 45,000 genomic sequences were submitted to global initiative on sharing all influenza databases (GISAID till July 2020.[33] This genetic variability may likely restrict virus detection using conventional RT-PCR assays. In such situation, microarrays and next-generation sequencing would be the alternative tools for surveillance and rapid detection of possible genetic variants of SARS-CoV-2.[34] [Table 1] comprises a list of emerging high-throughput molecular techniques for COVID-19 diagnosis.
Table 1: A list of high throughput nucleic acid tests for corona virus disease-19 diagnosis

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  Molecular Techno-Innovations for SARS-CoV-2 Testing in India Top


In India, the Indian Council of Medical Research (ICMR), the apex body for conducting biomedical research in India is actively working in formulating testing guidelines for SARS-CoV-2 infection. Till the time of manuscript writing, a total of 6, 53, 25,779 samples have been tested at 1770 testing centers (1062 Government laboratories and 715 Private laboratories) in India as per ICMR database.[35] ICMR has also build a fast-track system for validation of non US FDA approved kits for SARS-CoV-2 testing at ICMR National Institute for Cholera and Enteric Disease Kolkata, National Institute of Pathology New Delhi, National Institute of Virology (NIV) and National AIDS Research Institute, Pune.[36] NIV, the reference laboratory for viral diagnosis and research in India improved the conventional and real-time PCR assays targeting different genomic regions of SARS-CoV-2 and also serves as the resource center for the virus research and diagnostic laboratories network that provides the technical training for molecular and serological assays. Test kits with 100% concordance among true positive and true negative samples will be approved for commercial use in India.[37] ICMR has granted authorization to various types of molecular testing modalities and till the last week of June 2020, 133 RT PCR non US FDA kits were validated at ICMR centers.[38]

In India, Mylab Discovery Solutions Pvt. Ltd. has developed the first indigenous molecular diagnostic kit for SARS-CoV-2 named Mylab Patho Detect and received approval from ICMR and Central Drugs Standard Control Organization (CDSCO). It shows 100% sensitivity and specificity, reveals test results within 2.5 h.[39] A cost effective, rapid and confirmatory diagnostic test detects SARS-CoV-2 within 2 h invented by SreeChitra Tirunal Institute for Medical Sciences in India. It allows the testing of 30 samples in a single batch thus the large number of samples can be tested in a single day. This kit is highly specific as it detects two regions of N gene which ensures the sensitivity of the assay even after any mutation occurring in region of the N gene;[40] however, the approval for commercialization is pending. Scientists at Institute of Genomics and Integrative Biology have expanded India's first paper-strip test for rapid diagnosis of SARS-CoV-2 within <1 h using CRISPR technology named as FNCAS9 Editor Linked Uniform Detection Assay (Feluda).[15],[41]

Another RT-PCR kit has invented by Bhopal based 3B BLACK BIO Ltd. named as TRUPCR SARS-CoV-2RT-qPCR testing kit. TRUPCR Real-Time assay detects RNA genome of SARS-CoV-2 from a suspected infection patient. This kit has shown 100% concordance among true positive and true negative samples and received the commercial approval from ICMR, NIV and CDSCO. The assay design is based on WHO recommended primers and probes which identifies E, RdRP and N genes of virus in two tube formats. An endogenous internal control RNase P is used to avoid false negativity.[42] Similarly, an in vitro NAT kit for the detection of specific RNA of SARS-CoV-2 has been invented by Chennai based private firm Helini Biomolecules, it enables differentiation between PAN-coronavirus and novel coronavirus 2019.[43] The Indian Institute of Technology, Delhi, an academic and research institute has invented the first probe-free, affordable high throughput, sensitive and scalable assay for rapid diagnosis of SARS-CoV-2 and received the approval from ICMR on April 2020.[44] HUWEL Life Sciences has received the ICMR approval for RT-PCR COVID-19 testing kits which can provide results within 2.5 h.[45] A Faridabad, Uttar Pradesh, India, based company Medsource Ozone Biomedicals Pvt. Ltd. has developed a highly sensitive and specific diagnostic kit which can detect viral load of two genes up to 20 copies/μL and observed no cross reactivity with clinically positive samples of Influenza (A/B/H1N1), Corona Virus and MERS.[46] The one step multiplex, 100% sensitive and specific RT-PCR kit that identifies the viral genome in human serum, nasopharyngeal and throat swab samples was launched by M/s Meril Diagnostics Pvt Ltd. This assay shows the analytical accuracy of 127 RNA copies in single reaction with hands-on time of 65 min.[47] Recently, Genetic Diagnostics and BioGenomics, the two Indian firms have jointly developed RT-PCR testing kit, it shows 100% concordance to true positives and true negatives. The testing kit has received approval from ICMR and NIV.[48] [Table 2] comprises a list of Molecular Diagnostic Kits Developed in India Indigenously. In addition to kit development, the genome sequencing of 881 suspected cases of COVID-19 revealed the presence of two novel genetic variants of SARS-CoV-2 in India, and information on these novel strains was shared with GeneBank and GISAID.[49]
Table 2: Molecular Techno-innoin India indigenously

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In addition to the kits development, Indian scientists have been actively engaged in vaccine development and some targets for Novel inactivated COVID-19 vaccine has been identified at Bharat Biotech International Ltd. in collaboration with ICMR– NIV. The Drugs Controller General of India has gran ted permission to perform phase 1 and 2 clinical trial.[50]


  Limitations and Challenges Top


Timely diagnosis of COVID-19 is the key factor requires for effective management and prevention of the disease. In the context of COVID-19 diagnosis, ramping up the testing facilities and accessibility of population at larger extent are the current needs. USFDA is working on this direction as it has granting EU authorization to various types of testing modalities including rapid immunoassays with certain conditions. At the time of manuscript writing, there were 158 molecular tests and the catalog is available on the official website of USFDA updated regularly.[29] Although molecular methods are highly sensitive, specific and remain the mainstay of COVID-19 diagnosis, these also have some limitations. The development process of PCR tests is complex and expensive process as compared to serological tests. Moreover, the unprecedented global supply of PCR reagents, PCR primers and the positive/internal controls for molecular methods are the major challenges.[51] Various other problems encountered remains throughout the entire testing procedure that begin from the collection of samples from right anatomical site, adherence of safety procedures, lysing the virus, amplification glitches, detection of viral genome, the validation of kit, sensitivity, specificity and irregularity in equipment functioning.[51],[52] Other than these, widespread use and accessibility of molecular tests depends upon availability of special equipment, skilled staff especially in large government hospitals. In addition, funding source and cost involvement for setting up the molecular facilities may also influence the large scale accessibility to molecular testing. In context to cost calculation, a single RT-PCR test kit may cost over 100 USD, while setting up a diagnostic laboratory requires around 15,000 USD[10],[53] which makes it difficult to ramp up the testing facilities in low-middle income countries particularly those which have no indigenous manufacturing capacity for diagnostic tests and supplies purely relies on foreign imports. Time consumption (usually 4–6 h) in standard RT-PCR test comparatively higher than serological tests (up to 45 min) and use of molecular methods for viral genome detection after patient recovery may further limit the use in recurrence of disease as virus in samples is no longer detectable.[54],[55]

India is a low- and middle-income country (LMIC) with approximately 1.33 billion people and having current gross national income per capita of around $2130.[56] The widespread testing of SARS-CoV-2 infection in India remains a challenge as the country's COVID-19 tally is rising exponentially. The country has scientific potential and actively leverages the various technologies for rapid diagnosis of SARS-CoV-2 either molecular or serological. As per the National Health Profile-2019, India is spending only 1.28% of the GDP on the country's health sector[57] that would need to be increased further to accelerate indigenous manufacturing of diagnostic kits and health care devices. To accelerate research on COVID-19 diagnostics in India, recently, under the mentorship of central Government in collaboration with the Department of Biotechnology has launched various funding projects with an aim to accelerate the indigenous manufacturing of COVID-19 diagnostics in India through synchronization of all stakeholders.[58]


  Conclusion Top


The situation regarding COVID-19 is rapidly evolving and dynamic. The pandemic will no doubt change the world in the way we perceive it and working in the postpandemic period will never be the same. Increase in testing has led to the import of some critical reagents, especially the probes which makes the testing expensive. This indeed hinders the wide spread coverage of testing.

In India, there is a widespread network of universities and research intuitions across the country. The number of medical colleges and tertiary care research institutions are also growing gradually. Therefore, the current unprecedented situation created by COVID-19 and future outbreak of any health problem would merely resolve through convergence research. The collective and collaborative efforts of clinicians, basic scientists, technologists, innovative minds, investors, and policy makers of India together may create the sustainable research ecosystem to meet formidable health challenges like COVID-19.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.



 
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