Genetic sequencing data map shows how London became coronavirus hub

A fascinating video shows how London became a hub for the global spread of coronavirus after the initial outbreak in China.

Scientists have used genetic sequencing data to illustrate how different strands of the virus travelled to the UK via the capital and how it was passed on to other countries.

The map, produced by NextStrain.org, shows how COVID-19 started in Wuhan, before spreading across Asia to Singapore and South Korea, before being carried by travellers to London. From there, it was flown to the USA and across Europe.    

Yesterday saw the biggest increase in UK deaths in one day, with the figures jumping 260 to 1,016. There have now been more than 17,000 confirmed cases.    

A map based on genetic sequences reveal how coronavirus was spread across the globe, with London quickly becoming a hub

A map based on genetic sequences reveal how coronavirus was spread across the globe, with London quickly becoming a hub

A map based on genetic sequences reveal how coronavirus was spread across the globe, with London quickly becoming a hub 

The data also reveals there are eight different strands of the virus, but they all appear to mutate very slowly, with only tiny differences between them.

Data scientists behind the map say none of the strains of the virus are more deadly than any of the others. 

They also claim that the strains will not grow more lethal as they evolve.

‘The virus mutates so slowly that the virus strains are fundamentally very similar to each other,’ Charles Chiu, a professor of medicine and infectious disease at the University of California, San Francisco School of Medicine, told USA Today

Tracking the different strains of SARS-CoV-2, as the virus is officially named, allows scientists to see whether containment measures are working, by showing whether new cases are from community spread, or imported from a different hotspot.

Researchers stress that the different strains are fundamentally similar, because coronavirus mutates very slowly, about eight to 10 times slower than the common flu.

So far even in the virus’s most divergent strains scientists have found only 11 base pair changes, out of a genome of 30,000 base pairs.

A 'family tree' of SARS-CoV-2 shows how different mutations have developed

A 'family tree' of SARS-CoV-2 shows how different mutations have developed

A ‘family tree’ of SARS-CoV-2 shows how different mutations have developed

That means the different strains are not causing different symptoms, or inflicting different rates of fatality. 

Although different countries around the world have recorded significantly different fatality rates, this is almost certainly because they are testing their populations at different rates. 

Because many cases have no symptoms, aggressive and widespread testing makes the fatality rate appear to drop, because the total number of confirmed cases is much higher.

Researchers also say that when patients show no symptoms, or mild symptoms, it is not because they have contracted a ‘mild strain’ of the virus.

Rather, differences in symptoms most likely have more to do with an individual’s own immune system and general health. A strain that has little effect on one person could be deadly to another.

‘The current virus strains are still fundamentally very similar to each other,’ Chiu said. 

In the UK, widespread testing is not available, with only those admitted to hospital entitled to a swab. 

Over the weekend, it was announced that tests are to be rolled out among frontline NHS staff, starting with critical care doctors and nurses.  

This electron microscope image made available by the U.S. National Institutes of Health shows SARS-CoV-2, the virus that causes COVID-19

This electron microscope image made available by the U.S. National Institutes of Health shows SARS-CoV-2, the virus that causes COVID-19

This electron microscope image made available by the U.S. National Institutes of Health shows SARS-CoV-2, the virus that causes COVID-19

The slow mutation rate of the virus has given scientists hope that an eventual vaccine could provide protection for years, or even decades. 

Depending on how quickly a virus mutates, some vaccines have to be regularly updated, such a flu vaccines that have to be administered every year.

Other vaccines, such as for measles and chickenpox, provide protection for decades, or even a lifetime.

On Monday, Peter Thielen, a biologist with the Johns Hopkins Applied Physics Laboratory, said that it appears coronavirus mutates slowly, more like measles and chickenpox than the flu.

‘When this virus was first sequenced in China, that information was helpful in starting the process to develop a vaccine,’ Thielen explained in a statement. 

Peter Thielen (front), a biologist with the Johns Hopkins Applied Physics Laboratory, said that it appears coronavirus mutates slowly, more like measles and chickenpox than the flu

Peter Thielen (front), a biologist with the Johns Hopkins Applied Physics Laboratory, said that it appears coronavirus mutates slowly, more like measles and chickenpox than the flu

Peter Thielen (front), a biologist with the Johns Hopkins Applied Physics Laboratory, said that it appears coronavirus mutates slowly, more like measles and chickenpox than the flu

‘What we’re doing informs whether or not the virus is mutating away from that original sequence, and how quickly,’ he continued, describing his experiments to sequence the genome of SARS-CoV-2, the virus that causes COVID-19.

‘Based on the mutation rate, early data indicates that this would likely be a single vaccine rather than one that needs to be updated each year, like the flu shot,’ he said. 

Experts say that the earliest a vaccine for coronavirus could be widely available is a year to 18 months. 

Although vaccine trials are underway in the U.S., UK and elsewhere, time is needed to prove the shots safe and effective before they are rolled out to millions.   

How is coronavirus spreading in different parts of the world?

The researchers at NextStrain.org issued the following situation report on March 27, based on an analysis of 1,495 publicly shared viral genomes. 

By comparing these viral genomes to each other, they can characterize how the virus is moving around the world and spreading locally. They report:

Europe

‘We continue to see strong mixing of samples across Europe, suggesting that the virus has continued to move across borders in the last 3-5 weeks. As mitigation measures have time to take effect, we may see more clustering of cases by country.’

North America

‘Within the U.S., transmission patterns are complex: samples collected from opposite sides of the country still show close relationships.

‘Washington state has had at least two independent introductions (the first likely from China, the second likely from Europe), which have led to two separate transmission chains.

‘There is evidence for likely local transmission within several states, most clearly within California.’

Central and South America

‘We received new sequences from South America this week, but sampling remains sparse. There may be more COVID activity in this region than is captured in the available data, but we cannot say for sure.’

Asia

‘We find evidence for recent export of COVID-19 from Iran.’

Africa

‘The phylogeny suggests likely local transmission within Kinshasa, Democratic Republic of the Congo, for the last 11+ days.

‘We received new sequences from Africa this week, but sampling remains sparse; there may be much more COVID activity in this region than is captured in the available data.’

Oceania

‘There is evidence in the genetic data for local transmission in New South Wales, Australia.’

Link hienalouca.com

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