Science

Mutant ‘Kent strain’ of coronavirus has been in the US since November 6

The highly-infectious coronavirus variant B.1.1.7 which emerged in Kent in September 2020 had reached the US by November 6, new research shows.

It is thought to have mutated inside a single patient in England struggling with a critical case of Covid-19 which forced the virus to adapt, changing its genetic code. 

University of Arizona researchers studied the genomes of 50 B.1.1.7 infections in the US and traced their lineage to determine when the mutated variant first appeared in the US. 

They found two clusters of infections, one in California and one in Florida, which originated on November 6 and November 23 respectively – the first being roughly six weeks before SAGE told the government about the new variant and health secretary Matt Hancock announced it to the public. 

This retrospective study has the benefit of genomic analysis and hindsight, and the first actual case of the Kent strain was not diagnosed in an American until December 29. 

‘It is striking that this lineage may already have been established in the US for some 5-6 weeks before B.1.1.7 was first identified as a variant of concern in the UK in mid-December,’ the researchers write. 

‘And it may have been circulating in the US for close to two months before it was first detected, on 29 December 2020.’

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The new variants of the coronavirus have mutations on the spike protein, which are key for the immune system’s antibodies to latch onto and destroy it. Changing the shape of them makes it harder for the body to catch the virus

Kent variant timeline  

September 20 – Variant emerges in a chronically ill Covid-19 patient in Kent 

November 6 – Infected person takes the new strain to California  

November 2020 – Spike in cases occurs in Kent and Medway despite national lockdown squashing case numbers in the rest of the country 

November 23 – Air passenger brings new variant to  Florida

December 11 – SAGE tells the Government about the new variant 

December 14 –  Authorities of the United Kingdom of Great Britain and Northern Ireland reported to WHO that new SARS-CoV-2 variant was identified through viral genomic sequencing

Matt Hancock tells MPs about the new variant  

December 18 – SAGE tells the Government they are concerned about the new variant and its transmissibility

December 20 – London, South East and East of England go into new Tier 4 restrictions due to spike in cases due to new variant 

December 21 – More than 40 countries halt flights from UK due to new variant 

December 29 – First case is spotted in the US 

All dates are for the year 2020  

The study has not yet been peer-reviewed but is available online as a pre-print.  

The exact origin of the Kent variant is unknown but it is believed it sprung up in mid-September. 

Dr Susan Hopkins, a senior Public Health England (PHE) official said in December that originally there was ‘nothing to particularly highlight that this was something of major concern, as variants come and go’.

Mutations in viruses occur all the time, with the vast majority of them being harmless or deleterious to the pathogen.

However, by chance, sometimes the tweaks to the viral code give it a survival edge and increase its success, often by becoming more infectious and easier to spread. 

This is what is thought to have occurred in the B.1.1.7 variant, which previous studies have found is more abundant in the upper respiratory tract. 

A mutation on the spike protein — which protrudes from the coronavirus and hijacks human cells — made it better at infecting people. 

This so-called N501Y mutation is also found on the South African and Brazilian variants which have since been identified. 

The Arizona-based researchers found all the California cases share another minor mutation, which is seen in just 1.2 per cent of European B.1.1.7 cases.

This, they say, indicates a single introductory event, likely from international travel, seeded the variant in California where it then spread from person to person.  

A similar trend was seen for the Floridian batch of cases, which were very similar to the most common type of B.1.1.7 seen in the UK. 

This is a ‘strong indication that they too descend from a single introduction event’, the scientists say. 

At least three major coronavirus variants have been spotted in Britain in recent months – from Kent, South Africa and Brazil – and they appear to be evolving to spread faster and to evade some parts of the immune system, although scientists do not yet think any have yet got so far as to slip past the vaccines completely

At least three major coronavirus variants have been spotted in Britain in recent months – from Kent, South Africa and Brazil – and they appear to be evolving to spread faster and to evade some parts of the immune system, although scientists do not yet think any have yet got so far as to slip past the vaccines completely 

New strain of coronavirus is discovered in GERMANY 

Another mutant strain of coronavirus – different to those originating in the UK, South Africa and Brazil – has been discovered in Germany.

Health officials said the variant was identified in Bavarian hospital patients, but it isn’t yet known how transmissible it is.

Concerns have grown in recent weeks over the spread of the variants, the UK-based version of which forced Boris Johnson to cancel Christmas for millions and plunge the nation into a third national lockdown.

Discovery of the new German strain has also seen Angela Merkel take action, with the Chancellor declaring restrictions including the closure of schools and shops will be extended until mid-February.

Germany’s infection rate has stabilised in recent days, indicating that existing restrictions may have been effective in bringing down the numbers.

However, fears are growing after it was found that out of 73 newly infected people at Garmisch-Partenkirchen, in the southeast of the country, 35 had the new variation.

Experts continue to analyse samples after Clemens Stockklausner, deputy medical director at the Charité university hospital in Berlin, admitted it was too early to say whether this virus was more deadly than other variants.

He said: ‘At the moment we have discovered a small point mutation… and it is absolutely not clear whether it will be of clinical relevance.

‘We have to wait for the complete sequencing.’

On Tuesday, the country’s disease control center reported 11,369 newly confirmed infections and 989 deaths, for an overall death toll of 47,622.

When the UK Government revealed the variant was probably the reason for a spike in local cases in the UK in mid-December, it plunged the South-East, London and the East of England into Tier 3 restrictions. 

The UK Government’s scientific advisors proclaimed it is up to 70 per cent more infectious than the previously dominant variant and encourage people to stay at home to prevent transmission. 

It is now believed to account for more than 60 per cent of all UK cases but in California, between December 27 and January 2, only 0.4 per cent of cases were of the Kent variant. At a comparable point in the UK, this figure was 1.2 per cent. 

‘This suggests the dynamics of B.1.1.7 might be somewhat less explosive in California versus its original epicenter in England,’ the researchers say. 

‘Clade 2 in Florida (population 21 million), on the other hand, exhibited more rapid displacement of non-B.1.1.7.,’ the researchers write.

Here, it accounted for 0.7 per cent of cases 34 days after it first emerged in the state and ‘at a comparable point into the B.1.1.7 outbreak in England B.1.1.7 accounted for about 0.1 per cent of all cases’. 

‘Hence, while it is evidently younger than the California clade 1 lineage, the Florida clade 2 lineage already accounts for a larger proportion of the Florida SARS-CoV-2 epidemic than clade 1 does of the California SARS-CoV-2 outbreak.’

The B.1.1.7 lineage currently only accounts for 0.3 per cent of coronavirus infections in the US, the researchers say. 

The reason for the different rate at which B.1.1.7 is overtaking pre existing stains remains unknown but the researchers provide a few possibilities in their study.

‘One possibility is that B.1.1.7’s transmission advantage may vary with mitigation intensity,’ they say.

‘Perhaps this lineage of SARS-CoV-2, with demonstrably higher viral loads in the upper airway than other variants, is able to seed superspreader events with relative ease when mitigation efforts are comparatively lax, but its transmission advantage is less acute when the playing field is leveled by, for example, widespread mask use and indoor crowd avoidance. 

‘Another possibility is that the non-B.1.1.7 lineages circulating in the US, particularly in California, may be more transmissible than the non-B.1.1.7 lineages in England with which B.1.1.7 has been competing, giving B.1.1.7 less of a transmission advantage and, thus, a slower displacement rate of non-B.1.1.7 lineages.’ 

Future mutant strains of coronavirus could be detected faster by studying SEWAGE 

Scanning sewage for new coronavirus variants is a viable strategy for speeding up detection of new strains which may be more infectious, a study has found.  

Wastewater analysis has previously been identified as a good way of spotting signs of local infection, but now Covid is rife around the world the focus has shifted towards using sewage to spot new variants. 

Currently, emerging variants are spotted when coronavirus swabs are sent to a special lab for genomic analysis. 

However, only around one in ten swabs are sent for this analysis in the UK, and many people who have the virus are asymptomatic and do not receive a test.

To get a bigger sample size the researchers turned to sewage, which catches waste from thousands of people at a time. 

US-based academics from the University of California-Berkeley devised a way to spot trace amounts of SARS-CoV-2, the virus which causes Covid-19, amplify it and then scan its genetic code to spot any mutations.

The discovery means scientists can catch variants without the need to screen people individually. 

‘SARS CoV-2 virus is excreted by individuals that are infected by Covid-19 and the faecal waste ends up in the wastewater systems,’ explains Professor Kara Nelson, who led the investigation.

‘By sampling wastewater, we can get information on infections for a whole population. 

‘Some wastewater systems serve several thousand people. Some serve hundreds of thousands of people.’      


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