Improving knowledge of rare disorders since 1993: the Australian Paediatric Surveillance Unit.

The Australian Paediatric Surveillance Unit (APSU), established in 1993 to address the paucity of national data on rare childhood disorders, has become an invaluable research resource. It facilitates prospective, active surveillance for a variety of rare disorders, with monthly reporting by ~1500 paediatricians, who are invited to notify incident cases and provide demographic and clinical data. APSU is highly collaborative (used by >400 individuals/organisations), patient-informed and productive (>300 publications). In 30 years, 72 studies have been initiated on rare infections, and genetic, psychological and neurological disorders, and injuries. Return rates of monthly report cards were >90% for 30 years and paediatricians have provided data for >90% of notified cases. Although there are limitations, including case underascertainment in remote regions, APSU often provides the only available national data. APSU has assisted the government in reporting to the WHO, developing national strategies, informing inquiries and investigating disease outbreaks. APSU data have informed paediatrician education, practice, policy, and service development and delivery. APSU was integral in establishing the International Network of Paediatric Surveillance Units (INoPSU) and supporting development of other units. APSU's expanded remit includes one-off surveys, hospital audits, systematic reviews, studies on the impacts of rare disorders on families, surveillance evaluations, and joint studies with INoPSU members. Paediatricians value the APSU, reporting that APSU data inform their practice. They must be congratulated for an outstanding collective commitment to the APSU, in providing unique data that contribute to our understanding of rare disorders and support optimal, evidence-based care and improved child health outcomes.

Australian Paediatric Surveillance Unit (APSU) Annual Surveillance Report 2022.

For 30 years the Australian Paediatric Surveillance Unit (APSU) has conducted national surveillance of rare communicable diseases and rare complications of communicable diseases. In this report, we describe the results of thirteen such studies surveyed by the APSU in 2022, including reported case numbers and incidence estimates, demographics, clinical features, management and short-term outcomes. Conditions described are: acute flaccid paralysis (AFP); congenital cytomegalovirus (cCMV); neonatal and infant herpes simplex virus (HSV) infection; perinatal exposure to human immunodeficiency virus (HIV) and paediatric HIV infection; severe complications of influenza; juvenile-onset recurrent respiratory papillomatosis (JoRRP); congenital rubella infection/syndrome; congenital varicella syndrome (CVS) and neonatal varicella infection (NVI); and the new conditions dengue; Q fever; and severe acute hepatitis. In 2022, cases of severe complications of influenza were reported to the APSU for the first time since 2019. This likely reflects the easing of government-mandated restrictions imposed in 2020-2021 to curb the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the re-emergence of a range of infectious diseases. As previously, AFP surveillance by the APSU contributed to Australia achieving a minimum target incidence of one AFP case per 105 children aged less than 15 years. Cases of JoRRP and NVI were reported in 2022. This indicates potential gaps in human papillomavirus (HPV) and varicella vaccination coverage respectively, especially in high-risk groups such as young migrant and refugee women of childbearing age from countries without universal vaccination programs. Paediatric HIV case numbers resulting from mother-to-child-transmission (MTCT) of HIV remain low in Australia due to use of effective intervention strategies. However, there has been an increase in the number of imported cases of HIV in children (mainly perinatally-acquired) from countries with a high HIV prevalence. Without effective vaccines, there has been no decline in the incidence of congenital CMV and neonatal HSV, indicating the importance of early identification and management to reduce morbidity and mortality. The first cases of dengue, Q fever and severe acute hepatitis were received by APSU in 2022, including two cases of acute hepatitis in which aetiology has not been confirmed to date. The APSU has an important ongoing role in monitoring rare childhood infections.

Erratum to Commun Dis Intell (2018) 2023;47. (https://doi.org/10.33321/cdi.2023.47.46).

The text within this report, as originally published, incorrectly stated that the two included cases of dengue had not recently travelled to a dengue-endemic country. A reexamination of the case data has shown that both cases had recently travelled to a country where dengue is endemic. The paragraph below provides the corrected text for the dengue case descriptions, and replaces the paragraph at the foot of the right-hand column of text on page 10 of the published report. In 2022, two cases of dengue were notified to the APSU, one confirmed and one probable (Table 1), and the incidence estimate for the surveillance period (1 February - 31 December 2022) is shown in Table 2. Neither child had a prior history of dengue; however, both had recently travelled to an endemic country. One had DENV2 serotype and the serotype was not recorded for the second child. Both children were hospitalised and symptoms included fever, rash, cough, severe abdominal pain, diarrhoea, fatigue, retro-orbital pain and myalgia/arthralagia joint pains. One child had respiratory co-infection with human metapneumovirus. Both children received supportive therapies (intravenous fluids, pain relief) and one child received ceftriaxone. On discharge, one child had ongoing problems including arthralgia, fatigue, thrombocytopaenia and hepatitis.

Characteristics of neonatal herpes simplex central nervous system disease in Australia (1997-2020).

BACKGROUND: Neonatal herpes simplex virus (HSV) central nervous system (CNS) disease can occur in isolation or as part of disseminated infection. We sought to describe neonatal HSV CNS disease in Australia over 24 years. METHODS: Neonates (≤28 days) with confirmed HSV infection, reported prospectively to the Australian Paediatric Surveillance Unit (1997-2020), were evaluated for HSV CNS disease (laboratory confirmation with clinical evidence of encephalitis, e.g., lethargy, seizures, focal signs; and/or abnormalities on neuroimaging or electroencephalogram), and compared with neonates without CNS disease. CNS-restricted disease was compared with CNS-disseminated disease. FINDINGS: Of 195 neonates with HSV disease; 87 (45%) had CNS disease (1.29 cases/100,000 live births per year, 95% CI: 1·04-1·59). Neonates with CNS disease were significantly more likely to be male than neonates without CNS disease (60% versus 39%, OR=2·32, 95% CI 1·29-4·18). Of the neonates with CNS disease, those with CNS-restricted disease (52/87, 60%) presented later than neonates with CNS-disseminated disease (35/87, 40%), (mean 12 versus 6 days). Twenty (23%) neonates with CNS disease died, the majority with CNS-disseminated disease (n = 19). Most neonates received aciclovir therapy (94·3%), however five neonates with unrecognised CNS disseminated disease (diagnosed at autopsy) had not been treated. Survivors of CNS disease were significantly more likely to have adverse neurological sequelae, compared with those without CNS disease (30% versus 4%, OR: 9·60, 95% CI: 2·6-35·0). INTERPRETATION: Male neonates have a higher burden of HSV CNS disease. Despite the use of antiviral agents, morbidity following neonatal HSV CNS disease remains high. Evaluation of adjunctive therapies to improve outcomes is needed.

Active prospective national surveillance for congenital and neonatal varicella in Australia shows potential prevention opportunities.

To compare the incidence and outcomes of congenital and neonatal varicella in Australia in the pre-vaccination (1995-1997) and post-vaccination era (after 2005 to November 2020), active prospective national surveillance for congenital varicella syndrome (CVS) and neonatal varicella infection (NVI) was conducted through the Australian Paediatric Surveillance Unit (APSU). Compared with 1995-1997, there was a 91.5% reduction in the incidence of CVS and a 91.3% reduction in the incidence of NVI in 2009-2020. However, almost half of the mothers in 2009-2020 were born overseas and came from countries without a vaccination program. Although there has been a substantial and sustained decrease in the reported incidence of CVS and NVI in Australia since 2006, congenital and neonatal varicella infections persist. Thus, there is an opportunity for targeted screening of varicella in young migrant, asylum seeker and refugee women at risk of varicella infection and prioritisation for vaccination to prevent CVS and NVI.

Australian children living with rare diseases: health service use and barriers to accessing care.

BACKGROUND: Children with rare diseases experience challenges at home and school and frequently require multi-disciplinary healthcare. We aimed to determine health service utilization by Australian children with rare diseases and barriers to accessing healthcare. METHODS: Parents completed an online survey on health professional and emergency department (ED) presentations, hospitalization, and barriers to accessing services. Potential barriers to service access included residential location (city, regional, remote) and child health-related functioning, determined using a validated, parent-completed measure-of-function tool. RESULTS: Parents of 462 children with over 240 rare diseases completed the survey. Compared with the general population, these children were more likely to be hospitalized [odds ratio (OR) = 17.25, 95% confidence interval (CI) = 15.50-19.20] and present to the ED (OR = 4.15, 95% CI = 3.68-4.68) or a family physician (OR = 4.14, 95% CI = 3.72-4.60). Child functional impairment was nil/mild (31%), moderate (48%) or severe (22%). Compared to children with nil/mild impairment, those with severe impairment were more likely to be hospitalized (OR = 13.39, 95% CI = 7.65-23.44) and present to the ED (OR = 11.16, 95% CI = 6.46-19.27). Most children (75%) lived in major cities, but children from regional (OR = 2.78, 95% CI = 1.72-4.55) and remote areas (OR = 9.09, 95% CI = 3.03-25.00) experienced significantly more barriers to healthcare access than children from major cities. Barriers included distance to travel, out-of-pocket costs, and lack of specialist medical and other health services. CONCLUSIONS: Children with rare diseases, especially those with severe functional impairment have an enormous impact on health services, and better integrated multidisciplinary services with patient-centered care are needed. Access must be improved for children living in rural and remote settings.

Australian Paediatric Surveillance Unit (APSU) Annual Surveillance Report 2021.

Abstract: The Australian Paediatric Surveillance Unit (APSU) has been conducting surveillance of rare communicable and non-communicable conditions in children since its inception in 1993. In this report, the results are described of surveillance of ten communicable diseases (and complications) for 2021, including the numbers of cases and incidence estimates; demographics; clinical features; and management and short-term outcomes. The included diseases are: acute flaccid paralysis (AFP); congenital cytomegalovirus (CMV); neonatal herpes simplex virus (HSV) infection; paediatric human immunodeficiency virus (HIV) infection; perinatal exposure to HIV; severe complications from influenza; juvenile-onset respiratory papillomatosis (JoRRP); congenital rubella syndrome; congenital varicella syndrome; and neonatal varicella infection. In 2021, cases of JoRRP were reported to the APSU for the first time since 2017, indicating potential gaps in HPV vaccination. AFP surveillance by APSU again contributed to Australia achieving a minimum target incidence of one AFP case per 100,000 children aged < 15 years. There were no cases of children with severe complications of influenza. No cases of varicella or congenital rubella were reported; however, at-risk populations, especially young migrant and refugee women from countries without universal vaccination programs, need to be screened and prioritised for vaccination prior to pregnancy. Cases of perinatal exposure to HIV continue to increase; however, the rate of mother-to-child-transmission remains at low levels due to the use of effective intervention strategies. Case numbers of congenital CMV and neonatal HSV remain steady in the absence of vaccines, prompting the need for greater awareness and education, with recent calls for target screening of at-risk infants for congenital CMV.

Severe Influenza-Associated Neurological Disease in Australian Children: Seasonal Population-Based Surveillance 2008-2018.

BACKGROUND: Influenza-associated neurological disease (IAND) is uncommon but can result in death or neurological morbidity in children. We aimed to describe the incidence, risk factors, and outcome of children with IAND from seasonal influenza in Australia. METHODS: We analyzed national, population-based, surveillance data for children aged ≤ 14 years with severe influenza and neurological involvement, over 11 Australian influenza seasons, 2008-2018, by the Australian Paediatric Surveillance Unit. RESULTS: There were 633 laboratory-confirmed cases of severe influenza reported. Of these, 165 (26%) had IAND. The average annual incidence for IAND was 3.39 per million children aged ≤ 14 years. Compared to cases without neurological complications, those with IAND were more likely to have a pre-existing neurological disease (odds ratio [OR] 3.03, P < .001), but most children with IAND did not (n = 135, 82%). Children with IAND were more likely to receive antivirals (OR 1.80, P = .002), require intensive care (OR 1.79, P = .001), require ventilation (OR 1.99; P = .001), and die (OR 2.83, P = .004). CONCLUSIONS: IAND is a preventable cause of mortality, predominantly in otherwise well children. Incidence estimates validate previous sentinel site estimates from Australia. IAND accounted for a quarter of all severe influenza, is associated with intensive care unit admission, and accounted for half of all influenza deaths.

Health-related out-of-pocket expenses for children living with rare diseases - tuberous sclerosis and mitochondrial disorders: A prospective pilot study in Australian families.

AIM: We aimed to describe health-related out-of-pocket (OOP) expenses incurred by Australian families living with children with chronic and complex diseases. METHODS: A prospective pilot study of OOP expenses in families with children with tuberous sclerosis (TS) or mitochondrial disorders (MD) in 2016-2017. An initial survey assessed the family's financial situation, child's health functioning and estimated previous 6 months' and lifetime OOP expenses. Thereafter, families completed a survey each month for 6 months, prospectively tracking OOP expenses. RESULTS: Initial surveys were completed by 13 families with 15 children; median age 7 years (range: 1-12); 5 with MD, 10 with TS. All families reported OOP expenses: 38% paid $2000 per annum, more than double the annual per-capita OOP costs reported for Australia by the Organisation for Economic Co-operation and Development. Eight families estimated $5000-$25 000 in OOP expenses over their child's lifetime and 62% of mothers reduced or stopped work due to caring responsibilities. Eleven families paid annual private health insurance premiums of $2000-$5122, but 72% said this was poor value-for-money. Prospective tracking by eight families (9 children) identified the median OOP expenditure was $863 (range $55-$1398) per family for 6 months. OOP spending was associated with visits to allied health professionals, non-prescription medicines, special foods, supplements and disposable items. Eight families paid for 91 prescription medications over 6 months. CONCLUSION: All families caring for children with TS or MD reported OOP expenses. A larger study is needed to explore the affordability of health care for children living with a broader range of chronic diseases.

Australian Paediatric Surveillance Unit (APSU) Annual Surveillance Report 2020.

ABSTRACT: For 27 years, national prospective data on selected rare childhood diseases have been collected monthly by the Australian Paediatric Surveillance Unit (APSU) from paediatricians and other clinical specialists who report cases in children aged up to 16 years. We report here the annual results of APSU surveillance in 2020 for ten rare communicable diseases and complications of communicable diseases, namely: acute flaccid paralysis (AFP); congenital cytomegalovirus (CMV) infection; neonatal herpes simplex virus (HSV) infection; perinatal exposure to human immunodeficiency virus (HIV); paediatric HIV infection; severe complications of seasonal influenza; juvenile onset recurrent respiratory papillomatosis (JoRRP); congenital rubella syndrome; congenital varicella syndrome; and neonatal varicella infection. We describe the results for each disease in the context of the total period of study, including demographics, clinical characteristics, treatment and short-term outcomes. Despite challenges presented by the coronavirus disease 2019 (COVID-19) pandemic in 2020, more than 1,400 paediatricians reported regularly to the APSU and an overall monthly reporting rate of > 90% was achieved. The minimum AFP target of 1 case per 100,000 children aged less than 15 years was achieved and there were few cases of vaccine-preventable diseases (JoRRP, rubella, varicella). However, high cases of congenital CMV, neonatal HSV and perinatal exposure to HIV persist. There were no severe complications of seasonal influenza reported for the first time in 13 years. This is consistent with other surveillance data reporting a decline of influenza and other communicable diseases in 2020, and likely reflects the wider effects of public health measures to reduce transmission of SARS-CoV-2 in the Australian community.

Ten Years of National Seasonal Surveillance for Severe Complications of Influenza in Australian Children.

BACKGROUND: Severe complications of influenza in children are uncommon but may result in admission to hospital or an intensive care unit (ICU) and death. METHODS: Active prospective surveillance using the Australian Paediatric Surveillance Unit with monthly reporting by pediatricians of national demographic and clinical data on children with <15 years of age hospitalized with severe complications of laboratory-confirmed influenza during ten influenza seasons 2008-2017. RESULTS: Of 722 children notified, 613 had laboratory-confirmed influenza and at least one severe complication. Most (60%) were <5 years of age; 10% were <6 months, hence ineligible for vaccination. Almost half of all cases were admitted to ICU and 30 died. Most children were previously healthy: 40.3% had at least one underlying medical condition. Sixty-five different severe complications were reported; pneumonia was the most common, occurring in over half of all cases. Influenza A accounted for 68.6% hospitalizations; however, influenza B was more often associated with acute renal failure (P = 0.014), rhabdomyolysis (P = 0.019), myocarditis (P = 0.015), pericarditis (P = 0.013), and cardiomyopathy (P = 0.035). Children who died were more likely to be older (5-14 years), have underlying medical conditions, be admitted to ICU, and have encephalitis, acute renal failure, or myocarditis. Only 36.1% of all children reported received antiviral medications, and 8.5% were known to be vaccinated for seasonal influenza. CONCLUSIONS: Severe influenza complications cause morbidity and mortality in children, which may increase if coinfection with COVID-19 occurs in the 2020 season and beyond. Increased vaccination rates, even in healthy children, early diagnosis and timely antiviral treatment are needed to reduce severe complications and death.

Australian Paediatric Surveillance Unit (APSU) Annual Surveillance Report 2019.

The Australian Paediatric Surveillance Unit (APSU) has been prospectively collecting national data on rare childhood conditions since 1993, with monthly reporting of cases by paediatricians. In this report we describe annual results from studies for ten communicable diseases and complications of communicable diseases that were conducted using APSU surveillance in 2019 and place these in an historic context. Results are reported on acute flaccid paralysis, congenital cytomegalovirus infection, neonatal herpes simplex virus infection, perinatal exposure to HIV, paediatric HIV infection, severe complications of seasonal influenza, juvenile onset recurrent respiratory papillomatosis (JoRRP), congenital rubella syndrome, congenital varicella syndrome and neonatal varicella infection. APSU provides rich clinical data to complement data collected from other surveillance systems and to improve understanding and response to rare childhood infections.

Early Life Parechovirus Infection Neurodevelopmental Outcomes at 3 Years: A Cohort Study.

OBJECTIVE: To investigate the long-term developmental and behavioral outcomes in an established cohort of children hospitalized as infants with human parechovirus (HPeV) infection and sepsis-like illness. STUDY DESIGN: The HPeV cohort was composed of children 3 years of age after HPeV infection and hospitalization in early infancy that occurred during a well-documented HPeV genotype 3 outbreak in Australia. We assessed neurodevelopmental and behavioral outcomes using the Bayley Scales of Infant and Toddler Development-III and the Child Behavior Checklist. We compared their outcomes with a subsample of healthy control infants drawn from the independently sampled Triple B Pregnancy Cohort Study. RESULTS: Fifty children, with a mean age of 41 months, were followed for 3 years after hospital admission with HPeV infection. There were 47 children whose original illness was fever without source or sepsis-like illness and 3 who had encephalitis. All children in the HPeV cohort showed age-specific development within the population normal range on the Bayley Scales of Infant and Toddler Development-III. There was no difference in developmental attainment compared with 107 healthy control infants after adjusting for measured confounders. The HPeV cohort showed higher average scores on the Child Behavior Checklist and a higher frequency of clinical range scores compared with healthy controls. CONCLUSIONS: Although HPeV sepsis-like illness did not result in neurodevelopmental delay at 3 years of age, it was associated with increased behavioral problems compared with healthy controls. The behavioral problems reached a clinical threshold in a minority of children. Results inform clinical management and planning for children after severe HPeV infection in infancy.

High prevalence of developmental concern amongst infants at 12 months following hospitalised parechovirus infection.

AIM: The human parechovirus (HPeV) is an increasingly recognised cause of sepsis and central nervous system infection in young infants for which there are limited long-term outcome data. We aimed to assess neurodevelopmental outcome and quality of life in infants following hospitalised HPeV infection. METHODS: This cohort study was a 12-month follow-up of infants who were hospitalised with confirmed HPeV infection at the Sydney Children's Hospitals Network during an outbreak in Sydney in 2013. Telephone interviews were conducted with parents/guardians. We administered standardised questionnaires, including: Ages and Stages Questionnaire (ASQ), Liverpool Outcome Score-follow-up, Pediatric Quality of Life Inventory(PedsQL) Infant scales and Short-Form health survey (SF-12). RESULTS: We followed up 46 of 79 infants (58%) aged between 12 and 16 months who had been hospitalised with HPeV infection; 19% showed significant concern in developmental attainment (ASQ3 score <2 standard deviation below population mean), and 50% showed some concern (<1 standard deviation below mean). ASQ3 developmental outcome was associated with the presence of neurodevelopmental sequelae (lower total Liverpool Outcome Score) and poorer health-related quality of life (HRQOL) in physical functioning (PedsQL physical component score), but not overall HRQOL (total PedsQL score) or parental HRQOL (SF-12 scores). No significant associations were identified between clinical or laboratory features during acute hospitalisation and adverse outcome on ASQ3. CONCLUSIONS: A high proportion of infants show developmental concern at 12-month follow-up post-hospitalisation with HPeV infection. Clinical features during hospitalisation were not associated with adverse outcomes at 12 months. These results suggest that careful follow-up of young infants hospitalised with HPeV disease may be warranted.

HIV infection is associated with higher levels of monocyte chemoattractant protein-1 and eotaxin among people with recent hepatitis C virus infection.

BACKGROUND: Human immunodeficiency virus (HIV) infection leads to more rapid progression of hepatitis C virus (HCV)-related liver fibrosis, which could be linked to differences in the severity of liver inflammation among HIV/HCV co-infected individuals compared to HCV mono-infected individuals. This study assessed the association of HIV co-infection with pro-inflammatory and pro-fibrogenic cytokines and chemokines during recent HCV infection. METHODS: Participants from the ATAHC study, a prospective cohort of recent HCV infection, with detectable HCV RNA at the time of acute HCV detection were included. Concentrations of 27 plasma cytokines and chemokines were measured by multiplex immunoassays and compared between those with, and without, HIV co-infection. RESULTS: Out of 117 individuals with recent HCV infection included in analysis, 73 had HCV mono-infection and 44 had HIV/HCV co-infection. Individuals with HIV/HCV co-infection had significantly higher mean levels of eotaxin (1.79 vs. 1.62 log pg/mL; P < 0.001), monocyte chemotactic protein 1 (MCP-1; 2.10 vs. 1.98 log pg/mL; P < 0.001), and interferon-gamma inducible protein-10 (IP-10; 3.11 vs. 2.98 log pg/mL; P = 0.013). Linear regression analyses adjusting for age, alanine transaminase (ALT), HCV RNA levels, and assay run, higher eotaxin levels were independently associated with HIV/HCV co-infection (adjusted ß: 0.12; 95%CI: 0.01, 0.24; P = 0.039). Higher MCP-1 levels were also independently associated with HIV/HCV co-infection in adjusted analysis (adjusted ß: 0.11; 95%CI: 0.03, 0.18; P = 0.009). CONCLUSIONS: During recent HCV, those with HIV/HCV co-infection had a stronger pro-fibrogenic mediator profile compared to those with HCV mono-infection. These findings may provide a potential explanation for accelerated liver fibrosis in HIV/HCV co-infection. TRIAL REGISTRATION: Australian Trial in Acute Hepatitis C (ATAHC) study was registered with ClinicalTrials.gov registry on September 11, 2005. NCT00192569 .

Incident Hepatitis C Virus Genotype Distribution and Multiple Infection in Australian Prisons.

Hepatitis C virus (HCV) is a highly diverse pathogen that is classified into seven distinct genotypes. Simultaneous or sequential reinfection with multiple HCV genotypes is recognized in high-risk populations, such as injecting drug users (IDUs). Multiple infection is of clinical concern as different genotypes have various sensitivities to current antiviral therapies. Therefore, a better understanding of the frequency of multiple infection and of the genotypes currently being transmitted is clinically relevant. An Australian cohort of IDUs (n = 123), identified with primary incident infection, was followed for multiple infection by regular HCV RNA testing between 2005 and 2013. A total of 354 samples were tested. Sequencing of primary incident infections revealed that genotype 3a was the most common circulating genotype, followed by genotype 1a. Examination of longitudinally collected samples identified complex patterns of multiple infection, including reinfection and superinfection. In those with multiple infection, there was no apparent evidence of homotypic immunity conferring protection against reinfection of the same subtype. This study revealed frequent multiple infection in a high-risk prisoner cohort, illustrating the complex nature of HCV infection and reinfection and highlighting the need for pan-genotypic antiviral therapies.

HIV infection and hepatitis C virus genotype 1a are associated with phylogenetic clustering among people with recently acquired hepatitis C virus infection.

The aim of this study was to identify factors associated with phylogenetic clustering among people with recently acquired hepatitis C virus (HCV) infection. Participants with available sample at time of HCV detection were selected from three studies; the Australian Trial in Acute Hepatitis C, the Hepatitis C Incidence and Transmission Study - Prison and Community. HCV RNA was extracted and Core to E2 region of HCV sequenced. Clusters were identified from maximum likelihood trees with 1000 bootstrap replicates using 90% bootstrap and 5% genetic distance threshold. Among 225 participants with available Core-E2 sequence (ATAHC, n=113; HITS-p, n=90; and HITS-c, n=22), HCV genotype prevalence was: G1a: 38% (n=86), G1b: 5% (n=12), G2a: 1% (n=2), G2b: 5% (n=11), G3a: 48% (n=109), G6a: 1% (n=2) and G6l 1% (n=3). Of participants included in phylogenetic trees, 22% of participants were in a pair/cluster (G1a-35%, 30/85, mean maximum genetic distance=0.031; G3a-11%, 12/106, mean maximum genetic distance=0.021; other genotypes-21%, 6/28, mean maximum genetic distance=0.023). Among HCV/HIV co-infected participants, 50% (18/36) were in a pair/cluster, compared to 16% (30/183) with HCV mono-infection (P=<0.001). Factors independently associated with phylogenetic clustering were HIV co-infection [vs. HCV mono-infection; adjusted odds ratio (AOR) 4.24; 95%CI 1.91, 9.39], and HCV G1a infection (vs. other HCV genotypes; AOR 3.33, 95%CI 0.14, 0.61).HCV treatment and prevention strategies, including enhanced antiviral therapy, should be optimised. The impact of targeting of HCV treatment as prevention to populations with higher phylogenetic clustering, such as those with HIV co-infection, could be explored through mathematical modelling.