Covid variants identified in UK – latest updates

Latest update

UKHSA issues COVID-19 vaccination reminder as Omicron BA.4 and BA.5 become dominant in the UK, driving increase in infections

The UK Health Security Agency (UKHSA) is reminding people to ensure their COVID-19 vaccinations are up to date and to continue following COVID-safe behaviours, as latest technical data indicates BA.4 and BA.5 have become dominant in the UK and are driving the recent increase in infections.

The UKHSA’s COVID-19 variant technical briefing 43, published today, includes epidemiological analysis that shows that Omicron BA.4 and BA.5 now make up more than half of new COVID-19 cases in England, accounting for approximately 22% and 39% of cases, respectively.

Omicron BA.4 and Omicron BA.5 were designated as variants of concern on 18 May on the basis of an apparent growth advantage over the previously-dominant Omicron BA.2 variant.

UKHSA’s latest analysis suggests that Omicron BA.5 is growing 35.1% faster than Omicron BA.2, while Omicron BA.4 is growing approximately 19.1% faster. This suggests that BA.5 is likely to become the dominant COVID-19 variant in the UK.

The increasing prevalence of Omicron BA.4 and BA.5 is likely to be a factor in the recent increase in cases seen in the UK and elsewhere, though there is currently no evidence that Omicron BA.4 and BA.5 cause more severe illness than previous variants.

So far, vaccination means that the rise in cases is not translating to a rise in severe illness and deaths. UKHSA scientists are urging anyone who has not had all the vaccines they are eligible for to make sure that they get them as soon as possible.

COVID-19 has not gone away, so it is also vitally important that people continue to follow the guidance. Stay at home if you have any respiratory symptoms or a fever and limit contact with others until you are feeling better, particularly if they are likely to be at greater risk if they contract COVID-19.

Professor Susan Hopkins, Chief Medical Advisor at UKHSA said:

It is clear that the increasing prevalence of Omicron BA.4 and BA.5 are significantly increasing the case numbers we have observed in recent weeks. We have seen a rise in hospital admissions in line with community infections but vaccinations are continuing to keep ICU admissions and deaths at low levels.

As prevalence increases, it’s more important than ever that we all remain alert, take precautions, and ensure that we’re up to date with COVID-19 vaccinations, which remain our best form of defence against the virus. It’s not too late to catch up if you’ve missed boosters, or even first doses so please take your recommended vaccines.

Our data also show that 17.5 per cent of people aged 75 years and over have not had a vaccine within the past six months, putting them more at risk of severe disease. We urge these people in particular to get up-to-date.

If you have any symptoms of a respiratory infection, and a high temperature or feel unwell, try to stay at home or away from others – especially those who are elderly or vulnerable. Face coverings in crowded indoor spaces and hand washing will help to reduce transmission of infection and are especially important if you have any respiratory symptoms.

UKHSA encourage everyone to continue to follow the most up-to date guidance.

As we learn to live safely with COVID-19, there are actions we can all take to help reduce the risk of catching COVID-19 and passing it on to others.

The risk of catching or passing on COVID-19 is greatest when someone who is infected is physically close to, or sharing an enclosed or poorly ventilated space with, other people.

You will not always know whether someone you come into contact with is at higher risk of becoming seriously ill from respiratory infections, including COVID-19. They could be strangers (for example people you sit next to on public transport) or people you may have regular contact with (for example friends and work colleagues).

There are simple things you can do in your daily life that will help reduce the spread of COVID-19 and other respiratory infections and protect those at highest risk. Things you can choose to do are:

  • get vaccinated
  • let fresh air in if meeting others indoors
  • practise good hygiene:
    • wash your hands
    • cover your coughs and sneezes
    • clean your surroundings frequently
  • wear a face covering or a face mask, particularly if you are in crowded and enclosed spaces

Previous

Friday 6 May 2022

Omicron BA.4 and BA.5 designated as variant of concern by UKHSA

The UK Health Security Agency (UKHSA) has elevated the classification of the COVID-19 variants Omicron BA.4 and Omicron BA.5 to variants of concern (VOCs) on the basis of observed growth.

As of 17 May, 115 cases of BA.4 and 80 cases of BA.5 have been confirmed in England and the latest UKHSA variant technical briefing has been published today.

Whilst Omicron BA.4 and BA.5 are in the early stages of growth in the UK, analysis of the available data suggests that they are likely to have a growth advantage over the currently-dominant Omicron BA.2 variant.

There can be several reasons for growth advantage, but in the case of BA.4 and BA.5, laboratory data suggests a degree of immune escape which is likely to contribute.

Dr Meera Chand, Director of Clinical and Emerging Infections at UKHSA, said:

The reclassification of these variants as variants of concern reflects emerging evidence on the growth of BA.4 and BA.5 internationally and in the UK. Whilst the impact of these variants is uncertain, the variant classification system aims to identify potential risk as early as possible.

UKHSA is undertaking further detailed studies. Data and analysis will be released in due course through our regular surveillance reporting.

Friday 6 May 2022

The UK Health Security Agency (UKHSA) has released variant technical briefing 41.

This edition includes an update on the current circulating lineages, including several cases of Omicron BA.4 and BA.5 which have been detected in the UK.

UKHSA has also released a variant risk assessment for Omicron BA.4 and BA.5, summarising the emerging epidemiology and laboratory evidence.

As of 2 May 2022, 21 confirmed cases of Omicron BA.4 and 19 confirmed cases of Omicron BA.5 have been detected in England.

Dr Meera Chand, Director of Clinical and Emerging Infections at UKHSA, said:

UKHSA continues to monitor and study variants of SARS-CoV-2 closely and is working with academic partners to rapidly assess the significance of the lineages BA.4 and BA.5.

Our continued genomic surveillance allows us to further investigate variants that are growing within the UK.

Friday 25 March 2022

UKHSA releases updated analysis into recombinant COVID-19 variants in the UK

UKHSA’s most recent variant technical briefing includes examination of a number of recombinant variants which have been identified in the UK, as well as updated epidemiological and genomic analysis of Omicron BA.2.

A recombinant variant occurs when an individual becomes infected with 2 or more variants at the same time, resulting in a mixing of their genetic material within the patient’s body. This is not an unusual occurrence and several recombinant SARS-CoV-2 variants have been identified over the course of the pandemic.

As with any other coronavirus (COVID-19) variant, the vast majority do not confer any advantage to the virus and die out relatively quickly.

UKHSA’s new analysis examines 3 recombinants, known as XF, XE, and XD. Of these, XD and XF are recombinants of Delta and Omicron BA.1, while XE is a recombinant of Omicron BA.1 and BA.2.

In the UK, 38 cases of XF have been identified, though none have been seen since mid February. There is currently no evidence of community transmission within the UK.

XD has not been identified in the UK to date, though 49 cases have been reported to global databases, the majority of these are in France.

A total 637 cases of XE – a recombinant of Omicron BA.1 and BA.2 – have been confirmed in the UK so far. The earliest of these has a specimen date of 19 January 2022. There is currently insufficient evidence to draw conclusions about growth advantage or other properties of this variant. We continue to monitor all recombinants closely, routinely through our world-leading genomic surveillance and sequencing capability.

Professor Susan Hopkins, Chief Medical Advisor, UKHSA said:

Recombinant variants are not an unusual occurrence, particularly when there are several variants in circulation, and several have been identified over the course of the pandemic to date. As with other kinds of variant, most will die off relatively quickly.

This particular recombinant, XE, has shown a variable growth rate and we cannot yet confirm whether it has a true growth advantage. So far there is not enough evidence to draw conclusions about transmissibility, severity or vaccine effectiveness.

UKHSA will continue to monitor the situation closely as a matter of routine, as we do all data relating to SARS-CoV-2 variants both in the UK and internationally.

The variant technical briefing also includes updated analysis on Omicron BA.2, currently the dominant variant in the UK.

BA.2 is estimated to account for approximately 93.7% of cases in England, with the highest prevalence in the South East (96.4%) and the lowest in the East Midlands (91.1%). Data for Scotland, Wales and Northern Ireland is not included in the UKHSA Technical Briefing.

BA.2 continues to demonstrate a substantial growth advantage. Since the middle of February, this growth rate has settled at approximately 75% higher than other circulating Omicron lineages in England.

Ongoing analysis by UKHSA has found no evidence that infection with Omicron BA.2 results in a greater risk of hospitalisation, compared to Omicron BA.1.

UKHSA has also this week published further vaccine effectiveness data against hospitalisation following a booster dose. For the first time, this data includes analysis on vaccine effectiveness 15+ weeks after the booster dose.

This data shows that protection against severe illness from COVID-19 remains at over 90% in those aged 65 and over up to 14 weeks after a booster dose. While there is a suggestion that this wanes slightly after 15 weeks, protection in this age group remains high at over 85%.

This paper can be found as a pre-print, and the data is referred to in the latest vaccine surveillance report.

Change to variant classifications

UKHSA is updating its variant classification system to give a clearer indication of which variants have significant changes compared to the current dominant variant.

Under the new system, the variant of concern (VOC) label will be assigned to variants which are currently emerging or circulating, and which the following characteristics can be confirmed or predicted:

1. A detrimental change in biological properties (changes in transmissibility, severity or immune evasion) compared to the current dominant variant.

2. A growth rate potentially compatible with the eventual replacement of the current dominant variant.

There will be no other categorisation of variants, including no variant under investigation (VUI) category. Previous variants of concern which no longer meet the criteria will be redesignated.

UKHSA will continue to designate new variants, and these will receive a variant number (in the format V-date-number). We will continue to closely analyse all available biological, epidemiological and genomic evidence for any SARS-CoV-2 variant in the UK or internationally.

These changes will take effect as of 1 April 2022 and will be reflected in full in future technical briefings.

Friday 25 February 2022

The UK Health Security Agency (UKHSA) has published variant technical briefing 37.

Friday 28 January 2022

UKHSA publishes variant analyses of Omicron sub-lineage BA.2

The UK Health Security Agency (UKHSA) has published analyses of Omicron sub-lineage BA.2. Data by variant related to intensive care unit admissions is presented and an analysis into the effect of the recent surge of Omicron cases in care homes is also available in the latest technical briefing.

Omicron sub-lineage BA.2 (VUI-22JAN-01)

As of 24 January 2022, 1,072 genomically confirmed cases of BA.2 have been identified in England and all assessments remain preliminary whilst case numbers are relatively low.

BA.2 has an increased growth rate compared to BA.1 in all regions of England where there are enough cases to assess it. While growth rates can be overestimated in early analyses of a new variant, the apparent growth advantage is currently substantial.

Analysis from routine contact tracing data indicates that transmission is likely to be higher among contacts of BA.2 cases in households (13.4%) than those for contacts of other Omicron cases (10.3%) in the period 27 December 2021 to 11 January 2022. These early findings should be interpreted with caution as transmission data and dynamics can fluctuate, meaning that early findings can change quickly when new variants are identified.

A preliminary assessment did not find evidence of a difference in vaccine effectiveness against symptomatic disease for BA.2 compared to BA.1. After 2 doses, vaccine effectiveness was 9% and 13% respectively for BA.1 and BA.2, after 25+ weeks. This increased to 63% for BA.1 and 70% for BA.2 at 2 weeks following a third vaccine.

There is currently no data on the severity of BA.2. UKHSA will continue to carry out laboratory and epidemiological investigations to better understand the characteristics of this variant.

Dr Susan Hopkins, Chief Medical Advisor for UKHSA, said:

Ongoing variant analysis is an important part of our pandemic response. Thanks to the expertise of scientists at UKHSA and partner organisations, we’re able to respond quickly to new variations of the virus.

We now know that BA.2 has an increased growth rate which can be seen in all regions in England. We have also learnt that BA.2 has a slightly higher secondary attack rate than BA.1 in households.

Although hospitalisations and deaths remain low, cases are still high in some areas and some age groups so it’s important that we continue to act cautiously as restrictions are lifted. Consider wearing a face covering when in crowded places. Take a vaccine to protect yourself against COVID-19. If you have any symptoms, take a test.

Omicron data

UKHSA has also published analyses related to the original Omicron strain BA.1. Where variant information was available, the majority of intensive care unit (ICU) admissions from 24 November 2021 to 19 January 2022 had Delta infections. Overall numbers of ICU admissions have decreased over time, but where data was available admissions with Omicron have increased from 9% to more than 50% in the most recent week.

Although there was a rapid increase in SARS-CoV-2 infections in care homes during December 2021 in line with case rises in the community, there has not been an associated increase in hospital admissions.

Our findings suggest the current wave of Omicron infections is unlikely to lead to a major surge in severe disease in care home populations with high levels of vaccine coverage and/or natural immunity. There were very limited numbers of BA.2 in this study and no inferences can be made regarding BA.2.

Friday 21 January 2022

Omicron sub-lineage BA.2 designated as a variant under investigation (VUI)

The Omicron variant sub-lineage known as BA.2 has been designated a variant under investigation ( VUI-22JAN-01) by the UK Health Security Agency (UKHSA).

Overall, the original Omicron lineage, BA.1, is dominant in the UK and the proportion of BA.2 cases is currently low. The designation was made on the basis of increasing numbers of BA.2 sequences identified both domestically and internationally. There is still uncertainty around the significance of the changes to the viral genome, and further analyses will now be undertaken.

To date, there have been 426 cases of Omicron BA.2 confirmed by Whole Genome Sequencing (WGS), with the earliest dated 6 December 2021.

The areas with the largest number of confirmed cases are London (146) and the South East (97). Data for the devolved administrations will follow in due course.

Early analyses suggest an increased growth rate compared to BA.1, however, growth rates have a low level of certainty early in the emergence of a variant and further analysis is needed.

In total, 40 countries have uploaded 8,040 BA.2 sequences to GISAID since 17 November 2021. At this point it is not possible to determine where the sublineage may have originated. The first sequences were submitted from the Philippines, and most samples have been uploaded from Denmark (6,411). Other countries that have uploaded more than 100 samples are India (530), Sweden (181), and Singapore (127).

Omicron BA.2 lacks the genetic deletion on the spike protein which produces S-gene target failure (SGTF) in some polymerase chain reaction (PCR) tests, which has been used as a proxy for Omicron cases previously.

Dr Meera Chand, COVID-19 Incident Director at UKHSA, said:

It is the nature of viruses to evolve and mutate, so it’s to be expected that we will continue to see new variants emerge as the pandemic goes on. Our continued genomic surveillance allows us to detect them and assess whether they are significant.

So far, there is insufficient evidence to determine whether BA.2 causes more severe illness than Omicron BA.1, but data is limited and UKHSA continues to investigate.

Case rates remain high throughout the UK and we must remain vigilant and take up vaccinations. We should all continue to test regularly with LFDs and take a PCR test if symptoms develop.

Health and Social Care Secretary, Sajid Javid, said:

We are learning to live with this virus – and thanks to our world-leading surveillance system we can rapidly detect and carefully monitor any genetic changes to COVID-19.

Our exceptional vaccine rollout means the number of people severely affected by COVID-19 is low, and the UK’s innovation and research has discovered life-saving treatments for those most at risk from COVID-19.

As we cautiously return to Plan A, I encourage you to give yourself and your loved ones the best protection possible and Get Boosted Now.

As is routine for any new variants under investigation, UKHSA is carrying out laboratory and epidemiological investigations to better understand the characteristics of this variant. We will continue to monitor this situation closely and recommend appropriate public health measures if needed.

More detail will be available in UKHSA’s regular variant technical briefings.

Friday 14 January 2022

UKHSA publishes updated Omicron risk assessment and analysis on vaccine efficacy, sub-lineage and symptoms

The UK Health Security Agency (UKHSA) has published a new variant technical briefing containing an updated Omicron risk assessment, alongside analysis on vaccine efficacy, sub-lineages and symptoms.

The updated risk assessment includes indicators for infection severity in both adults and children.

There is now high confidence that the Omicron variant causes low severity of disease in adults. However, confidence levels for severity indicators for children are low because further analysis is required to compare the risk of hospitalisation between Omicron and Delta, and to assess the clinical nature of illness in children.

Susan Hopkins, Chief Medical Advisor at UKHSA, said:

This latest set of analysis once again demonstrates that a booster dose of the vaccine provides you with significant protection against hospitalisation from Omicron. Booster doses also increase the protection against symptomatic and asymptomatic infection which will reduce transmission in the population.

While signs remain encouraging on Omicron’s severity compared with Delta, the high levels of community transmission continue and may cause pressures on health services.

We’ll be undertaking further analysis to investigate the small rise in the number of children admitted to hospital but currently coronavirus (COVID-19) poses a very low health risk to children and infants. Early data shows that young children who are hospitalised experience mild illness and are discharged after short stays in hospital.

Getting your booster jab remains the most effective way of protecting yourself and others from infection and severe disease. While prevalence remains high, make sure to wear your mask in indoor settings and take a lateral flow test before meeting others. If you develop any symptoms, isolate immediately and get a PCR test.

BA.2 sub-lineage

As of January 10 2022, 53 sequences of the BA.2 sub-lineage of Omicron had been identified in the United Kingdom.

This sub-lineage, which was designated by Pangolin on 6 December 2021, does not have the spike gene deletion at 69-70 that causes S-gene target failure (SGTF), which has previously been used as a proxy to detect cases of Omicron. UKHSA are continuing to monitor data on the BA.2 sub-lineage closely.

Vaccine effectiveness

Vaccine effectiveness (VE) against Omicron has again been updated in this week’s briefing.

As previously published, data continues to show vaccine effectiveness against hospitalisation for Omicron remains high.

A booster dose was associated with a 74% reduced risk of hospitalisation in the first 2 to 4 weeks after vaccination, with the figure dropping to 66% 10 weeks or more after this dose. When combined with VE against symptomatic disease, the reduced risk of hospitalisation climbed to 92% 2 to 4 weeks after a third dose of the vaccine, down to 83% after 10 weeks or more.

There is further data showing that effectiveness against symptomatic disease is significantly lower compared to the Delta variant, and wanes more quickly.

Analysis shows that protection against symptomatic disease 2 to 4 weeks after a booster dose ranges from around 65% to 75%, dropping to 55% to 65% at 5 to 9 weeks – and 45% to 50% 10 weeks or more following the booster dose.

In the SIREN study, a large cohort of healthcare workers are tested regularly by PCR to detect asymptomatic infection in addition to normal testing practices for symptomatic infection. Updated analysis shows the additional incremental benefit from each vaccine exposure including for boosters, even in those who have had prior infection.

Prior infection is 44% effective at preventing future infection, increasing to 71% with 3 doses of the vaccine.

Symptoms

Technical Briefing 34 contains further analysis on symptom comparison on Omicron and Delta.

Of symptomatic cases, loss of smell and taste was found to be more common in people who tested positive for Delta than those who had Omicron. This matches a recent study led by Oxford University and the Office for National Statistics (ONS), using data from the COVID-19 Infection Survey produced by the latter.

Hospital admissions in children aged 0 to 5

There are indications of a small rise in children admitted to hospital, but these early signals need further investigations before we can draw any conclusions about whether Omicron causes more severe illness in children.

Early data shows that young children who are hospitalised experience mild illness and are discharged after short stays in hospital. Data continues to show COVID-19 poses a very low health risk to children and infants.

However, any stay in hospital for a child is too long if you’re a parent and it’s important we all take precautions to avoid the spread of infection.

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