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https://publichealthmatters.blog.gov.uk/2021/02/05/what-do-we-know-about-the-new-covid-19-variants/

What do we know about the new COVID-19 variants?

Posted by: , Posted on: - Categories: Coronavirus (COVID-19)
Coloured transmission electron micrograph (TEM) of a SARS-CoV-2 coronavirus particle
Coloured transmission electron micrograph (TEM) of a SARS-CoV-2 coronavirus particle isolated from a UK case of the disease Covid-19.

This blog was updated on 23 July

All viruses mutate over time. For this reason, very early on in the response to the COVID-19 pandemic, sequencing capability was established in the UK to monitor changes in the genome of the virus over time. Where variants are determined to have characteristics of interest or there is evidence of sustained transmission, PHE will monitor them closely to ensure appropriate and timely public health actions are taken.

This sequencing capability allowed us to detect the emergence of the variant first seen in South East England called Alpha, which went on to establish dominance before being outcompeted by a variant first identified in India, known as Delta. As case numbers remain high around the world, the virus will continue to naturally evolve and many more variants and mutations are likely to be identified in the coming months, both in the UK and in other countries.

Why are we now seeing these variants?

All viruses naturally mutate over time, and SARS-CoV-2, the virus that causes COVID-19 disease, is no exception. Over time, changes can build up in the genetic code of the virus, and these new viral variants can be passed from person to person. Most of the time the changes are so small that they have little impact on the virus.

But every so often a virus mutates in a way that benefits it, for example allowing it to spread more quickly, and causes us to be concerned about changes in the way the virus might behave. In this case the variant may be considered a ‘Variant of Concern’ by the UK public health authorities.

Most mutations are not a cause for concern. Scientists around the world have been monitoring these throughout the pandemic. In the UK, we have a comprehensive genomics system which allows us to detect these different mutations.

The UK has contributed around half of the sequences in the global SARS-COV-2 genome repository (GISAID). More samples are sent for sequencing than ever before and new rapid testing speeds up the detection of variants under close monitoring, which allows for public health interventions to be quickly put in place.

PHE, working with NHS Test and Trace alongside academic and international partners continues to bolster international capacity to identify variants of concern through the New Variant Assessment Platform.

Domestically, we work closely with PHE health protection teams, NHS Test and Trace and local authorities to quickly respond to variants of concern identified in the community. Public health interventions can include introducing enhanced contact tracing, targeted testing and increased vaccination in priority areas. The impact that variants can have on the effectiveness of vaccines is also closely monitored.

Everyone is now encouraged to take regular tests whether displaying symptoms or not, order online or call 119. We have a collective responsibility to follow local public health advice to help break the chains of transmission and reduce the virus spreading. Get vaccinated, work from home where you can and remember “hands, face, space, fresh air” at all times. These measures work, and they save lives.

What is the difference between a variant under investigation and a variant of concern?

Scientists and policy makers in the UK are working at pace to continually assess data and evidence emerging from our excellent genomics, epidemiology and virology capabilities to monitor all variants. Often starting out as signals under monitoring, mutations of the virus can be officially designated as under investigation (VUI) or of concern (VOC).

A VUI has mutations which are potentially concerning and UK or international community transmission. A VOC has demonstrated significant characteristics such as increased transmissibility, severity or ability to infect a person.

Which variants are currently VOCs and VUIs and how do we name them?

There are currently 4 designated Variants of Concern (VOC) and 10 Variants under Investigation (VUI). On 31 May 2021, the World Health Organisation (WHO) recommended a new SARS-CoV-2 variants naming system for VUIs and VOCs using the Greek alphabet for non-scientific audiences. PHE has incorporated this system but sometimes we designate a variant before WHO does so we need to assign our own name too. There are also variants PHE has previously designated VUIs and VOCs which are not covered by the WHO system.

Variants under Investigation Variants of Concern
Zeta (VUI-21JAN-01) Alpha (VOC-20DEC-01)
Beta (VOC-20DEC-02)
Eta (VUI-21FEB-03) Gamma (VOC-21JAN-02)
VUI-21FEB-04
Delta (VOC-21APR-02)
Theta (VUI-21MAR-02)
Kappa (VUI-21APR-01)

VUI-21APR-03

VUI-21MAY-01

 

 

VUI-21MAY-02

 

Lambda (VUI-21JUN-01)

 

VUI-21JUL-01

Every Friday we publish the total number of cases for each variant detected in the UK.

What does it mean when a variant is dominant?

When a variant establishes dominance, it is the strain most detected in the population and we have seen variants outcompete each other twice in the UK during the pandemic. The original, or wildtype virus was superseded by Alpha, the variant first detected in South East England in December 2020 before Delta, a variant first detected in India became dominant in June 2021.

Accelerating testing

As the UK’s testing and sequencing capability has increased so too has our ability to detect variants in the community. Advances in technology has seen the introduction of rapid tests, called reflex assays that allow specific variants to be detected quickly. Compared to the 5-10 days required for whole genome sequencing (WGS) laboratory and analysis, the reflex assay test can give a result for specific variants within 48 hours. Positive tests identified through reflex assay testing are subsequently confirmed through WGS and recent data has shown them to be extremely accurate in indicating a positive variant result.

This allows earlier detection of trends and provides a more complete picture of a variant’s spread across the country. It also helps to inform studies on transmissibility and how the variant interacts with vaccination. During a pandemic it is crucial to have as much information as possible, as early as possible. The tests can also be quickly adapted when a new variant is detected in the community, to provide intelligence on its spread and potential to become dominant.

Do vaccines work against variants?

Yes, studies point towards vaccination being effective against symptomatic disease, particularly after two doses. We are furthering our scientific understanding every day. Vaccines are even more effective at preventing severe disease and death. We expect vaccines to be even more effective at preventing severe disease and death. While no vaccine offers 100% protection for everyone, they are still our best line of defence. If you are eligible, we urge you to come forward and be vaccinated and remember that two doses provide significantly more protection than one.

What do we know about the Delta variant (VOC-21APR-02)?

The Delta variant was classified as a VOC by PHE on 06 May due to evidence that it was at least as transmissible as the Alpha variant, which was dominant at the time. Evidence has since emerged that Delta is significantly more transmissible and experts are working to establish by exactly how much. Now the dominant strain, Delta is found in over 90% of samples tested.

Targeted investigations are ongoing into cases and clusters across the UK to identify more cases and to ensure that people self-isolate when required. These measures, implemented by PHE health protection teams, NHS Test and Trace, and local authorities, are the most effective at breaking the chains of transmission and additional control measures, including surge testing and enhanced vaccination, can be implemented where there is evidence of increased spread.

A recent PHE study showed that 2 doses of vaccine offers high levels of protection against symptomatic disease from Delta. Another analysis shows that after 2 doses the vaccines are also highly effective against hospitalisation. PHE is continuing to carry out laboratory testing, in collaboration with academic and international partners to better understand the impact of the mutations on the behaviour of the virus.

What are the other VOCs?

There are 3 other VOCs in the UK: Alpha, Beta and Gamma.

Alpha

This variant, also known as VOC-20DEC-01 originated in the UK and includes multiple mutations in the spike protein, including N501Y. Genetic evidence suggests this variant emerged in September 2020 and it went on to spread widely across the globe. You can read our expert interview on finding this variant and the race to understand it here.

Beta

Beta was first identified in South Africa and appears to have emerged around the same time as the variant originating in the UK. It has the E484K mutation which laboratory studies have shown may be capable of escaping the body’s antibodies and is therefore of potential public health concern, so it’s one we’re monitoring closely. All cases with this mutation are followed-up closely UK. Additional surge testing has been deployed in a number of locations where the Beta has been found. It is also detectable through the rapid testing technology.

Over 1,000 cases have been identified in total.

Gamma

Gamma, also referred to as P.1, was first detected in Manaus, a city in North West Brazil, and in travellers in Japan from Brazil. It shares some important mutations with the variant first identified in South Africa, such as E484K and N501Y. Over 200 cases have been identified but we are watching it closely and all cases continue to be followed up through enhanced contact tracing.

What about the other VUIs?

There are currently 10 variants under investigation.

Zeta

Also known as P.2, this variant was first detected in Brazil and 60 cases have been detected in the UK since January 2021.

Eta

Declared a VUI in February 2021 when 38 cases were detected in the UK, the variant has also been found in countries including Nigeria and Denmark. Nearly 500 cases have been detected to date.

VUI-21FEB-04

This E484K containing variant was first detected in the UK and declared a VUI in February 2021. Just over 300 cases have been found in total.

Theta

Originally detected in the Philippines, Theta was declared a VUI in March 2021 after 2 cases linked to travel tested positive in the UK. It contains the notable mutations including E484K and N501Y. Only 7 cases have been identified in total since then.

VUI-21APR-03

Initially detected in India, this variant was designated a VUI in April. The variant is from the B.1.617 lineage, the same family as Delta and Kappa. 14 cases have been identified.

Kappa

Less than 500 cases have been identified in the UK since it was classified as a VUI. It too shares the same lineage as Delta and VUI-21APR-03. While closely related, their genetic profiles are different and were assigned as standalone variants so that we can track them properly and take fast public health action as needed.

VUI-21MAY-01

This is another VUI first detected in the UK, where cases were first found in Yorkshire and the Humber in May 2021. Where cases are identified, additional follow-up of cases, testing of contacts and targeted case finding will limit its spread.

VUI-21MAY-02

The second VUI to be declared in May 2021 was first found in someone who had travelled from Egypt to Thailand. It’s a VUI based on an unusual mutation profile and increased importation from a widening international area. Cases are dispersed across England.

Lambda (VUI-21JUN-01)

On 23 June, Lambda was declared a VUI by PHE due to international expansion and several notable mutations including L452Q and F4905. 8 cases have been detected in the England, all with links to overseas travel. All appropriate public health interventions will be undertaken to limit its spread.

VUI-21JUL-01

Previously a signal in monitoring and escalated to a VUI on 21 July, the variant shows international expansion and subsequent importation to the UK. There is currently no evidence that it causes more severe disease or renders the vaccines currently deployed any less effective.

Can a variant stop circulating?

PHE considers a variant provisionally extinct after 12 weeks without detection in the UK although we continue to monitor to see if they reappear. So far 3 variants have become provisionally extinct.

VUI-21MAR-01

Detected in the UK in two people returning from abroad, it was declared a VUI in March due to the mutations E484K and N501Y. No additional cases have been found.

VUI-21FEB-01

First detected in Liverpool variant, no cases of this variant have been detected since 23 February. The total case count was 79.

VOC-21FEB-02

With a final total case count of 43, the variant thought to have originated in Bristol, UK, has not been detected in England since 1 March 2021.

More information

You can access all the information that PHE publishes on variants here.

This collection includes detailed fortnightly Technical Briefings, which contain data and analyses from PHE’s domestic and international partners as we work together to better understand the significance of each variant. These investigations help us to put in place effective and proportionate interventions to keep the public safe and offer the best advice to Ministers.

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