A bank of molecular signatures has been constructed that will help identify the severity of virus infection from characteristic changes seen in cells.

Changes in lung cells infected with swine flu from the 2009 outbreak compared with seasonal flu have been investigated using a technique called stable isotope labeling by amino acids in cell culture (SILAC) to measure and compare thousands of different proteins in a sample.

A team of scientists at the University of Leeds (UK) working with others from the Health Protection Agency (Porton Down, UK) used the SILAC alongside mass spectrometry to identify the proteins most affected by viral infection and used these as molecular signatures to provide the “barcode” of disease.

The study revealed how several processes in the cell were affected by the virus, with most changes seen in proteins involved in cell replication. A total of 1,427 cellular proteins were identified by two or more peptides. Studies using SILAC-based quantitative proteomics vary in the cut off value used to analyze increases and decreases in the abundance of proteins. The abundance of proteins involved in mediating antiviral responses was changed in Influenza A Virus infected cells and several integrins were decreased in abundance in virus-infected cells. Taken together, both quantitative proteomics and transcriptomic approaches can be used to identify potential cellular proteins whose functions in the virus life cycle could be targeted for chemotherapeutic intervention.

Dr John Barr, one of the senior authors, said, "Swine flu affects the lungs in a similar way to seasonal flu and this was reflected in the barcodes we found for each. Using this test might have been a way to identify how lethal the 2009 swine flu pandemic was going to be, lessening worldwide panic. Our next step is to test more lethal strains of flu, such as bird flu, to see how the barcodes differ. Flu virus frequently mutates, resulting in new strains, which may be life threatening and become pandemic. If we can test new strains using our method, we can determine their potential impact on health by comparing their barcode of disease to those of viruses already studied." The study was published on May 14, 2012, in the journal Proteomics.

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