Infection forecasts powered by big data

Michael Eisenstein at Nature: “…The good news is that the present era of widespread access to the Internet and digital health has created a rich reservoir of valuable data for researchers to dive into….By harvesting and combining these streams of big data with conventional ways of monitoring infectious diseases, the public-health community could gain fresh powers to catch and curb emerging outbreaks before they rage out of control.

Going viral

Data scientists at Google were the first to make a major splash using data gathered online to track infectious diseases. The Google Flu Trends algorithm, launched in November 2008, combed through hundreds of billions of users’ queries on the popular search engine to look for small increases in flu-related terms such as symptoms or vaccine availability. Initial data suggested that Google Flu Trends could accurately map the incidence of flu with a lag of roughly one day. “It was a very exciting use of these data for the purpose of public health,” says Brownstein. “It really did start a whole revolution and new field of work in query data.”

Unfortunately, Google Flu Trends faltered when it mattered the most, completely missing the onset in April 2009 of the H1N1 pandemic. The algorithm also ran into trouble later on in the pandemic. It had been trained against seasonal fluctuations of flu, says Viboud, but people’s behaviour changed in the wake of panic fuelled by media reports — and that threw off Google’s data. …

Nevertheless, its work with Internet usage data was inspirational for infectious-disease researchers. A subsequent study from a team led by Cecilia Marques-Toledo at the Federal University of Minas Gerais in Belo Horizonte, Brazil, used Twitter to get high-resolution data on the spread of dengue fever in the country. The researchers could quickly map new cases to specific cities and even predict where the disease might spread to next (C. A. Marques-Toledo et al. PLoS Negl. Trop. Dis. 11, e0005729; 2017). Similarly, Brownstein and his colleagues were able to use search data from Google and Twitter to project the spread of Zika virus in Latin America several weeks before formal outbreak declarations were made by public-health officials. Both Internet services are used widely, which makes them data-rich resources. But they are also proprietary systems for which access to data is controlled by a third party; for that reason, Generous and his colleagues have opted instead to make use of search data from Wikipedia, which is open source. “You can get the access logs, and how many people are viewing articles, which serves as a pretty good proxy for search interest,” he says.

However, the problems that sank Google Flu Trends still exist….Additionally, online activity differs for infectious conditions with a social stigma such as syphilis or AIDS, because people who are or might be affected are more likely to be concerned about privacy. Appropriate search-term selection is essential: Generous notes that initial attempts to track flu on Twitter were confounded by irrelevant tweets about ‘Bieber fever’ — a decidedly non-fatal condition affecting fans of Canadian pop star Justin Bieber.

Alternatively, researchers can go straight to the source — by using smartphone apps to ask people directly about their health. Brownstein’s team has partnered with the Skoll Global Threats Fund to develop an app called Flu Near You, through which users can voluntarily report symptoms of infection and other information. “You get more detailed demographics about age and gender and vaccination status — things that you can’t get from other sources,” says Brownstein. Ten European Union member states are involved in a similar surveillance programme known as Influenzanet, which has generally maintained 30,000–40,000 active users for seven consecutive flu seasons. These voluntary reporting systems are particularly useful for diseases such as flu, for which many people do not bother going to the doctor — although it can be hard to persuade people to participate for no immediate benefit, says Brownstein. “But we still get a good signal from the people that are willing to be a part of this.”…(More)”.