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An international team of researchers has discovered an unknown hidden gene in SARS-CoV-2, which could contribute to the pandemic scale of viral infection. Scientific work published on eLife is summarized in a press release on Phys.org.
Scientists have designated the new gene that overlaps other genes as ORF3d. It is also present in the previously discovered pangolin coronavirus. Furthermore, ORF3d is capable of eliciting a strong antibody response in patients with COVID-19, which means that it encodes a protein produced during human infection. Furthermore, it is unrecognizable to immune T cells, and experts believe this may provide the coronavirus with benefits that have played a role in enhancing the pandemic potential.
The coronavirus RNA genome contains about 15 genes – regions of RNA where the amino acid sequence of a particular protein is encoded. Each amino acid corresponds to a certain combination of three nucleotides, called triplets. A triplet sequence that can encode a protein is called an open reading frame (ORF). However, a situation can arise where a shift of one or two nucleotides generates a new reading frame within the gene, which codes for a completely different amino acid sequence. Overlapping ORFs are quite rare, but they increase the number of proteins that viruses can synthesize.
ORFs are generally defined by triplets called start and end codons. They show you where to start reading information for protein synthesis and where to stop synthesis. However, sometimes adjacent nucleotides from different triplets purely randomly form a characteristic combination of such codons. This makes it difficult to find overlapping ORFs.
Scientists turned their attention to ORF3d because it encodes a peptide chain that is too long compared to a random read frame. The existence of a sufficiently large ORF usually indicates the existence of a gene in this region of the DNA or RNA (in the case of coronaviruses).
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