By Josiah Liew Liq Jong and Dr Tan Ju Lin
To date, there are over two million COVID-19 positive cases across the globe. While most cases have been traced via patients’ travel history or contact tracing, these methods are potentially misleading as it depends on the information provided by patients.
Viral genomes reveal identity and ancestry
The COVID-19 virus genome consists of approximately 30,000 bases (units that comprise a genome). As the virus replicates and is transferred from host to host, it starts to generate mutations, which are changes of bases at specific locations within the genome. These mutations are akin to molecular signatures that scientists and epidemiologists can trace and group together. By now, the term “clusters” has become ubiquitous within our society. In essence, “clusters” are groups of people that have been infected by COVID-19 strains with similar mutations.
To begin the process of uncovering the COVID-19 virus genome, nucleic acid sequencing methods and bioinformatics are employed. Computational tools process the raw data generated by DNA sequencing into useful forms, such as a map of how specific samples of COVID-19 in Malaysia are related to global samples.
Reading the Malaysian COVID-19 genomes
To date, eight COVID-19 genomes from samples collected in Malaysia. Of the eight, six samples were sequenced by the Malaysian Genome Institute (MGI), while the remaining two were sequenced by Universiti Malaya, in collaboration with GeneSEQ Sdn Bhd using a portable, pocket-sized device called the MinION. Coupled with a laptop, the COVID-19 viral genome was sequenced in less than an hour.
Both the sequenced COVID-19 viruses had near-identical genome sequences as the samples were collected from the same cluster. The near-identical nature also suggests infections from a similar source. It means that those infections potentially stemmed from the same route of transmission, or from the same country of origin.
Sequencing and COVID-19 mitigation strategies
Until a vaccine is created (optimistic estimates suggest late-2021), proper social distancing, aggressive contact tracing, and large-scale testing will remain the key factors in curbing the spread of the virus. Sequencing will be an important technology to inform public-health policies, in addition to its medical applications.
By studying genomic differences and mutation rates in COVID-19 viruses, researchers are able to examine how quickly the viruses are adapting to existing treatment regimes. Genomic data also reveals novel drug targets against the COVID-19 virus.
In addition to treatments, the genome sequencing of COVID-19 empowers the formation of targeted social distancing strategies and contact-tracing. As sequencing becomes more widespread, countries can begin to slowly reopen the borders for trade and trans-border travel. If and when a COVID-19 case arises, sequencing will reveal the origins of the virus by referencing it against known sequences.
For example, an individual may have contracted the virus with near-identical sequence to viruses sequenced in country X. Thus, health authorities can implement specific restrictions and testings for those travelling to-and-from country X. Finally, sequencing will work hand-in-hand with existing tests to improve traceability of asymptomatic patients (reports indicate a vast majority of patients are “silent spreaders”).
As the globe faces the COVID-19 epidemic, we will have to employ every possible strategy to ensure the safety of the population. Scientific technologies, like sequencing, may provide a way forward for public-health authorities to understand infection transmissions and to form targeted strategies of containment based upon viral origin. With these technologies, proper strategies, and effective treatments, we can begin to focus on getting back to our feet – sooner, rather than later.
*Dr Tan Ju Lin and Josiah Liew Liq Jong are part of the team from GeneSEQ Sdn Bhd, Malaysia’s first Next Generation Sequencing (NGS) service provider to cater for the food, aquaculture and agriculture industry. GeneSEQ Sdn Bhd has recently collaborated with University Malaya to carry out COVID-19 genome sequencing. NGS is a powerful platform that has enabled the sequencing of thousands to millions of DNA molecules simultaneously and thus revolutionised genomic research.
**All previous posts about COVID-19 here: https://sciencemediacentremalaysia.com/tag/covid-19/