Bioinformatics makes it possible to analyze large amounts of data from a variety of sources. In one notable use case, it enables the augmentation of contact tracing data with genomics data to create more detail mapping of COVID-19 spread. The disease is caused by the novel coronavirus, also known as SARS-CoV-2. By any name it is the biological threat that brought the world to a standstill and now endangers efforts for a restart.
Humankind has no choice but to try to resume normal activities such as employment since not doing so could soon lead to starvation and other life-threatening problems wrought by abject poverty. Yet the novel coronavirus cannot be ignored either as that too threatens lives. It is therefore imperative to find ways to control the spread of the disease.
Until recently, contact tracing was thought to be the best way, if not the only way, to do that. However, there is more than one way to do contact tracing, so success rates vary. Below is a CBC/Radio-Canada video on how Iceland was so very successful in how they did contact tracing.
Some countries opt to use a mobile phone API for app interoperability created by an Apple and Google partnership to keep track of who has come into contact with whom. Other countries take their own paths.
However employers, cities, and countries decide to do contact tracing, and no matter how well they implement it, there are limits to what the information can reveal. To overcome those limits, scientists are now supplementing contact tracing with genomics.
“Since the first whole-genome sequence of the new coronavirus, SARS-CoV-2, was shared online on 11 January, scientists have sequenced and shared some 32,000 viral genomes from around the world. Such a vast amount of data has allowed researchers to trace the origin of COVID-19 outbreaks in their countries and pinpoint when community transmission occurred,” according to an article in Nature.
The researchers say that genomics will be equally helpful in tracking and controlling new outbreaks as social restrictions are eased and humans enter the new normal stage. There are already a few reported success stories for this approach.
The Peter Doherty Institute for Infection and Immunity team in Melbourne sequenced the genomes of about three-quarters of the estimated 1700 cases in the state of Victoria. This was no small feat.
It is “thought to be the most comprehensive sequencing coverage in the world for an infectious-disease outbreak. By comparison, researchers working on the 2014–16 West Africa Ebola epidemic sequenced 5% (1,610 samples) of all infected cases in just under 3 years,” according to the Nature report.
The researchers were then able to determine whether an infected healthcare worker contracted SARS-CoV-2 from a patient or a social encounter.
“Without genomics, and only interviewing, you would never be able to tell which one it was,” Torsten Seemann, a bioinformatician at the Microbiological Diagnostic Unit Public Health Laboratory based at the Peter Doherty Institute for Infection and Immunity in Melbourne told Nature. This knowledge prevented a waste of resources in investigating a possible outbreak at the hospital by directing the investigation of the spread to its true source and where it had spread from there.
New Zealand is likewise sequencing all of its reported cases. So far, they have completed about 25% of their 1154 cases.
“But the sequence data is already proving useful in responding to outbreaks. Genomic data have identified links between cases that were missed by traditional contact tracing and have untangled two clusters that were thought to be one,” Joep de Ligt, lead bioinformatician at New Zealand’s Institute of Environmental Science and Research near Wellington, which is sequencing the country's cases told Nature.
However, there are obstacles to using genomics in this pursuit too. For one thing, wealthier countries tend to be the only ones currently using the technology in this way. And for another, widespread diagnostic testing is required. Some countries, even wealthy ones, are still struggling to achieve sufficient testing to make this approach work.