COVIPRIM_VAR2 - Monitoring of the whole genome sequencing (WGS) data of SARS-CoV-2 genomes to identify variants and their impact on detection methods

Last updated on 9-3-2021 by Mathieu Gand
February 1, 2021
December 31, 2021

Financial Source

In short

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic. Its presence is currently mostly detected by a molecular test called PCR. As the virus can evolve with time, as shown with the recent emergence of news variants in United Kingdom, South Africa and Brazil, it is of major importance to evaluate if SARS-CoV-2 can still be correctly detected by PCR methods, for accurate COVID-19 diagnosis and surveillance, to limit its spread.

Project summary

The Severe Acute Respiratory Syndrome related CoronaVirus 2 (SARS-CoV-2) is the virus responsible for the current COronaVIrus Disease 2019 (COVID-19) pandemic. The gold-standard method for COVID 19 diagnosis and SARS-CoV-2 surveillance (e.g. in wastewater) is the detection of viral RNA in various samples by Retro Transcription real-time PCR (RT-qPCR). The principle of this test is to detect small regions of the viral genome, specific for SARS-CoV-2, with a set of primers and probe. 

This detection is very important for: 

  • establishing a correct diagnosis so that patients can be given proper medical assistance
  • the control, containment and surveillance of SARS-CoV-2. It is important that COVID-19 positive cases are identified

Viruses constantly change through mutation, and new variants of a virus are expected to occur over time. New SARS-CoV-2 variants, carrying an abnormal number of mutations, have recently emerged in the United Kingdom, South-Africa and Brazil. These variants are considered as of concern because some of their mutations are estimated to enhance virus transmissibility and to have a potential effect on the immunological response and vaccine efficiency. Another consequence of SARS-CoV-2 mutations is that, if they are located in genomic regions targeted by the RT-qPCR tests, this can lower the performance of the test or result in a total test failure. The associated risk is that patients are misdiagnosed and do not receive the proper care, or do not go into quarantine, thus contributing to the further spread of the virus. It is therefore important to continuously verify that the PCR methods used to detect SARS-CoV-2 are still performing well.

In 2020, in the context of the COVIPRIM project, a research team of Sciensano was able to perform a preliminary in silico evaluation of 30 RT qPCR primers and probe sets used worldwide for SARS-CoV-2 detection, based on more than 4750 publically available genome sequences of the virus. In this study, it was assessed whether some mutations could potentially affect the correct detection of the SARS-CoV-2 strains circulating at that time. As new SARS-CoV-2 sequence data are continuously uploaded to the genomic databases (more than 400 000 genomes are now available), the same methodology is applied in 2021 in this COVIPRIM_VAR2 project. Here, we evaluate the in silico RT-qPCR tests’ performance on a regular basis, especially in the context of the emerging variants. Furthermore, it is important to verify if PCR based methods can be employed, as first line screening assays, to specifically and rapidly identify those variants. For doing this, COVIPRIM_VAR2 provides evidence-based results.  Using the several thousand SARS-CoV-2 genomes already publicly available, it is assessed if a specific genetic variation is representative of a variant and can be used as a target in a molecular method. This information will then be shared with the DIGICOVID_VAR2 project, in order to develop the corresponding dPCR assays.
 

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