A holistic approach to fragile X syndrome integrated guidance for person-centred care.

BACKGROUND: The Fragile X community has expressed a desire for centralised, national guidelines in the form of integrated guidance for Fragile X Syndrome (FXS). METHODS: This article draws on existing literature reviews, primary research and clinical trials on FXS, a Fragile X Society conference workshop and first-hand experience of clinicians who have worked with those living with FXS over many years. RESULTS: The article scopes proposed integrated guidance over the life course, including appendices of symptoms, comorbidities and referral options for FXS and Fragile X Premutation Associated Conditions. CONCLUSION: Integrated guidance would provide an authoritative source for doctors, health professionals, therapists, care workers, social workers, educators, employers, families and those living with FXS, so that a holistic, person-centred approach can be taken across the United Kingdom to garner the best outcomes for those with FXS.

Temper outbursts in Lowe syndrome: Characteristics, sequence, environmental context and comparison to Prader-Willi syndrome.

BACKGROUND: There is limited research into the nature and aetiology of temper outbursts in people with intellectual disabilities. In this study, we describe the phenomenology and environmental context of temper outbursts in Lowe syndrome, a rare genetic syndrome in which outbursts are purportedly frequent. METHOD: A temper outburst interview (TOI) was conducted with caregivers of seventeen individuals with Lowe syndrome to generate an account of the behavioural sequence, common antecedents and consequences of temper outbursts, and to enable comparisons with similar work on Prader-Willi syndrome. RESULTS: Outbursts in Lowe syndrome were frequently triggered by thwarted goal-directed behaviour and were associated with high levels of physical aggression and property destruction. CONCLUSIONS: Form and sequence of outbursts showed similarities to Prader-Willi syndrome and to behaviours reported in literature on typically developing children. The results highlight the importance of considering shared aetiology as well as syndrome-specific pathways in the development of outbursts.

Adaptation of HIV-1 to human leukocyte antigen class I.

The rapid and extensive spread of the human immunodeficiency virus (HIV) epidemic provides a rare opportunity to witness host-pathogen co-evolution involving humans. A focal point is the interaction between genes encoding human leukocyte antigen (HLA) and those encoding HIV proteins. HLA molecules present fragments (epitopes) of HIV proteins on the surface of infected cells to enable immune recognition and killing by CD8(+) T cells; particular HLA molecules, such as HLA-B*57, HLA-B*27 and HLA-B*51, are more likely to mediate successful control of HIV infection. Mutation within these epitopes can allow viral escape from CD8(+) T-cell recognition. Here we analysed viral sequences and HLA alleles from >2,800 subjects, drawn from 9 distinct study cohorts spanning 5 continents. Initial analysis of the HLA-B*51-restricted epitope, TAFTIPSI (reverse transcriptase residues 128-135), showed a strong correlation between the frequency of the escape mutation I135X and HLA-B*51 prevalence in the 9 study cohorts (P = 0.0001). Extending these analyses to incorporate other well-defined CD8(+) T-cell epitopes, including those restricted by HLA-B*57 and HLA-B*27, showed that the frequency of these epitope variants (n = 14) was consistently correlated with the prevalence of the restricting HLA allele in the different cohorts (together, P < 0.0001), demonstrating strong evidence of HIV adaptation to HLA at a population level. This process of viral adaptation may dismantle the well-established HLA associations with control of HIV infection that are linked to the availability of key epitopes, and highlights the challenge for a vaccine to keep pace with the changing immunological landscape presented by HIV.

CD8+ T-cell responses to different HIV proteins have discordant associations with viral load.

Selection of T-cell vaccine antigens for chronic persistent viral infections has been largely empirical. To define the relationship, at the population level, between the specificity of the cellular immune response and viral control for a relevant human pathogen, we performed a comprehensive analysis of the 160 dominant CD8(+) T-cell responses in 578 untreated HIV-infected individuals from KwaZulu-Natal, South Africa. Of the HIV proteins targeted, only Gag-specific responses were associated with lowering viremia. Env-specific and Accessory/Regulatory protein-specific responses were associated with higher viremia. Increasing breadth of Gag-specific responses was associated with decreasing viremia and increasing Env breadth with increasing viremia. Association of the specific CD8(+) T-cell response with low viremia was independent of HLA type and unrelated to epitope sequence conservation. These population-based data, suggesting the existence of both effective immune responses and responses lacking demonstrable biological impact in chronic HIV infection, are of relevance to HIV vaccine design and evaluation.

Measurement tools for behaviours that challenge and behavioural function in people with intellectual disability: A systematic review and meta-analysis of internal consistency, inter-rater reliability, and test-retest reliability.

Behaviours that challenge (BtC) are common in people with intellectual disability (ID) and associated with negative long-term outcomes. Reliable characterisation of BtC and behavioural function is integral to person-centred interventions. This systematic review and meta-analytic study quantitatively synthesised the evidence-base for the internal consistency, inter-rater reliability, and test-retest reliability of measures of BtC and behavioural function in people with ID (PROSPERO: CRD42021239042). Web of Science, Embase, PsycINFO and MEDLINE were searched from inception to March 2024. Retrieved records (n = 3691) were screened independently to identify studies assessing eligible measurement properties in people with ID. Data extracted from 83 studies, across 29 measures, were synthesised in a series of random-effects meta-analyses. Subgroup analyses assessed the influence of methodological quality and study-level characteristics on pooled estimates. COSMIN criteria were used to evaluate the measurement properties of each measure. Pooled estimates ranged across measures: internal consistency (0.41-0.97), inter-rater reliability (0.29-0.93) and test-retest reliability (0.52-0.98). The quantity and quality of evidence varied substantially across measures; evidence was frequently unavailable or limited to a single study. Based on current evidence, candidate measures with the most evidence for internal consistency and reliability are discussed; however, continued assessment of measurement properties in ID populations is a key priority.

Social Anxiety in Neurodevelopmental Disorders: The Case of Fragile X Syndrome.

Despite significant advances in understanding and treating social anxiety in the general population, progress in this area lags behind for individuals with intellectual disability. Fragile X syndrome is the most common cause of inherited intellectual disability and is associated with an elevated prevalence rate of social anxiety. The phenotype of fragile X syndrome encompasses multiple clinically significant characteristics that are posed as risk markers for social anxiety in other populations. Here, evidence is reviewed that points to physiological hyperarousal, sensory sensitivity, emotion dysregulation, cognitive inflexibility, and intolerance of uncertainty as primary candidates for underlying mechanisms of heightened social anxiety in fragile X syndrome. A multilevel model is presented that provides a framework for future research to test associations.

General practice experiences for parents of children with intellectual disability: a systematic review.

BACKGROUND: Parents of children diagnosed with intellectual disability are at increased risk of mental and physical health difficulties compared with other parents. They are likely to regularly seek medical treatment for their health concerns from general practice as well as on behalf of their child with intellectual disability, yet there is limited evaluation of the role general practice plays for this patient group. AIM: To explore parents' experiences of general practice support when caring for a child with intellectual disability. DESIGN & SETTING: Systematic review of studies reporting experiences of general practice as described by parents who care for children with intellectual disability. METHOD: Databases were searched using a pre-defined search strategy. Studies were included based on detailed inclusion criteria, title, abstract, and full-text screening. Quality assessment was conducted using the Mixed Methods Appraisal Tool (MMAT). A narrative synthesis was conducted. RESULTS: A total of nine studies were identified. There was a clear absence of data on parents' own health experience and consultation in general practice. Findings related to navigating general practice on behalf of their child's health including accessibility of general practice and positive and negative experiences of GPs. CONCLUSION: Findings from this review highlight priority areas for research, including further exploration of parents' perspectives on seeking support specifically for their own health concerns, while caring for a child with intellectual disability, to bring more awareness and understanding of the role general practice plays in supporting the health of this carer group. This review also considers implications for clinical services, including tailoring appointments for this patient group as a priority for continuity of care, which may result in improved experiences of general practice and encourage better communication.

Utilising Interview Methodology to Inform the Development of New Clinical Assessment Tools for Anxiety in Autistic Individuals Who Speak Few or no Words.

Autistic individuals with intellectual disability who speak few or no words are at high risk of anxiety but are underrepresented in research. This study aimed to describe the presentation of anxiety in this population and discuss implications for the development of assessments. Interviews were conducted with 21 parents/carers of autistic individuals and nine clinicians. Data were analysed using content analysis and interpretative phenomenological analysis. Anxiety behaviours described by parents/carers included increased vocalisation, avoidance and behaviours that challenge. Changes to routine were highlighted as triggering anxiety. Clinicians discussed the importance of identifying an individual's baseline of behaviour, knowing an individual well and ruling out other forms of distress. This study raises considerations for early identification of anxiety and for subsequent support.

Behaviours that Challenge in SATB2-associated Syndrome: Correlates of Self-injury, Aggression and Property Destruction.

SATB2-associated syndrome (SAS) is a genetic syndrome characterised by intellectual disability, severe speech delay, and palatal and dental problems. Behaviours that challenge (BtC) are reported frequently; however, there is limited research on specific forms of BtC and the correlates of these behaviours. The current study explores correlates of well-defined BtC, self-injury, aggression, and property destruction, in SAS. Eighty-one parents/caregivers of individuals with SAS (53.1% male, Mage 10.12 years) completed questionnaire measures of health, behavioural, emotional, and autism characteristics. Individuals with SAS were grouped based on caregiver responses to the presence or absence of self-injury, aggression, and property destruction on the Challenging Behaviour Questionnaire. Rates of self-injury, aggression and property destruction were 42%, 77% and 49%, respectively. Between-group comparisons were conducted to compare characteristics between behaviour groups. Significantly differing characteristics were entered into separate hierarchical logistic regressions for each form of BtC. Behavioural comparisons indicated variation in the characteristics associated with each behaviour. All hierarchical logistic regression models were significant (p < .001): self-injury (χ2(5) = 38.46, R2 = 0.571), aggression (χ2(4) = 25.12, R2 = 0.414), property destruction (χ2(4) = 23.70, R2 = 0.346), explaining between 34.6% and 57.1% of the variance in behaviour presence. This is the first study to identify correlates of self-injury, aggression, and property destruction in SAS. Variability in the characteristics associated with each behaviour highlights the importance of specificity when examining BtC. Understanding correlates of specific forms of BtC has important implications for informing SAS-associated pathways to behavioural outcomes and the implementation of tailored behavioural interventions.

Behavioural and physiological indicators of anxiety reflect shared and distinct profiles across individuals with neurogenetic syndromes.

Anxiety is heightened in individuals with intellectual disability, particularly in those with specific neurogenetic syndromes. Assessment of anxiety for these individuals is hampered by a lack of appropriate measures that cater for communication impairment, differences in presentation, and overlapping features with co-occurring conditions. Here, we adopt a multi-method approach to identify fine-grained behavioural and physiological (via salivary cortisol) responses to anxiety presses in people with fragile X (FXS; n = 27; Mage = 20.11 years; range 6.32 - 47.04 years) and Cornelia de Lange syndromes (CdLS; n = 27; Mage = 18.42 years; range 4.28 - 41.08 years), two neurogenetic groups at high risk for anxiety, compared to neurotypical children (NT; n = 21; Mage = 5.97 years; range 4.34 - 7.30 years). Results indicate that physical avoidance of feared stimuli and proximity seeking to a familiar adult are prominent behavioural indicators of anxiety/stress in FXS and CdLS. Heightened pervasive physiological arousal was identified in these groups via salivary cortisol. An association between autistic characteristics and anxiety was evident in the FXS group but not in the CdLS group pointing to syndrome-specific nuances in the association between anxiety and autism. This study furthers understanding of the behavioural and physiological presentation of anxiety in individuals with intellectual disability and progresses theoretical developments regarding the development and maintenance of anxiety at the intersection of autism.

The role of anxiety and depression in suicidal thoughts for autistic and non-autistic people: A theory-driven network analysis.

BACKGROUND: Autistic adults experience more frequent suicidal thoughts and mental health difficulties than non-autistic adults, but research has yet to explain how these experiences are connected. This study explored how anxiety and depression contribute to suicidal thoughts according to the Interpersonal Theory of Suicide for autistic and non-autistic adults. METHODS: Participants (autistic adults n = 463, 61% female; non-autistic n = 342, 64% female) completed online measures of anxiety, depression, thwarted belonging, and perceived burdensomeness. Network analysis explored whether: (i) being autistic is a risk marker for suicide; and (ii) pathways to suicidal thoughts are consistent for autistic and non-autistic adults. RESULTS: Being autistic connected closely with feeling like an outsider, anxiety, and movement, which connected to suicidal thoughts through somatic experiences, low mood, and burdensomeness. Networks were largely consistent for autistic and non-autistic people, but connections from mood symptoms to somatic and thwarted belonging experiences were absent for autistic adults. CONCLUSION: Autistic people experience more life stressors than non-autistic people leading to reduced coping, low mood, and suicidal thoughts. Promoting belonging, reducing anxiety, and understanding the role of movement could inform suicide prevention for autistic people. Research should accurately capture autistic lived experience when modeling suicide to ensure suicide prevention meets autistic needs.

Profiles of autism characteristics in thirteen genetic syndromes: a machine learning approach.

BACKGROUND: Phenotypic studies have identified distinct patterns of autistic characteristics in genetic syndromes associated with intellectual disability (ID), leading to diagnostic uncertainty and compromised access to autism-related support. Previous research has tended to include small samples and diverse measures, which limits the generalisability of findings. In this study, we generated detailed profiles of autistic characteristics in a large sample of > 1500 individuals with rare genetic syndromes. METHODS: Profiles of autistic characteristics based on the Social Communication Questionnaire (SCQ) scores were generated for thirteen genetic syndrome groups (Angelman n = 154, Cri du Chat n = 75, Cornelia de Lange n = 199, fragile X n = 297, Prader-Willi n = 278, Lowe n = 89, Smith-Magenis n = 54, Down n = 135, Sotos n = 40, Rubinstein-Taybi n = 102, 1p36 deletion n = 41, tuberous sclerosis complex n = 83 and Phelan-McDermid n = 35 syndromes). It was hypothesised that each syndrome group would evidence a degree of specificity in autistic characteristics. To test this hypothesis, a classification algorithm via support vector machine (SVM) learning was applied to scores from over 1500 individuals diagnosed with one of the thirteen genetic syndromes and autistic individuals who did not have a known genetic syndrome (ASD; n = 254). Self-help skills were included as an additional predictor. RESULTS: Genetic syndromes were associated with different but overlapping autism-related profiles, indicated by the substantial accuracy of the entire, multiclass SVM model (55% correctly classified individuals). Syndrome groups such as Angelman, fragile X, Prader-Willi, Rubinstein-Taybi and Cornelia de Lange showed greater phenotypic specificity than groups such as Cri du Chat, Lowe, Smith-Magenis, tuberous sclerosis complex, Sotos and Phelan-McDermid. The inclusion of the ASD reference group and self-help skills did not change the model accuracy. LIMITATIONS: The key limitations of our study include a cross-sectional design, reliance on a screening tool which focuses primarily on social communication skills and imbalanced sample size across syndrome groups. CONCLUSIONS: These findings replicate and extend previous work, demonstrating syndrome-specific profiles of autistic characteristics in people with genetic syndromes compared to autistic individuals without a genetic syndrome. This work calls for greater precision of assessment of autistic characteristics in individuals with genetic syndromes associated with ID.

The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms.

One proposed HIV vaccine strategy is to induce Gag-specific CD8(+) T-cell responses that can corner the virus, through fitness cost of viral escape and unavailability of compensatory mutations. We show here that the most variable capsid residues principally comprise escape mutants driven by protective alleles HLA-B*57, -5801, and -8101 and covarying HLA-independent polymorphisms that arise in conjunction with these escape mutations. These covarying polymorphisms are potentially compensatory and are concentrated around three tropism-determining loops of p24, suggesting structural interdependencies. Our results demonstrate complex patterns of adaptation of HIV under immune selection pressure, the understanding of which should aid vaccine design.

Divergent presentation of anxiety in high-risk groups within the intellectual disability population.

BACKGROUND: Anxiety symptomatology is common in individuals with intellectual disability (ID). Symptomatology includes both traditional Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM-5) anxiety disorders and autism spectrum disorder (ASD)-related anxiety traits. Some genetic disorders such as Cornelia de Lange (CdLS) and fragile X syndromes (FXS) are at very high risk of anxiety and afford the opportunity to examine prevalence, profiles and associated person characteristics. However, prevalence and associated characteristics of anxiety in these high-risk groups remain poorly described and understood. The aim of the current study was to examine the prevalence and profile of DSM-5 and ASD-related anxiety symptomatology in individuals with CdLS and FXS and associated behavioural and cognitive characteristics. METHODS: Questionnaires and interviews assessing DSM-5 and ASD-related anxiety were conducted with caregivers of individuals with CdLS (n = 49) and FXS (n = 36). RESULTS: DSM-5 anxiety symptomatology was present in both groups with high co-morbidity across anxiety diagnoses. ASD-related anxiety was also prevalent with specific difficulties related to intolerance of uncertainty identified in both groups. Symptomatology was persistent over the lifespan for both groups. Anxiety type was partially associated with repetitive behaviour but not measures of overall ASD phenomenology in CdLS. CONCLUSIONS: DSM-5 and ASD-related anxiety are common in these high-risk syndromes associated with ID. Prospective syndrome specific presentations and associations, which may implicate specific underlying mechanisms, are discussed. Clinicians should be aware of the risk and difficulties involved in assessment of anxiety in individuals with ID, including atypical types, to ensure these individuals do not "miss" diagnoses and support in general clinical practice.

Prevalence of anxiety symptomatology and diagnosis in syndromic intellectual disability: A systematic review and meta-analysis.

Individuals with syndromic intellectual disability are at increased risk of experiencing anxiety. Comparing prevalence estimates of anxiety will allow the identification of at-risk groups and inform causal pathways of anxiety. No known study has explored estimates of anxiety symptomatology and diagnosis, including specific anxiety profiles, across groups whilst accounting for methodological quality of studies. This systematic review and meta-analysis aimed to fill this gap. Prior to review completion, methodology and analysis plans were registered and documented in a protocol (CRD42019123561). Data from 83 papers, involving a pooled sample of 13,708 across eight syndromes were synthesised using a random effects model. Anxiety prevalence ranged from 9 % (95 % CI: 4-14) in Down syndrome to 73% in Rett syndrome (95 % CI: 70-77). Anxiety prevalence across syndromic intellectual disability was higher than for intellectual disability of mixed aetiology and general population estimates. Substantial variability between syndromes identified groups at higher risk than others. The identification of high-risk groups is crucial for early intervention, allowing us to refine models of risk and identify divergent profiles.

Executive function, repetitive behaviour and restricted interests in neurodevelopmental disorders.

BACKGROUND: Individuals with genetic syndromes show unique profiles of repetitive behaviours and restricted interests (RRBs). The executive dysfunction account of RRBs suggests that in autistic (AUT) individuals executive function impairments underpin RRBs, but not communication and social interaction autistic characteristics. AIMS: To 1) describe profiles of behavioural manifestations of executive function (EF behaviours) and 2) explore the relationship between EF behaviours and autistic traits across individuals with Cornelia de Lange (CdLS), fragile X (FXS) and Rubinstein-Taybi syndromes (RTS), and AUT individuals. METHOD: Carers completed the Behavior Rating Inventory of Executive Function - Preschool Version and the Social Communication Questionnaire. Data reporting on 25 individuals with CdLS (Mage = 18.60, SD = 8.94), 25 with FXS (Mage = 18.48, SD = 8.80), 25 with RTS (Mage = 18.60, SD = 8.65) and 25 AUT individuals (Mage = 18.52, SD = 8.65) matched on chronological age and adaptive ability were included in analyses. RESULTS: All groups showed impairments across EF behaviours compared to two-to-three-year-old typically developing normative samples with no differences between groups. Different EF behaviours predicted RRBs in the syndrome groups with no associations found in the AUT group. CONCLUSIONS: Syndrome related differences should be considered when developing targeted interventions that focus on EF behaviours and/or RRBs in these groups.

The behavioural phenotype of SATB2-associated syndrome: a within-group and cross-syndrome analysis.

BACKGROUND: SATB2-associated syndrome (SAS) is a multisystem neurodevelopmental disorder characterised by intellectual disability, speech delay, and craniofacial anomalies. Although the clinical presentation of SAS is well-delineated, behaviours associated with SAS are less well-defined. Given the varied social profile reported in SAS of a 'jovial' predisposition and autistic behaviours, there may be phenotypic overlap with both Angelman syndrome (AS) and non-syndromal autism. This study aimed to describe behaviours in SAS in relation to chronological age and level of ability and contrast aspects of the behavioural phenotype with AS and non-syndromal autism. METHODS: Informant report questionnaire measures of behaviour, emotion, and autism characteristics were completed for 81 individuals with SAS (aged 1-36 years; 43 male). Within-group associations were analysed, and categorical data were compared between pre-school (1-5 years), school-age (6-15 years), and adolescent and adult SAS sub-groups (16 years and over). Cross-syndrome subscale and item-level analyses were conducted for 63 individuals with SAS (aged 1-27 years; 31 male), who were matched according to age and level of ability to 63 individuals with AS (aged 2-25 years; 32 male) and 63 individuals with non-syndromal autism (aged 3-26 years; 53 male). RESULTS: In SAS, higher rates of overactivity were moderately associated with lower self-help ability, and higher general anxiety scores were reported for males compared with females. Cross-syndrome subscale analyses uncovered several significant differences (p < .01), with comparatively low rates of stereotyped behaviour, overactivity, insistence on sameness and positive affect, and comparatively greater interest and pleasure and compulsive behaviour in individuals with SAS. Item-level analyses revealed a distinct profile of repetitive and autistic behaviours. LIMITATIONS: Developmental analysis was based on a cross-sectional rather than a longitudinal research design, the contribution of pain and sleep to behaviour was not explored, and molecular genetic testing to determine genotype-phenotype behavioural relationships was not possible. CONCLUSIONS: This study highlights the importance of behavioural comparisons to well-delineated groups and the utility of fine-grained item-level analyses to elucidate aspects of behaviour that might be syndrome related or shared across neurodevelopmental disorders. Future research is needed to further describe the distinctive repetitive and autistic behavioural phenotype in SAS.

Genetic modifiers in rare disorders: the case of fragile X syndrome.

Methods employed in genome-wide association studies are not feasible ways to explore genotype-phenotype associations in rare disorders due to limited statistical power. An alternative approach is to examine relationships among specific single nucleotide polymorphisms (SNPs), selected a priori, and behavioural characteristics. Here, we adopt this strategy to examine relationships between three SNPs (5-HTTLPR, MAOA, COMT) and specific clinically-relevant behaviours that are phenotypic of fragile X syndrome (FXS) but vary in severity and frequency across individuals. Sixty-four males with FXS participated in the current study. Data from standardised informant measures of challenging behaviour (defined as physical aggression, property destruction, stereotyped behaviour, and self-injury), autism symptomatology, attention-deficit-hyperactivity-disorder characteristics, repetitive behaviour and mood/interest and pleasure were compared between each SNP genotype. No association was observed between behavioural characteristics and either 5-HTTLPR (serotonin) or MAOA (monoamine oxidase) genotypes. However, compared to the COMT (dopamine) AG and GG genotypes, the AA genotype was associated with greater interest and pleasure in the environment, and with reduced risk for property destruction, stereotyped behaviour and compulsive behaviour. The results suggest that common genetic variation in the COMT genotype affecting dopamine levels in the brain may contribute to the variability of challenging and repetitive behaviours and interest and pleasure in this population. This study identifies a role for additional genetic risk in understanding the neural and genetic mechanisms contributing to phenotypic variability in neurodevelopmental disorders, and highlights the merit of investigating SNPs that are selected a priori on a theoretical basis in rare populations.

HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering.

The selection of escape mutations has a major impact on immune control of infections with viruses such as human immunodeficiency virus (HIV). Viral evasion of CD8(+) T-cell responses leaves predictable combinations of escape mutations, termed HLA "footprints." The most clearly defined footprints are those associated with HLA alleles that are linked with successful control of HIV, such as HLA-B*57. Here we investigated the extent to which HLA footprint sites in HIV type 1 (HIV-1) are associated with viral evolution among and within clades. First, we examined the extent to which amino acid differences between HIV-1 clades share identity with sites of HLA-mediated selection pressure and observed a strong association, in particular with respect to sites of HLA-B selection (P < 10(-6)). Similarly, the sites of amino acid variability within a clade were found to overlap with sites of HLA-selected mutation. Second, we studied the impact of HLA selection on interclade phylogeny. Removing the sites of amino acid variability did not significantly affect clade-specific clustering, reflecting the central role of founder effects in establishing distinct clades. However, HLA footprints may underpin founder strains, and we show that amino acid substitutions between clades alter phylogeny, underlining a potentially substantial role for HLA in driving ongoing viral evolution. Finally, we investigated the impact of HLA selection on within-clade phylogeny and demonstrate that even a single HLA allele footprint can result in significant phylogenetic clustering of sequences. In conclusion, these data highlight the fact that HLA can be a strong selection force for both intra- and interclade HIV evolution at a population level.