SARS-CoV-2 variants of concern and  
variants under investigation in  
England  
Technical briefing 7  
1
1 March 2021  
This briefing provides an update on previous briefings up to 13 February 2021  
SARS-CoV-2 variants of concern and variants under investigation  
Contents  
Summary.................................................................................................................... 3  
Variants in Monitoring............................................................................................. 4  
Variant assessment tools........................................................................................ 4  
VOC 202012/01 (B.1.1.7)........................................................................................... 6  
VOC 202102/02 (B.1.1.7 cluster with E484K) .......................................................... 10  
Variant in monitoring B.1.1.7 with S494P Clade ................................................... 12  
VOC 202012/02 (B.1.351)........................................................................................ 13  
VOC 202101/02 (P.1)............................................................................................... 15  
VUI 202101/01 (P2).................................................................................................. 17  
VUI 202102/01 (A.23.1 with E484K)......................................................................... 20  
VUI 202102/03 (B.1.525).......................................................................................... 23  
VUI 202102/04 (B.1.1.318)....................................................................................... 25  
VUI 202103/01 (B.1.324.1 with E484K).................................................................... 29  
Appendices .............................................................................................................. 31  
Appendix 1. SGTF Surveillance............................................................................ 31  
Sources and acknowledgments ............................................................................... 34  
Data sources......................................................................................................... 34  
Variant Technical Group....................................................................................... 34  
2
SARS-CoV-2 variants of concern and variants under investigation  
Summary  
There are 4 variants of concern and 5 variants under investigation (Table 1).  
A slightly increased risk of hospitalisation has been now been detected for VOC  
2
02012/01 (B.1.1.7), supporting previous findings on fatality.  
The first VOC 202101/02 (P.1) cases have been detected in England. The VOC  
02101/02 (P.1) risk assessment indicates that it is plausible that there is some  
2
degree of either immune escape or increased transmissibility, or both. This is  
based on laboratory data and modelling; the magnitude and clinical significance  
of these effects have yet to be determined.  
VOCs (excluding VOC 202012/01 B.1.1.7) and VUIs remain low at less than 1%  
of samples with a sequence result available.  
Table 1. Total case numbers England per VOC/VUI as of 10 March 2021  
England genomic cases 10 March 2021, of 329734  
total sequences with unique identifier  
Variant  
Pangolin Confirmed  
lineage  
Probable  
Total confirmed  
and probable  
VOC 202012/01  
VOC 202102/02  
B1.1.7  
98,422  
34  
10,671  
0
109,093  
34  
B.1.1.7  
with  
E484K  
cluster  
VOC 202012/02  
VOC 202101/02  
VUI 202101/01  
VUI 202102/01  
B.1.351  
P1  
190  
5
76  
2
266  
7
P2  
46  
59  
0
46  
78  
A.23.1  
with  
19  
E484K  
VUI 202102/03  
VUI 202102/04  
VUI 202103/01  
B.1.525  
79  
28  
0
107  
18  
2
B.1.1.318 18  
B.1.324.1  
with  
2
0
E484K  
Case numbers on variants of concern (VOC) and variants under investigation (VUI) are  
updated online. Note table excludes variant cases not linked to a known COVID-19 case,  
which may represent duplicate results or non-England residents.  
3
SARS-CoV-2 variants of concern and variants under investigation  
Variants in Monitoring  
Variants in monitoring are those which have been identified through horizon scanning, do not  
have sufficient clear signals of concern to escalate further, but for which case numbers and  
available data are being monitored regularly. These variants are in the monitoring category:  
B.1.429 first detected in California (10/329,734 UK sequences as of 10 March  
021)  
B.1.1.7 with S494P first detected in the UK (761/329,734 UK sequences as of  
0 March 2021)  
2
1
A.27 first detected in Mayotte (4/329,734 UK sequences as of 10 March 2021)  
B.1.526 first detected in New York (2/329,734 UK sequences as of 10 March  
2
021)  
Variant assessment tools  
Repository of human and machine readable genomic case definitions  
A repository containing the up-to-date genomic definitions for all VOC and VUI as curated by  
Public Health England was created 5 March 2021. The repository can be accessed on  
GitHub. They are provided in order to facilitate standardised VOC and VUI calling across  
sequencing sites and bioinformatics pipelines and are the same definitions used internally at  
Public Health England. Definition files are provided in YAML format so are compatible with a  
range of computational platforms. The repository will be regularly updated.  
Variant risk assessment.  
Variant risk assessment includes the following confidence grading categorisations and  
utilises the framework in Table 2.  
Low: Little or poor-quality evidence, uncertainty or conflicting views amongst experts, no  
experience with previous similar incidents.  
Moderate: Adequate quality evidence, including consistent results published only in grey  
literature, reliable source(s), assumptions made on analogy and agreement between  
experts or opinion of at least 2 trusted experts.  
High: Good quality evidence, multiple reliable sources, verified, expert opinion concurs,  
experience of previous similar incidents.  
4
SARS-CoV-2 variants of concern and variants under investigation  
Table 2. Variant risk assessment framework.  
Indicator  
Risk assessment framework  
Zoonotic  
Animal reservoir  
identified but no  
evidence of  
transmission from  
animals to humans  
Sporadic transmission from  
animals to humans  
Frequent transmission  
from animals to humans  
emergence and  
transmission to  
humans  
Transmissibility  
between humans  
No demonstrated  
person to person  
transmission  
Limited human case clusters Established human to  
human transmission,  
which appears similar to  
Transmissibility appears  
greater than the wild type  
virus  
wild type virus  
Infection severity  
Evidence of less  
severe clinical  
picture or lower  
Similar clinical picture and  
infection fatality to wild type  
SARS-CoV-2 infections  
More severe clinical  
picture or higher infection or higher infection fatality  
fatality than from wild type than from wild type SARS-  
More severe clinical picture  
infection fatality than OR ex  
SARS-CoV-2 infections  
(limited to specific risk  
groups)  
CoV-2 infections  
from wild type  
SARS-CoV-2  
infections  
perimental animal data  
suggesting potential for  
increased disease severity in  
humans  
Susceptibility and  
immunity natural  
infection  
Evidence of no  
antigenic difference  
from other circulating other circulating wild type  
wild type virus  
Structural data suggesting  
antigenic difference from  
Experimental evidence of Evidence of frequent infection  
functional evasion of  
naturally acquired  
immunity  
in humans with known prior  
infection with earlier virus  
variant.  
virus  
Vaccines  
Evidence of no  
Structural data suggesting  
Experimental evidence of Evidence of frequent vaccine  
functional evasion of failure or decreased  
vaccine derived immunity effectiveness in humans  
structural or antigenic difference in vaccine target  
difference in vaccine epitopes  
targets  
Drugs and  
therapeutics  
Evidence of no  
structural or antigenic difference in therapeutic  
difference in  
Structural data suggesting  
Experimental evidence of Evidence of frequent drug or  
reduced drug susceptibility therapeutic failure or  
decreased effectiveness in  
target epitopes  
therapeutic targets  
humans  
5
SARS-CoV-2 variants of concern and variants under investigation  
VOC 202012/01 (B.1.1.7)  
This variant was designated VUI 202012/01 (B.1.1.7) on detection and on review re-  
designated as VOC 202012/01 (B.1.1.7) on 18 December 2020.  
Genomic profile  
Lineage defining mutations are shown in technical briefing 6. In addition, VOC 202012/01 has  
acquired other mutations in some cases. Mutation counts in the UK dataset are shown in  
Table 3.  
Table 3. VOC 202012/01 (B.1.1.7) Spike mutations acquired in addition to the variant  
defining mutations 11 December 2020 to 10 March 2021  
(Percentage indicates all sequences of VOC 202012/01 (B.1.1.7) per period in header).  
VOC 202012/01 (B.1.1.7) Spike variants  
Total number of  
instances in VOC 11 December  
11 January  
2021 to  
11 February  
2021 to  
Amino acid 202012/01  
2020 to  
change  
(B.1.1.7) (UK  
data) to 10 March 2021  
10 January  
10 February  
2021  
10 March  
2021  
2
021  
L18F  
3720 (2.7%)  
851 (0.6%)  
761 (0.6%)  
131 (0.1%)  
103 (0.1%)  
354 (0.3%)  
144 (0.1%)  
70 (0.1%)  
109 (0.1%)  
121 (0.1%)  
65 (0%)  
314 (0.7%)  
92 (0.2%)  
208 (0.4%)  
8 (0%)  
1431 (2.1%)  
366 (0.5%)  
339 (0.5%)  
25 (0%)  
549 (1.7%)  
348 (1.1%)  
88 (0.3%)  
84 (0.3%)  
42 (0.1%)  
37 (0.1%)  
30 (0.1%)  
27 (0.1%)  
24 (0.1%)  
23 (0.1%)  
13 (0%)  
Q677H  
S494P  
G142V  
S680F  
Y144F  
T678I  
13 (0%)  
120 (0.3%)  
25 (0.1%)  
7 (0%)  
36 (0.1%)  
164 (0.2%)  
54 (0.1%)  
23 (0%)  
H146Y  
F490S  
A475A  
E484K  
Q493K  
A684V  
10 (0%)  
11 (0%)  
10 (0%)  
0 (0%)  
64 (0.1%)  
64 (0.1%)  
37 (0.1%)  
1 (0%)  
14 (0%)  
11 (0%)  
51 (0%)  
8 (0%)  
23 (0%)  
10 (0%)  
Total VOC 202012/01 (B.1.1.7) 135,310  
6
SARS-CoV-2 variants of concern and variants under investigation  
Epidemiological profile  
Lineage B.1.1.7 is dispersed across the UK. Confirmed cases are those identified by whole  
genome sequencing. As of 10 March 2021, there were 109,093 confirmed and probable cases  
of VOC 202012/01 (B.1.1.7) in England (98,422 confirmed and 10,671 probable). The use of S  
gene target failure in the Taqpath assay as a good proxy for VOC 202012/01 (B.1.1.7) cases  
has been described in prior technical briefings. This continues to be supported by current data  
(Appendix 1). In samples tested with this assay in the Lighthouse Laboratories, samples with  
SGTF have predominated since mid December 2020, reaching 99% of cases in the week  
starting 3 March 2021. Proportions in all regions are >97% (Appendix 1). Confirmed and  
probable cases by specimen date are shown in Figure 1 and age-sex pyramid in Figure 2.  
7
SARS-CoV-2 variants of concern and variants under investigation  
Figure 1. Confirmed and probable VOC 202012/01 (B.1.1.7) cases by specimen date, 1 October 2020 to 10 March 2021  
3500  
3000  
2500  
2000  
1500  
1000  
500  
0
Specimen date  
8
SARS-CoV-2 variants of concern and variants under investigation  
Figure 2. Age-sex pyramid of VOC 202012/01 (B.1.1.7) cases, 1 October 2020 to  
1
0 March 2021  
80+  
70-79  
60-69  
50-59  
40-49  
30-39  
20-29  
<20  
15000  
10000  
5000  
0
5000  
10000  
15000  
Males  
Females  
Hospitalisations  
PHE undertook a record linkage to analyse sequenced confirmed VOC 202012/01 (B.1.1.7)  
cases between October and December 2020. A Cox proportional hazard analysis of 63,609  
sequenced cases identified a significantly increased risk of hospitalisation within 14 days of  
specimen date among VOC 202012/01 (B.1.1.7) cases compared to non-variant cases (HR  
1
.34, 95% CI:1.07-1.66, p=0.01), after adjusting for confounders (sex, age, ethnicity, residence  
type and week of diagnosis). This analysis used NHS hospital admission data from the NHS  
Digital Secondary Uses Service (SUS) which is subject to reporting delays, therefore these  
results represent a minimum estimate of hospital admission risk.  
Deaths  
As of 10 March 2021, there were 2,858 deaths (within 28 days) in the 109,093 cases with  
confirmed or probable VOC 202012/01 (B.1.1.7) (case fatality 2.6%).  
Immunisation  
Two interim assessments have been published covering B.1.1.7 and the UK vaccine  
programme1,2.  
1 Early effectiveness of COVID-19 vaccination with BNT162b2 mRNA vaccine and ChAdOx1 adenovirus vector  
vaccine on symptomatic disease, hospitalisations and mortality in older adults in the UK: a test negative case  
control study Jamie Lopez Bernal et al., 2021 Link  
2
Effectiveness of BNT162b2 mRNA Vaccine Against Infection and COVID-19 Vaccine Coverage in Healthcare  
Workers in England, Multicentre Prospective Cohort Study (the SIREN Study) Hall et al., 2021 Link  
9
SARS-CoV-2 variants of concern and variants under investigation  
International Epidemiology  
As of the 08 March 2021, there are 113 countries or territories (including the UK) reporting  
cases of the UK variants globally. Of countries/territories outside of the UK, 19 report, or there is  
evidence of, community transmission. However for many countries the information available on  
the extent of transmission within the country is not clear.  
GISAID (gisaid.org) includes data on sequences available internationally; as of the 10 March  
2
021 27,003 VOC 202012/01 (B.1.1.7) sequences (excluding UK) are available from 94  
countries/territories.  
VOC 202102/02 (B.1.1.7 cluster with E484K)  
Through routine scanning of variation in VOC 202012/01 (B.1.1.7) a small number of B.1.1.7  
sequences (65 of 135,310 sequences as of 10 March 2021), had acquired the spike protein  
mutation E484K. Information suggested more than one independent acquisition event and on  
investigation, this forms one predominant cluster and several separate cases or small clusters.  
The predominant cluster was designated VUI on detection and on review re-designated as VOC  
2
02102/02 (B.1.1.7 cluster with E484K) on 5 February 2021. The genomic and biological profile  
is as previously described.  
Epidemiological profile  
As of 10 March 2021, 34 genomically confirmed cases of VOC 202012/01 (B.1.1.7) have been  
identified; 21 with an epidemiological link to the South West and an additional 13 cases resident  
elsewhere in England (Table 4). Specimen dates range from 17 December 2020 to 20 February  
2
021, confirmed and probable cases by specimen date are shown in Figure 3.  
Table 4. Number of confirmed and probable VOC 202102/02 (B.1.1.7 cluster with E484K)  
cases, by region of residence (as of 10 March 2021)  
Region  
Confirmed  
Probable  
Total Percent of England total  
London  
1
11  
1
0
0
0
0
0
1
11  
1
2.9  
32.4  
2.9  
North West  
South East  
South West  
Total  
21  
34  
21  
34  
61.8  
100.0  
1
0
SARS-CoV-2 variants of concern and variants under investigation  
Figure 3. Confirmed and probable VOC 202102/02 (B.1.1.7 cluster with E484K) cases by specimen date, from 17 December  
2
020 as of 10 March 2021. Larger plot includes last 60 days only.  
1
1
SARS-CoV-2 variants of concern and variants under investigation  
Deaths  
As of 10 March 2021, one death (within 28 days) among 34 cases with confirmed VOC  
2
02102/02 (B.1.1.7 cluster with E484K) has been reported.  
International Epidemiology  
As of the 8 March 2021, international cases have been reported in 2 countries and 2  
sequences from the Netherlands have been identified on GISAID.  
Variant in monitoring B.1.1.7 with S494P Clade  
On 17 February 2021 the acquisition of Spike mutation S494P in VOC 202012/01 (B.1.1.7)  
samples was identified as a signal as part of the horizon scanning process for routine  
scanning of variation. Due to the large number of sequences identified, further analysis was  
undertaken. This mutation appears to have been acquired multiple times by VOC 202012/01  
(B.1.1.7). However, the majority of these sequences position within one clade, for which  
further information is presented here.  
Genomic and biological profile  
The cluster VOC 202102/02 (B.1.1.7) cluster with S494P has the mutations previously  
described for VOC 202012/01 (B.1.1.7) in technical briefing 6 with the addition of S494P in  
spike gene and 2 mutations in orf1ab (NSP8 Q24Rand NSP5 SNP G10870T). S494P allows  
evasion of binding or neutralization by several monoclonal antibodies but has not been  
shown to impact on neutralization by convalescent or vaccine-induced polyclonal antisera.  
S494P confers increased binding to hACE2.3,4  
Epidemiological profile  
As of 10 March 2021, there were 761 genomically confirmed cases. Cases of VOC  
2
02012/01 (B.1.1.7) with S494P have been increasing in recent weeks.  
The distribution of cases over time shows that the clade began in the South East in  
November 2020 and spread throughout this area in December 2020. It was also seen in the  
North West during December 2020, expanding in January 2021.  
3Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody Rappazzo  
et al., 2021 Science DOI: 10.1126/science.abf4830 link  
4
Whelan Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate  
monoclonal and serum antibody neutralization Liu et al., 2020. bioRxiv 2020.11.06.372037 link  
1
2
SARS-CoV-2 variants of concern and variants under investigation  
VOC 202012/02 (B.1.351)  
B.1.351 was initially detected in South Africa. This variant was designated VUI on detection  
and on review re-designated as VOC 202012/02 (B.1.351) on 24 December 2020.  
Epidemiological profile  
VOC 202012/02 (B1.351) is dispersed across the UK in low numbers. Confirmed cases are  
those identified by whole genome sequencing; probable cases are COVID-19 cases without  
sequencing, but who are contacts of confirmed cases. As of 10 March 2021, 266 cases of  
VOC 202012/02 (B.1.351) were identified (190 confirmed cases and 76 probable cases). An  
international travel link was identified for 181 cases, and 68 cases had no travel link (17  
awaiting further information). Confirmed and probable cases by specimen date are shown in  
Figure 4, age-sex pyramid in Figure 5, and regional breakdown in Table 5.  
Figure 4. Confirmed and probable VOC 202012/02 (B.1.351) cases by specimen date,  
from 10 December 2020 as of 10 March 2021 (3 cases are omitted without specimen  
date)  
1
1
1
4
2
0
8
6
4
2
0
Specimen date  
1
3
SARS-CoV-2 variants of concern and variants under investigation  
Figure 5. Age-sex pyramid of VOC 202012/02 (B.1.351) cases, from 10 December 2020 as  
of 10 March 2021  
80+  
70-79  
60-69  
50-59  
40-49  
30-39  
20-29  
<20  
30  
25  
20  
15  
10  
5
0
5
10  
15  
20  
25  
Males  
Females  
Table 5. Confirmed and probable cases by region, 10 December 2020 to 10 March 2021  
VOC 202012/02 (B.1.351)  
Region  
n
%
East Midlands  
East of England  
London  
6
2.3  
40  
83  
6
15.0  
31.2  
2.3  
North East  
North West  
South East  
South West  
West Midlands  
Yorkshire and Humber  
TBC  
32  
54  
13  
22  
10  
0
12.0  
20.3  
4.9  
8.3  
3.8  
0.0  
Total  
266  
1
4
SARS-CoV-2 variants of concern and variants under investigation  
Deaths  
As of 10 March 2021, there were 6 deaths (within 28 days) in the 266 cases with confirmed or  
probable VOC 202012/02 (B.1.351) (case fatality 2.3%).  
International Epidemiology  
As of 8 March 2021 there are 62 countries (including the UK) that have reported cases of this  
variant globally. As of 08 March 2021 the epidemiological profile in South Africa is as follows:  
The case incidence is continuing to decrease. Currently, the reported weekly  
incidence is 12.9 per 100,000 population. Weekly test positivity has also been  
decreasing with current test positivity of 4.3%. Testing rates have been declining  
since mid-January although remained relatively stable over the previous 2 weeks  
(current weekly testing rate is 3.0 per 1,000 population).  
The fatality rate is decreasing (the weekly fatality rate is 1.2 per 100,000  
population).  
The number of patients in hospital and ICU has also reduced slightly. As of 08  
March 2021, 914 COVID-19 patients are in ICU and 6,105 are in hospital.  
GISAID (gisaid.org) includes data on sequences available internationally. As of the 10 March  
021 2,643 sequences of VOC 202012/02 (B.1.351), excluding UK, are available from 46  
2
countries/territories.  
VOC 202101/02 (P.1)  
First identified in Japan amongst travellers from Brazil, the P.1 lineage is a descendant of  
B.1.1.28. This variant was designated VUI on detection and on review re-designated as VOC  
2
02101/02 (P.1) on 13 January 2021. The clinical risk assessment for P1 is shown in Table 6.  
Table 6. Risk assessment for VOC 202101/02 (P.1)  
Indicator  
RAG Confidence Assessment and rationale  
Zoonotic  
NA  
Not applicable  
emergence  
Transmissibility  
between humans  
MOD  
Transmissibility appears greater than wild  
type virus in the context of Manaus, and  
there is MODERATE confidence that this  
represents a true change in phenotype.  
1
5
SARS-CoV-2 variants of concern and variants under investigation  
Indicator  
RAG Confidence Assessment and rationale  
Infection severity  
NA  
Insufficient information. Reports from  
Manaus are confounded by healthcare  
system stresses. Clinical cohort studies  
currently underway in Brazil may provide  
data in the medium term.  
Naturally acquired  
immunity  
HIGH  
There is experimental evidence of evasion  
of naturally acquired immunity (HIGH  
confidence). There was a severe second  
wave in Manaus, despite apparently high  
seroprevalence. Better quality evidence, for  
example comparing the rate of confirmed  
reinfections in P1 and non P1 cohorts is  
required to raise the risk to red.  
Vaccine derived  
immunity  
MOD  
MOD  
There is experimental evidence of evasion  
of vaccine derived immunity in laboratory  
studies (MODERATE confidence). The  
magnitude of the effect may be less than  
that of B.1.351 (South Africa), based on  
limited laboratory data . Clinical trial and  
surveillance data are required.  
Drugs and  
Therapeutics  
There is experimental evidence that variants  
containing E484K may have reduced  
susceptibility to some monoclonal antibody  
based therapies in laboratory conditions  
(MODERATE confidence).  
Overall assessment  
of level and nature  
of risk, and level of  
confidence  
There are limited data available on P.1. It is a  
successful lineage in Brazil and is showing  
some evidence of international spread. The  
spread of P1 in the UK, where the prevalent  
virus is B.1.1.7, cannot be extrapolated from  
the trajectory observed in Manaus.  
There is laboratory evidence supporting  
antigenic change, and this is consistent with  
the epidemiology reported from Brazil. In the  
context of the situation in Manaus, it is difficult  
to differentiate immune escape and increased  
transmissibility, and some degree of both is  
plausible. . However, there are no robust,  
comparative clinical re-infection or vaccine  
efficacy data.  
There is an urgent need to assess severity.  
1
6
SARS-CoV-2 variants of concern and variants under investigation  
Epidemiological profile  
As of 10 March 2021, 7 genomically confirmed and probable cases of VOC 202101/02 (P.1) have been  
identified in England. All cases have been linked to international travel.  
Deaths  
As of 10 March 2021, there were no reported deaths in cases of VOC 202101/02 (P.1) in England.  
International Epidemiology  
As of 8 March 2021, cases of VOC 202101/02 (P.1) have been reported in 20 countries or territories. 8  
countries have reported cases of a Brazilian variant additional information is awaited to clarify if this is  
with VOC 202101/02 (P.1).  
GISAID (gisaid.org) includes data on sequences available internationally. As of the 10 March 2021 562  
sequences of VOC 202101/02 (P.1) are listed (Brazil 304, Italy 102, Belgium 29, Peru 24, USA 18,  
Colombia 17, Switzerland 16, Portugal 11, France 9, Japan 8, Ireland 6, Netherlands 4, French Guiana  
3
, Romania 2, South Korea 1, Canada 1, Mexico 1, Spain 1, Sint Maarten 1, Germany 1, Turkey 1,  
Australia 1, Faroe Islands 1).  
VUI 202101/01 (P2)  
First identified in Brazil, the P.2 lineage is a descendant of B.1.1.28. This variant was designated VUI  
on detection and on review re-designated as VUI 202101/01 (P.2) on 13 January 2021.  
Genomic profile  
VUI 202101/01 is lineage P.2 (first sequence detected in Brazil and was first sequenced in the UK in  
November 2020). The complete mutation profile of VUI 202101/01 (P.2) is shown in Table 7 and  
genomic case definition in Table 8.  
1
7
SARS-CoV-2 variants of concern and variants under investigation  
Table 7. VUI 202101/01 (P.2) Variant defining mutations  
Gene  
Amino Acid  
Actual Nucleotide  
Note  
not included in definition  
due to masking  
-
100>T  
L3468V  
-
10667T>G  
11824C>T  
nsp5:L205V  
nsp6:I248I  
orf1ab  
nsp9:G93G; not lineage  
defining  
-
12964A>G  
S Gene  
orf8  
E484K  
F120F  
A119S  
M234I  
23012G>A  
28253C>T  
28628G>T  
28975G>T  
N Gene  
not included in definition  
due to masking  
-
29754>T  
Table 8. VUI 202101/01 (P.2) Genomic case definition  
All variant defining changes called as alternate base or 6 of 7 changes  
called as alternate base and remaining position either N or mixed base  
CONFIRMED  
PROBABLE  
NA  
Fewer than 6 positions are called but at least one is called as alternate  
(variant) base and all other defining positions reported as N (unknown)  
or mixed bases.  
LOW_QC  
Epidemiological profile  
As of 10 March 2021, 46 cases of VUI 202101/01 (P.2) have been identified in England. 9 cases  
have been linked to international travel, and 32 cases had no travel link (5 awaiting further  
information). Confirmed and probable cases by specimen date are shown in Figure 6 and age-  
sex pyramid in Figure 7.  
1
8
SARS-CoV-2 variants of concern and variants under investigation  
Figure 6. Confirmed and probable VUI 202101/01 (P.2) cases by specimen date, from 14 November 2020 as of 10 March 2021  
5
4
3
2
1
0
Specimen date  
1
9
SARS-CoV-2 variants of concern and variants under investigation  
Figure 7. Age-sex pyramid of VUI 202101/01 (P.2) cases, 10 December 2020 to 10 March 2021  
80+  
70-79  
60-69  
50-59  
40-49  
30-39  
20-29  
<20  
8
6
4
2
0
2
4
6
8
Males  
Females  
International Epidemiology  
As of 8 March 2021, cases of VUI 202101/01 (P.2) have been reported in 11 countries or territories.  
GISAID (gisaid.org) includes data on sequences available internationally. As of the 10 March 2021 862  
sequences (excluding UK) of VUI 202101/01 (P.2) are listed ( Brazil 382, USA 267, French Guiana 42,  
Canada 23, Switzerland 22, Netherlands 21, Denmark 18, Portugal 16, Spain 11, Ireland 11, France  
1
1
0, Norway 6, Chile 6, Argentina 5, Germany 4, Australia 3, Japan 3, Sweden 3, Mexico 3, Singapore  
, Austria 1, Italy 1, Sint Maarten 1, Belgium 1, Malaysia 1).  
VUI 202102/01 (A.23.1 with E484K)  
This variant was first identified in Liverpool, UK, derived from a lineage first identified in Uganda  
without E484K. The variant was designated VUI on detection and on review re-designated as VUI  
2
02102/01 (A.23.1 with E484K) 5 February 2021.  
Genomic profile  
VUI 202102/01 (A.23.1 with E484K) is lineage A.23.1 (first sequence detected in the UK in  
December 2020). The complete mutation profile of VUI 202102/01 (A.23.1 with E484K) is shown  
in Table 9 and genomic case definition in Table 10.  
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SARS-CoV-2 variants of concern and variants under investigation  
Table 9. VUI 202102/01 (A.23.1 with E484K) Variant defining mutations  
Gene  
Amino Acid  
L1559F  
M3655I  
L3667F  
M3752I  
R102I  
Actual Nucleotide  
4940C>T  
Note  
nsp3:L741F  
nsp6:M86I  
nsp6:L98F  
nsp6:M183I  
11230G>T  
11266G>T  
11521G>T  
21867G>T  
22033C>A  
22661G>T  
23012G>A  
23401G>T  
23604C>G  
28144T>C  
28167G>A  
28878G>A  
orf1ab  
F157L  
V367F  
E484K  
Q613H  
P681R  
L84S  
S Gene  
orf8  
E92K  
N Gene  
S202N  
Table 10. VUI 202102/01 (A.23.1 with E484K) Genomic case definition  
CONFIRMED  
PROBABLE  
LOW_QC  
All variant defining changes called as alternate base  
At least 5 variant defining changes called as alternate base and all  
other positions either N or mixed base  
Fewer than 5 variant defining changes called as alternate base and all  
other positions either N or mixed base  
Epidemiological profile  
As of 10 March 2021, 59 genomically confirmed and 19 genomically probable cases of VUI  
2
02102/01 (A.23.1 with E484K) have been identified; 78 in total. The majority of these are  
residents of the North West of England (Table 11). Specimen dates range from 26 December  
020 to 23 February 2021 (Figure 8).  
2
Table 11. Number of confirmed and probable VUI 202102/01 (A.23.1 with E484K) cases,  
by region of residence (as of 10 March 2021)  
Percent of  
Region  
Confirmed  
Probable  
Total  
England total  
North West  
West Midlands  
Total  
58  
1
19  
0
77  
1
98.7  
1.3  
59  
2
19  
78  
100.0  
1
SARS-CoV-2 variants of concern and variants under investigation  
Figure 8. Confirmed and probable VUI 202102/01 (A.23.1 with E484K) cases by specimen date, from 26 December 2020 as of 10  
March 2021. Larger plot includes last 60 days only. Excludes 1 case with unknown specimen date.  
2
2
SARS-CoV-2 variants of concern and variants under investigation  
Deaths  
As of 10 March 2021, 1 death (within 28 days) in 78 cases with VUI 202102/01 (A.23.1 with  
E484K) has been reported (case fatality 1.3%).  
International Epidemiology  
The are no cases reported internationally as of the 8 March 2021.  
GISAID (gisaid.org) includes data on sequences available internationally. As of the 10 March  
2
021 1 sequence is listed of VUI 202102/01 (A.23.1 with E484K) (excluding UK) from  
Netherlands.  
VUI 202102/03 (B.1.525)  
First identified as a geographically dispersed cluster in UK on the 2 February 2021. This variant  
was designated VUI on detection and on review re-designated as VUI 202102/03 (B.1.525) on  
1
2 February 2021.  
Genomic profile  
VUI 202102/03 (B.1.525) is lineage B.1.525 (first sequence detected in the UK in February  
2
1
021). The complete mutation profile of VUI 202102/01 (A.23.1 with E484K) is shown in Table  
2 and genomic case definitions in Table 13.  
Table 12. VUI 202102/03 (B.1.525) Variant defining mutations  
Gene  
Amino Acid  
Actual Nucleotide  
1498C>T  
Note  
-
nsp2:F231F  
nsp2:G334G  
-
1807A>G  
-
2659G>A  
T2007I  
6285C>T  
nsp3:T1189I  
nsp4:V13V  
-
-
8593T>C  
orf1ab  
9565C>T  
nsp4:F337F  
nsp6:106_8del  
nsp12:P323S  
nsp14:G44G  
nsp16:L22L  
3
675_7del  
11288_96del  
14407C>T  
18171C>T  
20724A>G  
21717A>G  
21762C>T  
P4715S  
-
-
Q52R  
A67V  
S Gene  
2
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SARS-CoV-2 variants of concern and variants under investigation  
Gene  
Amino Acid  
Actual Nucleotide  
21765_70del  
21991_3del  
23012G>A  
23593G>C  
24224T>C  
Note  
6
1
9_70del  
44del  
E484K  
Q677H  
F888L  
-
24748C>T  
F1062F  
E Gene  
M Gene  
orf6  
L21F  
I82T  
26305C>T  
26767T>C  
2del  
27205_7del  
28278_80del  
28308C>G  
28699A>G  
29543G>T  
2
_3del  
N Gene  
A12G  
-
-
P142P  
Red text indicates acquisition in subset of isolates within the lineage, non-variant defining  
mutations. Indels (shaded in orange) are not currently included in variant definitions.  
Table 13. VUI 202102/03 (B.1.525) Genomic case definition  
CONFIRMED  
PROBABLE  
All variant defining changes called as alternate base  
At least 5 variant defining changes called as alternate base and all other  
positions either N or mixed base  
Fewer than 5 variant defining changes called as alternate base and all  
other positions either N or mixed base  
LOW_QC  
Biological profile  
The significance of E484K has been described previously in this briefing. Q677H is proximal to  
the furin cleavage site, it is unclear what the impact of this mutation might be, however  
mutations around the furin cleavage site are known to modulate transmissibility. The deletions  
in the NTD (Δ69-70 and Δ144) are also found in the VOC 202012/01  
(B.1.1.7) variant, Δ144 is an antigenic escape mutant and is highly associated with virus  
replication in immunocompromised patients. The deletion in NSP6 (Δ106-108) is found in  
multiple variants of concern (VOC 202012/01 (B.1.1.7) variant, VOC 202012/02 (B.1.351) and  
VOC 202101/02 (P.1) variants). NSP6 is involved in immune evasion but the impact of this  
deletion is currently unclear.  
2
4
SARS-CoV-2 variants of concern and variants under investigation  
Epidemiological profile  
As of 10 March 2021, there were 107 cases of VUI 202102/03 (B.1.525) in England (79  
confirmed cases and 28 probable cases). In this geographically dispersed genomic cluster, 27  
were linked to international travel, and 51 cases had no travel link. Travel history for 27 cases is  
pending and 2 cases were not contactable.  
Deaths  
As of 10 March 2021, 4 deaths in 107 cases with VUI 202102/03 (B.1.525) has been reported  
(case fatality 3.7%).  
International Epidemiology  
As of 8 March 2021, cases of VUI 202102/03 (B.1.525) have been reported in 11 countries or  
territories.  
GISAID (gisaid.org) includes data on sequences available internationally. As of the 10 March  
2
021 328 sequences of VUI 202102/03 (B.1.525) are listed, excluding UK. (Denmark 120,  
Nigeria 76, USA 42, Italy 15, Slovenia 41, Canada 8, Japan 7, Netherlands 7, Germany 7,  
Ireland 6, France 6, Norway 4, Belgium 3, Australia 2, Jordan 2, Cameroon 2, Malaysia 2,  
Switzerland 2, Austria 2, Singapore 1, Finland 1, Thailand 1, Mayotte 1, Spain 1).  
VUI 202102/04 (B.1.1.318)  
The VUI 202102/04 (B.1.1.318) was identified in England in mid February 2021 through routine  
horizon scanning for the development of new clusters within the E484K genomes. This analysis  
identified an initial cluster of 6 cases containing E484K and other spike mutations, designated  
VUI 202102/04 (B.1.1.318) 23 February 2021.  
Genomic profile  
VUI 202102/04 (B.1.1.318) is lineage B.1.1.318. The complete mutation profile of VUI  
2
02102/04 (B.1.1.318) is shown in Table 14 and genomic case definitions in Table 15.  
Table 14. VUI 202102/04 (B.1.1.318) Variant defining mutations  
Indels (shaded in orange) are not currently included in variant definitions.  
Gene  
Amino Acid  
E378V  
-
Nucleotide  
3852A>T  
3961C>T  
7798G>T  
9072C>T  
Note  
nsp3:E378V  
orf1ab  
K2511N  
T2936I  
nsp3K1693N  
nsp4:T173I  
2
5
SARS-CoV-2 variants of concern and variants under investigation  
Gene  
Amino Acid  
A3209V  
Nucleotide  
9891C>T  
Note  
nsp4:A446V  
nsp5:T21I  
T3284I  
10116C>T  
11288_96del  
20578G>A  
21846C>T  
21991_3del  
23012G>A  
23287T>C  
23604C>A  
23948G>C  
24382C>T  
25276C>A  
26767T>C  
27894_901del  
28209G>T  
28271A>G  
28896_8del  
3
675_7del  
nsp6:106_8del  
nsp15:V320M  
V6672M  
T95I  
1
44del  
E484K  
-
S
P681H  
D796H  
-
-
M
N
I82T  
1
_3del  
orf8  
E106  
-
A208_A209delinsG  
Table 15. VUI 202102/04 (B.1.1.318) Genomic case definition  
CONFIRMED  
PROBABLE  
LOW_QC  
All variant defining changes called as alternate base  
At least 5 variant defining changes called as alternate base and all other  
positions either N or mixed base  
Fewer than 5 variant defining changes called as alternate base and all  
other positions either N or mixed base  
Epidemiological profile  
As of 10 March 2021, there were 18 genomically confirmed cases of VUI 202102/04 (B.1.1.318).  
Cases are based across England (Table 16), with specimen dates ranging from 22 January 2021  
to 27 February 2021 (Figure 9). Three of the initial 6-person cluster are related to cases that  
travelled to Nigeria, however the wide geographic spread suggests this VUI may be a result of  
multiple importations or could be an undersampled within the UK.  
2
6
SARS-CoV-2 variants of concern and variants under investigation  
Table 16. Number of confirmed and probable VUI 202102/04 (B.1.1.318) cases, by region  
of residence (as of 10 March 2021)  
Percent of  
Region  
Confirmed  
Probable Total  
England total  
East Midlands  
East of England  
London  
1
1
0
0
0
0
0
0
0
0
1
1
5.6  
5.6  
5
5
27.8  
North West  
5
5
27.8  
South East  
2
2
11.1  
West Midlands  
Yorkshire and Humber  
Total  
1
1
5.6  
3
3
16.7  
18  
18  
100.2  
2
7
SARS-CoV-2 variants of concern and variants under investigation  
Figure 9. Confirmed and probable VUI 202102/04 (B.1.1.318) cases by specimen date, from 22 January 2021 as of 10 March 2021.  
Larger plot includes last 60 days only  
2
8
SARS-CoV-2 variants of concern and variants under investigation  
Deaths  
No deaths (within 28 days of specimen date) among confirmed or probable VUI 202102/04  
(B.1.1.318) have been reported as of 10 March 2021.  
International Epidemiology  
As of 8 March 2021 there are no cases reported internationally.  
GISAID (gisaid.org) includes data on sequences available internationally. As of the 10 March  
2
021, there are no international VUI 202102/04 (B.1.1.318) sequences.  
VUI 202103/01 (B.1.324.1 with E484K)  
First identified via horizon scanning of genomes with spike mutations characteristic of VOCs  
(
including both N501Y and E484K) on 3 March 2021, the variant VUI 202103/01 (B.1.324.1 with  
E484K) was designated VUI on detection as VUI 202103/01 (B.1.324.1 with E484K) on 4 March  
021.  
2
Genomic profile  
The complete mutation profile of VUI 202103/01 (B.1.324.1 with E484K) is shown in Table 17  
and genomic case definitions in Table 18.  
Table 17. VUI 202103/01 (B.1.324.1) Variant defining mutations  
Indels (shaded in orange) are not currently included in variant definitions.  
Gene  
Amino Acid  
Nucleotide  
1059C>T  
2945G>A  
3037C>T  
6730C>T  
6851A>C  
8704T>C  
8986C>T  
9120C>T  
9870C>T  
11005C>A  
12854C>T  
13458C>T  
13617G>A  
14408C>T  
14559G>A  
16852G>T  
Note  
T265I  
nsp2: T85I  
nsp3: G76S  
G894S  
-
-
T2196P  
-
nsp3: T1378P  
from wider lineage  
-
T2952I  
T3202M  
H3580Q  
P4197S  
S4398L  
-
nsp4: T189I  
orf1ab  
nsp4: T439M  
nsp6: H11Q  
nsp9: P57S  
nsp12: S6L  
from wider lineage  
nsp12: P323L  
P4715L  
-
G5530C  
nsp13: G206C  
2
9
SARS-CoV-2 variants of concern and variants under investigation  
-
22388C>T  
23012G>A  
23042T>C  
23063A>T  
23403A>G  
23604C>A  
24893G>A  
25563G>T  
27922_56del  
28272A>T  
28975G>A  
E484K  
S494P  
N501Y  
D614G  
P681H  
E1111K  
Q57H  
10_21del  
-
S Gene  
orf3a  
orf8  
from wider lineage  
N Gene  
M234I  
Table 18. VUI 202103/01 (B.1.324.1) Genomic case definition  
CONFIRMED  
PROBABLE  
LOW_QC  
All 8 variant defining changes called as alternate base  
N/A  
Fewer than 8 variant defining changes called as alternate base and all  
other positions either N or mixed base  
Epidemiological profile  
As of 10 March 2021, there are 2 confirmed cases in the UK in a single group of returning  
travellers. Two additional households note contact of which one has tested positive, sequence  
data not available. There is no current evidence of spread in the UK based on sequencing data.  
No deaths were reported.  
International Epidemiology  
As of 8 March 2021 there are no cases reported internationally.  
GISAID (gisaid.org) includes data on sequences available internationally. As of the 10 March  
2
021, 0 sequences are listed internationally of VUI 202103/01 (B.1.324.1 with E484K).  
3
0
SARS-CoV-2 variants of concern and variants under investigation  
Appendices  
Appendix 1. SGTF Surveillance  
One S gene mutation in VOC 202012/01 (B.1.1.7) causes deletion of amino acids 69 and 70  
(
Δ69-70), with a reproducible S gene target failure (SGTF). This is detected by the  
ThermoFisher TaqPath assay used in UK lighthouse laboratories (see Technical Briefing 1),  
TaqPath laboratories.’  
Considering pillar 2 samples where we know both the sequence and the SGTF status, 99.6% of  
Δ69-70 sequences are SGTF, compared to 0.05% of sequences without the deletion. Since 1  
January 2021, > 99.7% of Δ69-70 sequences are VOC 202012/01 (B.1.1.7) in all regions of  
England.  
Surveillance of SGTF, as a proxy for VOC 202012/01 (B.1.1.7), is based on positive tests  
reported by 3 lighthouse laboratories that use the Thermo Fisher TaqPath RT-PCR, and for  
which CT values are low enough to classify if the S gene is detectable. Specifically, positive  
tests with CT values >30 for any gene target are excluded. SGTF is defined as a positive test  
with CT values <=30 for the N and ORF1ab genes and an undetectable S gene. S gene positive  
is a positive test for which all 3 gene targets (N, ORF1ab, S) have CT values <=30.  
Samples with SGTF have predominated since mid-December 2020, and has remained above  
9
5% since the beginning of February 2021 (Figure 10). All regions in England are >98% SGTF  
in the most recent week (3 March to 9 March 2021; Figure 11). Total cases detected using the  
TaqPath assay have also been declining since the first week of 2021, reflecting the general  
decline in case rates across England.  
3
1
SARS-CoV-2 variants of concern and variants under investigation  
Figure 10. Weekly number and proportion of England Pillar 2 COVID-19 cases with SGTF among those tested with the TaqPath  
assay and with S gene detection results (1 September 2020 to 9 March 2021)  
3
2
SARS-CoV-2 variants of concern and variants under investigation  
Figure 11. Weekly number and proportion of England Pillar 2 COVID-19 cases with SGTF among those tested with the TaqPath  
assay and with S gene detection results, by region of residence (1 September 2020 to 9 March 2021)  
Data on coverage of TaqPath laboratories testing and numbers/proportions of cases with SGTF are shared daily with Local Authorities  
(Sunday to Friday) on the COVID-19 PHE Local Authorities Report Store (Sharepoint).  
3
3
SARS-CoV-2 variants of concern and variants under investigation  
Sources and acknowledgments  
Data sources  
Data used in this investigation is derived from the COG-UK dataset, the PHE Second  
Generation Surveillance System (SGSS), NHS Test and Trace, the Secondary Uses Service  
(SUS) dataset and Emergency Care Data Set (ECDS).  
Variant Technical Group  
Organisations  
This group includes representation from the following organisations: PHE, DHSC, BEIS, Wales  
NHS, PHScotland, NHS Scotland, Health and Social Care Northern Ireland, Imperial College  
London, London School of Hygiene and Tropical Medicine, University of Birmingham, University  
of Cambridge, University of Edinburgh, University of Liverpool, the Wellcome Sanger Institute.  
Acknowledgements  
The authors are grateful to those teams and groups provid  
ing data for this analysis, including: the Lighthouse Laboratories, COG-UK, the Wellcome  
Sanger Institute, the PHE Epidemiology Cell, Contact Tracing, Genomics and Outbreak  
Surveillance Teams.  
3
4
Contact: All enquiries should be addressed to [email protected]  
©
Crown copyright 2021  
Published: March 2021  
PHE gateway number: GW-1991