Science & Technology

Phylogenetic tools can help track COVID-19 variants faster. Here's how

Studying the evolutionary path of the virus can help countries assess their vaccine strategy

By DTE Staff
Published: Friday 05 March 2021
Scientists propose faster methods of tracking COVID-19 variants

Over 600,000 sequences of the novel coronavirus have emerged since the beginning of the pandemic. A group of scientists from across the globe have demonstrated the most effective ways to use this enormous volume of data to track variants of the SARS-CoV-2 virus faster.

These can help countries optimise their vaccine strategies and help prepare the world prepare better for pandemics in the future, they said.

The viral and genetic analysis specialists, in a paper published in Nature on March 1, called for more organised processes that will make the most of these analyses and also not burden the existing phylogenetic tools.

These tools were mostly developed by evolutionary biologists to study the lineage of organisms. In the case of analysing SARS-CoV-2 sequences, these tools have been helping countries understand how the virus is transmitting form one region to the other or how it is reaching newer clusters.

“Phylogenetics was key to public understanding that air travel was riskier than many understood,” the authors wrote in the paper.

The paper outlines two ways, apart from tracking transmission, genome sequencing data can be utilised by public health officials: To identify key mutations and estimating reproduction number, or R.

The reproduction number is a measure of how contagious a virus strain is: It tells us the average number of people who will contract COVID-19 from one person.

The paper cited the instance of South Africa which changed its vaccine strategy because the dominant variants were assumed to reduce the efficacy of existing vaccine candidates.

 “Individuals infected with certain strains might one day receive specific medical treatment or be managed differently in quarantine,” the researchers wrote.

The scientists proposed that computed genomic data of the virus should be read along with results of lab experiments of the variants to best understand the extent and pattern of spread.

Phylogenetic study can also improve R value estimates of SARS-COV-2 strains. This is because phylogeny can distinguish between imported and homegrown viruses in a community.

“Methods that combined information on epidemiology with phylogenetic data were used to show that a lockdown in New Zealand reduced Re from seven at the start of one outbreak to 0.2 at the end of March 2020 in one cluster of cases,” said the paper.

The paper suggested that phylogenetic tools should take stock of evolutionary uncertainties while tracing the path of coronavirus and communicate them for more accurate results.

Genomic data, like any computer code, is not error-free. Contaminated samples can dilute some mutations and hide others, the paper said.

To deal with this, the scientists highlighted the need for “stable and open infrastructures that allow the entire community to correct sequences and metadata throughout the pandemic”.

Also, countries do not have a uniform rate of sequencing (samples sequenced as a share of cases). The United Kingdom has so far sequenced almost 5,000 samples per 100,000 cases, compared with 320 per 100,000 in the United States and 30 per 100,000 in Brazil.

The tools currently in use for tracking variants do not take in to account this or other biases, the researchers observed. To understand the growth and geographical origins of new strains, the paper calls for systems that accommodate the same.

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