The Virus Analysis Tool (VAT) - A computational tool for the characterisation and monitoring of viruses during an acute outbreak
Lead Research Organisation:
University of Kent
Department Name: Sch of Biosciences
Abstract
A main limitation of the response to novel virus outbreaks is the lack of information. While virus identification by next generation sequencing is quick, the investigation of the clinical and biological virus properties takes much longer. Moreover, methods for the early detection of novel virus strains with changed pathogenicity, transmissibility, drug sensitivity, and/ or immunogenicity are needed. Computational approaches have the potential to fill these gaps. We have created a method that identifies determinants of virus behaviour by identifying amino acid sequence positions that are differently conserved between related viruses and subsequent computational modelling of their impact on protein structure/ function. Our research has already identified substantial differences between SARS-CoV-2 and SARS-CoV. Although SARS-CoV-2 and SARS-CoV share a sequence identity of about 80%, the majority of the remaining positions are differentially conserved, which is reflected in differences in clinical behaviour, cell tropism, and drug sensitivity. Here, we will develop this approach into a webserver (the 'Virus Analysis Tool', VAT) that can be used by everyone involved in SARS-CoV-2 research and treatment. In the current outbreak, VAT will enable researchers to compare the genomic sequences of novel SARS-CoV-2 isolates to those of other SARS-CoV-2 strains and to identify novel strains rapidly, which are likely to be characterised by changes in phenotype, for example in disease severity, drug sensitivity, or immunogenicity. Hence, VAT will be a tool for the effective monitoring of the emergence of novel virus variants. VAT will also increase our preparedness for future virus outbreaks.
Organisations
Publications
Bojkova D
(2021)
Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour.
in Bioinformatics (Oxford, England)
McLaughlin K
(2021)
A Potential Role of the CD47/SIRPalpha Axis in COVID-19 Pathogenesis
in Current Issues in Molecular Biology
Description | Previously, we have established a method to identify differences between related viruses that explain differences in their behaviour, for example, why some members of a virus family cause disease in humans but others do not. In this project, we developed this approach into a web tool so that it can be applied by other research groups on questions they are interested in. |
Exploitation Route | The resulting web tool can be used by research groups for the investigation of research questions of their interest. |
Sectors | Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology |
URL | https://www.wass-michaelislab.org/cat/ |
Description | The findings have attracted significant public and media interest and fostered public engagement. |
Sector | Pharmaceuticals and Medical Biotechnology |
Impact Types | Societal |
Title | CAT - Coronavirus Analysis Tool |
Description | This is a tool for the identification of mechanistically relevant differences between coronaviruses with different phenotypes (e.g. pathogenicity in humans). |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | First comparisons of SARS-CoV, the coronavirus that caused SARS, and SARS-CoV-2, the coronavirus that causes COVID-19, revealed that drug discovery approaches need to be performed using SARS-CoV-2 and not other coronaviruses as model systems. |
URL | https://www.wass-michaelislab.org/cat/ |
Description | Article in BuzzFeed News |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Interview with BuzzFeed News |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.buzzfeednews.com/article/danvergano/coronavirus-treatments-antivirals-fauci |
Description | BBC Radio Kent interview |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | BBC Radio Kent interview |
Year(s) Of Engagement Activity | 2021 |
Description | Ebiotrade article |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Ebiotrade article |
Year(s) Of Engagement Activity | 2021 |
URL | http://www.ebiotrade.com/newsf/2021-2/20210216081232303.htm |
Description | EurekaAlert release |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | EurekaAlert release |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.eurekalert.org/pub_releases/2021-02/uok-nss021121.php |
Description | ExBulletin article |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Article about research and the impact on the discovery of drugs against to COVID-19. |
Year(s) Of Engagement Activity | 2021 |
URL | https://exbulletin.com/world/health/777977/ |
Description | FR24News |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Article in FR24News |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.fr24news.com/fr/a/2021/03/pourquoi-navons-nous-pas-plus-de-medicaments-covid-19.html |
Description | Frankfurter Allgemeine Zeitung articlw |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Newspaper article |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.faz.net/aktuell/rhein-main/region-und-hessen/protein-analysen-zeigen-unterschiede-zwisch... |
Description | Infosurhoy article |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Infosurhoy article |
Year(s) Of Engagement Activity | 2021 |
URL | https://infosurhoy.com/health/new-study-suggests-better-approach-in-search-for-covid-19-drugs.html |
Description | KMTV interview |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | KMTV interview |
Year(s) Of Engagement Activity | 2021 |
Description | MedicalXpress article |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | MedicalXpress article |
Year(s) Of Engagement Activity | 2021 |
URL | https://medicalxpress.com/news/2021-02-approach-covid-drugs.html |
Description | Press release |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Press release |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.kent.ac.uk/news/science/27826/new-study-suggests-better-approach-in-search-for-covid-19-... |
Description | Scienmag article |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Scienmag article |
Year(s) Of Engagement Activity | 2021 |
URL | https://scienmag.com/new-study-suggests-better-approach-in-search-for-covid-19-drugs/ |
Description | VarietyInfo Article |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | VarietyInfo article. |
Year(s) Of Engagement Activity | 2021 |
URL | https://verietyinfo.com/germany/warum-haben-wir-nicht-mehr-covid-19-medikamente/ |