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

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7 Comments

  1. Pink David

     /  8th May 2020

    There are over 4,000 mutations of CV-19 identified so far. Good luck with that vaccine.

    Reply
    • From the article:

      “In comparison to other RNA viruses, it’s a little bit more stable because it has a way of correcting some of the errors that it makes while it replicates,” Geoghegan said.

      “The stability is actually a good thing. It doesn’t necessarily mutate as quickly as some other viruses do and it’s quite encouraging news, for example, for the hope of creating a long-lasting vaccine.”

      “The parts of the genome that have accumulated many mutations are more flexible. They can tolerate changes to their genetic sequence without causing harm to the virus. The parts with few mutations are more brittle. Mutations in those parts may destroy the coronavirus by causing catastrophic changes to its proteins. Those essential regions may be especially good targets for attacking the virus with antiviral drugs,” the New York Times reported in April.

      That’s part of why New Zealand scientists are seeking to sequence the genome of all 1138 of our confirmed cases. This could help with vaccine research and the quest for an effective antiviral.

      Reply
  2. duperez

     /  8th May 2020

    Who would have thought it eh? It’s all sciencey and complicated and to do with things like DNA) and RNA, cell biology and reading of genetic information that underpins all life! Genomes, mutations and strains?

    I can see why the scientist Siouxsie Wiles was attacked on here and needed to be told to shut up. All she did was research on animals after all. What you she know indeed? 🙃

    Reply
    • Alan Wilkinson

       /  8th May 2020

      Multi levels of science, dups. There’s the molecular level, the medical level, the transmission level and the economic level. Just like there are multiple levels in a functioning economy.

      Which is why the limited information available to central controllers is always inadequate for optimal decisions.

      Reply
  3. Alan Wilkinson

     /  8th May 2020

    A useful study of blood pressure medications finds no correlation with likelihood of contracting Covid19 or severity of symptoms:
    https://www.health24.com/Medical/Infectious-diseases/Coronavirus/blood-pressure-medications-do-not-increase-covid-19-risk-20200507-2

    Reply
  4. Alan Wilkinson

     /  8th May 2020

    Some indications of the b.s. around the lockdown rules are starting to emerge:
    The Government’s coronavirus warnings have “effectively terrorised” Britons “into believing that this is a disease that is going to kill you” even though most those infected will not be hospitalised, one of its advisers has warned.

    Professor Robert Dingwall also told today’s Chopper’s Politics podcast, which you can listen to on the player below. that the Government should let people come within 1.5 metres of each other inside and outside as part of measures to ease lockdown.

    Prof Dingwall is based at Nottingham Trent University and sits on the Government’s New and Emerging Respiratory Virus Threats Advisory Group (Nervtag), which feeds into its Scientific Advisory Group for Emergencies (Sage).

    Speaking in a personal capacity, he said: “We have this very strong message which has effectively terrorised the population into believing that this is a disease that is going to kill you. And mostly it isn’t.

    Prof Dingwall said the mandatory social distancing level was set at two metres because Britons had not been trusted to observe one metre – and it could be cut to 1.5 metres.

    The academic told Chopper’s Politics podcast: “There is a fair degree of consensus now among people who are more expert on these things than I am that outdoor transmission is negligible…

    “Personally I think we could quite safely go to 1.5 metres which seems to be an internationally acceptable standard, inside and outside.”

    Prof Dingwall said he had been told by a senior public health specialist that “we knew it was one metre but we doubled it to two because we did not think the British population would understand what one metre was and we could not trust them to observe it so we doubled it to be on the safe side”.

    He said: “If you think of it as a circle around a person that you are trying to protect, if it is 2 metres, that circle is 12 square metres, 1.5 metres that circle is roughly 7 sq m, if you come down to 1 metre it is three and a bit sq m.

    “You can immediately see what difference that makes to any shop, any leisure or retail place. As you reduce the distance the area that is sterilised shrinks quite dramatically.”

    He added: “Fleeting contacts are really irrelevant – if a jogger runs past you in the park, this is not a big deal.

    https://www.telegraph.co.uk/politics/2020/05/07/government-has-terrorised-britons-believing-coronavirus-will/

    Reply
  1. Covid-19 genome mutations used for tracking — Your NZ – Health Matters

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