Through this achievement, the research center seeks to decentralize the management carried out by the Public Health Institute (PHI) in terms of monitoring the geographical and temporal spread of the virus, early detection of mutations that could influence its virulence, and assessing the response to the vaccines used.
Researchers from MELISA Institute Genomics & Proteomics SpA, a biotechnology company and research center located in San Pedro de la Paz, successfully sequenced and for the first time in the region, 48 SARS-CoV-2 RNA samples extracted from nasopharyngeal swabs of patients with COVID-19.
In relation to this, Cristián Vargas, surgeon and CEO of MELISA Institute, expressed: “Being able to execute the complete flow of mass sequencing of SARS-CoV-2 in our research center will allow us to contribute enormously to the medicine of the Region of the Biobío. This event inaugurates the era of personalized precision medicine applied to public health with human and technological capabilities installed in the region. "
Currently, it only remains to be included in the Registry of sequencing capabilities for SARS-CoV-2 Genomic surveillance to be carried out by the Public Health Institute (PHI). Regarding this, Vargas added: "In the next few days we will present the background information to the PHI to begin the accreditation process, which would allow us to process up to 384 samples per week, positioning ourselves as the public or private center with the greatest capacity in the south-central zone of Chile to carry out the genomic monitoring strategy”.
Mutability of the virus
SARS-CoV-2, unlike other viruses composed of RNA (such as HIV or influenza), mutates at a slower rate, since it is able to correct the errors produced in replication. However, as there is a high rate of infection, the chances that after replication there will be a change in some of the components of its nucleic acid increase. In other words, for a new variant to emerge.
These changes that the RNA undergoes are the reason that not all vaccines have the same degree of efficiency against certain variants or that not all diagnostic tests are equally effective.
Broadly speaking, the sequencing process begins with the extraction of SARS-CoV-2 RNA from the nasopharyngeal swabs of patients with COVID-19. To be able to analyze these samples, it is necessary to convert the total RNA of the sample into coding DNA (cDNA). The next thing is to create a large number of copies of the virus cDNA and sequence them. Finally, by means of a bioinformatic analysis it is possible to identify the variants present in the community.
Before carrying out the procedure, researchers from the MELISA Institute were trained in the generation of sequencing libraries and bioinformatic analysis of viral variants at the University of Santiago de Chile (Usach) facilities.
On the other hand, for sequencing they used their Illumina NextSeq 500 system (the only one in mass sequencing of new generation by synthesis available in the south-central macrozone of Chile), libraries of SARS-CoV-2 positive samples carried out at the Usach, in addition to the COVIDSeq kit (validated by the FDA for the study of new variants) delivered by the company Arquimed. Likewise, the analysis of the variants was carried out through the Nextclade and Pangolin platforms, obtaining results that were reproducible to those carried out in Santiago.
This achievement will improve the genomic monitoring capacity and with it, the response and defense protocols against COVID-19. Along these lines, Vargas concluded: “The sequencing of SARS-CoV-2 variants carried out by the team of scientists from the MELISA Institute will contribute to the monitoring of the geographical and temporal spread of the virus, to the early detection of mutations that could influence the virulence and evaluate the response to vaccines, thus complying with the recommendation to sequence between 5% and 10% of positive samples made by the WHO and the member states of the European Community. "