Covid-19 genome mutations used for tracking

For those who wanted some science…

Genome sequencing has been used to identify mutations of the Covid-19 virus, and while there is no evidence any known mutations have changed the characteristics of Covid-19 yet, it has provided a useful way of tracking the spread of the virus.

This phylogeny tree from Nextstrain, with each shade representing a different country and each branch a separate mutation, shows how mutations tend to be linked to a specific geographic location. Each dot represents a genome from the GISAID database.

Newsroom – The NZ strains: How the virus got here

On average, the virus is thought to undergo about 23.92 mutations a year, or two every month. This figure can help us backdate its emergence. If there is an average of 10 mutations from the supposed index case, then the virus likely entered the human population around five months ago – or early December.

Even the two most divergent strains have just 35 mutations, representing about 0.12 percent of the genome. By comparison, SARS, which is significantly deadlier but still very similar to Covid-19, is 21 percent distinct from SARS-CoV-2.

While the mutations may not make the virus more deadly or more transmissible, understanding where in the virus these mutations occur could help with efforts to create an antiviral medication.

One interesting example, in March a father and son arrived in New Zealand from the US and both tested positive, but they had different mutations that made it extremely unlikely they caught the virus from the same source.

“A Wellington man in his 30s and his father in his 70s have tested positive on their return from the United States. The man in his 30s became unwell on the flight and his father became unwell the day after they arrived,” Bloomfield said.

These two men, however, did not infect one another. Instead, they were likely infected in separate circumstances, each with one of the two strains detailed above. One of the viruses had five mutations that the other did not, making it extremely unlikely that one man had infected the other.”

Here the ESR has now sequenced 171 of the more than 600 cases referred to them, and has just received a new sequencer that wil double their testing capacity to 100 genomes a week. Their aim is to sequence all New Zealand cases.

This map charts the progress of the strains that made up the eight New Zealand cases on Nextstrain.

Our aim is to sequence every positive case in New Zealand,” Geoghegan said.

“Fortunately, that seems like a very realistic goal because we haven’t had that many cases. We’re in a really unique position to be able to do that. That will really provide us with an amazing dataset and a great case study, especially for international collaborations, to be able to understand how the virus spread here, what happened after we closed our borders, what happened after we went into Level 4 lockdown and as we begin to lift those lockdown restrictions, what happens to the transmission of the virus?”

Since New Zealand is a closed population, such studies could help researchers understand how the virus changes, without having to deal with the pressures of managing an active outbreak.

For example, an examination of different clusters in New Zealand could show cluster-specific mutations, allowing health officials to link closed cases with unknown origins to where they came from. Similarly, if a new case emerges out of nowhere, sequencing the genome of the patient’s virus could link it to another extant case or, through ruling out genomic connections to any of New Zealand’s cases, declare it an imported case.

A lengthy article but worth reading in you like a bit more depth and more science.

It’s incredible how science is now capable of sequencing RNA like this (as they do with DNA).

A bit more science: DNA vs. RNA – 5 Key Differences and Comparison

Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) are perhaps the most important molecules in cell biology, responsible for the storage and reading of genetic information that underpins all life. They are both linear polymers, consisting of sugars, phosphates and bases, but there are some key differences which separate the two. These distinctions enable the two molecules to work together and fulfil their essential roles. Here, we look at 5 key differences between DNA and RNA.

DNA vs. RNA – 5 Key Differences and Comparison