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Big Data Detectives Investigate Harmful Microbes

What do viruses and the X-Men have in common? Their ability to mutate! As they reproduce, random errors occur in their DNA or RNA sequences – they mutate – and like the villains in X-Men, they end up with ‘superpowers’ that resist antibiotics and even cause diseases. These ‘superpowers’ are a curse to us, but fear not – A*STAR can break this curse by the power of genome sequencing!

 

Sequencing is a key first step in modern infectious disease outbreak investigation.

 

– Dr. Swaine Chen, Senior Research Scientist in the GIS Infectious Diseases Group and Assistant Professor in the Department of Medicine at National University of Singapore Yong Loo Lin School of Medicine (Source: ChannelNewsAsia)

Genome sequencing is the process of understanding the genetic order that makes up the bacteria or virus’ DNA. This is especially crucial when epidemics occur, as it is a race against time to figure out the who, what, where, why, when and how of the diseases before they claim further casualties, including ourselves and our loved ones.

 

Each person has an average of 10-100 trillion bacteria and it might only be a strain in that sea of bacteria which is responsible for the infection. How do we trace that one culprit?

 

Only when equipped with the knowledge of the origin of the bacteria or virus strains can the appropriate treatment and vaccine be developed, thereby curbing the spread of these infections.

Remember the swine flu outbreak in 2009? Or the more recent Zika threat that is probably fresher in our memories? When Zika was first reported here, it was widely assumed that ‘Singapore Zika’ was imported. However, genomics analytics eventually revealed to researchers at the Bioinformatics Institute (BII) together with the Ministry of Health that ‘Singapore Zika’ actually originated from a strain that had been spreading within Southeast Asia for more than five decades!

 

Knowledge (Really) Is King

In 2015, a puzzling infection broke out in Singapore – the Group B Streptococcus (GBS) infection. Scientists at the Genome Institute of Singapore utilized the long read, single molecule PacBio sequencer to deduce the full sequence of the GBS strain. The eventual conclusion was that this was a relatively rare strain that had only been seen in Southeast Asia previously. Together with the Ministry of Health (MOH), the Environmental Health Institute (EHI), as well as an army of medical professionals specialising in infectious diseases, a detailed analysis of the genome sequence verified that the GBS outbreak was caused by a popular local hawker delight – yusheng (sliced raw freshwater fish served with rice porridge or tossed in sauces as an appetiser). Streptococcus infection had not been known to be a food-borne disease until this point.

The initial analysis of the full GBS genome sequence performed in 2015 took approximately a week to derive initial answers. Since then, however, advances in analytics have shortened the time taken to a mere six hours – a whopping 95% of savings in precious time!

This was made possible through the GIS GERMS platform, which employs cutting-edge genomic technology to collect thousands of genomes to examine the evolution of bacteria in specific environments. GERMS is a key contributor to ROUTES, which in turn is the pathogen tracking arm of the centre for Big Data and Integrative Genomics (c-BIG).

 

Flu "Facebook"

Given the rapid mutation of viruses and their omnipresence throughout the world, potent ones such as the influenza virus require an effective tracking method.

Responding to this need, the BII came up with the ultimate stalking tool (think Facebook) to track the spread of the common flu – the FluSurver! This is an online tool housing genomics data that allows for the identification and matching of flu strains across the world.

Researchers worldwide can upload information on different strains of viruses and bacteria from everywhere and mark its location on the FluSurver, much like Facebook’s check-in function! In the same way as Facebook posts can be tagged with emojis such as the thumbs-up or the sad face, the FluSurver tags strains with “bad” mutations such as drug resistance (thumbs-down and angry face for this post).

With this elaborate flu-stalking gizmo, researchers are now better able to compare and evaluate strains of flu variants. More than just an edgy name, the FluSurver is such a comprehensive database that even the World Health Organisation (WHO) surveillance network uses it!

Now that genomic sequencing is well-positioned to combat and conquer nasty viruses and bacteria, it is time for these little troublemakers to face their just ‘con-sequences’!