A few months after the announcement of the Covid-19 pandemic, in early 2020, scientists sequenced the genome of the virus, SARS-CoV-2, but many of the protein coding genes remain unknown. Now, the study of comparative genomics has made it possible to create the most accurate and complete genetic map of the virus.
Made by researchers from Massachusetts Institute of Technology (MIT) And it was published on Tuesday in the magazine Nature Communications, The study confirmed several protein-coding genes and found that others – which have been proposed as genes – did not code for any protein.
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Says Manolis Kelis, lead author of the study and professor of computer science at the Massachusetts Institute of Technology, and a fellow of the Broad Institute of Massachusetts Institute of Technology and Harvard University.
In the second part of the study, the research team also analyzed nearly 2,000 mutations that have appeared in SARS-CoV-2 since the outbreak of the epidemic, allowing them to assess the significance of these mutations and their ability to avoid infection. The immune system becomes more or more contagious.
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With approximately 30,000 bases of RNA, the SARS-CoV-2 genome was known to contain many regions coding for protein genes and other genes suspected but not definitively classified. To determine which parts of the SARS-CoV-2 genome actually contain the genes, the researchers turned to comparative genomics, comparing SARS-CoV-2 (which belongs to a subspecies of viruses called Sarbecovirus, which infects bats) with SARS-CoV (which caused it). In the 2003 SARS outbreak) and 42 strains of the sorbic bat virus.
Thus, they confirmed six protein-coding genes in the SARS-CoV-2 genome, in addition to the five genes that are anchored in all coronaviruses. They also determined that the region encoding a gene called ORF3a also encodes an additional gene, ORF3c, which contains RNA bases that interfere with ORF3a, but that in a different reading frame, it is rare in large genomes, but common in many viruses, in the case of SARS-CoV-2. His job is not yet known.
The researchers also showed that five other regions have been proposed as potential genes that do not code for functional proteins, and they ruled out that other regions remain to be explored.
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In addition, the authors found that many of the earlier works not only used incorrect gene combinations, but also sometimes contradictory names, so, in a parallel article recently published in the Journal of Virology, they made recommendations for naming SARS genes. -CoV-2.
In the study, the researchers also analyzed more than 1,800 mutations that appeared in SARS-CoV-2 and found that in most cases, the genes that evolved rapidly before the epidemic continued to do so, and those that tended to evolve slowly they maintained that trend.
They also looked at mutations that arose in variants of concern, such as the British, Brazilian, and South African strains, and found that many of the mutations that make these variants more dangerous are present in the spike protein, helping the virus to spread rapidly and bypass the immune system.
However, each of these variants has “more than 20 other mutations, and it is important to know which ones can do something and which ones cannot,” says Erwin Jongres, lead author of the study and a researcher at MIT. For the authors, this data could help other scientists focus their attention on the mutations that seem to have the most important effects on virus infection.
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