COVID-19 (SARS-CoV-2) Surveillance

Identification and prevention of future coronavirus threat

  • In India, from 3 January 2020 to 1 July 2021, there have been 30,411,634 confirmed cases of COVID-19 with 399,459 deaths, reported to WHO.[3]

  • The world is now facing an unprecedented crisis due to the novel variants of coronavirus. There are no specific treatments for coronaviruses to date.

  • Scientists are working to understand several novel coronavirus variants now circulating in India, where a ferocious second wave of COVID-19 has devastated the nation and caught authorities unawares. The country recorded nearly 400,000 new infections on 9 May 2021. [1]

  • The U.S. Food and Drug Administration (FDA) is alerting clinical laboratory staff and health care providers that false-negative results may occur with any molecular test for the detection of SARS-CoV-2.[2]

Covid-19 Statistics of India

COVID-19 Surveillance
  • Real-Time RT-PCR and antibody-based methods are the main tools for detecting infectious agents, however, such methods can only focus on a limited number of targets and can at times suffer from low assay sensitivity and false-negative results. These methods only provide qualitative diagnoses. Whole-genome sequencing of SARS-CoV-2 via NGS allows you to confirm the results of RT PCR and it helps you to detect new emerging variants.

  • Next-generation sequencing (NGS) technologies are now challenging current molecular technologies as the tool of choice for genome analysis. The ability to sequence genetic material at full-genome depth will change the types of questions that we ask in many disciplines of biology.

NGS Complements the Existing Molecular Technologies for Covid-19 Surveillance.

  • Track the transmission routes of the virus globally

  • Detect mutations quickly to prevent the spread of new strain types

  • Identify viral mutations that can avoid detection by established molecular diagnostic assays

  • Identify viral mutations that can affect vaccine potency

  • Screen targets for possible COVID-19 therapeutics

  • Identify and characterize respiratory co-infections and antimicrobial resistance alleles​

NGS opening doors for vast genomic applications

NGS workflow for COVID-19

RNA extraction

Reverse Transcription

Library Preparation

Sequencing

Data Analysis

Figure: Background cleaning chemistry with and without CleanPlex digestion. Efficient background removal achieved with CleanPlex digestion.

Figure: Low viral copy number of 20 and high viral copy number of 230,000 both through CleanPlex SARS-CoV-2 NGS Panel are showing high genome coverage i.e, Approx. 100%.

To overcome shortcomings in existing target enrichment techniques and to bridge the gap between amplicon- and hybrid capture-based methods, scientists at Paragon Genomics have developed the CleanPlex® technology to provide a better tool to prepare NGS libraries for targeted sequencing. This technology is an ultra-high multiplex PCR-based target enrichment method that features a proprietary background cleaning chemistry, which allows tens of thousands of amplicons to be pooled in one reaction to target genomic regions as large as a few megabases in size.

Case Study

Prof. Hakan Akca from Pamukkale University, Turkey, performed whole-genome sequencing on 15 COVID-19 positive patients using CleanPlex SARS-CoV-2 Panel . They identified 32 missense, 21 synonymous, and 4 non-coding allele mutations. Out of the missense mutations identified, 11 were rare missense mutations in the virus compared to the reference genome. Phylogenetic analysis revealed that most of the isolates were similar to European sequences. The phylogenetic tree constructed with all the complete SARS-CoV-2 genomes of Turkey showed that the viruses were spread nearly homogenous on eastern and western sides of Turkey.

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