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Friday, February 24, 2017

Mathematics supports a new way to classify viruses based on structure | Science Daily and The Okinawa Institute of Science and Technology

Photo: The Okinawa Institute of Science and Technology

"Professor Robert Sinclair at the Okinawa Institute of Science and Technology Graduate University (OIST) and Professor Dennis Bamford and Dr. Janne Ravantti from the University of Helsinki have found new evidence to support a classification system for viruses based on viral structure." reports ScienceDaily.

Professor Robert Sinclair,
head of OIST’s Mathematical Biology Unit,
holds a model of a Zika virus.
(from left)
Professor Dennis Bamford and
Dr. Janne Ravantti of the
University of Helsinki

The team developed a new highly-sensitive computational prototype tool, and used it to detect similarities in the genetic code of viruses with similar outer structures, that conventional tools have failed to detect, suggesting that they share a common ancestor. This is not what would have been expected if similarities in the structure of viruses were due to similar environmental pressures -- a phenomenon known as convergence.

The results, published in the Journal of Virology, suggest that viral structure could provide a means of categorizing viruses with their close relatives -- a potentially superior approach to current classification systems. Application of this new structure-based classification system could make it easier to identify and treat newly emerging viruses that cannot easily be classified with existing classification systems.

Viruses are notoriously difficult to classify due to their enormous diversity, high rates of change and tendency to exchange genetic material. They challenge the very concept of a clear distinction between the living and the dead, with many characteristics resembling those of living things, but lacking the ability to reproduce themselves, without the help of a host cell. As such, they do not fit neatly into the established biological classification system for cellular organisms.

Existing classification systems are imperfect and often lead to very similar viruses being categorized as entirely different entities. These systems are also unable to account for the fact that viruses are constantly changing.

If scientists could identify something that viruses are unable to change, it could provide a basis for a more meaningful approach to classification and enable the scientific community to tackle emerging viruses, such as HIV, SARS coronavirus and Zika virus, more easily.

Previously observed similarities between the protein shell, or 'capsid', of viruses -- that encloses and protects the genetic material -- provide a basis for a classification system based on capsid structure, as previously proposed by Prof. Bamford. The few ways in which viruses package themselves are very similar, even between viruses that are likely to have had their common relative more than a billion years ago. Whether this conservation is due to convergence or common descent has been disputed.

For a classification system based on virus capsid structure to be meaningful, the amino acids that provide the building blocks of the capsid proteins should be similar in related viruses. A seeming lack of sufficient amino acid sequence similarity picked up by conventional sequence analysis tools previously undermined capsid structure as a viable way to classify viruses.

Using ideas from mathematics and computer science, Professor Sinclair from OIST's Mathematical Biology Unit worked with scientists at the University of Helsinki to reinvestigate whether the structure-based classification for viral capsids is in fact supported by previously undetected sequence similarity.
"The conventional tools for detecting sequence similarity are very fast but they can miss things," says Professor Sinclair. "We used a more classical approach that takes longer but is much more sensitive."

Additional resources
Journal Reference:

1. Robert M. Sinclair, Janne J. Ravantti, Dennis H. Bamford. Nucleic and amino acid sequences support structure-based viral classification. Journal of Virology, 2017; JVI.02275-16 DOI: 10.1128/JVI.02275-16 

Mathematics Supports a New Way to Classify Viruses Based on Structure - The Okinawa Institute of Science and Technology
New research supports a structure-based classification system for viruses which could help in the identification and treatment of emerging viruses.

Source: ScienceDaily and The Okinawa Institute of Science and Technology

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