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Variations in diagnostic methods for newer COVID-19 variants

Healthcare establishments and research centres have come up with better strategies to tackle the fast spreading SAR-CoV-2 virus and accordingly, the virus found a way to survive through mutating itself. This gave rise to new variants of concern that have defied diagnosis and management methods which has led to developing newer methods to detect and thus, curtail further COVD-19 infections. 

MedPiper Technologies and JournoMed along with the All India Institute of Hygiene and Public Health had conducted a webinar on 7th December, 2021, titled “Newer Alternatives for Diagnosis and Management of COVID-19” where expert speaker, Dr. Sayan Bhattacharya elaborated on the recent treatment strategies for detecting and treating the upcoming strains of the COVID-19 virus. Dr. Sayan Bhattacharya is the Assistant Professor at the Department of Microbiology, All India Institute of Hygiene and Public Health, Kolkata and the Chief Editor, Eastern Journal of Medical Sciences.

Dr. Bhattacharya focussed on the methods that can detect the latest “Variant of Concern”, the Omicron Variant. The Omicron Variant is tricky to decipher as it has upto 30 mutations in the spike protein and is not easily detected through the established RT-PCR test. The main concern regarding this variant is that the established vaccines fail to protect against it, as almost 50% of the omicron strain infections have occurred in vaccinated individuals. The Omicron strain is suspected to have risen from genetic reassortment with the Deer coronaviruses and was first detected in South Africa. 

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The virus can be detected by either determining the amount of viral RNA from the antigen (via nasopharyngeal swabs) or neutralising antibodies against the virus (via blood samples). The detection can be done using point of care tests which don’t require any sophisticated equipment. Each point of care tests are authorised for certain specimen types and should only be used for those specimen types. Some of these tests that help to detect the newer COVID-19 strains are: 

  1. RT-PCR: An RT-PCR (Reverse Transcriptase Polymerase Chain Reaction) test looks for the load of the Spike Protein gene (S), the Nucleocapsid gene (N2) and the RNA polymerase gene (RDP). With the omicron variant, there is an S-gene dropout (which was also seen in the alpha variant), as the test is unable to identify the Spike Protein mutation. If the S-gene is not  detected in an RT-PCR test, there is a possibility that it could be the omicron variant. 
  2. Rapid Antigen Test: This is a test that is cheap and can be easily done at home. However it lacks sensitivity.
  3. CB-NAAT and True NAAT: Nucleic Acid Amplification Tests (NAAT), whether it be cartridge based or otherwise, can detect the viral RNA within 15 to 20 minutes. These tests are portable and run on battery. True NAAT can also help to detect other types of diseases and is advised by the ICMR for the detection of the SARS-CoV-2 virus. 
  4. SMART Test: Researchers from the Antimicrobial Resistance Interdisciplinary Research Group at the Singapore-MIT Alliance for Research and Technology (SMART) developed a new kind of rapid test that detects the neutralising antibodies against the SARS-CoV-2 virus from the blood or serum sample of the patient. The drawback of this test is that it may not indicate neutralising antibodies are present due to an active infection or from a previous infection. 
  5. Lateral Flow Tests: Test kits such as Mylab’s Coviself, and Abbott’s BinaxNow can help to detect the infection but cannot confirm the variant. These tests give results in 15-20 mins and can be done at home. Electrochemical sensors are also used to confirm the infection. 
  6. RT-LAMP test: The Reverse Transcriptase Loop Mediated Isothermal Amplification Test follows the sample principles of an RT-PCR test. The Reverse Transcriptase enzyme converts the SARS-CoV-2 RNA to cDNA which is amplified at a single temperature of 65℃ (isothermal), unlike PCR where three different temperatures are used. The RT-LAMP is a single step process and is thus more advantageous over the PCR method. 
  7. FELUDA test: FELUDA stands for FNCas9 Editor Limited Uniform Detection Assay is a CRISPR Cas9 based rapid test developed by the TATA Group and launched by the DCGI. The FELUDA Test combined with HybriDirect assay can decode the genomic sequence and thus identify the variant.
  8. SHERLOCK test: Specific High-Sensitivity Enzymatic Reporter Unlocking (SHERLOCK) is a Cas12 based test that detects the S-gene of the virus. 
  9. Use of Animals: Dogs can be trained to sniff out the Volatile Organic Compound that is generated from SARS-CoV-2 positive samples. However, the sensitivity and specificity of this test is very low. 
  10. Genome Sequencing: Many of the above tests can identify the infection but not the variant. Genome sequencing is required to confirm the variant and this method is only done in a few institutions throughout the country. 

Treatment options for the developing strains: 

Molnupiravir, previously used to treat influenza, is now repurposed to treat COVID-19 as it interferes with SARS-CoV-2 viral replication. This drug  is 50% effective in reducing hospitalisation and death, however it is mutagenic. Paxlovid, an investigational drug, is also capable of inhibiting viral replication at the proteolytic step in the cycle and is given along with Ritonavir. Paxlovid is so far 89% effective in reducing hospital admissions and death and is not mutagenic. Amlodipine is another drug that is helpful in treating COVID-19 in hypertension patients. 

The SARS-CoV-2 virus has drastically changed the way of life since it was first identified in March 2020 and researchers are working to keep up with the structural mutations of the virus so as to avoid claiming any more lives through future pandemic waves. Newer treatments and diagnostic methods have to be updated as newer aspects of the virus are being uncovered. 

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