Covid-19 genomics bulletin
COVID-19 Genomics Bulletin
30 October 2024
This report describes the epidemiology of SARS-CoV-2 (the virus that causes COVID-19) variants in Northern Ireland.
The availability of SARS-CoV-2 sequencing results is affected the current COVID-19 testing policy and practice. We continue to monitor the circulating lineages detected through clinical testing and community sentinel surveillance for changes in prevalence of genomic variants and emergence of novel variants. We use intelligence from UKHSA and other public health authorities to monitor prevalence of mutations that may be associated with changes in immunity or severity.
It should be noted that date ranges in this report are different from those reported in the Respiratory Surveillance Report, available here.
Grouping of lineages into their parent lineages is subject to change, as variant definitions and lineages under monitoring are revised.
1 Summary
-
In the 8 epidemiological weeks (19 August 2024 to 08 October 2024), 269 COVID-19 samples were sequenced in Northern Ireland.
-
The current most common SARS-CoV-2 variant in Northern Ireland is KP.3 (V-23DEC-01), with 48 sequenced samples, or 92.3% of all sequenced samples (100% of those with a lineage assigned) in the week commencing 30 September 2024.
-
More information about prevalence and growth rates of SARS-CoV-2 lineages circulating in the UK can be found in UKHSA reports published here.
2 Current Variant View - last 8 weeks
This section summarises the SARS-CoV-2 sequencing data for Northern Ireland for the last 8 weeks of sequencing data available (19 August 2024 to 08 October 2024).
In the last 8 weeks of sequencing data, the following parent lineages have been detected: KP.3, XEC, KP, JN.1, BA.3, and BA.2. The number of sequenced samples can be seen in Table 2.1 and Figure 2.1, and the numbers as a percentage of total sequenced samples are shown in Figure 2.2. The age group distribution by parent lineage is shown in Figure 2.3.
Please note that numbers of sequenced samples per week may change retrospectively due to the delay in sequencing.
Recombinant refers to any lineage starting with “X” that does not fall under any other parent lineage definition.
Table 2.1. Number (Percentage) of sequenced samples for variants in Northern Ireland over the last 8 epidemiological weeks (week commencing) |
||||||||
---|---|---|---|---|---|---|---|---|
Variant (parent lineage) |
2024-08-19 |
2024-08-26 |
2024-09-02 |
2024-09-09 |
2024-09-16 |
2024-09-23 |
2024-09-30 |
2024-10-07 |
Unassigned (Unassigned) |
5 (13.2%) |
5 (11.6%) |
1 (3.6%) |
5 (20.8%) |
4 (9.1%) |
2 (5.7%) |
4 (7.7%) |
0 (0) |
V-23DEC-01 (KP) |
1 (2.6%) |
3 (7%) |
2 (7.1%) |
2 (8.3%) |
0 (0) |
0 (0) |
2 (3.8%) |
0 (0) |
V-23DEC-01 (KP.3) |
30 (78.9%) |
31 (72.1%) |
19 (67.9%) |
11 (45.8%) |
32 (72.7%) |
25 (71.4%) |
36 (69.2%) |
4 (80%) |
V-23DEC-01 (XEC) |
1 (2.6%) |
2 (4.7%) |
4 (14.3%) |
4 (16.7%) |
7 (15.9%) |
8 (22.9%) |
9 (17.3%) |
1 (20%) |
VOC-21NOV-01 (BA.3) |
1 (2.6%) |
1 (2.3%) |
0 (0) |
1 (4.2%) |
0 (0) |
0 (0) |
0 (0) |
0 (0) |
V-23DEC-01 (JN.1) |
0 (0) |
1 (2.3%) |
1 (3.6%) |
1 (4.2%) |
1 (2.3%) |
0 (0) |
1 (1.9%) |
0 (0) |
VOC-22JAN-01 (BA.2) |
0 (0) |
0 (0) |
1 (3.6%) |
0 (0) |
0 (0) |
0 (0) |
0 (0) |
0 (0) |
Week Total |
38 |
43 |
28 |
24 |
44 |
35 |
52 |
5 |
This chart only shows counts for lineages with at least 5 sequenced samples in a given age group.
Age band information is not available for all sequences, so age band distributions should be interpreted with caution.
3 Variant View - last 12 months
This section summarises the COVID-19 sequencing data for Northern Ireland over the past 12 months (08 October 2023 to 08 October 2024).
The number of sequenced samples over the past 12 months can be seen in Figure 3.1 and supplementary Table 6.2, and the numbers as a percentage of total sequenced samples are shown in Figure 3.2. The age-sex distribution by parent lineages is shown in Figure 3.3.
This chart only shows counts for lineages with at least 5 sequenced samples in a given age group.
4 Percentage of Specimens Sequenced
Not all PCR samples are sequenced; sequencing can only be carried out on samples that have a sufficiently high viral load, which is largely determined by when the sample is taken during the course of the infection. Other factors affecting how many samples are sequenced include volume of sample available, sample quality, and sequencing laboratory capacity.
The number of COVID-19 positive PCR samples (sequenced and not sequenced) in Northern Ireland over the past 12 months (02 October 2023 to 07 October 2024) is shown in Figure 4.1. The percentage of COVID-19 positive PCR samples that have been sequenced in on a weekly basis over the past 12 months is shown in Figure 4.2, with 6.33% sequenced (4 week rolling average of 17.22%) in the week commencing 07 October 2024.
5 Key Definitions and Interpretation
5.1 Definitions
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Variant nomenclature - UKHSA made changes to the variant classification system from the 1st April 2022, resulting in previously assigned Variants Under Investigation (VUIs) or Variants of Concern (VOCs) to be assigned with the V nomenclature. Details of the change to the classification system can be found in Technical briefing 39 here.
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Lineage assignment algorithm - on 29th November 2022, the lineage assignment algorithm was switched from PangoLEARN to UShER for lineage counts. PangoLEARN uses a machine learning algorithm, whereas UShER uses phylogenetic placement and produces few unassigned lineages.
5.2 Interpretation of variant data
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Lineage counts for recent weeks may increase due to the time lag associated with whole genome sequencing.
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Lineage calls are subject to change following analysis of genomic sequence results, which may result in fluctuations in lineage/variant counts.
6 Appendix
6.1 Total counts by lineage for the last 8 weeks of sequencing data (19 August 2024 to 08 October 2024)
Table 6.1. Summary of variants sequenced in Northern Ireland over the past 8 weeks |
|||
---|---|---|---|
Lineage |
Parent Lineage |
Variant |
Sequenced count |
BA.2 |
BA.2 |
VOC-22JAN-01 |
1 |
BA.3 |
BA.3 |
VOC-21NOV-01 |
3 |
KP.2.19 |
KP |
V-23DEC-01 |
1 |
KP.2.2 |
KP |
V-23DEC-01 |
1 |
KP.2.3 |
KP |
V-23DEC-01 |
6 |
KP.2.3.4 |
KP |
V-23DEC-01 |
1 |
KP.2.3.5 |
KP |
V-23DEC-01 |
1 |
KP.3.1 |
KP.3 |
V-23DEC-01 |
16 |
KP.3.1.1 |
KP.3 |
V-23DEC-01 |
136 |
KP.3.2 |
KP.3 |
V-23DEC-01 |
2 |
KP.3.3 |
KP.3 |
V-23DEC-01 |
3 |
KP.3.3.2 |
KP.3 |
V-23DEC-01 |
2 |
KP.3.3.4 |
KP.3 |
V-23DEC-01 |
1 |
LB.1 |
JN.1 |
V-23DEC-01 |
1 |
LB.1.3 |
JN.1 |
V-23DEC-01 |
1 |
LB.1.3.1 |
JN.1 |
V-23DEC-01 |
1 |
LB.1.7 |
JN.1 |
V-23DEC-01 |
2 |
MC.1 |
KP.3 |
V-23DEC-01 |
5 |
MC.10 |
KP.3 |
V-23DEC-01 |
3 |
MC.11 |
KP.3 |
V-23DEC-01 |
2 |
MC.13 |
KP.3 |
V-23DEC-01 |
4 |
MC.15 |
KP.3 |
V-23DEC-01 |
1 |
MC.16 |
KP.3 |
V-23DEC-01 |
5 |
MC.2.1 |
KP.3 |
V-23DEC-01 |
1 |
MC.5 |
KP.3 |
V-23DEC-01 |
1 |
MC.6 |
KP.3 |
V-23DEC-01 |
2 |
MC.8.1 |
KP.3 |
V-23DEC-01 |
1 |
MC.9 |
KP.3 |
V-23DEC-01 |
1 |
MK.1 |
KP.3 |
V-23DEC-01 |
1 |
MM.1 |
KP.3 |
V-23DEC-01 |
1 |
Unassigned |
Unassigned |
Unassigned |
26 |
XEC |
XEC |
V-23DEC-01 |
36 |
Total |
- |
- |
269 |
6.2 Total counts and percentage sequenced by parent lineage for the last 12 months of sequencing data (08 October 2023 to 08 October 2024)
Table 6.2. Summary of variants sequenced in Northern Ireland over the past 12 months |
||||
---|---|---|---|---|
Parent Lineage |
Variant |
WHO variant name |
Sequence count |
Percentage sequenced |
JN.1 |
V-23DEC-01 |
Omicron |
507 |
27.8 |
KP.3 |
V-23DEC-01 |
Omicron |
489 |
26.8 |
Unassigned |
Unassigned |
|
388 |
21.3 |
XBB |
V-22OCT-02 |
Recombinant |
76 |
4.2 |
BA.2.86 |
V-23AUG-01 |
Omicron |
73 |
4.0 |
EG.5.1 |
V-23JUL-01 |
Recombinant |
65 |
3.6 |
KP |
V-23DEC-01 |
Omicron |
65 |
3.6 |
XEC |
V-23DEC-01 |
Omicron |
40 |
2.2 |
BA.3 |
VOC-21NOV-01 |
Omicron |
31 |
1.7 |
XBB.1.5 |
V-23JAN-01 |
Recombinant |
31 |
1.7 |
XBB.1.16 |
V-23APR-01 |
Recombinant |
30 |
1.6 |
BA.2 |
VOC-22JAN-01 |
Omicron |
22 |
1.2 |
JN.1 |
Unassigned |
|
4 |
0.2 |
CH.1.1 |
V-22DEC-01 |
Omicron |
1 |
0.1 |
Recombinant |
Recombinant |
Recombinant |
1 |
0.1 |