Researchers have discovered a new “hidden” gene SARS-CoV-2 -Causes a virus Coronavirus disease -May have contributed to its unique biology and pandemic potential. In a virus with only about 15 genes in total, knowing more about this gene and other overlapping genes (or “genes within genes”) may have a major impact on how we fight the virus.Described this new gene in the magazine today Electronic life.
“Overlapping genes may be one of the means by which the coronavirus evolves to effectively replicate, hinder the host’s immunity or spread itself,” said Chase Nelson, a postdoctoral researcher at the Academia Sinica in China and a visiting researcher at the Academia Sinica in Taiwan. American Museum of Natural History. “Knowing the existence of overlapping genes and how they function may reveal new ways to control the coronavirus, such as through antiviral drugs.”
The research team identified ORF3d, a new overlapping gene in SARS-CoV-2, with the potential to encode proteins that may be longer than expected by chance. They found that this gene is also present in the previously discovered pangolin coronavirus, which may reflect the repeated loss or acquisition of this gene in the evolution of SARS-CoV-2 and related viruses. In addition, ORF3d has been independently identified and shown to cause a strong antibody response in COVID-19 patients, indicating that the protein of this new gene is produced during human infection.
Nielsen said: “We don’t yet know its function or whether it has clinical significance.” “But we predict that compared with antibody response, this gene is relatively unlikely to be detected by T cell response. Perhaps this is related to the way the gene is produced. related.”
At first glance, genes look like written language because they are made up of strings of letters (in Ribonucleic acid Viruses, the nucleotides A, U, G and C that convey information). However, although the units of language (words) are discrete and non-overlapping, genes can overlap and are multifunctional, and the way information is encrypted depends on where you start “reading”. Overlapping genes are difficult to find, and most scientific computer programs are not designed to find them. However, they are very common in viruses. Part of the reason is that RNA viruses have a high mutation rate, so they tend to keep their gene counts low to prevent large numbers of mutations. As a result, the virus has developed a data compression system in which a letter in the genome can contribute two or even three different genes.
Nielsen said: “The lack of overlapping genes puts us in danger of ignoring important aspects of virus biology.” In terms of genome size, SARS-CoV-2 and its relatives are among the longest existing RNA viruses. Therefore, they may be more prone to “genome deception” than other RNA viruses. “
Before the pandemic, while working as a Gerstner scholar in bioinformatics and computational biology at the museum, Nelson developed a computer program to screen the genome for patterns of genetic changes unique to overlapping genes.In this study, Nielsen worked with the Technical University of Munich and UC Berkeley, In order to apply this software and other methods to a large amount of new sequence data that can be used for SARS-CoV-2. The team hopes that other scientists will investigate the genes they found in the laboratory to define their functions and possibly determine their possible role in the emergence of a pandemic virus.
References: Chase W Nelson, Zachary Ardern, Tony L Goldberg, Chen Meng, Chen-Hao Kuo, Christina Ludwig, Sergios-Orestis Kolokotronis, and Xinzhu Wei, “The dynamically evolving new overlapping gene is one of the SARS-CoV-2 pandemics Factors” October 1, 2020, Electronic life.
DOI: 10.7554 / eLife.59633
Funding for this work was partly provided by the Academia Sinica, the Bavarian State Government and the 12 National Charitable Foundations, the National Science Foundation (Grant Nos. 1755370 and 1758800, and the University of Wisconsin-Madison).