230 results found
Kraemer MUG, Pybus OG, Fraser C, et al., 2022, Publisher Correction: Monitoring key epidemiological parameters of SARS-CoV-2 transmission, Nature Medicine, ISSN: 1078-8956
Kraemer MUG, Pybus OG, Fraser C, et al., 2021, Monitoring key epidemiological parameters of SARS-CoV-2 transmission, NATURE MEDICINE, Vol: 27, Pages: 1854-1855, ISSN: 1078-8956
Clemens SAC, Folegatti PM, Emary KRW, et al., 2021, Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil, NATURE COMMUNICATIONS, Vol: 12
Pickles M, Cori A, Probert WJM, et al., 2021, PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial, PLoS Computational Biology, Vol: 17, ISSN: 1553-734X
Mathematical models are powerful tools in HIV epidemiology, producing quantitative projections of key indicators such as HIV incidence and prevalence. In order to improve the accuracy of predictions, such models need to incorporate a number of behavioural and biological heterogeneities, especially those related to the sexual network within which HIV transmission occurs. An individual-based model, which explicitly models sexual partnerships, is thus often the most natural type of model to choose. In this paper we present PopART-IBM, a computationally efficient individual-based model capable of simulating 50 years of an HIV epidemic in a large, high-prevalence community in under a minute. We show how the model calibrates within a Bayesian inference framework to detailed age- and sex-stratified data from multiple sources on HIV prevalence, awareness of HIV status, ART status, and viral suppression for an HPTN 071 (PopART) study community in Zambia, and present future projections of HIV prevalence and incidence for this community in the absence of trial intervention.
Hinch R, Probert WJM, Nurtay A, et al., 2021, OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing, PLOS COMPUTATIONAL BIOLOGY, Vol: 17, ISSN: 1553-734X
Wymant C, Ferretti L, Tsallis D, et al., 2021, The epidemiological impact of the NHS COVID-19 app, NATURE, Vol: 594, Pages: 408-+, ISSN: 0028-0836
Thomas R, Probert W, Sauter R, et al., 2021, Cost and cost-effectiveness of a universal HIV testing and treatment intervention in Zambia and South Africa: evidence and projections from the HPTN 071 (PopART) trial, The Lancet Global Health, Vol: 9, Pages: e668-e680, ISSN: 2214-109X
BackgroundThe HPTN 071 (PopART) trial showed that a combination HIV prevention package including universal HIV testing and treatment (UTT) reduced population-level incidence of HIV compared with standard care. However, evidence is scarce on the costs and cost-effectiveness of such an intervention.MethodsUsing an individual-based model, we simulated the PopART intervention and standard care with antiretroviral therapy (ART) provided according to national guidelines for the 21 trial communities in Zambia and South Africa (for all individuals aged >14 years), with model parameters and primary cost data collected during the PopART trial and from published sources. Two intervention scenarios were modelled: annual rounds of PopART from 2014 to 2030 (PopART 2014–30; as the UNAIDS Fast-Track target year) and three rounds of PopART throughout the trial intervention period (PopART 2014–17). For each country, we calculated incremental cost-effectiveness ratios (ICERs) as the cost per disability-adjusted life-year (DALY) and cost per HIV infection averted. Cost-effectiveness acceptability curves were used to indicate the probability of PopART being cost-effective compared with standard care at different thresholds of cost per DALY averted. We also assessed budget impact by projecting undiscounted costs of the intervention compared with standard care up to 2030.FindingsDuring 2014–17, the mean cost per person per year of delivering home-based HIV counselling and testing, linkage to care, promotion of ART adherence, and voluntary medical male circumcision via community HIV care providers for the simulated population was US$6·53 (SD 0·29) in Zambia and US$7·93 (0·16) in South Africa. In the PopART 2014–30 scenario, median ICERs for PopART delivered annually until 2030 were $2111 (95% credible interval [CrI] 1827–2462) per HIV infection averted in Zambia and $3248 (2472–3963) per HIV infection averted in South Afric
Abueg M, Hinch R, Wu N, et al., 2021, Modeling the effect of exposure notification and non-pharmaceutical interventions on COVID-19 transmission in Washington state, NPJ DIGITAL MEDICINE, Vol: 4, ISSN: 2398-6352
Zhang Y, Wymant C, Laeyendecker O, et al., 2021, Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052, CLINICAL INFECTIOUS DISEASES, Vol: 72, Pages: 30-37, ISSN: 1058-4838
Fogel JM, Bonsall D, Cummings V, et al., 2020, Performance of a high-throughput next-generation sequencing method for analysis of HIV drug resistance and viral load, JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, Vol: 75, Pages: 3510-3516, ISSN: 0305-7453
Kendall M, Milsom L, Abeler-Dorner L, et al., 2020, Epidemiological changes on the Isle of Wight after the launch of the NHS Test and Trace programme: a preliminary analysis, LANCET DIGITAL HEALTH, Vol: 2, Pages: E658-E666
Azarian T, Martinez PP, Arnold BJ, et al., 2020, Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae, PLOS BIOLOGY, Vol: 18, ISSN: 1544-9173
Bonsall D, Golubchik T, de Cesare M, et al., 2020, A comprehensive genomics solution for HIV surveillance and clinical monitoring in low-income settings, Journal of Clinical Microbiology, Vol: 58, Pages: 1-13, ISSN: 0095-1137
Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing. This method overcomes several major technical challenges that have prevented HIV sequencing from being used routinely in public health efforts; it is fast, robust, and cost-efficient, and generates full genomic sequences of diverse strains of HIV without bias. The complete veSEQ-HIV pipeline provides viral load estimates and quantitative summaries of drug resistance mutations; it also exploits information on within-host viral diversity to construct directed transmission networks. We evaluated the method’s performance using 1,620 plasma samples collected from individuals attending 10 large urban clinics in Zambia as part of the HPTN 071-2 study (PopART Phylogenetics). Whole HIV genomes were recovered from 91% of samples with a viral load of >1,000 copies/ml. The cost of the assay (30 GBP per sample) compares favorably with existing VL and HIV genotyping tests, proving an affordable option for combining HIV clinical monitoring with molecular epidemiology and drug resistance surveillance in low-income settings.
Pickles M, Cori A, Probert W, et al., 2020, PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial
<jats:title>Abstract</jats:title><jats:p>Mathematical models are powerful tools in HIV epidemiology, producing quantitative projections of key indicators such as HIV incidence and prevalence. In order to improve the accuracy of predictions, such models need to incorporate a number of behavioural and biological heterogeneities, especially those related to the sexual network within which HIV transmission occurs. An individual-based model, which explicitly models sexual partnerships, is thus often the most natural type of model to choose. In this paper we present PopART-IBM, a computationally efficient individual-based model capable of simulating 50 years of an HIV epidemic in a large, high-prevalence community in under a minute. We show how the model calibrates within a Bayesian inference framework to detailed age- and sex-stratified data from multiple sources on HIV prevalence, awareness of HIV status, ART status, and viral suppression for an HPTN 071 (PopART) study community in Zambia, and present future projections of HIV prevalence and incidence for this community in the absence of trial intervention.</jats:p>
Kendall M, Milsom L, Abeler-Dörner L, et al., 2020, COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme
<jats:title>Abstract</jats:title><jats:p>In May 2020 the UK introduced a Test, Trace, Isolate programme in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included Version 1 of the NHS contact tracing app. We used COVID-19 daily case data to infer incidence of new infections and estimate the reproduction number R for each of 150 Upper Tier Local Authorities in England, and at the National level, before and after the launch of the programme on the Isle of Wight. We used Bayesian and Maximum-Likelihood methods to estimate R, and compared the Isle of Wight to other areas using a synthetic control method. We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch. These results are robust across each of our approaches. Our results show that the sub-epidemic on the Isle of Wight was controlled significantly more effectively than the sub-epidemics of most other Upper Tier Local Authorities, changing from having the third highest reproduction number R (of 150) before the intervention to the tenth lowest afterwards. The data is not yet available to establish a causal link. However, the findings highlight the need for further research to determine the causes of this reduction, as these might translate into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination becomes available.</jats:p>
Parker MJ, Fraser C, Abeler-Dorner L, et al., 2020, Ethics of instantaneous contact tracing using mobile phone apps in the control of the COVID-19 pandemic, JOURNAL OF MEDICAL ETHICS, Vol: 46, Pages: 427-431, ISSN: 0306-6800
Aanensen DM, Abudahab K, Adams A, et al., 2020, An integrated national scale SARS-CoV-2 genomic surveillance network, The Lancet Microbe, Vol: 1, Pages: E99-E100, ISSN: 2666-5247
El Bouzidi K, Kemp SA, Datir RP, et al., 2020, High prevalence of integrase mutation L74I in West African HIV-1 subtypes prior to integrase inhibitor treatment, JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, Vol: 75, Pages: 1575-1579, ISSN: 0305-7453
Ferretti L, Wymant C, Kendall M, et al., 2020, Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing, SCIENCE, Vol: 368, Pages: 619-+, ISSN: 0036-8075
Lehtinen S, Chewapreecha C, Lees J, et al., 2020, Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae, SCIENCE ADVANCES, Vol: 6, ISSN: 2375-2548
Bbosa N, Ssemwanga D, Ssekagiri A, et al., 2020, Phylogenetic and demographic characterization of directed HIV-1 transmission using deep sequences from high-risk and general population cohorts/groups in Uganda, Viruses, Vol: 12, ISSN: 1999-4915
Across sub-Saharan Africa, key populations with elevated HIV-1 incidence and/or prevalence have been identified, but their contribution to disease spread remains unclear. We performed viral deep-sequence phylogenetic analyses to quantify transmission dynamics between the general population (GP), fisherfolk communities (FF), and women at high risk of infection and their clients (WHR) in central and southwestern Uganda. Between August 2014 and August 2017, 6185 HIV-1 positive individuals were enrolled in 3 GP and 10 FF communities, 3 WHR enrollment sites. A total of 2531 antiretroviral therapy (ART) naïve participants with plasma viral load >1000 copies/mL were deep-sequenced. One hundred and twenty-three transmission networks were reconstructed, including 105 phylogenetically highly supported source-recipient pairs. Only one pair involved a WHR and male participant, suggesting that improved population sampling is needed to assess empirically the role of WHR to the transmission dynamics. More transmissions were observed from the GP communities to FF communities than vice versa, with an estimated flow ratio of 1.56 (95% CrI 0.68-3.72), indicating that fishing communities on Lake Victoria are not a net source of transmission flow to neighboring communities further inland. Men contributed disproportionally to HIV-1 transmission flow regardless of age, suggesting that prevention efforts need to better aid men to engage with and stay in care.
Ferretti L, Wymant C, Kendall M, et al., 2020, Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing
<jats:title>Abstract</jats:title><jats:p>The newly emergent human virus SARS-CoV-2 is resulting in high fatality rates and incapacitated health systems. Preventing further transmission is a priority. We analysed key parameters of epidemic spread to estimate the contribution of different transmission routes and determine requirements for case isolation and contact-tracing needed to stop the epidemic. We conclude that viral spread is too fast to be contained by manual contact tracing, but could be controlled if this process was faster, more efficient and happened at scale. A contact-tracing App which builds a memory of proximity contacts and immediately notifies contacts of positive cases can achieve epidemic control if used by enough people. By targeting recommendations to only those at risk, epidemics could be contained without need for mass quarantines (‘lock-downs’) that are harmful to society. We discuss the ethical requirements for an intervention of this kind.</jats:p>
Ratmann O, Kagaayi J, Hall M, et al., 2020, Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda, The Lancet HIV, Vol: 7, Pages: e173-e183, ISSN: 2352-3018
BackgroundInternational and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits of geo-targeted control, we assessed the extent to which HIV hotspots along Lake Victoria sustain transmission in neighbouring populations in south-central Uganda.MethodsWe did a population-based survey in Rakai, Uganda, using data from the Rakai Community Cohort Study. The study surveyed all individuals aged 15–49 years in four high-prevalence Lake Victoria fishing communities and 36 neighbouring inland communities. Viral RNA was deep sequenced from participants infected with HIV who were antiretroviral therapy-naive during the observation period. Phylogenetic analysis was used to infer partial HIV transmission networks, including direction of transmission. Reconstructed networks were interpreted through data for current residence and migration history. HIV transmission flows within and between high-prevalence and low-prevalence areas were quantified adjusting for incomplete sampling of the population.FindingsBetween Aug 10, 2011, and Jan 30, 2015, data were collected for the Rakai Community Cohort Study. 25 882 individuals participated, including an estimated 75·7% of the lakeside population and 16·2% of the inland population in the Rakai region of Uganda. 5142 participants were HIV-positive (2703 [13·7%] in inland and 2439 [40·1%] in fishing communities). 3878 (75·4%) people who were HIV-positive did not report antiretroviral therapy use, of whom 2652 (68·4%) had virus deep-sequenced at sufficient quality for phylogenetic analysis. 446 transmission networks were reconstructed, including 293 linked pairs with inferred direction of transmission. Adjusting for incomplete sampling, an estimated 5·7% (95% credibility interval 4·4–7·3) of transmissions occurred within lakeside areas, 89·2% (86·0–91·
Pellis L, Cauchemez S, Ferguson NM, et al., 2020, Systematic selection between age and household structure for models aimed at emerging epidemic predictions, NATURE COMMUNICATIONS, Vol: 11, ISSN: 2041-1723
Grant HE, Hodcroft EB, Ssemwanga D, et al., 2020, Pervasive and non-random recombination in near full-length HIV genomes from Uganda., Virus Evol, Vol: 6, Pages: 1-12, ISSN: 2057-1577
Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
Rose R, Hall M, Redd AD, et al., 2019, Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort, JOURNAL OF INFECTIOUS DISEASES, Vol: 220, Pages: 1406-1413, ISSN: 0022-1899
Hall MD, Holden MTG, Srisomang P, et al., 2019, Improved characterisation of MRSA transmission using within-host bacterial sequence diversity, ELIFE, Vol: 8, ISSN: 2050-084X
Kwun M, Oggioni MR, Bentley SD, et al., 2019, Synergistic activity of mobile genetic element defences in Streptococcus pneumoniae, Genes, Vol: 10, ISSN: 2073-4425
A diverse set of mobile genetic elements (MGEs) transmit between Streptococcus pneumoniae cells, but many isolates remain uninfected. The best-characterised defences against horizontal transmission of MGEs are restriction-modification systems (RMSs), of which there are two phase-variable examples in S. pneumoniae. Additionally, the transformation machinery has been proposed to limit vertical transmission of chromosomally integrated MGEs. This work describes how these mechanisms can act in concert. Experimental data demonstrate RMS phase variation occurs at a sub-maximal rate. Simulations suggest this may be optimal if MGEs are sometimes vertically inherited, as it reduces the probability that an infected cell will switch between RMS variants while the MGE is invading the population, and thereby undermine the restriction barrier. Such vertically inherited MGEs can be deleted by transformation. The lack of between-strain transformation hotspots at known prophage att sites suggests transformation cannot remove an MGE from a strain in which it is fixed. However, simulations confirmed that transformation was nevertheless effective at preventing the spread of MGEs into a previously uninfected cell population, if a recombination barrier existed between co-colonising strains. Further simulations combining these effects of phase variable RMSs and transformation found they synergistically inhibited MGEs spreading, through limiting both vertical and horizontal transmission.
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