Genetic mutation study finds new coronavirus spread swiftly in late 2019

By Kate Kelland

 

FILE PHOTO: The ultrastructural morphology exhibited by the 2019 Novel Coronavirus (2019-nCoV), which was identified as the cause of an outbreak of respiratory illness first detected in Wuhan, China, is seen in an illustration released by the Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia, U.S. January 29, 2020. Alissa Eckert, MS; Dan Higgins, MAM/CDC/Handout via REUTERS.

 

LONDON (Reuters) - A genetic analysis of samples from more than 7,500 people infected with COVID-19 suggests the new coronavirus spread quickly around the world late last year and is adapting to its human hosts, scientists said on Wednesday.

 

A study by scientists at University College London's (UCL) Genetics Institute found almost 200 recurrent genetic mutations of the new coronavirus - SARS-CoV-2 - which the researchers said showed how it may be evolving as it spreads in people.

 

Francois Balloux, a UCL professor who co-led the research, said results showed that a large proportion of the global genetic diversity of SARS-CoV-2 is found in all of the hardest-hit countries. That suggests that the virus was already being transmitted extensively around the globe from early on in the epidemic.

 

"All viruses naturally mutate. Mutations in themselves are not a bad thing and there is nothing to suggest SARS-CoV-2 is mutating faster or slower than expected," said Balloux. "So far we cannot say whether SARS-CoV-2 is becoming more or less lethal and contagious."

 

More than 3.68 million people have been reported to be infected by the novel coronavirus globally and 256,000 have died, according to a Reuters tally. Infections have been reported in more than 210 countries and territories since cases were first identified in China in December 2019.

 

The UCL team's findings, published on Wednesday in the journal Infection, Genetics and Evolution, confirm that the virus emerged in late 2019, Balloux said, before quickly spreading across the globe.

 

The study was not able to confirm the exact starting point or location.

 

Balloux's team screened the genomes of more than 7,500 viruses from infected patients around the world. Their results add to a growing body of evidence that SARS-CoV-2 viruses share a common ancestor from late 2019, suggesting this was when the virus jumped from a previous animal host into people.

 

This means it is most unlikely the virus causing Covid-19 was in human circulation for long before it was first detected, Balloux said.

 

A study by French scientists published earlier this week found a man there was infected with COVID-19 as early as Dec. 27, nearly a month before France confirmed its first cases.

 

The World Health Organization said the French case was "not surprising" and urged countries to investigate any other early suspicious cases.

 

Balloux said the 198 small genetic changes, or mutations, that the study identified appeared to have independently occurred more than once. These may hold clues to how the virus is adapting and help in efforts to develop drugs and vaccines.

 

"A major challenge to defeating viruses is that a vaccine or drug might no longer be effective if the virus has mutated," Balloux said. "If we focus our efforts on parts of the virus that are less likely to mutate, we have a better chance of developing drugs that will be effective in the long run."

 

-- © Copyright Reuters 2020-05-06

 

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I'd venture to guess their data source was GISAID, the same as Nextstrain uses for visualization.

 

https://nextstrain.org/ncov

https://www.gisaid.org/

 

https://edition.cnn.com/2020/05/05/health/genetics-coronavirus-spread-study/index.html

Quote

Balloux and colleagues pulled viral sequences from a giant global database that scientists around the world are using to share data.

 

https://www.sciencedirect.com/science/article/pii/S1567134820301829

Quote

There are thousands of global SARS-CoV-2 whole-genome sequences available on the rapid data sharing service hosted by the Global Initiative on Sharing All Influenza Data (GISAID; https://www.epicov.org) (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017). 

 

Looks like Thailand has uploaded more genomes. Search for "Thai" in the box.

 

They used to have only one from the early Wuhan days. Now it seems there's another one that came back in late February. Press Play in the map.

 

Here's one that seems to have come back from Germany: https://nextstrain.org/ncov/asia?s=Thailand/Bangkok-0017/2020 . Note the date, in 21.3.2020. My going theory has been that Thailand got a lesser strain in the beginning. Now we'll see what happens when the German strain has arrived.

I got sick end of November 2019, and I got better for about a week than got sick again.....

 

I am curious how many members here were sick around that time?

5 minutes ago, Pravda said:

I got sick end of November 2019, and I got better for about a week than got sick again.....

 

I am curious how many members here were sick around that time?

Now that you mentioned, I think I did have a week or so in early December when I felt something was not 100%. I just shrugged it off. I travelled a fair bit in that period so would not be surprised at all if that was it. One of these days I'll get some antibody tests from somewhere.

7 minutes ago, DrTuner said:

Now that you mentioned, I think I did have a week or so in early December when I felt something was not 100%. I just shrugged it off. I travelled a fair bit in that period so would not be surprised at all if that was it. One of these days I'll get some antibody tests from somewhere.

I had a very strange persistent cough, I remarked to the woman how this cough was very strange, because it did not go away for so long. Dry cough. Just shrugged it off as well and it went away. I had exposure to Chinese.

17 minutes ago, Pravda said:

I got sick end of November 2019, and I got better for about a week than got sick again.....

 

I am curious how many members here were sick around that time?

Concur !  Early December.

3 hours ago, Pravda said:

I got sick end of November 2019, and I got better for about a week than got sick again.....

 

I am curious how many members here were sick around that time?

 

Me. Mid November. Horrible bout of coughing the likes I have never had. Spent several nights on the sofa because I didn't want to annoy the family trying to sleep. Was delerious for about a day. (Oxygen deprivation...another recently discovered feature of Covid-19) No fever, but had the chills. It eventually passed, but I thought it was one of the most brutal colds I had ever contracted.

 

No way to know for sure, but I suspect that it may have been Corona. If so, it means it was circulating through Thailand in early November, long before they even officially recognized it.

 

And this is why I think Thailand has done so well with their infections. The country may already have herd immunity, especially as it appears that 50% or more of infections are asymptomatic.

 

Interesting article suggesting this was possibly spreading as early as October:

 

https://www.express.co.uk/news/world/1278723/France-coronavirus-october-athletes-covid19-symptoms-wuhan-china-who

 

14 minutes ago, Monomial said:

Interesting article suggesting this was possibly spreading as early as October:

 

https://www.express.co.uk/news/world/1278723/France-coronavirus-october-athletes-covid19-symptoms-wuhan-china-who

This would suggest that people were expiring from this virus well into last year. So, assuming, unrealistically, that the virus was never really identified, and simply assumed to be a very bad Influenza season, what would have been the government's response to this situation?

And slowly the Blame America First version takes shape. Before long, it will likely be traced to some Trump supporters who were waving Confederate flags.

13 hours ago, snoop1130 said:

London's (UCL) Genetics Institute found almost 200 recurrent genetic mutations of the new coronavirus

How do they want to develop a vaccine against that ...?

 

13 hours ago, snoop1130 said:

it may be evolving as it spreads in people

and people who were infected already , can become reinfected ...

 

13 hours ago, snoop1130 said:

"So far we cannot say whether SARS-CoV-2 is becoming more or less lethal and contagious."

 

May become more lethal ... anyway , it is far from over , it changed the world forever .

 

13 hours ago, snoop1130 said:

growing body of evidence that SARS-CoV-2 viruses share a common ancestor from late 2019, suggesting this was when the virus jumped from a previous animal host into people.

The revenge of the pangolin ...

 

8 hours ago, Monomial said:

The country may already have herd immunity,

How can a country ever develop ' herd immunity ' if the individual's immunity is not lasting a long time ...?

11 hours ago, Pravda said:

I got sick end of November 2019, and I got better for about a week than got sick again.....

 

I am curious how many members here were sick around that time?

 

This is very interesting.

 

I got sick end on November too, a couple of days after a flight Bangkok to CNX. Lasted 8 days. Fever, cough, extreme high blood pressure and rapid pulse, splitting headaches.

 

Point is that I have never had anything like it - no flu or colds - for 20 years. I pride myself on my general health. It was a mystery at the time. Got some medications for the cough from a pharmacist, didn't see a doctor.

Same here (north Thailand) We got sick with dry cough late December-early January

Dry cough lasted weeks but no severe symptoms other than that

1 hour ago, nobodysfriend said:

How can a country ever develop ' herd immunity ' if the individual's immunity is not lasting a long time ...?

It can't, that why some diseases are seasonal. It's still too early to know how long the B and T-cells remember the virus and can produce antibodies. 

 

If I'd have to guess, acquired immunity will not last for more than a few months. I base that on the coronaviruses causing the common cold. A guess as good as any at this point.

9 hours ago, Monomial said:

Interesting article suggesting this was possibly spreading as early as October:

 

https://www.express.co.uk/news/world/1278723/France-coronavirus-october-athletes-covid19-symptoms-wuhan-china-who

 

Could have been anything. At any given point there are dozens of viruses and bacteria out there to get you. Testing them for presence of antibodies could be interesting.

 

What these could imply is that it took a lot longer time for the virus to really take flight than previously thought. Thailand had some strange anomaly in Jan-Feb with hordes of Wuhanese flying in, yet no catastrophic outbreak occurred. I'm still going with the mutated EU/US strain theory.

 

The real question is, when did CCP know?

1 hour ago, bbudd said:

Same here (north Thailand) We got sick with dry cough late December-early January

Dry cough lasted weeks but no severe symptoms other than that

Probably all that PM in the smoke.

13 hours ago, Pravda said:

I got sick end of November 2019, and I got better for about a week than got sick again.....

 

I am curious how many members here were sick around that time?

Where were you?

Yeah, in late November early December the doctors told me that I had a combination of the flue and asthma, and it felt strange as I have not had any problems with my asthma since I moved to Thailand as it used to be triggered by cold winter weather... so I can just hope that I had this s*** already back then!
(This was about the same time as we got Chinese exchange students to the school)

35 minutes ago, DrTuner said:

Could have been anything. At any given point there are dozens of viruses and bacteria out there to get you. Testing them for presence of antibodies could be interesting.

 

What these could imply is that it took a lot longer time for the virus to really take flight than previously thought. Thailand had some strange anomaly in Jan-Feb with hordes of Wuhanese flying in, yet no catastrophic outbreak occurred. I'm still going with the mutated EU/US strain theory.

 

The real question is, when did CCP know?

I would say when did China know what.

 

Could be similar to Spanish flu, possibly originated in China in not too virulent form, and when it returned to China in a more aggressive form there was some kind of immunity. Similar could have happened here in Thailand, and maybe even China.

What has amazed me and others is that covid 19 contaminated the world very quickly as opposed to sars which was less contagious .  I have not read yet if the virus can be spread by being airborne  because that would explain the rapid global coverage . The UK lock down has not been particularly effective as would have been expected with new cases hitting around 4000 a day and that some 7 weeks after the lock down began . I watched a UK doctor who said that when new patients are asked how they think they caught the virus they say they have no idea . Lock down should mean just that with no daily exercising and food delivering should have been a priority by issuing basic food parcels to begin with and seconding the armed forces to help .   

16 hours ago, snoop1130 said:

Genetic mutation study finds new coronavirus spread swiftly in late 2019

Maybe Mother Earth is going to look after herself , A few more Real Bad Viruses and the words population will be Halved or more.  ???? 

1 hour ago, superal said:

What has amazed me and others is that covid 19 contaminated the world very quickly as opposed to sars which was less contagious .  I have not read yet if the virus can be spread by being airborne  because that would explain the rapid global coverage . The UK lock down has not been particularly effective as would have been expected with new cases hitting around 4000 a day and that some 7 weeks after the lock down began . I watched a UK doctor who said that when new patients are asked how they think they caught the virus they say they have no idea . Lock down should mean just that with no daily exercising and food delivering should have been a priority by issuing basic food parcels to begin with and seconding the armed forces to help .   

SARS was far more deadly, thereby also killing itself.

 

What I find funny is that you see the virus spread itself, more or less, like a wave over the world, in spite of globalisation.

18 minutes ago, digger70 said:

Maybe Mother Earth is going to look after herself , A few more Real Bad Viruses and the words population will be Halved or more.  ???? 

There has to be a limit on the worlds population . A quick Google shows 25000 people die every day from starvation or 9 million a year . 11 % of the globe are undernourished .

1 hour ago, DrTuner said:

Thailand had some strange anomaly in Jan-Feb with hordes of Wuhanese flying in, yet no catastrophic outbreak occurred. I'm still going with the mutated EU/US strain theory.

In Jan-Feb my family of six got sick. Two elderly, one pregnant, myself (50 years old), my brother-in-law and my wife. My Brother-in-law came back from Bangkok after a business trip and got sick as. Fever, cough - really wreaked him.  Then over a two week period, everyone else got sick. Sore throat first, followed by sore limbs followed by fever and then a bad cough. It went through the whole family very quick and we were all sick for about 14 to 25 days in total. I had a sore throat first, then got a fever and got a sore chest and started coughing. I recovered in about 14 days but the rest of my family took about 3 weeks.

 

The whole funny part about this was just how contagious it was and that was what concerned me most. I just passed around us so quickly. So many it was maybe it  wasn't Covid but it seems strange we all got sick at this time specially after the visit to Bangkok.

16 hours ago, Pravda said:

I got sick end of November 2019, and I got better for about a week than got sick again.....

 

I am curious how many members here were sick around that time?

You must have been the worlds first. Nov ??????????????

We are immerse in coronviruses. It's nothing new. We are and have been since birth, immersed in a bath of viruses and this one they call SARS-COV-2 is no different. It's all int he labelling. One label which you may call the flu will get your hospital zero bucks while if it's labelled SARS-COV-2, you get $19,000 in some hospitals in Amerika.

2 hours ago, stevenl said:

SARS was far more deadly, thereby also killing itself.

 

What I find funny is that you see the virus spread itself, more or less, like a wave over the world, in spite of globalisation.

Or maybe because of it.

Here's more study on a possible mutation in EU/US: https://www.biorxiv.org/content/10.1101/2020.04.29.069054v2

 

Quote

 The mutation Spike D614G is of urgent concern; after beginning to spread in Europe in early February, when introduced to new regions it repeatedly and rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections.

 

"A major challenge to defeating viruses is that a vaccine or drug might no longer be effective if the virus has mutated," Balloux said. 

 

You can't help laughing. We can't even find a cure for the corona viruses which cause the common cold, let alone their nasty big brother who gives us COVID 19.

 

Why? Because viruses have an inconvenient habit of mutating. This explains why flu shots either stop working or become less effective over time. 

 

All the more reason not to wait for Big Pharma to rush to our rescue with their latest batch of expensive snake oil.

 

It's time to lift the lock-down, end the curfew and bin the social distancing for everyone except the vulnerable elderly. We need fresh air, and exercise, and social interaction for mental as well as physical health.

 

Mixing with our fellow humans once more is also the best way to boost immune systems weakened by months of enforced isolation. This will improve our chances - already very high unless we are elderly - of repelling or shaking off the virus with serious harm.

 

The "old normal" beats any vaccine.