Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia.
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ABSTRACT:
SUBMITTER: Di Giallonardo F
PROVIDER: S-EPMC6563510 | biostudies-literature | 2019 May
REPOSITORIES: biostudies-literature
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Project description:IntroductionThe human immunodeficiency virus 1 (HIV-1) pandemic is characterized by numerous distinct sub-epidemics (clusters) that continually fuel local transmission. The aims of this study were to identify active growing clusters, to understand which factors most influence the transmission dynamics, how these vary between different subtypes and how this information might contribute to effective public health responses.MethodsWe used HIV-1 genomic sequence data linked to demographic factors that accounted for approximately 70% of all new HIV-1 notifications in New South Wales (NSW). We assessed differences in transmission cluster dynamics between subtype B and circulating recombinant form 01_AE (CRF01_AE). Separate phylogenetic trees were estimated using 2919 subtype B and 473 CRF01_AE sequences sampled between 2004 and 2018 in combination with global sequence data and NSW-specific clades were classified as clusters, pairs or singletons. Significant differences in demographics between subtypes were assessed with Chi-Square statistics.ResultsWe identified 104 subtype B and 11 CRF01_AE growing clusters containing a maximum of 29 and 11 sequences for subtype B and CRF01_AE respectively. We observed a > 2-fold increase in the number of NSW-specific CRF01_AE clades over time. Subtype B clusters were associated with individuals reporting men who have sex with men (MSM) as their transmission risk factor, being born in Australia, and being diagnosed during the early stage of infection (p < 0.01). CRF01_AE infections clusters were associated with infections among individuals diagnosed during the early stage of infection (p < 0.05) and CRF01_AE singletons were more likely to be from infections among individuals reporting heterosexual transmission (p < 0.05). We found six subtype B clusters with an above-average growth rate (>1.5 sequences / 6-months) and which consisted of a majority of infections among MSM. We also found four active growing CRF01_AE clusters containing only infections among MSM. Finally, we found 47 subtype B and seven CRF01_AE clusters that contained a large gap in time (>1 year) between infections and may be indicative of intermediate transmissions via undiagnosed individuals.ConclusionsThe large number of active and growing clusters among MSM are the driving force of the ongoing epidemic in NSW for subtype B and CRF01_AE.
| S-EPMC7817915 | biostudies-literature
Project description:Australia has a low tuberculosis incidence rate with most cases occurring among recent immigrants. Given suboptimal cluster resolution achieved with 24-locus mycobacterium interspersed repetitive unit (MIRU-24) genotyping, the added value of whole genome sequencing was explored. MIRU-24 profiles of all Mycobacterium tuberculosis culture-confirmed tuberculosis cases diagnosed between 2009 and 2013 in New South Wales (NSW), Australia, were examined and clusters identified. The relatedness of cases within the largest MIRU-24 clusters was assessed using whole genome sequencing and phylogenetic analyses. Of 1841 culture-confirmed TB cases, 91.9% (1692/1841) had complete demographic and genotyping data. East-African Indian (474; 28.0%) and Beijing (470; 27.8%) lineage strains predominated. The overall rate of MIRU-24 clustering was 20.1% (340/1692) and was highest among Beijing lineage strains (35.7%; 168/470). One Beijing and three East-African Indian (EAI) clonal complexes were responsible for the majority of observed clusters. Whole genome sequencing of the 4 largest clusters (30 isolates) demonstrated diverse single nucleotide polymorphisms (SNPs) within identified clusters. All sequenced EAI strains and 70% of Beijing lineage strains clustered by MIRU-24 typing demonstrated distinct SNP profiles. The superior resolution provided by whole genome sequencing demonstrated limited M. tuberculosis transmission within NSW, even within identified MIRU-24 clusters. Routine whole genome sequencing could provide valuable public health guidance in low burden settings.
| S-EPMC5063377 | biostudies-literature
Project description:Changes over time in HIV-1 subtype diversity within a population reflect changes in factors influencing the development of local epidemics. Here we report on the genetic diversity of 2364 reverse transcriptase sequences from people living with HIV-1 in New South Wales (NSW) notified between 2004 and 2018. These data represent >70% of all new HIV-1 notifications in the state over this period. Phylogenetic analysis was performed to identify subtype-specific transmission clusters. Subtype B and non-B infections differed across all demographics analysed (p < 0.001). We found a strong positive association for infections among females, individuals not born in Australia or reporting heterosexual transmission being of non-B origin. Further, we found an overall increase in non-B infections among men who have sex with men from 50 to 79% in the last 10 years. However, we also found differences between non-B subtypes; heterosexual transmission was positively associated with subtype C only. In addition, the majority of subtype B infections were associated with clusters, while the majority of non-B infections were singletons. However, we found seven non-B clusters (?5 sequences) indicative of local ongoing transmission. In conclusion, we present how the HIV-1 epidemic has changed over time in NSW, becoming more heterogeneous with distinct subtype-specific demographic associations.
| S-EPMC7762219 | biostudies-literature
Project description:There is concern in Australia that droughts substantially increase the incidence of suicide in rural populations, particularly among male farmers and their families. We investigated this possibility for the state of New South Wales (NSW), Australia between 1970 and 2007, analyzing data on suicides with a previously established climatic drought index. Using a generalized additive model that controlled for season, region, and long-term suicide trends, we found an increased relative risk of suicide of 15% (95% confidence interval, 8%-22%) for rural males aged 30-49 y when the drought index rose from the first quartile to the third quartile. In contrast, the risk of suicide for rural females aged >30 y declined with increased values of the drought index. We also observed an increased risk of suicide in spring and early summer. In addition there was a smaller association during unusually warm months at any time of year. The spring suicide increase is well documented in nontropical locations, although its cause is unknown. The possible increased risk of suicide during drought in rural Australia warrants public health focus and concern, as does the annual, predictable increase seen each spring and early summer. Suicide is a complex phenomenon with many interacting social, environmental, and biological causal factors. The relationship between drought and suicide is best understood using a holistic framework. Climate change projections suggest increased frequency and severity of droughts in NSW, accompanied and exacerbated by rising temperatures. Elucidating the relationships between drought and mental health will help facilitate adaptation to climate change.
| S-EPMC3435226 | biostudies-literature
Project description:This paper describes three datasets of seamless bathymetry and coastal topography for Sydney Harbour (Port Jackson), Botany and Bate Bays, and the Hawkesbury River. The datasets used to form these compilations were the most recent and highest quality available to the authors and were originally collated using the software ESRI ArcGIS. The original compilation of this data was undertaken to support tsunami modelling research by the authors of this paper. Before processing, all data were adjusted and/or reprojected to conform to the vertical datum Australian Height Datum (AHD) and horizontal projection WGS84 UTM zone 56. Data resolution and density was highly variable and grid resolutions of the final datasets were selected as the highest resolutions possible using the most sparse data in the compilation in question. For areas where no data were available, the ESRI ArcGIS interpolation tool, Topo to Raster, was used to provide a best estimate. These dastasets of three important Australian waterways provide a useful tool for coastal research and scientific interest.
| S-EPMC6007089 | biostudies-literature
Project description:BACKGROUND: Molecular epidemiology of Mycobacterium tuberculosis, its transmission dynamics and population structure have become important determinants of targeted tuberculosis control programs. Here we describe recent changes in the distribution of M. tuberculosis genotypes in New South Wales (NSW), Australia and compared strain types with drug resistance, site of disease and demographic data. METHODS: We evaluated all culture-confirmed newly identified tuberculosis cases in NSW, Australia, from 2010-2012. M. tuberculosis population structure and clustering rates were assessed using 24-loci Mycobacterial interspersed repetitive unit (MIRU) analysis and compared to MIRU data from 2006-2008. RESULTS: Of 1177 tuberculosis cases, 1128 (95.8%) were successfully typed. Beijing and East African Indian (EAI) lineage strains were most common (27.6% and 28.5%, respectively) with EAI strains increasing in relative abundance from 11.8% in 2006-2008 to 28.5% in 2010-2012. Few cases of multi-drug resistant tuberculosis were identified (18; 1.7%). Compared to 12-loci, 24-loci MIRU provided improved cluster resolution with 695 (61.6%) and 227 (20.1%) clustered cases identified, respectively. Detailed analysis of the largest cluster identified (an 11 member Beijing cluster) revealed wide geographic diversity in the absence of documented social contact. CONCLUSIONS: EAI strains of M. tuberculosis recently overtook Beijing family as a prevalent cause of tuberculosis in NSW, Australia. This lineage appeared to be less commonly related to multi-drug resistant tuberculosis as compared to Beijing strain lineage. The resolution provided by 24-loci MIRU typing was insufficient for reliable assessment of transmissions, especially of Beijing family strains.
| S-EPMC4262242 | biostudies-other
Project description:BackgroundThere is uncertainty about factors associated with involuntary in-patient psychiatric care. Understanding these factors would help in reducing coercion in psychiatry.AimsTo explore variables associated with involuntary care in the largest database of involuntary admissions published.MethodWe identified 166 102 public mental health hospital admissions over 5 years in New South Wales, Australia. Demographic, clinical and episode-of-care variables were examined in an exploratory, multivariable logistic regression.ResultsA total of 54% of eligible admissions included involuntary care. The strongest associations with involuntary care were referral from the legal system (odds ratio 4.98, 95% CI 4.61-5.38), and psychosis (odds ratio 4.48, 95% CI 4.31-4.64) or organic mental disorder (odds ratio 4.40, 95% CI 3.85-5.03). There were moderately strong associations between involuntary treatment and substance use disorder (odds ratio 2.68, 95% CI 2.56-2.81) or affective disorder (odds ratio 2.06, 95% CI 1.99-2.14); comorbid cannabis and amphetamine use disorders (odds ratio 1.65, 95% CI 1.57-1.74); unmarried status (odds ratio 1.62, 95% CI 1.49-1.76) and being born in Asia (odds ratio 1.42, 95% CI 1.35-1.50), Africa or the Middle East (odds ratio 1.32, 95% CI 1.24-1.40). Involuntary care was less likely for people aged >75 years (odds ratio 0.68, 95% CI 0.62-0.74), with comorbid personality disorder (odds ratio 0.90, 95% CI 0.87-0.94) or with private health insurance (odds ratio 0.89, 95% CI 0.86-0.93).ConclusionsThis research strengthens the evidence linking diagnostic, socioeconomic and cultural factors to involuntary treatment. Targeted interventions are needed to reduce involuntary admissions in disadvantaged groups.
| S-EPMC10951846 | biostudies-literature
Project description:The presented dataset relates to a research project titled "My Home My Community" undertaken at University of Technology Sydney (UTS) which has been funded by the National Disability Insurance Agency (NDIA) Australia. The dataset reports estimated prevalence rates of Intellectual Disability in NSW by local government area (LGA) from 2010 - 2015. The dataset is a re-examination of a cohort of 92, 542 people with intellectual disability from a larger linked research dataset built by the Department of Developmental Disability Neuropsychiatry, School of Psychiatry, UNSW. The dataset in this paper is presented in a multi-year cross-sectional format. The cohort of people with Intellectual Disability was analysed to estimate, quantify and visualise where people with intellectual disability live in New South Wales (NSW). The cohort analysed in this dataset had been generated in an earlier project undertaken by the UNSW-based authors. This dataset was generated to share with local governments in Australia and has the potential to be more widely used in a range of health policy and planning research, and city and regional planning research environments. It represents one of the only datasets currently available in Australia on Intellectual Disability describing prevalence rates at a local government area level. This dataset allows for population comparisons in other Australian states and internationally and can be examined in combination with other social and economic datasets to continue to build evidence about disability, planning and geography.
| S-EPMC7243054 | biostudies-literature
Project description:During the Early Cretaceous, dinosaur communities of the Australian-Antarctic rift system (Eumeralla and Wonthaggi formations) cropping out in Victoria were apparently dominated by a diverse small-bodied 'basal ornithopod' fauna. Further north, in Queensland (Winton and Mackunda formations), poorly-represented small-bodied ornithopods coexisted with large-bodied iguanodontians. Our understanding of the ornithopod diversity from the region between the Australian-Antarctic rift and Queensland, represented by Lightning Ridge in central-northern New South Wales (Griman Creek Formation), has been superficial. Here, we re-investigate the ornithopod diversity at Lightning Ridge based on new craniodental remains. Our findings indicate a diverse ornithopod fauna consisting of two-to-three small-bodied non-iguanodontian ornithopods (including Weewarrasaurus pobeni gen. et sp. nov.), at least one indeterminate iguanodontian, and a possible ankylopollexian. These results support those of previous studies that favour a general abundance of small-bodied basal ornithopods in Early to mid-Cretaceous high-latitude localities of southeastern Australia. Although these localities are not necessarily time-equivalent, increasing evidence indicates that Lightning Ridge formed a 'meeting point' between the basal ornithopod-dominated localities in Victoria and the sauropod-iguanodontian faunas in Queensland to the north.
| S-EPMC6284429 | biostudies-literature
Project description:INTRODUCTION:The HIV Strategy in New South Wales (NSW) Australia aims to virtually eliminate HIV transmission by 2020. We estimated the 2016 HIV diagnosis and care cascade for the state of NSW, with a focus on introducing population-based data to improve data quality and assess progress towards the UNAIDS 90-90-90 targets. METHODS:To estimate the number of people living with diagnosed HIV (PLDHIV) we used NSW data from the Australian National HIV Registry, enhanced by surveillance among people recently diagnosed with HIV to improve migration estimates. The number of undiagnosed PLHIV was estimated using back-projection modelling by CD4 count at diagnosis. De-duplicated prescription claims data were obtained from the Australian Pharmaceutical Benefits Scheme (PBS), and were combined with an estimate for those ineligible, to determine the number of PLDHIV on antiretroviral therapy (ART). Data from a clinic network with 87% coverage of PLDHIV in NSW enabled the estimation of the number on ART who had HIV suppression. RESULTS AND DISCUSSION:We estimated that 10,110 PLHIV resided in NSW in 2016 (range 8400 to 11,720), among whom 9230 (91.3%) were diagnosed, and 8490 (92.0% of those diagnosed) were receiving ART. Among PLDHIV receiving ART, 8020 (94.5%) had suppressed viral load (<200 HIV-1 RNA copies/mL). Overall, 79.3% of all PLHIV had HIV virological suppression. CONCLUSION:NSW has met each of the UNAIDS 90-90-90 targets. The enhanced surveillance methods and data collection systems improved data quality. Measuring and meeting the 90-90-90 targets is feasible and could be achieved in comparable parts of the world.
| S-EPMC5909111 | biostudies-other