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Genetic sleuths identify three COVID-19 lineages

University of Tasmania researchers have applied their expertise in disease ecology and mathematics to track the COVID-19 pandemic, distinguishing three different lineages of the virus around the world and suggesting another unique lineage may yet emerge.

Two of these lineages emerged from China in November and December last year, the first being the likely lineage that made the switch from bats to humans. A third lineage emerged in Europe with a high growth rate in late February.

A team from the University’s School of Natural Sciences, working with researchers based at Imperial College, London, and the University of Warwick, explored the idea of different lineages by applying some recently developed statistical approaches to nearly 800 COVID-19 genomes.

“Understanding how a virus evolves and mutates is not only crucial for the development of effective vaccines and treatments but also offer important insights into a pandemic,” lead researcher Nick Fountain-Jones, a disease ecologist with expertise in phylodynamics, explained.

“For example, geographic patterns of virus spread, periods of epidemic growth and control efforts imprint themselves on genetic code of a virus.

“Since COVID-19 spilt over from wildlife to humans sometime in late 2019, and spread across the world, the genome of the virus has mutated and evolved.

“Some mutations allow the virus to be more easily transmitted, but most will be of no consequence or a hindrance to the virus and will be rapidly lost. Interestingly, when there are lots of infections, it is likely that there will also be lots of mutations occurring.”

The researchers found a ‘roller coaster-like pattern’ of growth and decline in genetic diversity of each lineage. This rollercoaster closely followed China’s experience with the virus, followed by the expansion of COVID-19 across the world.

“Initially, Lineage A experienced lots of growth in genetic diversity as the epidemic intensified in Wuhan followed by a decline as the virus was controlled in the region,” Dr Fountain-Jones said.

“We have some evidence that Lineage B started to spread at the height of the outbreak in China and then went into a decline when the virus was controlled.

“Both lineages then entered, based on our estimates, a period of growth in late February into early March when the outbreak turned into a pandemic, and the virus spread into Europe in particular.

“At this point, Lineage C came onto the scene, having picked up some important mutations along the way. This lineage likely originated in Europe and appears to be the most common linage present now.

“The mutations that make Lineage C distinctive may have made the virus more easily transmitted from person to person, but more research is required to support this hypothesis.”

The researchers found no evidence that infection by one lineage may make a person sicker than an infection by another.

“This study not only shows some interesting insights into the pandemic, it also demonstrates that our approach is sensitive enough to pick up when, for example, control measures are (or aren’t) working,” Dr Fountain-Jones said.

“If we go through another period of growth in genetic diversity, we may find yet another lineage diverging.”

Comic explaining virus evolution

Illustration: Dr Fountain-Jones has worked with artist Jai Sutton-Bassett to produce a comic introducing the public to phylodynamics and why understanding virus evolution can help fight COVID-19.

Published on: 15 Jun 2020 10:13am