COVID: how worried should we be about the new AY.4.2 lineage of the coronavirus?

Asia's Tech News Daily

SARS-CoV-2, the virus that causes COVID-19, with its spike proteins shown in blue. Design_Cells/Shutterstock

No sooner than you thought all the talk of new COVID variants was over, there’s news of yet another one: AY.4.2. But what is it, where did it come from, and should we be concerned?

AY.4.2 is what’s termed a “lineage”. These are labels given to branches of the COVID evolutionary tree to illustrate their relatedness. They are overseen by the diligent Pango network, a joint team of researchers from the universities of Edinburgh and Oxford, who act as the custodians of lineages and handle the assignment of new ones.

If we go back to April of this year, we can trace the origins of AY.4.2. Our team in Northumbria, working as part of Cog-UK – the British consortium that sequences the genomes of COVID samples to see how the virus is changing – had just sequenced two samples connected via travel history to India.

At the time we knew the lineage circulating in India was B.1.617, but the cases we had sampled didn’t matching this. Variants are distinguished by the different mutations they have in their genetic material and, looking at the mutations in our samples, it appeared our cases were missing some of the commonly accepted mutations of B.1.617 but also had some additional ones.

What we were reporting to colleagues in Cog-UK was classified the following week as B.1.617.2, one of three main sub-lineages of B.1.617, and which was later named delta by the World Health Organization.

AY is a further evolutionary step forward from here. Once a lineage’s labelling gets five levels deep, a new letter combination is started to avoid the name getting too long. So the AY forms of the virus aren’t vastly different from what’s come before, even though their labelling is different. They are all sub-lineages of delta.

There are now 75 AY lineages identified, each with different additional defining mutations in their genome. One of these – AY.4 – has been steadily growing in proportion in the UK over the last few months, accounting for 63% of new UK cases in the last 28 days.

Does AY.4 have an advantage?

We’re still not sure if AY.4’s mutations confer a genuine advantage or if the increasing frequency of the lineage is simply down to what’s called a “founder effect”. This is when a subset of viruses get separated from the overall viral population, and then reproduce in isolation. In the area where the separated viruses are, all subsequent viruses will therefore be descendants of this subset.

AY.4 may have spread because of favourable conditions, rather than having a distinct advantage over earlier lineages. Rawpixel.com/Shutterstock

With COVID, this might have happened by there being a single case at a large event. This lone virus would have been the “founder”, the only virus spreading at the event. If it infected a sizeable number of people, who later infected others, this may have quickly built up a large amount of virus all from the same origin. Sometimes, for a certain form of a virus to dominate, it doesn’t have to be better than others – it simply needs to be in the right place at the right time.

But, given its rise to dominance in the UK, AY.4 might well have a selective advantage. The defining change in AY.4 is the mutation A1711V, which affects the virus’s Nsp3 protein, which plays a number of roles in viral replication. However, the impact of this mutation is unknown.

This brings us to AY.4.2 – a sub-lineage of AY.4 – which was first noted at the end of September, though it appears it surfaced in the UK around June. It’s defined by two additional genetic mutations, Y145H and A222V, that affect the spike protein. The spike protein is a key part of the virus’s outer surface, and is the part of its structure that it uses to get inside cells.

AY.4.2 has grown steadily in volume to the point where it now accounts for about 9% of UK cases in the last 28 days. It has also been observed in a few European nations: Denmark, Germany and Ireland, to name a few.

But whether its two mutations offer the virus a selective advantage is unclear as well. A222V was previously seen last year in the B.1.177 lineage that probably emerged in Spain and was then spread across northern Europe, most likely by holidaymakers. At the time, many were sceptical that A222V conferred an advantage. Indeed, the increase in the form of the virus that’s become known as AY.4.2 seems to have only occurred since it acquired its Y145H mutation.

This mutation is within an “antigenic supersite” of the spike protein – a part of the protein that antibodies frequently recognise and target. We know that this part of the spike protein has already been modified once before by a mutation in delta’s genetic material, and that this possibly contributes to delta’s greater ability to escape immunity, as antibodies have a harder time targeting it as a result. However, the research exploring this is still in preprint, meaning it is yet to be formally reviewed – so we need to treat its findings with caution.

If the shape of AY.4.2’s spike proteins (red) has changed, antibodies (white) may struggle to bind to them to destroy the virus. Leonid Altman/Shutterstock

But it’s therefore possible the Y145H mutation could give the virus an even greater ability to escape immunity by making this supersite less recognisable to antibodies.

The counterargument is that, despite introduction into several European countries, AY.4.2 has failed to take hold, dropping off the radar in Germany and Ireland – though it is lingering in Denmark. This would suggest its ability to get around immunity isn’t any greater than delta’s. Equally, it might just be that there wasn’t enough of AY.4.2 arriving in these places for it to take hold.

Really, it’s too early to tell if this is the beginning of the next dominant lineage. Any ability it might have to escape immunity needs to be confirmed by experimental work. Clearly, though, it’s emergence shows that there’s a continued need for genomic surveillance of the virus.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

The Conversation

Matthew Bashton holds Cog-UK funding and is currently supporting SARS-CoV-2 sequencing funded by the UK Health Security Agency.

Darren Smith receives funding from Cog-UK/the UK Health Security Agency/UK Research and Innovation. He is currently a deputy director of Cog-UK and leads the funded Northumbria University hub. He also leads continuing SARS-CoV-2 genome sequencing at Northumbria University funded by the UK Health Security Agency.

Internet Explorer Channel Network
Asia's Tech News Daily
News Related

OTHER NEWS

HP is keeping the savings going with a massive pre-Cyber Monday flash sale—here's what to buy

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Tech gifts are at a premium during Cyber Monday, and right ... Read more »

Dyson vacuums and fans are majorly marked down ahead of Cyber Monday 2021—here are the best Dyson deals

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Cyber Monday 2021 deals are here early, and now is the ... Read more »

This is where you can get Cyber Monday deals on the Oculus Quest 2

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. For a standalone virtual reality headset you can use for video ... Read more »

Customers and staff prepare to spend third night trapped at highest pub in Britain due to Storm Arwen

Stranded guests at the Tan Hill Inn, in the Yorkshire Dales have been entertained with a quiz, films and music. (PA) Staff and customers trapped at Britain's highest pub were ... Read more »

Keira Knightley says she is ‘feeling pretty rubbish' with Covid while her ‘smug' husband is asymptomatic

Keira Knightley has said she feels “pretty rubbish” due to Covid-19. In an interview with The Times’s Stella magazine, the actor asked: “Do you mind if we don’t turn our ... Read more »

These are the absolute best Verizon, T-Mobile and AT&T Cyber Monday 2021 deals

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. If a new phone is what you’re after this Cyber Monday, ... Read more »

The best Cyber Monday laptop deals you can get at HP, Best Buy and more

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Laptops are some of the priciest gadgets on the market, but ... Read more »

Best GPS Watches For Ladies

­­Wearable technology has evolved considerably over recent years and GPS golf watches now offer an impressive amount of detailed information that could previously only be found on handheld devices. © ... Read more »

This Nuna car seat is $50 off ahead of Cyber Monday, but act fast—this sale won't last

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. During Cyber Monday 2021, we’re seeing all kinds of amazing deals ... Read more »

Best Cyber Monday web hosting deals in 2021: from Hostinger, Bluehost, Hostgator and more

The number of Cyber Monday web hosting deals that have come through over the last few days can be a little overwhelming to some. Luckily, we’ve done all the hard ... Read more »

Cyber Monday coffee machine live blog: the best Keurig and Nespresso offers

Refresh 2021-11-27T18:43:54.549Z Welcome to TechRadar’s Cyber Monday coffee machine deals live blog, where we’re pointing you towards all the very best offers. Whether you prefer a creamy latte, a smooth ... Read more »

The best Apple Cyber Monday 2021 deals on AirPods, iPhones, iPads and more

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Cyber Monday is almost here, but the savings are already in ... Read more »

Amazon's top Cyber Monday laptop deal is this $160 convertible Chromebook

With only a few hours remaining until Cyber Monday officially starts, there is a clear winner when it comes to laptops. The current best selling laptop this Sunday, at Amazon ... Read more »

COVID-19: UK calls meeting of G7 health ministers to discuss Omicron variant as third case found in Britain

The UK has called a meeting of G7 health ministers on Monday to discuss the Omicron COVID variant – after a third infected person was found in Britain. The individual, ... Read more »

Covid booster rollout could be rapidly expanded to tackle Omicron

Photograph: Maureen McLean/Rex/Shutterstock Change to criteria could happen as soon as Monday as No 10 tries to combat variant’s spread The Covid booster vaccination scheme could be significantly expanded as ... Read more »

Hulu Cyber Monday deal: You can still get a full year of Hulu for 99 cents per month through Cyber Monday

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Update 1:57 PM EST: Hulu’s Black Friday deal is running right ... Read more »

Rams vs Packers live stream: how to watch NFL online from anywhere

Switching that golden West Coast sun for a freezing Sunday night in Wisconsin is probably most Californians’ idea of hell, and the Packers will be looking to use the icy ... Read more »

Lady Gaga and Tony Bennett will perform tonight 'One Last Time'—here's how to watch it for free

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Though there’s a 60-year age difference between them, Tony Bennett and ... Read more »

Cyber Monday headphone deals are stellar—save on headphones from Bose, Sony and AirPods

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Winter’s here, which means you’ve got plenty of time to cozy ... Read more »

The Omicron variant has a 'record' number of mutations that may hinder vaccine effectiveness, NIH director says

NIH Director Francis Collins during a November 28, 2021, appearance on “Fox News Sunday.”Fox News/Fox News Sunday NIH Director Francis Collins said Sunday that the Omicron variant could present challenges ... Read more »

SoftBank in investment talks with mRNA vaccine firm Abogen: Sources

Chinese mRNA vaccine developer Suzhou Abogen Biosciences is in talks with Japan’s SoftBank and other investors to raise $300 million-$400 million, people familiar with the matter said. The fundraising by ... Read more »

Black Panther 2: cast, release date changes and all you need to know about Wakanda Forever

Read more »

Christmas and commerce have long gone together like two turtle doves

The author of this article is Philip Hancock, Professor of Work and Organization at the University of Essex. The “spirit of Christmas” is all about universal goodwill, caring about others ... Read more »

Shop huge markdowns during the Michael Kors Cyber Monday sale

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Whether you’re looking to upgrade your winter wardrobe or are simply ... Read more »

The best Cyber Monday Nintendo Switch SD card deals are right here

The Cyber Monday deals are starting to land, and whether you’re looking for a massive 1TB or smaller 128GB storage expansion we’ve found the best Cyber Monday SD card deals ... Read more »

Cyber Monday GPU deals 2021 - all sales and what to look out for

Cyber Monday graphics card deals are popping up all over now that we’re on the cusp of Cyber Monday itself. Until the big day, you’ll still find a range of ... Read more »

Woman punched in the face after asking teenager to wear facemask

Woman punched in the face after asking teenager to wear facemask Read more »

Ola and James Jordan's Strictly verdict: Why we'll be devastated if Rhys leaves the competition

Tensions rose in the Strictly Come Dancing ballroom as the competition reached its tenth week. While John Whaite and Johannes Radebe tangoed their way to the top of the leaderboard, ... Read more »

How to build a dev knowledge base ahead of your next job

Disclaimer: this is not an ad for Obsidian. Onboarding to a new company is hard work. Keeping all the information straight is its own work stream that deserves thought and ... Read more »

Score Cyber Monday golf deals at Dick's Sporting Goods, Callaway, Academy Sports and more

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Hunting for impressive Cyber Monday golf deals? We’re tracking all the ... Read more »

‘He's missing': anxious wait in Calais camps for news on Channel victims

Photograph: David Levene/The Guardian On Saturday Gharib Ahmed spent five hours outside the police station in Calais, desperately waiting for news. “It was so cold. There was no answer,” he ... Read more »

Best Cyber Monday TV deals: the best cheap TV deals right now

The Black Friday deals are waning but in their place plenty of new Cyber Monday deals are appearing. The relentless cycle of new TVs means there are plenty of savings ... Read more »

Cyber Monday PS5 SSD and hard drive deals 2021: all the latest sales live now

Cyber Monday PS5 SSD deals are going live across the internet as the weekend rolls into its final hours, marking new savings to stay on the lookout for even as ... Read more »

You can already shop massive KitchenAid mixer Cyber Monday sales—here are the best ones

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. KitchenAid is known for quality products that range from large appliances ... Read more »

Cyber Monday PS5 live blog: restocks, games and accessories

Refresh 2021-11-28T16:35:26.426Z (Image credit: Activision) Call of Duty: Vanguard was only released a few weeks ago, but Walmart is already offering a decent discount on the PS5 version of the ... Read more »

Cyber Monday Xbox live blog: restocks, games and accessories

Refresh 2021-11-28T16:37:56.677Z (Image credit: Double Fine) Psychonauts 2 is my personal Game of the Year. Sure, the combat is a bit clunky, but it’s a brilliant tongue-in-cheek (but evocative) adventure ... Read more »

Boris Johnson tightens rules on travel and mask-wearing over Omicron concerns

Boris Johnson has announced fresh measures to curb the spread of coronavirus including mandatory masks in shops and PCR tests for travellers entering England after two cases of the Omicron ... Read more »

Third person identified with Omicron in UK visited central London

© PA PA-57506430.jpg A third case of the Omicron Covid variant has been detected in the UK. The individual, who is no longer in the UK, visited central London while ... Read more »

Apple AirPods Cyber Monday live blog: the best Pro, Max and 3rd gen deals

Refresh 2021-11-28T16:15:15.031Z (Image credit: Apple) Let’s kick off with the best Cyber Monday AirPods deal out there right now in the US – the AirPods Max have dropped to their ... Read more »

The best robot vacuum Cyber Monday deals you can already get on iRobot, Eufy and more

— Recommendations are independently chosen by Reviewed’s editors. Purchases you make through our links may earn us a commission. Get your home holiday-ready by picking up a robot vacuum for ... Read more »
On free-english-test.com you will find lots of free English exam practice materials to help you improve your English skills: grammar, listening, reading, writing, ielts, toeic