Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology

Background: Despite the passing of more than a year since the first outbreak of Severe Acute Respiratory Syndrome (SARS), efficient counter-measures are still few and many believe that reappearance of SARS, or a similar disease caused by a coronavirus, is not unlikely. For other virus families like the picornaviruses it is known that pathology is related to proteolytic cleavage of host proteins by viral proteinases. Furthermore, several studies indicate that virus proliferation can be arrested using specific proteinase inhibitors supporting the belief that proteinases are indeed important during infection. Prompted by this, we set out to analyse and predict cleavage by the coronavirus main proteinase using computational methods. Results: We retrieved sequence data on seven fully sequenced coronaviruses and identified the main 3CL proteinase cleavage sites in polyproteins using alignments. A neural network was trained to recognise the cleavage sites in the genomes obtaining a sensitivi...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom
• Keywords: BMCBI 2004, Cleavage Sites, Coronavirus, Severe Acute Respiratory Syndrome