The UK Health Security Agency (UKHSA) is working with the NHS and the general public well being businesses of the 4 nations to analyze the monkeypox outbreak. This briefing is produced to share knowledge helpful to different public well being investigators and tutorial companions endeavor associated work. It contains early proof and preliminary analyses which can be topic to alter.

Data reported within the technical briefing is as of 1 August 2022 (or as specified within the textual content) to permit time for evaluation.

Potential ranges of the outbreak in England

The outbreak will be thought-about to fall into one in every of 4 potential ranges of transmission:

Level 1

Incursions from remainder of the world – small numbers of imported circumstances with restricted onward transmission.

Level 2

Transmission inside an outlined sub-population.

Level 3

Transmission inside a number of sub-populations or bigger sub-population.

Level 4

Wider vital group transmission – with potential for endemic and native epi-zoonotic illness.

These could also be refined with higher understanding of modes of transmission.

At current, England is judged to be in stage 2.

Part 1. Risk evaluation as of 1 August 2022

UK trajectory

Nowcast and development

Over the previous couple of weeks there was roughly no change within the each day variety of confirmed circumstances. Case ascertainment continues to problem our understanding of the outbreak.

Assessment (confidence): zero (or low) each day case development (excessive).

Geographic unfold

The proportion of circumstances resident in London was greater than 75% from the beginning of the incident as much as 20 June 2022. This proportion stayed at round 66% in July 2022.

Assessment (confidence): remaining concentrated in London (average) however with proof of accelerating geographic unfold (low).


Whilst testing is freely out there and a blended inhabitants group is being examined, it’s doubtless that there’s below ascertainment. Atypical signs, together with single or scarce lesions, are reported and there are worldwide studies of subclinical an infection.

Assessment (confidence): inadequate data.

UK transmission

Outbreak stage

Level 2 is outlined as transmission inside an outlined sub-population, at present homosexual, bisexual and males who’ve intercourse with males (GBMSM) related by sexual networks. Enhanced surveillance knowledge doesn’t counsel a change in case combine, though it’s out there on solely 26% (703 out of two,638) of circumstances and is probably not consultant of the entire cohort. There are 22 girls with confirmed or extremely possible monkeypox in England (out of two,615 with identified gender). There isn’t any sturdy proof of sustained transmission outdoors some sexual networks of GBMSM, though the rise in feminine circumstances requires shut surveillance.

Assessment (confidence): stage 2 (average).

Route of transmission

Whilst the first reported route is thru shut or sexual contact, monkeypox virus has been detected in air and environmental samples within the hospital room of contaminated sufferers. There are not any confirmed cases of airborne transmission. Limited family transmission has been described within the UK. Detailed investigations of some circumstances have discovered small numbers with no identified route of acquisition, as a consequence of reporting no intercourse or different potential exposures throughout their incubation interval.

Assessment (confidence): transmitting primarily by shut or sexual contact (average).


Observed scientific severity

There are not any reported deaths within the UK. There is important morbidity within the majority of people who find themselves admitted to hospital for scientific care causes, together with extreme ache and problems as a consequence of secondary bacterial an infection. 

Assessment (confidence): in present inhabitants group, low mortality however vital morbidity (average). In wider inhabitants, inadequate knowledge.

Virological characterisation

UK genomic knowledge is now out there. The majority of outbreak circumstances are at present in a definite lineage (B.1) which has mutations of unknown significance in comparison with the closest beforehand characterised monkeypox virus genomes. A small variety of circumstances, together with 2 UK circumstances and a few worldwide circumstances, are in lineage A.2. Phylogeny counsel there could also be below sampled circulation of this lineage alongside B.1, and this virus and outbreak requires separate characterisation. There is proof suggestive of sustained human transmission previous to the 2022 outbreak however not clear-cut proof of adaptation for improved human transmission. There isn’t any phenotypic knowledge out there for this clade up to now.

Assessment (confidence): inadequate knowledge.

International trajectory

Global development

There is now indication of various trajectories in several international locations, with a number of international locations in all probability having a plateau in each day circumstances, and a few persevering with to have rising variety of each day circumstances. Given the various reporting practices globally, additional time is required to substantiate adjustments in trajectory.

Assessment (confidence): the outbreak continues to develop in some international locations, with indications of plateauing or decline in others (average).

International transmission

Routes of transmission reported by different international locations

Cases in beforehand non-endemic international locations are reported as primarily in GBMSM. Small variety of circumstances are reported in girls and youngsters. In international locations with an extended historical past of monkeypox, obvious wider inhabitants transmission is reported with unclear routes. Phylogenetic knowledge means that human transmission has been occurring for quite a few years in some areas previous to the looks of the outbreak clade and there may be at current no purpose to imagine that the epidemic as a complete will naturally scale back with out interventions globally. 

Assessment (confidence): transmitting primarily by shut or sexual contact in non-endemic international locations (low), unknown transmission routes in endemic international locations.

Part 2. Research and proof gaps prioritisation and exercise

2.1 Identification of analysis and proof questions

UKHSA has carried out a analysis and proof gaps evaluation regarding the monkeypox outbreak within the UK. We are working collaboratively with tutorial companions, together with National Institute for Health and Care Research Health Protection Research Units (NIHR HPRU) and nationwide analysis funders, to develop and implement fast research to deal with these. The precedence proof gaps are proven in Table 1 and a full checklist of analysis questions developed with companions and shared with funding our bodies in Table 2.

Table 1. Priority analysis and proof gaps

Research subject
Priority proof gaps

Levels of undiagnosed illness
Determining the beginning of the outbreak
Level of asymptomatic an infection
Wastewater surveillance

Transmission dynamics
Transmission threat to contacts
Modes of transmission

Biological characterisation and virology
Genome sequencing and in-host variation
Viral dynamics
Virus characterisation, together with organic significance of mutations

Clinical characterisation
Clinical presentation and outcomes. Groups prone to worse outcomes

Vaccine response and immunology
Immune response to an infection and vaccines
Immunological correlates of safety
Post-implementation effectiveness research

Is put up publicity prophylaxis tecovirimat higher or worse than vaccine?
Does tecovirimat assist with lowering isolation interval?
Does early therapy scale back threat of transmission? Impact on illness development – extreme illness

Diagnostics and analysis
Best web site to check
Home sampling and testing
Evaluation of Lateral Flow Devices (LFDs)
Development of serology take a look at

Evaluation of different interventions
Effectiveness of contact tracing

Behavioural and different social sciences
Public notion of threat
Public understanding of illness
Help searching for behaviour
Vaccine acceptability
Adherence to self-isolation
Media protection, behaviour and stigmatisation

Longer time period penalties of an infection
Are there longer-term penalties of an infection?

Reverse zoonosis threat

Table 2. Monkeypox analysis questions


How a lot undiagnosed illness is there? Prevalence
How many circumstances might have been missed as a consequence of a presumption of a unique trigger, for instance syphilis, herpes, chickenpox?
Risk components for an infection
When was virus launched?

Understanding the extent of unfold and assessing potential approaches to surveillance
Genomic Analysis of Wastewater from websites below investigation – direct deep sequencing
Can the virus be detected in wastewater? Can wastewater be used to watch epidemic?

Transmission dynamics
What proportion of circumstances are contaminated in UK?
What is the infectious interval?
What is the incubation interval?
Analysis of routine case and get in touch with tracing knowledge (and co-creation of enhanced contact cluster intelligence with key group, venue and occasion organisers)

Transmission dynamics
Risk of transmission to totally different teams on the inhabitants and get in touch with classes.
Risk of transmission in flights

Transmission dynamics
Can phylogeny present any data on transmission?
What data can we achieve about intrinsic transmissibility of West African clade?
Sequence and evaluation. Is there any proof that this can be a new clade or that there was any biologically vital change in comparison with beforehand described West African monkeypox? – In host variation

Transmission dynamics
Is there pre-symptomatic or prodromal transmission?
How a lot transmission is asymptomatic, presymptomatic or symptomatic?
Viral presence in semen

Transmission dynamics
What are the doubtless modes of transmission, together with
is there proof of airborne transmission? Fomites
Role of huge droplets, aerosols and steam rooms
Decontamination and mitigations – what’s efficient and wanted in several settings?

Transmission dynamics
Risk to UK home animals
Understanding reverse zoonotic threat, attainable animal reservoirs

Transmission dynamics
Inference of organic traits from epidemic trajectories and mitigation efforts by modelling. Can interrupted chains of transmission inform organic traits?

Biological characterisation and virology
Viral dynamics

Clinical characterisation
What are the signs and may the case definition be refined?

Clinical characterisation
Does the present syndrome differ from the classical description of West African monkeypox?

Clinical characterisation
Do the outcomes (together with essential sickness and fatality) differ from the prevailing descriptions of West African monkeypox?

Clinical characterisation
Is extra extreme illness skilled by any inhabitants subgroup?

Clinical characterisation
What are the dangers in being pregnant?

Clinical characterisation
Do totally different ages or demographics differ on scientific presentation?
Does that result in under- ascertainment of circumstances?

Vaccine response and immunology
What is the length of the serological response to Imvanex after 1 or 2 doses?
What are the immune responses to an infection and vaccination?

Vaccine response and immunology
Intrinsic and innate immune limitations to monkeypox

Vaccine response and immunology
What are the immunological correlates of safety together with cell-mediated immunity after vaccination, safety from smallpox vaccine?

Vaccine response and immunology
What is post-implementation vaccine effectiveness for the at present circulating pressure?
How can we deploy vaccine to maximise profit? Effectiveness of vaccine for pre-exposure prophylaxis

Is post-exposure prophylaxis tecovirimat higher or worse than vaccine?
Does tecovirimat assist with lowering isolation interval?
Does early therapy scale back threat of transmission?
Impact on illness development – extreme illness (occurring or anticipated, for instance, immunosuppressed)

Evaluation of different antivirals

Pharmacokinetics and pharmacodynamic research; both as a part of scientific trials above, or probably separate earlier section research in particular susceptible populations (the place the dosing is unclear)

Best web site to check, which web site goes constructive first

What would allow dwelling or point-of-care sampling and testing, together with self-testing? Evaluation of swabs with inactivating buffer to allow group testing

Development of serology take a look at.

Rapid LFD antigen take a look at improvement and validation

Evaluation of different interventions
What is the effectiveness of contact tracing and activation? How do interventions act synergistically to cut back onward transmission?

Behavioural and different social sciences and equalities concerns
How are the general public and affected teams perceiving the danger from monkeypox?
What is the general public understanding of the illness and What actions they should take?
What proportion of symptomatic circumstances search care? Vaccine acceptability and supposed or precise uptake
What are present ranges of adherence to self-isolation?
What components are related to poor adherence or profitable adherence to self-isolation?
Is size of self-isolation a deterrent to assist searching for?
What components are related to compliance with different management measures?
What components are related to efficient symptom recognition and help-seeking when signs develop?
How has media protection of this as a sexual well being drawback affecting homosexual, bisexual, and different males who’ve intercourse with males (GBMSM) particularly affected public responses, together with well being searching for behaviours?
How does the homosexual group want to self-organise monkeypox transmission prevention and management?
What characterises monkeypox misinformation and what are the scalable countermeasures?
What are the potential harms from stigmatising monkeypox communications connected to particular threat teams?
Impact of vaccination methods

Longer time period penalties of an infection
What are the longer-term penalties of an infection?
Cohort for long-term comply with up? Including: what are the implications of an infection in being pregnant, infancy or childhood?

Systems context – how can we optimise surveillance, understanding transmission, destigmatised testing, behavioural insights, focused vaccination, group involvement and so forth as a system of action-research? In explicit, bringing extra behavioural understanding into adaptive commentary or sampling to know transmission?

What can we study from analysis of the response to monkeypox to boost our responses to future outbreaks of concern?
Include consideration of mechanisms for collaborative working with worldwide companions

Are there any causes to imagine that this outbreak could also be indirectly associated to coronavirus (COVID-19) and/or components associated to GBMSM?

2.2 Studies underway to deal with recognized gaps

UKHSA has developed proposals to deal with particular analysis and proof questions associated to monkeypox, each as leaders and in collaboration with companions, together with NIHR HPRUs. Any queries about analysis in UKHSA ought to be directed to the Monkeypox Research and Science cell.

Studies led by UKHSA embody:

monkeypox virus tradition from longitudinal samples from 7 sufferers to find out threat of onwards transmission, funded by the Healthcare Infection Society
evaluation of monkeypox ranges in wastewater to evaluate incidence in group
prevalence of monkeypox an infection in England
measuring environmental contamination with monkeypox virus in healthcare and different settings
estimating the danger of transmission to contacts of monkeypox circumstances (in collaboration with the Behavioural Science and Evaluation HPRU)
monkeypox prognosis by way of near-patient lateral stream machine (LFD)
evaluation of the length of protecting immunity to at present circulation monkeypox
improvement of serology assessments to extend diagnostic capability

Other research underway and in planning with UKHSA involvement embody these designed to reply the next questions:

threat of transmission to totally different inhabitants teams (in collaboration with the Behavioural Science and Evaluation HPRU)
understanding transmission dynamics together with infectivity and incubation interval

In addition, UKHSA and the Medicine and Healthcare merchandise Regulatory Authority (MHRA) have additionally acquired funding from the Coalition for Epidemic Preparedness Innovations) (CEPI) for the event of a monkeypox antibody normal and assays:

The instruments CEPI is supporting the event of are: assays, with UKHSA, to check for the presence of particular antibodies – indicative of an immune response to monkeypox – following both pure an infection or vaccination. A reference antibody normal, with the UK MHRA, to harmonise how totally different laboratories assess the energy and length of immune responses generated by present vaccines and people in improvement in opposition to monkeypox.

2.3 Published literature

UKHSA researchers have authored or contributed to peer-reviewed publications for the present incident response. These will be accessed by way of the UKHSA Research Portal.

Part 3. Epidemiology replace

3.1 Current epidemiological scenario

Cases of monkeypox an infection had been confirmed in England from 6 May 2022. As of 1 August 2022, there have been 2,759 laboratory-detected circumstances of monkeypox within the UK. This contains 2,672 confirmed and 87 extremely possible circumstances, collectively known as ‘circumstances’ on this briefing for simplicity and outlined respectively as those that examined constructive with a monkeypox and orthopox polymerase chain response (PCR) take a look at. Positive outcomes for orthopox, the genus of viruses that features monkeypox, are thought-about extremely possible because of the rarity of different orthopox viruses within the UK.

Of all circumstances, 65 had been in Scotland, 24 had been in Northern Ireland, 32 had been in Wales and a couple of,638 had been in England. The median age of circumstances within the UK was 37 years previous (interquartile vary 31 to 44).

Table 3. Number of confirmed and extremely possible monkeypox circumstances by devolved administrations, May 2022 to 1 August 2022

Devolved administrations
Highly possible


Northern Ireland




Figure 1 reveals the specimen dates of monkeypox circumstances over time in England. While the primary reported case in England was recognized 6 May 2022 in a traveller from an endemic nation for monkeypox, the earliest identified case in England has a specimen date of seven March 2022. This case was recognized in late July by retrospective testing of a residual pattern. An further small variety of circumstances have additionally been detected with specimen dates in May 2022 however with symptom onset dates in early April 2022. Some of those early circumstances had no journey historical past of their incubation interval.

Figure 1. Incidence of confirmed and extremely possible monkeypox circumstances by specimen date in England as of 4 August 2022

Where specimen date is lacking, the date the laboratory acquired the specimen is used. The knowledge used on this graph will be discovered within the accompanying spreadsheet]

In England, a excessive proportion of circumstances had been identified to be London residents (total 73%, 1,906 out of two,626 with reported dwelling handle), see Table 4. The variety of circumstances in different areas has been steadily rising, significantly within the South East and North West of England (Figure 2). The proportion of circumstances in London has stayed round 66% in July 2022 (Figure 3).

Where gender data was out there, 2,593 out of two,615 (99.1%) circumstances in England had been males, and 22 had been girls (Figure 4).

Table 4. Number of laboratory confirmed and extremely possible monkeypox circumstances by area of residence, England, May 2022 to 1 August 2022

Region of residence
Total confirmed

East of England

East Midlands


North East

North West

South East

South West

West Midlands

Yorkshire and Humber



Figure 2. Cumulative rely of confirmed and extremely possible monkeypox circumstances by area of residence in England as of 1 August 2022*

The knowledge used on this graph will be discovered within the accompanying spreadsheet.

*If residential postcode is thought, then area of residence is used, in any other case the area of the healthcare facility the place testing occurred at is used

Figure 3. Seven-day rolling common of the proportion of confirmed and extremely possible monkeypox circumstances in London, by specimen date

The knowledge used on this graph will be discovered within the accompanying spreadsheet.

Figure 4. Age and gender distribution of confirmed and extremely possible monkeypox circumstances in England as of 1 August 2022

The knowledge used on this graph will be discovered within the accompanying spreadsheet.

3.2 Findings from enhanced surveillance questionnaires

Of the two,638 circumstances recognized in England as much as 1 August 2022, a complete of 703 (26%) had accomplished enhanced surveillance questionnaires. This contains knowledge collected by way of fast sexual well being questionnaires administered throughout the preliminary weeks of the outbreak (used from 27 to 31 May 2022), questionnaires accomplished by well being safety groups throughout phone interviews (used from 1 to 24 June 2022), and self-completed questionnaires despatched electronically to circumstances (used from 25 June 2022 onwards). Information from enhanced questionnaires ought to be interpreted with warning, because of the low uptake and since uptake has modified extra time. People finishing questionnaires is probably not consultant of all these affected.

Most respondents had been of white ethnicity (76%), adopted by blended (9%) and Asian (7%) ethnicities. Additionally, most circumstances had been born within the UK or different European international locations, though 10% reported being born in Latin American or Caribbean international locations.

Table 5. Ethnicity and area of delivery from enhanced surveillance questionnaires in confirmed monkeypox circumstances in England as of 1 August 2022


Percentage (%)







Region of Birth
Percentage (%)



Latin America and the Caribbean




Northern America


As proven in Table 6 and reported in earlier technical briefings, monkeypox is predominantly being transmitted in interconnected sexual networks of GBMSM: the vast majority of circumstances report a number of sexual companions within the final 3 months, historical past of a sexually transmitted an infection (STI) within the final 12 months, and/or use of human immunodeficiency pre-exposure prophylaxis (HIV PrEP).

Table 6. Selected epidemiological metrics from enhanced surveillance questionnaires in confirmed monkeypox circumstances in England as of 1 August 2022

N=703, some metrics have smaller denominators as a consequence of lacking values

Denominator (excluding circumstances with lacking responses)
Percentage (%)

Gay, bisexual, or males who’ve intercourse with males

History of STI within the final 12 months

One or no sexual companions in final 3 months

10+ sexual companions in final 3 months

Living with HIV

Ever used PrEP (amongst HIV damaging)

Figure 5 reveals developments of the chosen epidemiological metrics over time, amongst circumstances with accomplished questionnaires and with symptom onset dates between epidemiological weeks 18 to twenty-eight (from 1 May 2022 to 16 July 2022). Cases with onset dates earlier than or after these dates had been excluded from these analyses as a consequence of small numbers. These metrics had been constant over time, suggesting transmission of monkeypox virus in England has continued to happen in outlined sexual networks of GBMSM.

More detailed analyses of questionnaire knowledge, together with guide evaluation of case administration notes, was undertaken to explain the small variety of circumstances which are identified to not be GBMSM together with attainable routes of acquisition. Of 22 circumstances who had been girls, 9 (41%) had been transgender girls. From all 22 girls, 8 had proof of attainable transmission throughout sexual contact, 5 appeared to have non-sexual routes of acquisition (both family or no recognized publicity route), and 9 had no data on transmission. Additionally, there have been 15 cisgender heterosexual males who had not reported having intercourse with one other man previously 21 days. Of these, a small quantity had proof of attainable transmission throughout sexual contact with cisgender girls.

Figure 5. Trends of chosen epidemiological metrics in monkeypox circumstances with accomplished questionnaires, by week of symptom onset in England, epidemiological weeks 18 to 26 (1 May 2022 to 16 July 2022)

Supplementary knowledge just isn’t out there for this determine. Due to delays between symptom onset and questionnaire completion, knowledge for the latest epidemiological weeks could change and ought to be interpreted with warning.

3.3 Testing knowledge

Testing for monkeypox within the UK is carried out by the UKHSA Rare and Imported Pathogen Laboratory (RIPL) in addition to a number of different NHS and personal laboratories which have begun utilizing monkeypox or orthopox PCR assessments since early July 2022.

Testing analyses can be found for RIPL, though these are at present not consultant of testing throughout the UK and more likely to under-represent testing in London.

Up to 29 July 2022, 4,921 monkeypox assessments had been carried out in RIPL, of which 48% (2,204) had been constructive. Figure 6 reveals positivity by intercourse. Positivity in females has elevated barely in current weeks, whereas positivity in males was larger between weeks 25 and 28 however extra not too long ago has decreased to 50%.

Figure 6. Monkeypox take a look at positivity over time amongst samples examined by UKHSA RIPL by intercourse, 1 May to 29 July 2022

Part 4. Transmission dynamics

There is further proof that transmission has slowed since technical briefing 3. Nowcasting by each specimen date and reporting date suggests the epidemic has plateaued.

4.1 Nowcasting by specimen date

As the epidemic has grown, the supply of information with recorded symptom onset date has declined. This biases the epidemic curve by symptom onset date, because the proportion of circumstances being recorded will decay over time, even when adjusting for reporting delays. Therefore, right here we mannequin the epidemic utilizing specimen date, which is the date the pattern is collected from a affected person. This displays an epidemic curve lagged by the delay between an infection and searching for healthcare.

Visualising the epidemic curve by specimen date is affected by the delay from specimen date to the case being reported to UKHSA. To appropriate for this delay, nowcasting strategies alter the noticed knowledge by the distribution of reporting delays to create predictions of the particular frequency. We use a generalised additive mannequin to nowcast present circumstances and apply this to non-travel related circumstances in England.

The nowcasting means that the expansion in confirmed each day circumstances is zero, albeit with some uncertainty (Figure 7), with development charges estimated between a 39-day doubling time and a 35-day halving time. Negative doubling occasions symbolize halving occasions. The nowcast estimate of circumstances is round 35 per day. The swathe that spans zero reveals development has slowed and is now persistently near zero.

Figure 7. 7a reveals estimates of nowcast development fee and incidence by specimen date, 7b reveals estimates of the expansion fee and incidence by report date of monkeypox circumstances in England

The charts exclude circumstances related to journey. The shaded space is the 90% Credible Interval (CrI). The darkish shaded space is the 50% CrI and the lighter space is the 90% CrI.
Note: y-axis denotes incidence of circumstances by specimen date.
Supplementary knowledge just isn’t out there for these figures.

Figure 7a

Figure 7b

4.2 Temporal developments in gender distribution

Thus far, the vast majority of circumstances have occurred in outlined networks of GBMSM. To assess whether or not the outbreak is shifting away from this preliminary subpopulation, we examine temporal developments within the proportion of circumstances that don’t establish as girls. Assuming Monkeypox is being transmitted in sexual networks of GBMSM, the proportion of circumstances that establish as girls ought to stay fixed (permitting for random fluctuations within the noticed proportion).

A small variety of sporadic transmission occasions from GBMSM networks to girls is predicted. However, if the proportion of circumstances in girls is rising, this might counsel that there’s sustained transmission outdoors GBMSM networks. If the proportion of circumstances in girls with no identified hyperlinks to GBMSM networks is rising, that could possibly be even stronger proof of sustained onward transmission.

To assess the proof, we assemble a null speculation of no change within the transmission community based mostly on the gender-distribution of circumstances during the last 6 weeks. We then alter this noticed proportion to the variety of circumstances within the present week, to create a 95% confidence area the place we’d count on the at present noticed gender-distribution to lie if it follows the null speculation. By overlaying the at present noticed gender-distribution, we are able to establish statistically vital perturbations. Note that though statistically vital, these perturbations could not replicate underlying transmission adjustments, because it may be affected by adjustments within the relative ascertainment of circumstances in girls relative to males, or unknown circumstances. We plot the statistical take a look at as a rolling perform of time for every week of the outbreak.

The proportion of circumstances in girls is at present according to the null speculation, so there may be inadequate proof to help a change within the transmission dynamics (Figure 8). This is true whether or not circumstances in girls which have a identified hyperlink to a GBMSM main case are included or excluded. However, over the previous couple of weeks the proportion of circumstances in girls has been rising, so this pattern must be monitored intently.

Figure 8. Binomial chance of male circumstances utilizing a binomial precise take a look at

The purple shaded space is the null speculation (which suggests no change within the fee). The strong black line is the proportion noticed within the newest week, plotted by the primary day of the focal week.

Plot a) removes 5 circumstances (at time of research) which had been identified to have a hyperlink to a GBMSM main case. Plot b) evaluation together with all girls.

Figure 8a

Figure 8b

Supplementary knowledge just isn’t out there for these figures.

Part 5. UK Genomics knowledge


The majority of UK genomes up to now sequenced fall within the identified outbreak lineage B.1, however 2 are designated as lineage A.2, which can be co-circulating internationally.
There is proof of genetic variation inside particular person lesion samples, which could possibly be both acquired or transmitted variety.
This variety could trigger uncertainty in any makes an attempt to undertake detailed molecular epidemiology at current.
In host variety requires additional detailed exploration.

5.1 Samples sequenced

A complete of 87 monkeypox genomes have been produced utilizing Illumina metagenomics. Samples which have a monkeypox PCR cycle threshold (Ct) lower than or equal to twenty, are pre-treated to take away free nucleic acid earlier than extraction and library preparation. This evaluation contains data on the latest 81 genomes which have been generated. This contains 2 pairs of sequences from the identical samples in several runs. Both duplicates produced the identical outcomes.

5.2 Genomic variety

A phylogenetic tree is proven in Figure 9. A complete of 79 of the sequences include the 11 B.1 mutations described in technical briefing 3. This clade has been collapsed within the picture because of the massive variety of sequences throughout the clade internationally. The remaining 2 sequences belong to clade A.2, which incorporates 16 mutations not present in different clades. The UK genomes which are throughout the B.1 clade include 105 distinct level mutations when in comparison with ON563414.3. A complete of 79 of the mutations (75.24%) are according to the motion of host apolipoprotein B mRNA enhancing enzyme catalytic polypeptide 3 (APOBEC3) as described within the linked virological post. An extra 15 mutations (14.29%) are both C>T or G>A adjustments however will not be the canonical dinucleotides seen in APOBEC3 associated mutations.

Figure 9. Phylogenetic tree of monkeypox genomes

The tree features a pattern of the worldwide knowledge out there in Genbank and the 87 UK genomes from the 2022 outbreak, together with some historic samples for context. Clades B.1 and A.2 are labelled on the tree. B.1 (containing 85 UK genomes) has been collapsed because of the massive variety of sequences out there internationally. Sequences are labelled by accession quantity for publicly out there knowledge, and by inner identifier for brand spanking new UK genomes. Country and specimen assortment date are included within the label and indicated by the color and form, respectively. Underlying knowledge just isn’t out there for this determine.

Approximately 38% of samples include at the least one blended base (Figure 10). Mixtures are known as throughout the sequence knowledge if 2 bases are current at a given place and the whole learn depth at that place is greater than or equal to 20X. Reads will need to have a MapQ rating greater than or equal to 30 and particular person bases will need to have a QUAL rating greater than or equal to 33 to be included in depth calculations. In one set of duplicate sequences, the identical 5 blended positions had been noticed in each units of learn knowledge. The potential for blended populations has implications for inferences made concerning the construction of the B.1 clade. The utility of genomic knowledge in assessing transmission could also be diminished as samples from totally different people could have acquired distinctive mutations within the time between transmission and sampling.

Figure 10. Number of blended bases noticed in UK sequences

The knowledge used on this graph will be discovered within the accompanying spreadsheet.

Evidence for spontaneous technology of variation inside a lesion

Fifty-one of the 61 distinctive mutations (83.61%) noticed at blended positions are according to the motion of host APOBEC3. The high-quality thresholds for calling blended bases, and native nature of the sequencing protocol (that’s, no PCR enrichment) mixed with the APOBEC3 fashion mutations helps the speculation that variety is acquired inside a lesion. Additionally, sequence knowledge from 2 totally different swabs taken from the identical affected person present 2 totally different units of blended bases, suggesting this variety is acquired inside a person lesion over time.

Sequencing a single lesion is probably not consultant of the preliminary viral inhabitants acquired by a person, or equally of the inhabitants subsequently transmitted to contacts.

Detection of minority variants shared with different sequences

Sequencing of a UK pattern confirmed 5 blended bases at a frequency between 45 and 50% of reads. Four of the 5 blended positions noticed on this pattern had been current within the consensus sequence of two totally different B.1 subclades. It just isn’t attainable right now to find out the possible reason for this commentary, nonetheless superinfection, transmission of variation and convergent evolution are all attainable explanations. The presence of blended bases shared with different genomes as an alternative of wildtype or alternate calls within the consensus genomes resulted in uncertainty within the placement of those sequences inside phylogenies of the B.1 lineage.

Further sequencing of samples from totally different lesions or websites (for instance, lesion versus blood), and the identical lesion over time is required to totally perceive the relevance of blended bases within the genomic knowledge. The detection of blended bases in 38% of the sequenced samples coupled with the low total variety within the B.1 clade resulted in vital uncertainty in any phylogenetic illustration of the clade. Uncertainty within the phylogeny will restrict the molecular epidemiological inferences which are attainable from the genomic knowledge, subsequently it’s essential, as an preliminary step, that the extent and mechanisms resulting in the technology of intra-host variety are described.

Sources and acknowledgments

Data sources

Monkeypox virus PCR outcomes are submitted to UKHSA each day by the Rare and Imported Pathogens Laboratory, Porton, UKHSA regional laboratories and NHS laboratories endeavor testing. Data on individuals testing constructive since 6 May 2022 is enhanced with demographic, symptom, epidemiological, and publicity data extracted from the UKHSA Health Protection Team case administration system (HPZone), or collected in enhanced surveillance questionnaires.

Enhanced surveillance questionnaires embody knowledge collected by way of fast sexual well being questionnaires administered throughout the preliminary weeks of the outbreak (used from 27 to 31 May 2022), questionnaires accomplished by well being safety groups throughout phone interviews (used from 1 to 24 June 2022), and self-completed questionnaires despatched electronically to circumstances (used from 25 June 2022 onwards).

Authors of this report

Zahidul Abedin, Carolina Arevalo, Paula Blomquist, Jessica Bridgen, Chloe Byers, Meera Chand, Kristine Cooper, Fergus Cumming, Julie Day, Jake Dunning, Ashley Goddard, Irene Gonsalvez, Alice Graham, Natalie Groves, James Guilder, Susan Hopkins, Luke Hounsome, Christopher I Jarvis, Nicholas Loman, Nicola Love, Richard Myers, Isabel Oliver, Karthik Paranthaman, Mateo Prochazka, Thomas Ward, Nick Watkins, William Welfare, Katie Wrenn.


UKHSA Data, Epidemiology and Analytics Cell

UKHSA Research and Science Cell

UKHSA Modelling Cell

UKHSA Genomics Public Health Analysis

UKHSA Sexual Health Liaison Group

UKHSA Monkeypox Incident Management Team

Monkeypox Technical Group

The Monkeypox Technical Group contains members with experience in scientific infectious ailments, scientific analysis, epidemiology, genomics, modelling and virology:

Meera Chand (Chair), UKHSA

Andre Charlett, UKHSA

Andrew Rambaut, University of Edinburgh
Allan Bennett, UKHSA

Ashley Otter, UKHSA

Calum Semple, University of Liverpool
Christophe Fraser, University of Oxford
Claire Dewsnap, British Association for Sexual Health and HIV
Claire Gordon, UKHSA

David Ulaeto, Defence Science and Technology Laboratory
Erik Volz, Imperial College London
Emma Thomson, Medical Research Council-University of Glasgow Centre for Virus Research
Fergus Cumming, UKHSA

Giri Shankar, Public Health Wales
Geoffrey L. Smith, University of Cambridge
Geraldine O’Hara, High Consequence Infectious Diseases Network
Helen Fifer, UKHSA

Isabel Oliver, UKHSA

Jake Dunning, University of Oxford and Royal Free Hospital
Jason Mercer, University of Birmingham
Maria Rossi, Public Health Scotland
Matt Keeling, Warwick University
Matt Phillips, British Association for Sexual Health and HIV
Natalie Groves, UKHSA

Neil Ferguson, Imperial College London
Nicholas Loman, University of Birmingham and UKHSA

Obaghe Edeghere, UKHSA

Health and Social Care Northern Ireland

Richard Myers. UKHSA

Steven Riley, UKHSA

Susan Hopkins, UKHSA

Tommy Rampling, UKHSA


The authors are grateful to these groups and teams offering knowledge for these analyses together with:

British HIV Association (BHIVA)
British Association for Sexual Health and HIV (BASHH)
Sexual Health Services
NHS England and Improvement
High Consequence Infectious Diseases Network
Public Health Scotland
Public Health Wales
Public Health Agency, Northern Ireland


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#Investigation #monkeypox #outbreak #England #technical #briefing

By Seth A. Dunbar

Seth Dunbar leads clinical research study operations and quality & compliance. He is experienced working with teams to help drug sponsors better leverage eSource data. With 10+ years of experience Seth brings expertise developing eClinical services that integrate data and technology to help companies optimise study execution.

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