Imperial College London

DrMichaelPickles

Faculty of MedicineSchool of Public Health

Advanced Research Fellow
 
 
 
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m.pickles

 
 
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Praed StreetSt Mary's Campus

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Publications

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111 results found

Hall M, Golubchik T, Bonsall D, Abeler-Dörner L, Limbada M, Kosloff B, Schaap A, de Cesare M, MacIntyre-Cockett G, Otecko N, Probert W, Ratmann O, Bulas Cruz A, Piwowar-Manning E, Burns DN, Cohen MS, Donnell DJ, Eshleman SH, Simwinga M, Fidler S, Hayes R, Ayles H, Fraser C, HPTN 071 PopART Phylogenetics protocol team, PANGEA consortiumet al., 2024, Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study, The Lancet Microbe, Vol: 5, Pages: E62-E71, ISSN: 2666-5247

BACKGROUND: In the last decade, universally available antiretroviral therapy (ART) has led to greatly improved health and survival of people living with HIV in sub-Saharan Africa, but new infections continue to appear. The design of effective prevention strategies requires the demographic characterisation of individuals acting as sources of infection, which is the aim of this study. METHODS: Between 2014 and 2018, the HPTN 071 PopART study was conducted to quantify the public health benefits of ART. Viral samples from 7124 study participants in Zambia were deep-sequenced as part of HPTN 071-02 PopART Phylogenetics, an ancillary study. We used these sequences to identify likely transmission pairs. After demographic weighting of the recipients in these pairs to match the overall HIV-positive population, we analysed the demographic characteristics of the sources to better understand transmission in the general population. FINDINGS: We identified a total of 300 likely transmission pairs. 178 (59·4%) were male to female, with 130 (95% CI 110-150; 43·3%) from males aged 25-40 years. Overall, men transmitted 2·09-fold (2·06-2·29) more infections per capita than women, a ratio peaking at 5·87 (2·78-15·8) in the 35-39 years source age group. 40 (26-57; 13·2%) transmissions linked individuals from different communities in the trial. Of 288 sources with recorded information on drug resistance mutations, 52 (38-69; 18·1%) carried viruses resistant to first-line ART. INTERPRETATION: HIV-1 transmission in the HPTN 071 study communities comes from a wide range of age and sex groups, and there is no outsized contribution to new infections from importation or drug resistance mutations. Men aged 25-39 years, underserved by current treatment and prevention services, should be prioritised for HIV testing and ART. FUNDING: National Institute of Allergy and Infectious Diseases, US President's Emergency Plan for AI

Journal article

Lazarus L, Herpai N, Pavlova D, Gill A, Cholette F, McClarty LM, Isac S, Lopatenko A, Pickles M, Mishra S, Shaw SY, Lorway R, McKinnon LR, Sandstrom P, Blanchard J, Balakireva O, Becker ML, Dynamics Study Teamet al., 2023, A cross-sectional survey exploring HIV and HCV prevalence among men who purchase sex in Dnipro, Ukraine, BMC Public Health, Vol: 23, ISSN: 1471-2458

BACKGROUND: HIV programming in Ukraine largely targets "key population" groups. Men who purchase sex are not directly reached. The aim of our study was to explore the prevalence of sexually transmitted and blood-borne infections (STBBIs) among men who purchase sex from female sex workers. METHODS: Following geographic mapping and population size estimation at each "hotspot", we conducted a cross-sectional bio-behavioural survey with men who purchase sex between September 2017 and March 2018 in Dnipro, Ukraine. Eligibility criteria included purchasing sex services at a "hotspot" and being ≥ 18 years. Participants completed a structured questionnaire, followed by HIV/HCV rapid testing and a dried blood spot (DBS) sample collection for confirmatory serology. RESULTS: The study enrolled 370 participants. The median age was 32 (interquartile range [IQR] = 27-38) and the median age of first purchase of sexual services was 22 (IQR = 19-27). Over half (56%) of participants reported ever testing for HIV; four participants (2%, N = 206) reported having tested positive for HIV, with three out of the four reporting being on ART. Forty percent of participants had ever tested for HCV, with three (2%, N = 142) having ever tested positive for HCV. In DBS testing, nine participants (2.4%) tested positive for HIV and 24 (6.5%) tested positive for ever having an HCV infection. CONCLUSION: Prevalence of HIV and HCV in this population was high. Given high rates of study enrolment and testing, efforts should be made to reach men who purchase sex with expanded STBBI programming.

Journal article

Davis K, Pickles M, Gregson S, Hargreaves JR, Ayles H, Bock P, Pliakas T, Thomas R, Ohrnberger J, Bwalya J, Bell-Mandla N, Shanaube K, Probert W, Hoddinott G, Bond V, Hayes R, Fidler S, Hauck Ket al., 2023, The effect of universal testing and treatment for HIV on health-related quality of life – an analysis of data from the HPTN 071 (PopART) cluster randomised trial, SSM: Population Health, Vol: 23, Pages: 1-10, ISSN: 2352-8273

BackgroundHIV treatment has clear Health-Related Quality-of-Life (HRQoL) benefits. However, little is known about how Universal Testing and Treatment (UTT) for HIV affects HRQoL. This study aimed to examine the effect of a combination prevention intervention, including UTT, on HRQoL among People Living with HIV (PLHIV).MethodsData were from HPTN 071 (PopART), a three-arm cluster randomised controlled trial in 21 communities in Zambia and South Africa (2013–2018). Arm A received the full UTT intervention of door-to-door HIV testing plus access to antiretroviral therapy (ART) regardless of CD4 count, Arm B received the intervention but followed national treatment guidelines (universal ART from 2016), and Arm C received standard care. The intervention effect was measured in a cohort of randomly selected adults, over 36 months. HRQoL scores, and the prevalence of problems in five HRQoL dimensions (mobility, self-care, performing daily activities, pain/discomfort, anxiety/depression) were assessed among all participants using the EuroQol-5-dimensions-5-levels questionnaire (EQ-5D-5L). We compared HRQoL among PLHIV with laboratory confirmed HIV status between arms, using adjusted two-stage cluster-level analyses.ResultsAt baseline, 7,856 PLHIV provided HRQoL data. At 36 months, the mean HRQoL score was 0.892 (95% confidence interval: 0.887–0.898) in Arm A, 0.886 (0.877–0.894) in Arm B and 0.888 (0.884–0.892) in Arm C. There was no evidence of a difference in HRQoL scores between arms (A vs C, adjusted mean difference: 0.003, -0.001-0.006; B vs C: -0.004, -0.014-0.005). The prevalence of problems with pain/discomfort was lower in Arm A than C (adjusted prevalence ratio: 0.37, 0.14–0.97). There was no evidence of differences for other HRQoL dimensions.ConclusionsThe intervention did not change overall HRQoL, suggesting that raising HRQoL among PLHIV might require more than improved testing and treatment. However, PLHIV had fewer problems with p

Journal article

Shaw SY, Leung S, Isac S, Musyoki H, Mugambi M, Kioko J, Musimbi J, Olango K, Kuria S, Ongaro MK, Walimbwa J, Melon M, Emmanuel F, Moses S, Blanchard JF, Pickles M, Lazarus L, Lorway RR, Becker ML, Mishra S, Bhattacharjee Pet al., 2023, Assessing awareness and use of HIV self-testing kits after the introduction of a community-based HIV self-testing programme among men who have sex with men in Kenya, PLOS Global Public Health, Vol: 3, ISSN: 2767-3375

Men who have sex with men (MSM) bear a disproportionate burden of new HIV infections in Kenya, while experiencing discrimination, leading to suboptimal levels of HIV care. HIV self-testing (HIVST) is a tool to increase HIV screening and earlier diagnosis; however, questions remain regarding how best to scale-up HIVST to MSM in Kenya. The main objective of this study was to examine changes in knowledge and use of HIVST after implementation of a community-led HIVST project. Participants were MSM recruited from Kisumu, Mombasa, and Kiambu counties. Data were collected from two rounds (Round 1: 2019; Round 2: 2020) of serial cross-sectional integrated biological and behavioural assessments (IBBA), pre-, and post-project implementation. Two main outcomes were measured: 1) whether the respondent had ever heard of HIVST; and 2) whether they had ever used HIVST kits. Changes in outcomes between IBBA rounds were examined using modified multivariable Poisson regression models; adjusted prevalence ratios (aPR) and 95% confidence intervals (95% CI) are reported. A total of 2,328 respondents were included in main analyses. The proportion of respondents who had heard of HIVST increased from 75% in Round 1 to 94% in Round 2 (aPR: 1.2, 95% CI: 1.2-1.3), while those reporting using an HIVST kit increased from 20% to 53% (aPR: 2.3, 95% CI: 2.0-2.6). Higher levels of education and HIV programme awareness were associated with both outcomes. Awareness and use of HIVST kits increased after implementation of a community-led HIVST implementation project, demonstrating the importance of integration with existing community groups.

Journal article

Bhattacharjee P, Isac S, Musyoki H, Gichangi P, Ma H, Becker M, Hontelez J, Mishra S, Transitions teamet al., 2023, Changes in context, typology and programme outcomes between early and recent periods of sex work among young female sex workers in Mombasa, Kenya: a cross-sectional study, PLoS One, Vol: 18, ISSN: 1932-6203

INTRODUCTION: The sex work context and typology change continuously and influence HIV related risk and vulnerability for young female sex workers (YFSW). We sought to describe changes in the context and typology of sex work between the first (early) and past month (recent) of sex work among YFSW to inform HIV prevention programming for sex workers. METHODS: We used data from a cross-sectional survey (April-November 2015), administered using physical location-based sampling to 408 cis-women, aged 14-24 years, who self-identified as sex workers, in Mombasa, Kenya. We collected self-reported data on the early and recent month of sex work. The analysis focused on changes in a) sex work context and typology (defined by setting where sex workers practice sex work) where YFSW operated, b) primary typology of sex work, and c) HIV programme outcomes among YFSW who changed primary typology, within the early and recent month of sex work. We analysed the data using a) SPSS27.0 and excel; b) bivariate analysis and χ2 test; and c) bivariate logistic regression models. RESULTS: Overall, the median age of respondents was 20 years and median duration in sex work was 2 years. Higher proportion of respondents in the recent period managed their clients on their own (98.0% vs. 91.2%), had sex with >5 clients per week (39.3% vs.16.5%); were able to meet > 50% of living expenses through sex work income (46.8% vs. 18.8%); and experienced police violence in the past month (16.4% vs. 6.5%). YFSW reported multiple sex work typology in early and recent periods. Overall, 37.2% reported changing their primary typology. A higher proportion among those who used street/ bus stop typology, experienced police violence, or initiated sex work after 19 years of age in the early period reported a change. There was no difference in HIV programme outcomes among YFSW who changed typology vs. those who did not. CONCLUSIONS: The sex work context changes even in a short duration of two years. Hence

Journal article

Pickles M, Gregson S, Moorhouse L, Dadirai T, Dzamatira F, Mandizvidza P, Maswera R, Museka T, Schaefer R, Skovdal M, Thomas R, Tsenesa B, Mugurungi O, Nyamukapa C, Hallett Tet al., 2023, Strengthening the HIV prevention cascade to maximise epidemiological impact in Eastern Zimbabwe: a modelling study, The Lancet Global Health, Vol: 11, Pages: e1105-e1113, ISSN: 2214-109X

Background HIV prevention cascades provide a systematic understanding of barriers to prevention. In this study we use mathematical modelling to understand the consequences of these barriers and how the cascade could be strengthened to maximise epidemiological impact, providing potentially important insights for programmes. Methods We use an individual-based model of HIV transmission (PopART-IBM), calibrated to cohort data from eastern Zimbabwe. HIV prevention cascade estimates from this cohort are used as probabilities for indicators in the model representing an individual’s ‘motivation’, ‘access’ and ‘capacity to use effectively’ pre-exposure prophylaxis, voluntary male medical circumcision and condom use. We examine how current barriers affect the number and distribution of HIV infections compared to a no-barrier scenario. Using assumptions about how interventions could strengthen the HIV prevention cascade, we estimate the reduction in HIV infections over a ten-year period through addressing different elements of the cascade.Findings 22,000 new potentially ‘avertable’ HIV infections will occur over the next ten years due to existing HIV prevention cascade barriers, 74·2% of the 28,000 new infections that would occur with existing barriers in a population of approximately 1·2 million adults. Removing these barriers would reduce HIV incidence below the benchmarks for epidemic elimination. Addressing all cascade steps in one priority population is much more impactful than addressing one step across all populations. Interpretation Interventions exists in eastern Zimbabwe to reduce HIV towards elimination, but barriers of motivation, access and effective use prevent their full effect being realised. Interventions need to be multi-layered, and address all steps along the HIV prevention cascade. Models incorporating the HIV prevention cascade can help identify the main barriers to greater impact.Funding

Journal article

Neufeld B, Cholette F, Sandstrom P, Musyoki H, Ma H, Kaosa S, Kioko J, Isac S, Bhattacharjee P, Cheuk E, Pickles M, Mwatelah R, Capiña R, Daniuk C, Mckinnon LR, Blanchard J, Mishra S, Becker M, Transitions Study Teamet al., 2023, HIV acquisition prior to entry into formal sex work: inference from next-generation viral sequencing., AIDS, Vol: 37, Pages: 987-992, ISSN: 0269-9370

OBJECTIVE: To infer the timing of HIV acquisition in relation to self-reported events in the sexual life course of adolescent girls and young women (AGYW) who self-identify as female sex workers (FSW) in Mombasa, Kenya. DESIGN: Next-generation viral sequencing of samples of AGYW living with HIV in the Transitions study, a cross-sectional bio-behavioural survey of AGYW aged 14-24 years in Mombasa, Kenya. METHOD: Dried blood spot specimens were collected from study participants ( n  = 37, all FSW). A portion of the HIV pol gene was sequenced using an in-house next-generation sequencing assay for HIV drug resistance mutation genotyping. Estimated time since infection (ETI) was inferred using the HIV EVO web-based tool ( https://hiv.biozentrum.unibas.ch/ETI/ ), and data on self-reported events were obtained from the survey. RESULTS: The median ETI among FSW was 3.4 (interquartile range = 1.7, 6.3) years, with a median ETI of 1.5 years prior to entry into formal sex work. We estimated that 74.1% (95% confidence interval = 53.7-88.9%) of participants living with HIV and who self-identified as FSW likely acquired HIV prior to self-identification as a sex worker. CONCLUSIONS: Findings suggest a large fraction of prevalent HIV infection among AGYW engaged in sex work stems from acquisition prior to entry into formal sex work. Current HIV prevention programs tailored for sex workers may miss key opportunities for HIV prevention as they are designed to reach women after entry into formal sex work, signaling a need for tailored programs to reach high-risk AGYW earlier on in their sexual life course.

Journal article

Zewdie K, Pickles M, Floyd S, Fidler S, Ayles H, Bock P, Hoddinott G, Mandla N, Shanaube K, Simwinga M, Fraser C, Seeley J, Piwowar-Manning E, Hayes R, Donnell Det al., 2023, Uptake of medical male circumcision with household-based testing, and the association of traditional male circumcision and HIV infection, AIDS, Vol: 37, Pages: 795-802, ISSN: 0269-9370

OBJECTIVES: Voluntary medical male circumcision (VMMC) is an important component of combination HIV prevention. Inclusion of traditionally circumcised HIV negative men in VMMC uptake campaigns may be important if traditional male circumcision is less protective against HIV acquisition than VMMC. METHODS: We used data from the HIV Prevention Trials Network (HPTN) 071 (PopART) study. This cluster-randomized trial assessed the impact of a combination prevention package on population-level HIV incidence in 21 study communities in Zambia and South Africa. We evaluated uptake of VMMC, using a two-stage analysis approach and used discrete-time survival analysis to evaluate the association between the types of male circumcision and HIV incidence. RESULTS: A total of 10 803 HIV-negative men with self-reported circumcision status were included in this study. At baseline, 56% reported being uncircumcised, 26% traditionally circumcised and 18% were medically circumcised. During the PopART intervention, 11% of uncircumcised men reported uptake of medical male circumcision. We found no significant difference in the uptake of VMMC in communities receiving the PopART intervention package and standard of care {adj. rate ratio=1·10 [95% confidence interval (CI) 0.82, 1.50, P  = 0.48]}. The rate of HIV acquisition for medically circumcised men was 70% lower than for those who were uncircumcised adjusted hazard ratio (adjHR) = 0.30 (95% CI 0.16-0.55; P  < 0.0001). There was no difference in rate of HIV acquisition for traditionally circumcised men compared to those uncircumcised adjHR = 0.84 (95% CI 0.54, 1.31; P  = 0.45). CONCLUSIONS: Household-based delivery of HIV testing followed by referral for medical male circumcision did not result in substantial VMMC uptake. Traditional circumcision is not associated with lower risk of HIV acquisition.

Journal article

Davis K, Moorhouse L, Maswera R, Mandizvidza P, Dadirai T, Dzamatira F, Nyamukapa C, Pickles M, Gregson Set al., 2023, Association between symptoms of depression and sexual risk behaviours among young people in Manicaland, East Zimbabwe: a cohort study, AIDSImpact

Conference paper

Lazarus L, Herpai N, Pavlova D, Murney MA, Balakireva O, Tarasova T, McClarty L, Pickles M, Mishra S, Forget E, Becker M, Lorway Ret al., 2023, Exploring the impact of military conflict on sex work in Ukraine: Women's experiences of economic burden, Global Public Health, Vol: 18, ISSN: 1744-1692

Little is known about the impact of military conflict on sex work from the perspective of sex workers. We attempt to explore the meaning of conflict on sex work by asking women about the changes that they have experienced in their lives and work since the beginning of the 2014 military conflict in eastern Ukraine. The findings in this article are based on qualitative interviews with 43 cisgender women living and practicing sex work in Dnipro, eastern Ukraine. Our analysis highlights the meanings that sex workers have linked to the conflict, with financial concerns emerging as a dominant theme. The conflict therefore functions as a way of understanding changing economic circumstances with both individual and broader impacts. By better understanding the meaning of conflict as expressed by sex workers, we can begin to adapt our response to address emerging, and unmet, needs of the community.

Journal article

Yang L, Boily M-C, Rönn MM, Obiri-Yeboah D, Morhason-Bello I, Meda N, Lompo O, Mayaud P, Pickles M, Brisson M, Hodgins C, Delany-Moretlwe S, Maheu-Giroux Met al., 2023, Regional and country-level trends in cervical cancer screening coverage in sub-Saharan Africa: a systematic analysis of population-based surveys (2000-2020), PLoS Medicine, Vol: 20, Pages: 1-18, ISSN: 1549-1277

BACKGROUND: Sub-Saharan Africa (SSA) has the highest cervical cancer (CC) burden globally-worsened by its HIV epidemics. In 2020, the World Health Organization (WHO) introduced a CC elimination strategy with goals for vaccination, screening, and treatment. To benchmark progress, we examined temporal trends in screening coverage, percent screened at least twice by the age of 45, screening coverage among women living with HIV (WLHIV), and pre-cancer treatment coverage in SSA. METHODS AND FINDINGS: We conducted a systematic analysis of cross-sectional population-based surveys. It included 52 surveys from 28 countries (2000 to 2020) with information on CC screening among women aged 25 to 49 years (N = 151,338 women). We estimated lifetime and past 3-year screening coverage by age, year, country, and HIV serostatus using a Bayesian multilevel model. Post-stratification and imputations were done to obtain aggregate national, regional, and SSA-level estimates. To measure re-screening by age 45, a life table model was developed. Finally, self-reported pre-cancer treatment coverage was pooled across surveys using a Bayesian meta-analysis. Overall, an estimated 14% (95% credible intervals [95% CrI]: 11% to 21%) of women aged 30 to 49 years had ever been screened for CC in 2020, with important regional and country-level differences. In Eastern and Western/Central Africa, regional screening coverages remained constant from 2000 to 2020 and WLHIV had greater odds of being screened compared to women without HIV. In Southern Africa, however, screening coverages increased and WLHIV had equal odds of screening. Notably this region was found to have higher screening coverage in comparison to other African regions. Rescreening rates were high among women who have already been screened; however, it was estimated that only 12% (95% CrI: 10% to 18%) of women had been screened twice or more by age 45 in 2020. Finally, treatment coverage among 4 countries with data was 84% (95% CrI: 70% to

Journal article

Shanaube K, Gachie T, Hoddinott G, Schaap A, Floyd S, Mainga T, Bond V, Hayes R, Fidler S, Ayles H, HPTN071 PopART Study Teamet al., 2022, Depressive symptoms and HIV risk behaviours among adolescents enrolled in the HPTN071 (PopART) trial in Zambia and South Africa, PLoS One, Vol: 17, ISSN: 1932-6203

BACKGROUND: Mental health is a critical and neglected public health problem for adolescents in sub-Saharan Africa. In this paper we aim to determine the prevalence of depressive symptoms and the association with HIV risk behaviours in adolescents aged 15-19 years in Zambia and SA. METHODS: We conducted a cross-sectional survey from August-November 2017 in seven control communities of HPTN 071 (PopART) trial (a community-randomised trial of universal HIV testing and treatment), enrolling approximately 1400 eligible adolescents. HIV-status was self-reported. Depressive symptoms were measured with the Short Mood and Feelings Questionnaire (SMFQ), with a positive screen if adolescents scored ≥12. We fitted a logistic regression model to identify correlates of depressive symptoms with subgroup analyses among those who self-reported ever having had sex, by gender and country. RESULTS: Out of 6997 households approached, 6057 (86.6%) were enumerated. 2546 adolescents were enumerated of whom 2120 (83.3%) consented to participate and were administered the SMFQ. The prevalence of depressive symptoms was 584/2120 (27.6%) [95%CI: 25.7%-29.5%]. Adolescents in SA were less likely to experience depressive symptoms (Adjusted Odds Ratio [AOR] = 0.63 (95% CI: 0.50, 0.79), p-value<0.0001). Female adolescents (AOR = 1.46 (95% CI: 1.19, 1.81), p-value<0.0001); those who reported ever having sex and being forced into sex (AOR = 1.80 (95% CI: 1.45, 2.23), p-value<0.001) and AOR = 1.67 (95% CI: 0.99, 2.84); p-value = 0.057 respectively) were more likely to experience depressive symptoms. Among 850 (40.1%) adolescents who self-reported to ever having had sex; those who used alcohol/drugs during their last sexual encounter were more likely to experience depressive symptoms (AOR = 2.18 (95% CI: 1.37, 3.47); p-value = 0.001), whereas those who reported using a condom were less likely to experience depressive symptoms (AOR = 0.74 (95% CI: 0.55, 1.00); p-value = 0.053). CONCLUSION: Th

Journal article

Probert WJM, Sauter R, Pickles M, Cori A, Bell-Mandla NF, Bwalya J, Abeler-Dörner L, Bock P, Donnell DJ, Floyd S, Macleod D, Piwowar-Manning E, Skalland T, Shanaube K, Wilson E, Yang B, Ayles H, Fidler S, Hayes RJ, Fraser C, Hayes R, Fidler S, Beyers N, Ayles H, Bock P, El-Sadr W, Cohen M, Eshleman S, Agyei Y, Piwowar-Manning E, Bond V, Hoddinott G, Donnell D, Floyd S, Wilson E, Emel L, Noble H, Macleod D, Burns D, Fraser C, Cori A, Sista N, Griffith S, Moore A, Headen T, White R, Miller E, Hargreaves J, Hauck K, Thomas R, Limbada M, Bwalya J, Pickles M, Sabapathy K, Schaap A, Dunbar R, Shanaube K, Yang B, Simwinga M, Smith P, Vermund S, Mandla N, Makola N, van Deventer A, James A, Jennings K, Kruger J, Phiri M, Kosloff B, Mwenge L, Kanema S, Sauter R, Probert W, Kumar R, Sakala E, Silumesi A, Skalland T, Yuhas Ket al., 2022, Projected outcomes of universal testing and treatment in a generalised HIV epidemic in Zambia and South Africa (the HPTN 071 [PopART] trial): a modelling study, The Lancet HIV, Vol: 9, Pages: e771-e780, ISSN: 2352-3018

BackgroundThe long-term impact of universal home-based testing and treatment as part of universal testing and treatment (UTT) on HIV incidence is unknown. We made projections using a detailed individual-based model of the effect of the intervention delivered in the HPTN 071 (PopART) cluster-randomised trial.MethodsIn this modelling study, we fitted an individual-based model to the HIV epidemic and HIV care cascade in 21 high prevalence communities in Zambia and South Africa that were part of the PopART cluster-randomised trial (intervention period Nov 1, 2013, to Dec 31, 2017). The model represents coverage of home-based testing and counselling by age and sex, delivered as part of the trial, antiretroviral therapy (ART) uptake, and any changes in national guidelines on ART eligibility. In PopART, communities were randomly assigned to one of three arms: arm A received the full PopART intervention for all individuals who tested positive for HIV, arm B received the intervention with ART provided in accordance with national guidelines, and arm C received standard of care. We fitted the model to trial data twice using Approximate Bayesian Computation, once before data unblinding and then again after data unblinding. We compared projections of intervention impact with observed effects, and for four different scenarios of UTT up to Jan 1, 2030 in the study communities.FindingsCompared with standard of care, a 51% (95% credible interval 40–60) reduction in HIV incidence is projected if the trial intervention (arms A and B combined) is continued from 2020 to 2030, over and above a declining trend in HIV incidence under standard of care.InterpretationA widespread and continued commitment to UTT via home-based testing and counselling can have a substantial effect on HIV incidence in high prevalence communities.FundingNational Institute of Allergy and Infectious Diseases, US President's Emergency Plan for AIDS Relief, International Initiative for Impact Evaluation, Bill &

Journal article

Herpai N, Lazarus L, Forget E, Balakireva O, Pavlova D, McClarty L, Lorway R, Pickles M, Isac S, Sandstrom P, Aral S, Mishra S, Ma H, Blanchard J, Becker Met al., 2022, Exploring the dynamics of workplace typologies for sex workers in Eastern Ukraine, Global Public Health, Vol: 17, Pages: 2034-2053, ISSN: 1744-1692

We examine the typologies of workplaces for sex workers in Dnipro, Ukraine as part of the larger Dynamics Study, which explores the influence of conflict on sex work. We conducted a cross-sectional survey with 560 women from September 2017 to October 2018. The results of our study demonstrate a diverse sex work environment with heterogeneity across workplace typologies in terms of remuneration, workload, and safety. Women working in higher prestige typologies earned a higher hourly wage, however client volume also varied which resulted in comparable monthly earnings from sex work across almost all workplace types. While sex workers in Dnipro earn a higher monthly wage than the city mean, they also report experiencing high rates of violence and a lack of personal safety at work. Sex workers in all workplaces, with the exception of those working in art clubs, experienced physical and sexual violence perpetrated by law enforcement officers and sex partners. By understanding more about sex work workplaces, programmes may be better tailored to meet the needs of sex workers and respond to changing work environments due to ongoing conflict and COVID-19 pandemic.

Journal article

Davis K, Pickles M, Gregson S, Hargreaves J, Ayles H, Bock P, Pliakas T, Thomas R, Ohrnberger J, Bwalya J, Bell-Mandla N, Shanaube K, Probert W, Hoddinott G, Bond V, Hayes R, Fidler S, Hauck Ket al., 2022, The effect of universal testing and treatment for HIV on health-related quality of life - data from the HPTN 071 (PopART) cluster randomised trial in Zambia and South Africa, AIDS 2022, Publisher: International AIDS Society, ISSN: 1758-2652

Conference paper

Yang L, Boily M-C, Ronn M, Delany-Moretlwe S, Obiri-Yeboah D, Morhason-Bello I, Meda N, Gauthier T, Mayaud P, Pickles M, Brisson M, Maheu-Giroux Met al., 2022, Cervical cancer screening among women living with HIV: a systematic analysis of population-based surveys in sub-Saharan Africa, 24th International AIDS Conference, Publisher: Wiley, Pages: 83-83, ISSN: 1758-2652

Conference paper

Derksen J, Pavlova D, McClarty LM, Balakireva O, Herpai N, Lazarus L, Tennakoon A, Tarasova T, Lorway R, Pickles M, Mishra S, Shaw SY, Becker MLet al., 2022, Awareness and utilization of HIV testing and prevention services among female sex workers in Dnipro, Ukraine: implications for prevention program strengthening from the dynamics study, Frontiers in Reproductive Health, Vol: 4, ISSN: 2673-3153

INTRODUCTION: Approximately 240,000 people live with HIV in Ukraine, concentrated among key populations, including sex workers. Non-governmental organizations (NGOs) play an important role in the funding and delivery of HIV testing and prevention services in Ukraine. These services are set within the context of national healthcare reforms as well as ongoing armed conflict. This study seeks to describe and understand the usage of HIV testing and prevention services among sex workers in the eastern Ukrainian city of Dnipro. METHODS: A cross-sectional bio-behavioral survey was administered in September 2017-March 2018 among 560 sex workers working in Dnipro. Descriptive analyses of survey data are presented alongside multivariable logistic regression models identifying factors associated with NGO awareness and HIV testing in the past 12 months; adjusted odds ratios (AOR) and 95% confidence intervals (95% CI) are reported. RESULTS: Sixty-two percent of respondents were aware of NGOs offering HIV services. Sixty-eight percent had tested for HIV in the past 12 months, and 51% of those who reported the location of their most recent test were tested at an NGO. Those with 5-9 years in sex work had greater odds of being aware of NGOs (AOR = 5.5, 95%CI: 3.2-9.7) and testing for HIV (AOR = 3.4, 95%CI: 2.0-6.0) compared to those new to the profession. Contact with outreach workers was strongly associated with increased odds of testing (AOR = 13.0, 95%CI: 7.0-24.0). Sex workers in "offices" (brothel-like venues) reported higher odds of testing than all other workplaces, while those in entertainment venues (AOR = 0.3, 95%CI: 0.2-0.5) and public places (AOR = 0.2, 95%CI: 0.1-0.3) reported lower rates. Receiving prevention services, such as free condoms, was associated with increased testing (AOR = 16.9, 95%CI: 9.7-29.3). DISCUSSION: NGOs in Dnipro, Ukraine play an important role in HIV testing and prevention for women involved in sex work. However, focused efforts should

Journal article

Hall E, Davis K, Ohrnberger J, Pickles M, Gregson S, Thomas R, James H, Pliakas T, Justin B, Dunbar R, Shanaube K, Graeme H, Virginia B, Bock P, Ayles H, Stangl A, Donnell D, Hayes R, Fidler S, Hauck Ket al., 2022, Associations between HIV stigma and health-related quality of life among people living with HIV in Zambia and South Africa: Cross-sectional analysis of data from the HPTN071 (PopART) study, AIDS 2022

Conference paper

Limbada M, Macleod D, Situmbeko V, Muhau E, Shibwela O, Chiti B, Floyd S, Schaap AJ, Hayes R, Fidler S, Ayles Het al., 2021, Rates of viral suppression in a cohort of people with stable HIV from two community models of ART delivery versus facility-based HIV care in Lusaka, Zambia: a cluster-randomised, non-inferiority trial nested in the HPTN 071 (PopART) trial, The Lancet HIV, Vol: 9, Pages: E13-E23, ISSN: 2405-4704

BackgroundNon-facility-based antiretroviral therapy (ART) delivery for people with stable HIV might increase sustainable ART coverage in low-income and middle-income countries. Within the HPTN 071 (PopART) trial, two interventions, home-based delivery (HBD) and adherence clubs (AC), which included groups of 15–30 participants who met at a communal venue, were compared with standard of care (SoC). In this trial we looked at the effectiveness and feasibility of these alternative models of care. Specifically, this trial aimed to assess whether these models of care had similar virological suppression to that of SoC 12 months after enrolment.MethodsThis was a three-arm, cluster-randomised, non-inferiority trial, done in two urban communities in Lusaka, Zambia included in the HPTN 071 trial. The two communities were split into zones, which were randomly assigned (1:1:1) to the three treatment strategies: 35 zones to the SoC group, 35 zones to the HBD group, and 34 zones to the AC group. ART and adherence support were delivered once every 3 months at home for the HBD group, in groups of 15–30 people in the AC group, or in the clinic for the SoC group. Adults with HIV who were receiving first-line ART for at least 6 months, virally suppressed using national HIV guidelines in the last 12 months, had no other health conditions requiring the clinicians attention, live in the study catchment area, and provided written informed consent, were eligible for inclusion. The primary endpoint was viral suppression at 12 months (with a 6 month final measurement window [ie, 9–15 months]), defined as less than 1000 HIV RNA copies per mL, with a non-inferiority margin of 5%.FindingsBetween May 5 and Dec 19, 2017, 9900 individuals were screened for inclusion, of whom 2489 (25·1%) participants were enrolled into the trial: 781 (31%) in the SoC group, 852 (34%) in the HBD group, and 856 (34%) in the AC group. A higher proportion of participants had viral load measurem

Journal article

Davis K, Muzariri K, Mangenah C, Dadirai T, Mandizvidza P, Maswera R, Nyamukapa C, Hauck K, Gregson S, Pickles Met al., 2021, Modelling the interaction between depression and HIV incidence in Manicaland, East Zimbabwe, Fast Track Cities 2021

Conference paper

Pickles M, Cori A, Probert WJM, Sauter R, Hinch R, Fidler S, Ayles H, Bock P, Donnell D, Wilson E, Piwowar-Manning E, Floyd S, Hayes RJ, Fraser C, HPTN 071 PopART Study Teamet 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 Comput Biol, Vol: 17

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.

Journal article

Thomas R, Probert W, Sauter R, Mwenge L, Singh S, Kanema S, Vanqa N, Harper A, Burger R, Cori A, Pickles M, Bell-Mandla N, Yang B, Bwalya J, Phiri M, Shanaube K, Floyd S, Donnell D, Bock P, Ayles H, Fidler S, Hayes R, Fraser C, Hauck Ket 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

Journal article

Amiri L, Torabi M, Deardon R, Pickles Met al., 2021, Spatial modeling of individual-level infectious disease transmission: Tuberculosis data in Manitoba, Canada, Statistics in Medicine, Vol: 40, Pages: 1678-1704, ISSN: 0277-6715

Geographically dependent individual level models (GD-ILMs) are a class of statistical models that can be used to study the spread of infectious disease through a population in discrete-time in which covariates can be measured both at individual and area levels. The typical ILMs to illustrate spatial data are based on the distance between susceptible and infectious individuals. A key feature of GD-ILMs is that they take into account the spatial location of the individuals in addition to the distance between susceptible and infectious individuals. As a motivation of this article, we consider tuberculosis (TB) data which is an infectious disease which can be transmitted through individuals. It is also known that certain areas/demographics/communities have higher prevalent of TB (see Section 4 for more details). It is also of interest of policy makers to identify those areas with higher infectivity rate of TB for possible preventions. Therefore, we need to analyze this data properly to address those concerns. In this article, the expectation conditional maximization algorithm is proposed for estimating the parameters of GD-ILMs to be able to predict the areas with the highest average infectivity rates of TB. We also evaluate the performance of our proposed approach through some simulations. Our simulation results indicate that the proposed method provides reliable estimates of parameters which confirms accuracy of the infectivity rates.

Journal article

Bhattacharjee P, Ma H, Musyoki H, Cheuk E, Isac S, Njiraini M, Gichangi P, Mishra S, Becker M, Pickles Met al., 2020, Prevalence and patterns of gender-based violence across adolescent girls and young women in Mombasa, Kenya, BMC Women's Health, Vol: 20, ISSN: 1472-6874

Background We sought to estimate the prevalence and describe heterogeneity in experiences of gender-based violence (GBV) across subgroups of adolescent girls and young women (AGYW). MethodsWe used data from a cross-sectional bio-behavioural survey among 1299 AGYW aged 14-24 in Mombasa, Kenya in 2015. Respondents were recruited from hotspots associated with sex work, and self-selected into one of three subgroups: young women engaged in casual sex (YCS), young women engaged in transactional sex (YTS), and young women engaged in sex work (YSW). We compared overall and across subgroups: prevalence of lifetime and recent (within previous year) self-reported experience of physical, sexual, and police violence; patterns and perpetrators of first and most recent episode of physical and sexual violence; and factors associated with physical and sexual violence. ResultsThe prevalences of lifetime and recent physical violence were 18.0% and 10.7% respectively. Lifetime and recent sexual violence respectively were reported by 20.5% and 9.8% of respondents. Prevalence of lifetime and recent experience of police violence were 34.7% and 25.8% respectively. All forms of violence were most frequently reported by YSW, followed by YTS and then YCS. 62%/81% of respondents reported having sex during the first episode of physical/sexual violence, and 48%/62% of those sex acts at first episode of physical/sexual violence were condomless. In the most recent episode of violence when sex took place levels of condom use remained low at 53-61%. The main perpetrators of violence were intimate partners for YCS, and both intimate partners and regular non-client partners for YTS. For YSW, first-time and regular paying clients were the main perpetrators of physical and sexual violence. Alcohol use, ever being pregnant and regular source of income were associated with physical and sexual violence though it differed by subgroup and type of violence. ConclusionsAGYW in these settings experience high vu

Journal article

Foss AM, Prudden HJ, Mitchell KM, Pickles M, Washington R, Phillips AE, Alary M, Boily M-C, Moses S, Watts CH, Vickerman PTet al., 2020, Using data from 'visible' populations to estimate the size and importance of 'hidden' populations in an epidemic: A modelling technique., Infectious Disease Modelling, Vol: 5, Pages: 798-813, ISSN: 2468-2152

We used reported behavioural data from cisgender men who have sex with men and transgender women (MSM/TGW) in Bangalore, mainly collected from 'hot-spot' locations that attract MSM/TGW, to illustrate a technique to deal with potential issues with the representativeness of this sample. A deterministic dynamic model of HIV transmission was developed, incorporating three subgroups of MSM/TGW, grouped according to their reported predominant sexual role (insertive, receptive or versatile). Using mathematical modelling and data triangulation for 'balancing' numbers of partners and role preferences, we compared three different approaches to determine if our technique could be useful for inferring characteristics of a more 'hidden' insertive MSM subpopulation, and explored their potential importance for the HIV epidemic. Projections for 2009 across all three approaches suggest that HIV prevalence among insertive MSM was likely to be less than half that recorded in the surveys (4.5-6.5% versus 13.1%), but that the relative size of this subgroup was over four times larger (61-69% of all MSM/TGW versus 15%). We infer that the insertive MSM accounted for 10-20% of all prevalent HIV infections among urban males aged 15-49. Mathematical modelling can be used with data on 'visible' MSM/TGW to provide insights into the characteristics of 'hidden' MSM. A greater understanding of the sexual behaviour of all MSM/TGW is important for effective HIV programming. More broadly, a hidden subgroup with a lower infectious disease prevalence than more visible subgroups, has the potential to contain more infections, if the hidden subgroup is considerably larger in size.

Journal article

Cheuk E, Mishra S, Balakireva O, Musyoki H, Isac S, Pavlova D, Bhattacharjee P, Lorway R, Pickles M, Ma H, Gichangi P, Sandstrom P, McKinnon LR, Lazarus L, Moses S, Blanchard J, Becker Met al., 2020, Transitions: novel study methods to understand early HIV risk among adolescent girls and young women in Mombasa, Kenya, and Dnipro, Ukraine, Frontiers in Reproductive Health, Vol: 2, ISSN: 2673-3153

Transitions aims to understand the human immunodeficiency virus (HIV) risk at critical transition points in the sexual life course of adolescent girls and young women (AGYW) who engage in casual sex, transactional sex, and sex work. In this article, we present the Transitions study methods. The Transitions study has the following objectives: (1) to describe how the characteristics and length of the transition period and access gap vary across two epidemiological contexts (Mombasa, Kenya, and Dnipro, Ukraine); (2) to understand how the risk of HIV varies by length and characteristics of the transition period and access gap across epidemiologic contexts; and (3) to assess the extent to which HIV infections acquired during the transition period and access gap could mitigate the population-level impact of focused interventions for female sex workers and explore the potential marginal benefit of expanding programs to reach AGYW during the transition period and access gap. Cross-sectional biobehavioral data were collected from young women aged 14 to 24 years who were recruited from locations in Mombasa County, Kenya, and Dnipro, Ukraine, where sex work took place. Data are available for 1,299 Kenyan and 1,818 Ukrainian participants. The survey addressed the following areas: timing of transition events (first sex, first exchange of sex for money or other resources, self-identification as sex workers, entry into formal sex work, access to prevention program services); sexual behaviors (condom use, anal sex, sex under the influence of drugs or alcohol); partnerships (regular and first-time clients, regular and first-time transactional sex partners, and husbands and boyfriends); alcohol use; injection and non-injection illicit drug use; experience of violence; access to HIV prevention and treatment program; testing for sexually transmitted and blood-borne infections and HIV; and reproductive health (pregnancies, abortions, contraceptives). HIV and hepatitis C virus prevalence

Journal article

Hogan A, Jewell B, Sherrard-Smith E, Watson O, Whittaker C, Hamlet A, Smith J, Winskill P, Verity R, Baguelin M, Lees J, Whittles L, Ainslie K, Bhatt S, Boonyasiri A, Brazeau N, Cattarino L, Cooper L, Coupland H, Cuomo-Dannenburg G, Dighe A, Djaafara A, Donnelly C, Eaton J, van Elsland S, Fitzjohn R, Fu H, Gaythorpe K, Green W, Haw D, Hayes S, Hinsley W, Imai N, Laydon D, Mangal T, Mellan T, Mishra S, Parag K, Thompson H, Unwin H, Vollmer M, Walters C, Wang H, Ferguson N, Okell L, Churcher T, Arinaminpathy N, Ghani A, Walker P, Hallett Tet al., 2020, Potential impact of the COVID-19 pandemic on HIV, TB and malaria in low- and middle-income countries: a modelling study, The Lancet Global Health, Vol: 8, Pages: e1132-e1141, ISSN: 2214-109X

Background: COVID-19 has the potential to cause substantial disruptions to health services, including by cases overburdening the health system or response measures limiting usual programmatic activities. We aimed to quantify the extent to which disruptions in services for human immunodeficiency virus (HIV), tuberculosis (TB) and malaria in low- and middle-income countries with high burdens of those disease could lead to additional loss of life. Methods: We constructed plausible scenarios for the disruptions that could be incurred during the COVID-19 pandemic and used established transmission models for each disease to estimate the additional impact on health that could be caused in selected settings.Findings: In high burden settings, HIV-, TB- and malaria-related deaths over five years may increase by up to 10%, 20% and 36%, respectively, compared to if there were no COVID-19 pandemic. We estimate the greatest impact on HIV to be from interruption to antiretroviral therapy, which may occur during a period of high health system demand. For TB, we estimate the greatest impact is from reductions in timely diagnosis and treatment of new cases, which may result from any prolonged period of COVID-19 suppression interventions. We estimate that the greatest impact on malaria burden could come from interruption of planned net campaigns. These disruptions could lead to loss of life-years over five years that is of the same order of magnitude as the direct impact from COVID-19 in places with a high burden of malaria and large HIV/TB epidemics.Interpretation: Maintaining the most critical prevention activities and healthcare services for HIV, TB and malaria could significantly reduce the overall impact of the COVID-19 pandemic.Funding: Bill & Melinda Gates Foundation, The Wellcome Trust, DFID, MRC

Journal article

Skovdal M, Pickles MR, Hallett TB, Nyamukapa C, Gregson Set al., 2020, Complexities to consider when communicating risk of COVID-19, Public Health, Vol: 186, Pages: 283-285, ISSN: 0033-3506

Journal article

Bhattacharjee P, Isac S, Musyoki H, Emmanuel F, Olango K, Kuria S, Ongaro MK, Walimbwa J, Musimbi J, Mugambi M, Kaosa S, Kioko J, Njraini M, Melon M, Onyoni J, Bartilol K, Becker M, Lorway R, Pickles M, Moses S, Blanchard J, Mishra Set al., 2020, HIV prevalence, testing and treatment among men who have sex with men through engagement in virtual sexual networks in Kenya: a cross-sectional bio-behavioural study, Journal of the International AIDS Society, Vol: 23, ISSN: 1758-2652

INTRODUCTION: In Kenya, men who have sex with men (MSM) are increasingly using virtual sites, including web-based apps, to meet sex partners. We examined HIV testing, HIV prevalence, awareness of HIV-positive status and linkage to antiretroviral therapy (ART), for HIV-positive MSM who solely met partners via physical sites (PMSM), compared with those who did so in virtual sites (either solely via virtual sites (VMSM), or via both virtual and physical sites (DMSM)). METHODS: We conducted a cross-sectional bio-behavioural survey of 1200 MSM, 15 years and above, in three counties in Kenya between May and July 2019, using random sampling of physical and virtual sites. We classified participants as PMSM, DMSM and VMSM, based on where they met sex partners, and compared the following between groups using chi-square tests: (i) proportion tested; (ii) HIV prevalence and (iii) HIV care continuum among MSM living with HIV. We then performed multivariable logistic regression to measure independent associations between network engagement and HIV status. RESULTS: 177 (14.7%), 768 (64.0%) and 255 (21.2%), of participants were classified as PMSM, DMSM and VMSM respectively. 68.4%, 70.4% and 78.5% of PMSM, DMSM and VMSM, respectively, reported an HIV test in the previous six months. HIV prevalence was 8.5% (PMSM), 15.4% (DMSM) and 26.7% (VMSM), p < 0.001. Among those living with HIV, 46.7% (PMSM), 41.5% (DMSM) and 29.4% (VMSM) were diagnosed and aware of their status; and 40.0%, 35.6% and 26.5% were on antiretroviral treatment. After adjustment for other predictors, MSM engaged in virtual networks remained at a two to threefold higher risk of prevalent HIV: VMSM versus PMSM (adjusted odds ratio 3.88 (95% confidence interval (CI) 1.84 to 8.17) p < 0.001); DMSM versus PMSM (2.00 (95% CI 1.03 to 3.87), p = 0.040). CONCLUSIONS: Engagement in virtual networks is associated with elevated HIV risk, irrespective of individual-level risk factors. Und

Journal article

Mellan T, Hoeltgebaum H, Mishra S, Whittaker C, Schnekenberg R, Gandy A, Unwin H, Vollmer M, Coupland H, Hawryluk I, Rodrigues Faria N, Vesga J, Zhu H, Hutchinson M, Ratmann O, Monod M, Ainslie K, Baguelin M, Bhatia S, Boonyasiri A, Brazeau N, Charles G, Cooper L, Cucunuba Perez Z, Cuomo-Dannenburg G, Dighe A, Djaafara A, Eaton J, van Elsland S, Fitzjohn R, Fraser K, Gaythorpe K, Green W, Hayes S, Imai N, Jeffrey B, Knock E, Laydon D, Lees J, Mangal T, Mousa A, Nedjati Gilani G, Nouvellet P, Olivera Mesa D, Parag K, Pickles M, Thompson H, Verity R, Walters C, Wang H, Wang Y, Watson O, Whittles L, Xi X, Okell L, Dorigatti I, Walker P, Ghani A, Riley S, Ferguson N, Donnelly C, Flaxman S, Bhatt Set al., 2020, Report 21: Estimating COVID-19 cases and reproduction number in Brazil

Brazil is an epicentre for COVID-19 in Latin America. In this report we describe the Brazilian epidemicusing three epidemiological measures: the number of infections, the number of deaths and the reproduction number. Our modelling framework requires sufficient death data to estimate trends, and wetherefore limit our analysis to 16 states that have experienced a total of more than fifty deaths. Thedistribution of deaths among states is highly heterogeneous, with 5 states—São Paulo, Rio de Janeiro,Ceará, Pernambuco and Amazonas—accounting for 81% of deaths reported to date. In these states, weestimate that the percentage of people that have been infected with SARS-CoV-2 ranges from 3.3% (95%CI: 2.8%-3.7%) in São Paulo to 10.6% (95% CI: 8.8%-12.1%) in Amazonas. The reproduction number (ameasure of transmission intensity) at the start of the epidemic meant that an infected individual wouldinfect three or four others on average. Following non-pharmaceutical interventions such as school closures and decreases in population mobility, we show that the reproduction number has dropped substantially in each state. However, for all 16 states we study, we estimate with high confidence that thereproduction number remains above 1. A reproduction number above 1 means that the epidemic isnot yet controlled and will continue to grow. These trends are in stark contrast to other major COVID19 epidemics in Europe and Asia where enforced lockdowns have successfully driven the reproductionnumber below 1. While the Brazilian epidemic is still relatively nascent on a national scale, our resultssuggest that further action is needed to limit spread and prevent health system overload.

Report

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