[{"command":"openDialog","selector":"#drupal-modal","settings":null,"data":"\u003Cdiv id=\u0022republish_modal_form\u0022\u003E\u003Cform class=\u0022modal-form-example-modal-form ecl-form\u0022 data-drupal-selector=\u0022modal-form-example-modal-form\u0022 action=\u0022\/en\/article\/modal\/7221\u0022 method=\u0022post\u0022 id=\u0022modal-form-example-modal-form\u0022 accept-charset=\u0022UTF-8\u0022\u003E\u003Cp\u003EHorizon articles can be republished for free under the Creative Commons Attribution 4.0 International (CC BY 4.0) licence.\u003C\/p\u003E\n \u003Cp\u003EYou must give appropriate credit. We ask you to do this by:\u003Cbr \/\u003E\n 1) Using the original journalist\u0027s byline\u003Cbr \/\u003E\n 2) Linking back to our original story\u003Cbr \/\u003E\n 3) Using the following text in the footer: This article was originally published in \u003Ca href=\u0027#\u0027\u003EHorizon, the EU Research and Innovation magazine\u003C\/a\u003E\u003C\/p\u003E\n \u003Cp\u003ESee our full republication guidelines \u003Ca href=\u0027\/horizon-magazine\/republish-our-stories\u0027\u003Ehere\u003C\/a\u003E\u003C\/p\u003E\n \u003Cp\u003EHTML for this article, including the attribution and page view counter, is below:\u003C\/p\u003E\u003Cdiv class=\u0022js-form-item form-item js-form-type-textarea form-item-body-content js-form-item-body-content ecl-form-group ecl-form-group--text-area form-no-label ecl-u-mv-m\u0022\u003E\n \n\u003Cdiv\u003E\n \u003Ctextarea data-drupal-selector=\u0022edit-body-content\u0022 aria-describedby=\u0022edit-body-content--description\u0022 id=\u0022edit-body-content\u0022 name=\u0022body_content\u0022 rows=\u00225\u0022 cols=\u002260\u0022 class=\u0022form-textarea ecl-text-area\u0022\u003E\u003Ch2\u003ECovid-19: How unprecedented data sharing has led to faster-than-ever outbreak research\u003C\/h2\u003E\u003Cp\u003EWhen the new coronavirus (formally known as SARS-CoV-2) was identified in China in January, scientists around the world were ready to respond. The virus\u2019s entire genetic makeup, or genome, was published \u003Ca href=\u0022https:\/\/www.thelancet.com\/journals\/lancet\/article\/PIIS0140-6736(20)30251-8\/fulltext\u0022 target=\u0022_blank\u0022 rel=\u0022noopener noreferrer\u0022\u003Eonline\u003C\/a\u003E within days. By comparison, during the SARS coronavirus outbreak in 2003, this took almost three months, after the disease was \u003Ca href=\u0022https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1550436\/\u0022 target=\u0022_blank\u0022 rel=\u0022noopener noreferrer\u0022\u003Eoriginally blamed on chlamydia\u003C\/a\u003E.\u003C\/p\u003E\u003Cp\u003EAdvances in the technology have brought down the cost of gene sequencing significantly and the machines are now small enough to fit in the palm of your hand. This has made it easier for a large number of samples to be sequenced around the world.\u003C\/p\u003E\u003Cp\u003E\u2018You can see from the sequences how the virus spreads, the speed at which it\u0027s spreading and estimate the number of people that are infected. As we get more and more sequences, the more and more accurate the numbers are,\u2019 said Professor Anne-Mieke Vandamme from KU Leuven, Belgium.\u003C\/p\u003E\u003Cp\u003ENext-generation sequencing, or NGS, can generate enormous amounts of data, and the challenge becomes finding ways to analyse it properly.\u003C\/p\u003E\u003Cp\u003EIn 2015, Prof. Vandamme led a project called \u003Ca href=\u0022https:\/\/cordis.europa.eu\/project\/id\/634650\/en\u0022 target=\u0022_blank\u0022 rel=\u0022noopener noreferrer\u0022\u003EVIROGENESIS\u0026nbsp;\u003C\/a\u003Eto develop new tools to help analyse and interpret the data that comes from sequencing, particularly for laboratories that were not used to dealing with sophisticated genetic analysis.\u003C\/p\u003E\u003Cp\u003E\u2018When we were doing the project, there were only mainly research labs that had NGS. Now everyone has NGS,\u2019 she said.\u003C\/p\u003E\u003Cp\u003EOne of the tools developed, called \u003Ca href=\u0022https:\/\/www.genomedetective.com\/\u0022 target=\u0022_blank\u0022 rel=\u0022noopener noreferrer\u0022\u003EGenome Detective\u003C\/a\u003E, can take the raw data from the sequencing machine, filter out results from non-viruses, piece together the genome and use that to identify the virus. It does not rely on any prior guesses or hypotheses, so it can even identify viruses that have not been seen before. This was used to confirm the first case of COVID-19 in Belgium, identifying it as a SARS-related coronavirus.\u003C\/p\u003E\u003Cp\u003E\u003Cblockquote class=\u0022tw-text-center tw-text-blue tw-font-bold tw-text-2xl lg:tw-w-1\/2 tw-border-2 tw-border-blue tw-p-12 tw-my-8 lg:tw-m-12 lg:tw--ml-16 tw-float-left\u0022\u003E\n \u003Cspan class=\u0022tw-text-5xl tw-rotate-180\u0022\u003E\u201c\u003C\/span\u003E\n \u003Cp class=\u0022tw-font-serif tw-italic\u0022\u003E\u2018You can see from the sequences how the virus spreads, the speed at which it\u0026#039;s spreading and estimate the number of people that are infected.\u2019\u003C\/p\u003E\n \u003Cfooter\u003E\n \u003Ccite class=\u0022tw-not-italic tw-font-normal tw-text-sm tw-text-black\u0022\u003EProfessor Anne-Mieke Vandamme, KU Leuven, Belgium\u003C\/cite\u003E\n \u003C\/footer\u003E\n\u003C\/blockquote\u003E\n\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EOnline sharing\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003EThe power of gene sequencing comes from comparing the results across different cases. Prof. Vandamme says that it has been \u2018fantastic\u2019 to see the level of collaboration internationally: \u2018There is a lot more online sharing of data and sequences ... compared to the past because we have a lot more online sharing tools available.\u2019\u003C\/p\u003E\u003Cp\u003EOne of these tools is \u003Ca href=\u0022https:\/\/nextstrain.org\/\u0022 target=\u0022_blank\u0022 rel=\u0022noopener noreferrer\u0022\u003ENextStrain\u003C\/a\u003E, an online resource that uses genome data to monitor the evolution of disease-causing organisms such as viruses in real time. It has tracked several outbreaks including Zika, Ebola and Dengue and has even been used to inform World Health Organization policy on seasonal flu.\u003C\/p\u003E\u003Cp\u003EResearch papers typically take months to be published \u2013 an aeon in the current race to tackle the pandemic. The need to share information quickly has encouraged greater sharing of \u2018preprints\u2019, drafts of papers that have not yet been through peer review.\u003C\/p\u003E\u003Cp\u003E\u2018The push towards open science, open data and preprinting has really changed the way we experience the scientific discourse in this outbreak compared to previous ones,\u2019 said Professor Richard Neher, from the University of Basel, Switzerland, who leads the NextStrain project.\u003C\/p\u003E\u003Cp\u003ENextStrain already has over 700 genomes of the new coronavirus, which it can use to trace the outbreak by detecting new mutations in the virus. The mutations do not necessarily affect how the virus behaves, but they can act as a genetic signature to link cases that are related. Like tracing your ancestry through a DNA test, a virus sequenced in Madrid, for instance, could have mutations that suggest it originated from an outbreak in Italy.\u003C\/p\u003E\u003Cp\u003E\u2018In the current pandemic, it gives us a lower bound on how often the virus has been introduced to a specific location,\u2019 Prof. Neher said.\u003C\/p\u003E\u003Cp\u003ENextStrain publishes a weekly situation report that analyses these trends. The team was able to estimate that the \u003Ca href=\u0022https:\/\/nextstrain.org\/narratives\/ncov\/sit-rep\/2020-03-13?n=6\u0022 target=\u0022_blank\u0022 rel=\u0022noopener noreferrer\u0022\u003Eoutbreak in Iran\u003C\/a\u003E may have been introduced by a single person, whereas at least four different introductions were responsible for the outbreak in the UK, as of 13 March.\u003C\/p\u003E\u003Cp\u003E\u2018(Sequencing cases) will become even more important because as we start cracking down on (the pandemic), which we hopefully will achieve, it will tell us how many transmission chains are still circulating and whether the virus is being transported from one region to another,\u2019 said Prof. Neher.\u003C\/p\u003E\u003Cp\u003EHe believes that, as the virus continues to spread, it will accumulate more genetic diversity and it will give us more information on how the virus is being transmitted.\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EGenetic blueprint\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003EDespite the genetic blueprint of the new coronavirus being readily available, it still does not tell us very much about how it differs from other coronaviruses. Much of what we know has come from seeing how it has spread through the population. It is now clear how different it is to previous coronavirus outbreaks, such as SARS and MERS.\u003C\/p\u003E\u003Cp\u003E\u2018They were certainly much less easy to transmit, and also had a very different presentation in that only a few people were asymptomatic. One of the many challenges that we are facing here is that people that have only very mild symptoms have been substantial in transmitting this virus,\u0027 said Prof. Neher.\u003C\/p\u003E\u003Cp\u003E\u2018That is much harder to control because you have to convince somebody who is basically healthy to distance themselves from others.\u2019\u0026nbsp;\u003C\/p\u003E\u003Cp\u003EYet, it is not clear why that is the case. The traits of the virus, such as its infectiousness and severity, are driven by its proteins that are responsible for invading our cells and replicating the viral genome.\u003C\/p\u003E\u003Cp\u003E\u2018Sequencing a genome these days is pretty fast, but for proteins it\u2019s different,\u2019 said Dr Charlotte Uetrecht, from the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Germany. She studies coronavirus proteins through a project called\u0026nbsp;\u003Ca href=\u0022https:\/\/cordis.europa.eu\/project\/id\/759661\u0022\u003ESPOCkS MS\u003C\/a\u003E.\u003C\/p\u003E\u003Cp\u003E\u2018My lab is producing the proteins (of the new coronavirus) right now. So we want to see whether they behave the same (as other coronaviruses). We usually need to produce the proteins and purify them to a certain extent so we can look at them. So it\u0027s a lot more laborious than sequencing.\u2019\u003C\/p\u003E\u003Cp\u003EEven small changes to the viral proteins can significantly influence how they interact with each other. Dr Uetrecht studies these fleeting associations, which are crucial for the virus to replicate.\u003C\/p\u003E\u003Cp\u003E\u2018We know a bit about how that looks, but we don\u0027t really understand which of the proteins need to associate for a new genome to be produced,\u2019 she said.\u003C\/p\u003E\u003Cp\u003EAlthough understanding these processes could provide new targets for antiviral drugs, Dr Uetrecht says that historically there has been little interest in studying coronaviruses as they have had little relative impact until now.\u0026nbsp;\u003C\/p\u003E\u003Cp\u003EThe case numbers were low for SARS and MERS and\u0026nbsp;interest fell after the outbreaks, she says. \u0027The common-cold-causing coronaviruses were not (considered) dangerous.\u0027\u003C\/p\u003E\u003Cp\u003E\u2018There was not much research into coronaviruses at all, until SARS. I know a few people who have been working on coronaviruses since the \u002790s, and they were not very well regarded \u2013 they had a hard time getting funding. It was considered a boring, irrelevant virus.\u003C\/p\u003E\u003Cp\u003E\u2018Now, it is very interesting again.\u2019\u003C\/p\u003E\u003Cp\u003E\u003Cem\u003EThe research in this article\u0026nbsp;is supported\u0026nbsp;by the EU. 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