Imperial College London

DrOliverRatmann

Faculty of Natural SciencesDepartment of Mathematics

Lecturer in Statistics
 
 
 
//

Contact

 

oliver.ratmann05 Website

 
 
//

Location

 

525Huxley BuildingSouth Kensington Campus

//

Summary

 

Publications

Publication Type
Year
to

73 results found

Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete Jr CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro M, Costa S, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim D, Miscoridou X, Mishra S, Monod M, Moreira FRR, Ranzani O, Schnekenberg R, Semenova E, Sonnabend R, Souza RP, Xi X, Sabino E, Faria NR, Bhatt S, Ratmann Oet al., 2022, Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals, Nature Medicine, ISSN: 1078-8956

The SARS-CoV-2 Gamma variant of concern spread rapidly across Brazil since late 2020, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 between 20 January 2020 and 26 July 2021 to document temporary, sweeping shocks in hospital fatality rates that followed Gamma’s spread across 14 state capitals, during which typically more than half of hospitalised patients aged 70 and over died. We show that such extensive shocks in COVID-19 in-hospital fatality rates also existed prior to detection of Gamma. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil’s COVID-19 in-hospital fatality rates were primarily associated with geographic inequities and shortages in healthcare capacity. We estimate that approximately half of the COVID-19 deaths in hospitals in the 14 cities could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.

Journal article

Unwin HJT, Hillis S, Cluver L, Flaxman S, Goldman PS, Butchart A, Bachman G, Rawlings L, Donnelly CA, Ratmann O, Green P, Nelson CA, Blenkinsop A, Bhatt S, Desmond C, Villaveces A, Sherr Let al., 2022, Global, regional, and national minimum estimates of children affected by COVID-19-associated orphanhood and caregiver death, by age and family circumstance up to Oct 31, 2021: an updated modelling study, The Lancet Child & Adolescent Health, Vol: 6, ISSN: 2352-4642

BACKGROUND: In the 6 months following our estimates from March 1, 2020, to April 30, 2021, the proliferation of new coronavirus variants, updated mortality data, and disparities in vaccine access increased the amount of children experiencing COVID-19-associated orphanhood. To inform responses, we aimed to model the increases in numbers of children affected by COVID-19-associated orphanhood and caregiver death, as well as the cumulative orphanhood age-group distribution and circumstance (maternal or paternal orphanhood). METHODS: We used updated excess mortality and fertility data to model increases in minimum estimates of COVID-19-associated orphanhood and caregiver deaths from our original study period of March 1, 2020-April 30, 2021, to include the new period of May 1-Oct 31, 2021, for 21 countries. Orphanhood was defined as the death of one or both parents; primary caregiver loss included parental death or the death of one or both custodial grandparents; and secondary caregiver loss included co-residing grandparents or kin. We used logistic regression and further incorporated a fixed effect for western European countries into our previous model to avoid over-predicting caregiver loss in that region. For the entire 20-month period, we grouped children by age (0-4 years, 5-9 years, and 10-17 years) and maternal or paternal orphanhood, using fertility contributions, and we modelled global and regional extrapolations of numbers of orphans. 95% credible intervals (CrIs) are given for all estimates. FINDINGS: The number of children affected by COVID-19-associated orphanhood and caregiver death is estimated to have increased by 90·0% (95% CrI 89·7-90·4) from April 30 to Oct 31, 2021, from 2 737 300 (95% CrI 1 976 100-2 987 000) to 5 200 300 (3 619 400-5 731 400). Between March 1, 2020, and Oct 31, 2021, 491 300 (95% CrI 485 100-497 900) children

Journal article

Xi X, Spencer SEF, Hall M, Grabowski MK, Kagaayi J, Ratmann Oet al., 2022, Inferring the sources of HIV infection in Africa from deep-sequence data with semi-parametric Bayesian Poisson flow models, Journal of the Royal Statistical Society Series C: Applied Statistics, ISSN: 0035-9254

Pathogen deep-sequencing is an increasingly routinely used technology in infectious disease surveillance. We present a semi-parametric Bayesian Poisson model to exploit these emerging data for inferring infectious disease transmission flows and the sources of infection at the population level. The framework is computationally scalable in high-dimensional flow spaces thanks to Hilbert Space Gaussian process approximations, al-lows for sampling bias adjustments, and estimation of gender- and age-specific transmis-sion flows at finer resolution than previously possible. We apply the approach to densely sampled, population-based HIV deep-sequence data from Rakai, Uganda, and find sub-stantive evidence that adolescent and young women are predominantly infected through age-disparate relationships.

Journal article

Bareng OT, Moyo S, Zahralban-Steele M, Maruapula D, Ditlhako T, Mokaleng B, Mokgethi P, Choga WT, Moraka NO, Pretorius-Holme M, Mine MO, Raizes E, Molebatsi K, Motswaledi MS, Gobe I, Mohammed T, Gaolathe T, Shapiro R, Mmalane M, Makhema JM, Lockman S, Essex M, Novitsky V, Gaseitsiwe Set al., 2022, HIV-1 drug resistance mutations among individuals with low-level viraemia while taking combination ART in Botswana, JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, ISSN: 0305-7453

Journal article

Unwin HJ, Hillis S, Cluver L, Flaxman S, Goldman P, Butchart A, Bachman G, Rawlings L, Donnelly C, Ratmann O, Green P, Nelson C, Blenkinsop A, Bhatt S, Desmond C, Villaveces A, Sherr Let al., 2022, More than 5.2 million children affected by global surges in COVID-associated orphanhood and caregiver death: new evidence for national responses, The Lancet Child & Adolescent Health, ISSN: 2352-4642

Background: In the past six months, proliferation of new coronavirus variants, updated mortality data, and disparities in vaccine access have increased estimates of children experiencing COVID-19-associated orphanhood. To inform responses, we modelled increases in numbers of children affected by COVID-19-associated orphanhood and caregiver death; and cumulative orphanhood age-group distribution and circumstance (maternal/paternal).Methods: We used updated excess mortality and fertility data to model increases in minimum estimates of COVID-19-associated orphanhood and caregiver deaths between May 1,2021 — October 31, 2021, for 21 countries. Using yearly fertility contributions, we grouped children by age (0-4, 5-9, 10-17), maternal/paternal orphanhood, and modelled global and regional extrapolations. Findings: The number of children affected by COVID-19-associated orphanhood and caregiver death increased by 90% from April 30 to October 31, 2021: from 2,737,300 [95% CrI 1,976,100- 2,987,000] to 5,209,000 [95% CrI 3,751,400-5,826,300]. From March 1, 2020 - October 31, 2021, 491,900 [95% CrI 485,800 - 498,300] children ages 0-4, 737,700 [95% 727,600 - 747,100] children 5-9, and 2,149,100 [95% CrI 2,123,400 - 2,176,800] children 10-17 experienced COVID associated parental death. In each age-group/region, paternal orphanhood prevalence exceeded maternal orphanhood for children 0-4, 11.5% vs. 3.1%, children 5-9, 17.0% vs. 4.8%, and children 10-17, 48.0% vs. 15.6% respectively.Interpretation: Our findings show that numbers of children affected by COVID-associated orphanhood almost doubled in 6 months compared to the first 14 months of the pandemic with 5.0 million COVID-19 deaths and 5.2 million children having lost a parent or caregiver over the entire 20-month period. We provide data on children’s ages and circumstances, to support response planning for children globally.

Journal article

Hillis S, Blenkinsop A, Villaveces A, Annor F, Liburd L, Massetti G, Demissie Z, Mercy J, Nelson C, Cluver L, Flaxman S, Sherr L, Donnelly C, Ratmann O, Unwin Jet al., 2021, COVID-19-associated orphanhood and caregiver death in the United States, Pediatrics, Vol: 148, Pages: 1-13, ISSN: 0031-4005

Background: Most COVID-19 deaths occur among adults, not children, and attention has focused on mitigating COVID-19 burden among adults. However, a tragic consequence of adult deaths is that high numbers of children might lose their parents and caregivers to COVID-19-associated deaths.Methods: We quantified COVID-19-associated caregiver loss and orphanhood in the US and for each state using fertility and excess and COVID-19 mortality data. We assessed burden and rates of COVID-19-associated orphanhood and deaths of custodial and co-residing grandparents, overall and by race/ethnicity. We further examined variations in COVID-19-associated orphanhood by race/ethnicity for each state. Results: We found that from April 1, 2020 through June 30, 2021, over 140,000 children in the US experienced the death of a parent or grandparent caregiver. The risk of such loss was 1.1 to 4.5 times higher among children of racial and ethnic minorities, compared to Non-Hispanic White children. The highest burden of COVID-19-associated death of parents and caregivers occurred in Southern border states for Hispanic children, Southeastern states for Black children, and in states with tribal areas for American Indian/Alaska Native populations.Conclusions: We found substantial disparities in distributions of COVID-19-associated death of parents and caregivers across racial and ethnic groups. Children losing caregivers to COVID-19 need care and safe, stable, and nurturing families with economic support, quality childcare and evidence-based parenting support programs. There is an urgent need to mount an evidence-based comprehensive response focused on those children at greatest risk, in the states most affected.

Journal article

Mousa A, Winskill P, Watson OJ, Ratmann O, Monod M, Ajelli M, Diallo A, Dodd P, Grijalva CG, Kiti MC, Krishnan A, Kumar R, Kumar S, Kwok KO, Lanata C, Le Polain de Waroux O, Leung K, Mahikul W, Melegaro A, Morrow CD, Mossong J, Neal EFG, Nokes DJ, Pan-ngum W, Potter GE, Russel FM, Saha S, Sugimoto JD, Wei WI, Wood RR, Wu JT, Zhang J, Walker PGT, Whittaker Cet al., 2021, Social contact patterns and implications for infectious disease transmission: a systematic review and meta-analysis of contact surveys, eLife, Vol: 10, ISSN: 2050-084X

Background: Transmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of contact patterns to date have focussed on high-income settings.Methods: Here, we conduct a systematic review and individual-participant meta-analysis of surveys carried out in low- and middle-income countries and compare patterns of contact in these settings to surveys previously carried out in high-income countries. Using individual-level data from 28,503 participants and 413,069 contacts across 27 surveys we explored how contact characteristics (number, location, duration and whether physical) vary across income settings.Results: Contact rates declined with age in high- and upper-middle-income settings, but not in low-income settings, where adults aged 65+ made similar numbers of contacts as younger individuals and mixed with all age-groups. Across all settings, increasing household size was a key determinant of contact frequency and characteristics, with low-income settings characterised by the largest, most intergenerational households. A higher proportion of contacts were made at home in low-income settings, and work/school contacts were more frequent in high-income strata. We also observed contrasting effects of gender across income-strata on the frequency, duration and type of contacts individuals made.Conclusions: These differences in contact patterns between settings have material consequences for both spread of respiratory pathogens, as well as the effectiveness of different non-pharmaceutical interventions.

Journal article

Mousa A, Winskill P, Watson OJ, Ratmann O, Monod M, Ajelli M, Diallo A, Dodd PJ, Grijalva CG, Kiti MC, Krishnan A, Kumar R, Kumar S, Kwok KO, Lanata CF, de Waroux OLP, Leung K, Mahikul W, Melegaro A, Morrow CD, Mossong J, Neal EFG, Nokes DJ, Pan-ngum W, Potter GE, Russell FM, Saha S, Sugimoto JD, Wei WI, Wood RR, Wu JT, Zhang J, Walker PGT, Whittaker Cet al., 2021, Social contact patterns and implications for infectious disease transmission - a systematic review and meta-analysis of contact surveys, ELIFE, Vol: 10, ISSN: 2050-084X

Journal article

Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonnabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann Oet al., 2021, Report 46: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals., medRxiv

The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital fatality rates that followed Gamma's spread across 14 state capitals, and in which more than half of hospitalised patients died over sustained time periods. We show that extensive fluctuations in COVID-19 in-hospital fatality rates also existed prior to Gamma's detection, and were largely transient after Gamma's detection, subsiding with hospital demand. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil's COVID-19 in-hospital fatality rates are primarily associated with geographic inequities and shortages in healthcare capacity. We project that approximately half of Brazil's COVID-19 deaths in hospitals could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries. NOTE: The following manuscript has appeared as 'Report 46 - Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals' at https://spiral.imperial.ac.uk:8443/handle/10044/1/91875 . ONE SENTENCE SUMMARY: COVID-19 in-hospital fatality rates fluctuate dramatically in Brazil, and these fluctuations are primarily associated with geographic inequities and shortages in healthcare capacity.

Journal article

Gurdasani D, Bhatt S, Costello A, Denaxas S, Flaxman S, Greenhalgh T, Griffin S, Hyde Z, Katzourakis A, McKee M, Michie S, Ratmann O, Reicher S, Scally G, Tomlinson C, Yates C, Ziauddeen H, Pagel Cet al., 2021, Vaccinating adolescents against SARS-CoV-2 in England: a risk-benefit analysis., Journal of the Royal Society of Medicine, Vol: 114, Pages: 513-524, ISSN: 0141-0768

OBJECTIVE: To offer a quantitative risk-benefit analysis of two doses of SARS-CoV-2 vaccination among adolescents in England. SETTING: England. DESIGN: Following the risk-benefit analysis methodology carried out by the US Centers for Disease Control, we calculated historical rates of hospital admission, Intensive Care Unit admission and death for ascertained SARS-CoV-2 cases in children aged 12-17 in England. We then used these rates alongside a range of estimates for incidence of long COVID, vaccine efficacy and vaccine-induced myocarditis, to estimate hospital and Intensive Care Unit admissions, deaths and cases of long COVID over a period of 16 weeks under assumptions of high and low case incidence. PARTICIPANTS: All 12-17 year olds with a record of confirmed SARS-CoV-2 infection in England between 1 July 2020 and 31 March 2021 using national linked electronic health records, accessed through the British Heart Foundation Data Science Centre. MAIN OUTCOME MEASURES: Hospitalisations, Intensive Care Unit admissions, deaths and cases of long COVID averted by vaccinating all 12-17 year olds in England over a 16-week period under different estimates of future case incidence. RESULTS: At high future case incidence of 1000/100,000 population/week over 16 weeks, vaccination could avert 4430 hospital admissions and 36 deaths over 16 weeks. At the low incidence of 50/100,000/week, vaccination could avert 70 hospital admissions and two deaths over 16 weeks. The benefit of vaccination in terms of hospitalisations in adolescents outweighs risks unless case rates are sustainably very low (below 30/100,000 teenagers/week). Benefit of vaccination exists at any case rate for the outcomes of death and long COVID, since neither have been associated with vaccination to date. CONCLUSIONS: Given the current (as at 15 September 2021) high case rates (680/100,000 population/week in 10-19 year olds) in England, our findings support vaccination of adolescents against SARS-CoV2.

Journal article

Hall M, Golubchik T, Bonsall D, Abeler-Dörner L, Limbada M, Kosloff B, Schaap A, de Cesare M, Mackintyre-Cockett G, Probert W, Ratmann O, Cruz AB, Piwowar-Manning E, Burns DN, Cohen MS, Donnell DJ, Eshleman SH, Simwinga M, Hayes R, Fidler S, Ayles H, Fraser Cet al., 2021, Demographic characteristics of sources of HIV-1 transmission in Zambia

<jats:title>Abstract</jats:title><jats:sec><jats:title>BACKGROUND</jats:title><jats:p>In the last decade, universally available antiretroviral therapy has led to reduced HIV incidence in sub-Saharan Africa. Sources of remaining transmission need to be characterised to design effective prevention strategies.</jats:p></jats:sec><jats:sec><jats:title>METHODS</jats:title><jats:p>We used phylogenetics to understand the population characteristics of people who are sources of infection. HIV samples from 6,864 individuals from Zambia were deep-sequenced as part of HPTN 071-02 (PopART) Phylogenetics between 2014 and 2018. We identified 300 likely directed transmission pairs and analysed their sources to better understand transmission in the general population.</jats:p></jats:sec><jats:sec><jats:title>RESULTS</jats:title><jats:p>After demographic weighting of the recipient population to match the estimated total population infected during the trial period, 59.4% (95% CI: 53.1%-65.8%) of transmissions were male-to-female, with 43.1% (36.6%-49.5%) of transmissions from males aged 25-40. Since the adult HIV prevalence was 2.0 times higher in women than men, the per-capita transmission rate was 2.93 times higher per infected male than per infected female. 25.6% (19.9%-31.3%) of sources were estimated to have themselves been infected less than a year before the transmission event. 16.8% (12%-21.7%) of sources transmitted viruses resistant to first-line ART. 13% (8.6%-17.4%) of transmissions occurred between individuals from different study communities.</jats:p></jats:sec><jats:sec><jats:title>CONCLUSIONS</jats:title><jats:p>Our findings suggest that HIV transmission in the study communities took place as part of common sexual mixing, and that there was no outsized contribution of importation, from drug resistance, or recent infection. Men

Journal article

Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete Jr CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos A, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonnabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann Oet al., 2021, Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

The SARS‐CoV‐2 Gamma variant spread rapidly across Brazil, causing substantial infection and death wa ves. We use individual‐level patient records following hospitalisation with suspected or confirmed COVID‐19 to document the extensive shocks in hospital fatality rates that followed Gamma’s spread across 14 state capitals, and in which more than half of hospitalised patients died over sustained time pe riods. We show that extensive fluctuations in COVID‐19 in‐hospital fatality rates also existed prior to Gamma’s detection, and were largely transient after Gamma’s detection, subsiding with hospital d emand. Using a Bayesian fatality rate model, we find that the geo‐graphic and temporal fluctuations in Brazil’s COVID‐19 in‐hospital fatality rates are primarily associated with geo‐graphic inequities and shortages in healthcare c apacity. We project that approximately half of Brazil’s COVID‐19 deaths in hospitals could have been avoided without pre‐pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly trans‐missible and deadly pathogens such as SARS‐CoV‐2, especially in low‐ and middle‐income countries.

Report

Bezemer D, Blenkinsop A, Hall M, Van Sighem A, Cornelissen M, Wessels E, van Kampen J, van de Laar T, Reiss P, Fraser C, Ratmann Oet al., 2021, Many but small HIV-1 non-B transmission chains in the Netherlands, AIDS, Vol: 36, Pages: 83-94, ISSN: 0269-9370

Objective To investigate introductions and spread of different HIV-1 subtypes in the Netherlands. Design We identified distinct HIV-1 transmission chains in the Netherlands within the global epidemic context through viral phylogenetic analysis of partial HIV-1 polymerase sequences from individuals enrolled in the ATHENA national HIV cohort of all persons in care since 1996, and publicly available international background sequences. Methods Viral lineages circulating in the Netherlands were identified through maximum parsimony phylogeographic analysis. The proportion of HIV-1 infections acquired in-country among heterosexuals and men having sex with men (MSM) was estimated from phylogenetically observed, national transmission chains using a branching process model that accounts for incomplete sampling. Results As of January 1st 2019, 2,589 (24%) of 10,971 (41%) HIV-1 sequenced individuals in ATHENA had non-B subtypes (A1, C, D, F, G) or circulating recombinant forms (CRF01AE, CRF02AG, CRF06-cpx). The 1,588 heterosexuals were in 1,224, and 536 MSM in 270 phylogenetically observed transmission chains. After adjustments for incomplete sampling, most heterosexual (75%) and MSM (76%) transmission chains were estimated to include only the individual introducing the virus (size=1). Onward transmission occurred mostly in chains size 2-5 amongst heterosexuals (62%) and in chains size ≥10 amongst MSM (64%). Considering some chains originated in-country from other risk-groups, 40% (95%CI: 36-44%) of non-B-infected heterosexuals and 62% (95%CI: 49%-73%) of MSM acquired infection in-country. Conclusions Whilst most HIV-1 non-B introductions showed no or very little onward transmission, a considerable proportion of non-B infections amongst both heterosexuals and MSM in the Netherlands have been acquired in-country.

Journal article

Whittaker C, Ratmann O, Dye C, Sabino EC, Faria NRet al., 2021, Altered demographic profile of hospitalizations during the second COVID-19 wave in Amazonas, Brazil, The Lancet Regional Health - Americas, Vol: 2, ISSN: 2667-193X

Journal article

Ratmann O, Bhatt S, Flaxman S, 2021, Implications of a highly transmissible variant of SARS-CoV-2 for children, Archives of Disease in Childhood, Vol: 106, Pages: 1-1, ISSN: 0003-9888

Journal article

Mishra S, Scott JA, Laydon DJ, Flaxman S, Gandy A, Mellan TA, Unwin HJT, Vollmer M, Coupland H, Ratmann O, Monod M, Zhu HH, Cori A, Gaythorpe KAM, Whittles LK, Whittaker C, Donnelly CA, Ferguson NM, Bhatt Set al., 2021, Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling, SCIENTIFIC REPORTS, Vol: 11, Pages: 1-9, ISSN: 2045-2322

The UK and Sweden have among the worst per-capita COVID-19 mortality in Europe. Sweden stands out for its greater reliance on voluntary, rather than mandatory, control measures. We explore how the timing and effectiveness of control measures in the UK, Sweden and Denmark shaped COVID-19 mortality in each country, using a counterfactual assessment: what would the impact have been, had each country adopted the others’ policies? Using a Bayesian semi-mechanistic model without prior assumptions on the mechanism or effectiveness of interventions, we estimate the time-varying reproduction number for the UK, Sweden and Denmark from daily mortality data. We use two approaches to evaluate counterfactuals which transpose the transmission profile from one country onto another, in each country’s first wave from 13th March (when stringent interventions began) until 1st July 2020. UK mortality would have approximately doubled had Swedish policy been adopted, while Swedish mortality would have more than halved had Sweden adopted UK or Danish strategies. Danish policies were most effective, although differences between the UK and Denmark were significant for one counterfactual approach only. Our analysis shows that small changes in the timing or effectiveness of interventions have disproportionately large effects on total mortality within a rapidly growing epidemic.

Journal article

Hillis S, Unwin H, Chen Y, Cluver L, Sherr L, Goldman P, Ratmann O, Donnelly C, Bhatt S, Villaveces A, Butchart A, Bachman G, Rawlings L, Green P, Nelson C, Flaxman Set al., 2021, Global minimum estimates of children affected by COVID-19-associated orphanhood and deaths of caregivers: a modelling study, The Lancet, Vol: 398, Pages: 391-402, ISSN: 0140-6736

Background: The COVID-19 pandemic response has focused on prevention, detection, and response. Beyond morbidity and mortality, pandemics carry secondary impacts, such as children orphaned or bereft of their caregivers. Such children often face adverse consequences, including poverty, abuse, and institutionalization. We provide estimates for the magnitude of this problem resulting from COVID-19 and describe the need for resource allocation.Methods: We use mortality and fertility data to model minimum estimates and rates of COVID-19-associated orphanhood (death of 1 or both parents) and deaths of custodial and co-residing grandparents for 21 countries. We use these estimates to model global extrapolations for the number of children experiencing COVID-19-associated deaths of parents and grandparents ages 60-84.Results: Globally, from March 1, 2020-March 31, 2021, we estimate 974,000 children experienced death of primary caregivers, including parents or custodial grandparents; >1.3 million experienced death of primary caregivers and co-residing grandparents (or kin). Countries with rates of primary caregiver deaths >1/1000 children included Peru, South Africa, Mexico, Colombia, Brazil, I.R. Iran, U.S.A., and Russia (range, 1.0-8.5/1000). Numbers of children orphaned exceeded numbers of deaths among those aged 15 – 44; 2 – 5 times more children had deceased fathers than deceased mothers. Conclusions: Orphanhood and caregiver deaths are a hidden pandemic resulting from COVID-19-associated deaths. Accelerating equitable vaccine delivery is key to prevention. Psychosocial and economic support can help families nurture children bereft of caregivers and help ensure institutionalization is avoided. These data demonstrate the need for an additional pillar of our response: prevent, detect, respond, and care for children.

Journal article

Mishra S, Mindermann S, Sharma M, Whittaker C, Mellan TA, Wilton T, Klapsa D, Mate R, Fritzsche M, Zambon M, Ahuja J, Howes A, Miscouridou X, Nason GP, Ratmann O, Semenova E, Leech G, Sandkuehler JF, Rogers-Smith C, Vollmer M, Unwin HJT, Gal Y, Chand M, Gandy A, Martin J, Volz E, Ferguson NM, Bhatt S, Brauner JM, Flaxman Set al., 2021, Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England, ECLINICALMEDICINE, Vol: 39

Journal article

Meyerowitz-Katz G, Bhatt S, Ratmann O, Brauner JM, Flaxman S, Mishra S, Sharma M, Mindermann S, Bradley V, Vollmer M, Merone L, Yamey Get al., 2021, Is the cure really worse than the disease? The health impacts of lockdowns during COVID-19, BMJ Global Health, Vol: 6, Pages: 1-6, ISSN: 2059-7908

Journal article

Mousa A, Winskill P, Watson OJ, Ratmann O, Monod M, Ajelli M, Diallo A, Dodd PJ, Grijalva CG, Kiti MC, Krishnan A, Kumar R, Kumar S, Kwok KO, Lanata CF, Le Polain de Waroux O, Leung K, Mahikul W, Melegaro A, Morrow CD, Mossong J, Neal EF, Nokes DJ, Pan-Ngum W, Potter GE, Russell FM, Saha S, Sugimoto JD, Wei WI, Wood RR, Wu JT, Zhang J, Walker PG, Whittaker Cet al., 2021, Social Contact Patterns and Implications for Infectious Disease Transmission: A Systematic Review and Meta-Analysis of Contact Surveys., medRxiv

BACKGROUND: Transmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of contact patterns to date have focussed on high-income settings. METHODS: Here, we conduct a systematic review and individual-participant meta-analysis of surveys carried out in low- and middle-income countries and compare patterns of contact in these settings to surveys previously carried out in high-income countries. Using individual-level data from 28,503 participants and 413,069 contacts across 27 surveys we explored how contact characteristics (number, location, duration and whether physical) vary across income settings. RESULTS: Contact rates declined with age in high- and upper-middle-income settings, but not in low-income settings, where adults aged 65+ made similar numbers of contacts as younger individuals and mixed with all age-groups. Across all settings, increasing household size was a key determinant of contact frequency and characteristics, but low-income settings were characterised by the largest, most intergenerational households. A higher proportion of contacts were made at home in low-income settings, and work/school contacts were more frequent in high-income strata. We also observed contrasting effects of gender across income-strata on the frequency, duration and type of contacts individuals made. CONCLUSIONS: These differences in contact patterns between settings have material consequences for both spread of respiratory pathogens, as well as the effectiveness of different non-pharmaceutical interventions. FUNDING: This work is primarily being funded by joint Centre funding from the UK Medical Research Council and DFID (MR/R015600/1).

Journal article

Bogers SJ, Schim van der Loeff MF, Davidovich U, Boyd A, van der Valk M, Brinkman K, de Bree GJ, Reiss P, van Bergen JEAM, Geerlings SE, HIV Transmission Elimination AMsterdam H-TEAM Consortiumet al., 2021, Promoting HIV indicator condition-guided testing in hospital settings (PROTEST 2.0): study protocol for a multicentre interventional study, BMC Infectious Diseases, Vol: 21, ISSN: 1471-2334

BACKGROUND: Late presentation remains a key barrier towards controlling the HIV epidemic. Indicator conditions (ICs) are those that are AIDS-defining, associated with a prevalence of undiagnosed HIV > 0.1%, or whose clinical management would be impeded if an HIV infection were undiagnosed. IC-guided HIV testing is an effective strategy in identifying undiagnosed HIV, but opportunities for earlier HIV diagnosis through IC-guided testing are being missed. We present a protocol for an interventional study to improve awareness of IC-guided testing and increase HIV testing in patients presenting with ICs in a hospital setting. METHODS: We designed a multicentre interventional study to be implemented at five hospitals in the region of Amsterdam, the Netherlands. Seven ICs were selected for which HIV test ratios (proportion of patients with an IC tested for HIV) will be measured: tuberculosis, cervical/vulvar cancer or high-grade cervical/vulvar dysplasia, malignant lymphoma, hepatitis B and C, and peripheral neuropathy. Prior to the intervention, a baseline assessment of HIV test ratios across ICs will be performed in eligible patients (IC diagnosed January 2015 through May 2020, ≥18 years, not known HIV positive) and an assessment of barriers and facilitators for HIV testing amongst relevant specialties will be conducted using qualitative (interviews) and quantitative methods (questionnaires). The intervention phase will consist of an educational intervention, including presentation of baseline results as competitive graphical audit and feedback combined with discussion on implementation and opportunities for improvement. The effect of the intervention will be assessed by comparing HIV test ratios of the pre-intervention and post-intervention periods. The primary endpoint is the HIV test ratio within ±3 months of IC diagnosis. Secondary endpoints are the HIV test ratio within ±6 months of diagnosis, ratio ever tested f

Journal article

Dijkstra M, van Rooijen MS, Hillebregt MM, van Sighem A, Smit C, Hogewoning A, Davidovich U, Heijman T, Hoornenborg E, Reiss P, van der Valk M, Prins M, Prins JM, van der Loeff MFS, de Bree GJet al., 2021, Decreased Time to Viral Suppression After Implementation of Targeted Testing and Immediate Initiation of Treatment of Acute Human Immunodeficiency Virus Infection Among Men Who Have Sex With Men in Amsterdam, CLINICAL INFECTIOUS DISEASES, Vol: 72, Pages: 1952-1960, ISSN: 1058-4838

Journal article

Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FS, de Lima AB, Silva JDP, Zauli DAG, Ferreira ACDS, Schnekenberg RP, Laydon DJ, Walker PGT, Schlueter HM, dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, dos Santos HM, Aguiar RS, Proenca-Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Prete CA, Nascimento VH, Suchard MA, Bowden TA, Pond SLK, Wu C-H, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino ECet al., 2021, Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil, Science, Vol: 372, Pages: 815-821, ISSN: 0036-8075

Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

Journal article

Mishra S, Mindermann S, Sharma M, Whittaker C, Mellan T, Wilton T, Klapsa D, Mate R, Fritzsche M, Zambon M, Ahuja J, Howes A, Miscouridou X, Nason G, Ratmann O, Leech G, Fabienne Sandkühler J, Rogers-Smith C, Vollmer M, Unwin H, Gal Y, Chand M, Gandy A, Martin J, Volz E, Ferguson N, Bhatt S, Brauner J, Flaxman Set al., 2021, Report 44: Recent trends in SARS-CoV-2 variants of concern in England, Report 44: Recent trends in SARS-CoV-2 variants of concern in England, Publisher: Imperial College London, 44

Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when, whether, and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital. This is particularly true for England, which has high coverage from vaccines that are likely more protective against B.1.1.7 than some other VOCs. We examine trends in B.1.1.7’s prevalence in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. Our results suggest shifts in the composition of SARS-CoV-2 lineages driving transmission in England between March and April 2021. Local transmission of non-B.1.1.7 VOCs may be increasing; this warrants urgent further investigation.

Report

Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, Hinsley WR, Laydon DJ, Dabrera G, O'Toole Á, Amato R, Ragonnet-Cronin M, Harrison I, Jackson B, Ariani CV, Boyd O, Loman NJ, McCrone JT, Gonçalves S, Jorgensen D, Myers R, Hill V, Jackson DK, Gaythorpe K, Groves N, Sillitoe J, Kwiatkowski DP, COVID-19 Genomics UK COG-UK consortium, Flaxman S, Ratmann O, Bhatt S, Hopkins S, Gandy A, Rambaut A, Ferguson NMet al., 2021, Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England, Nature, Vol: 593, Pages: 266-269, ISSN: 0028-0836

The SARS-CoV-2 lineage B.1.1.7, designated a Variant of Concern 202012/01 (VOC) by Public Health England1, originated in the UK in late Summer to early Autumn 20202. Whole genome SARS-CoV-2 sequence data collected from community-based diagnostic testing shows an unprecedentedly rapid expansion of the B.1.1.7 lineage during Autumn 2020, suggesting a selective advantage. We find that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S-gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases. Time-varying reproduction numbers for the VOC and cocirculating lineages were estimated using SGTF and genomic data. The best supported models did not indicate a substantial difference in VOC transmissibility among different age groups. There is a consensus among all analyses that the VOC has a substantial transmission advantage with a 50% to 100% higher reproduction number.

Journal article

Cabras S, Castellanos ME, Ratmann O, 2021, Goodness of fit for models with intractable likelihood, TEST, Vol: 30, Pages: 713-736, ISSN: 1133-0686

Journal article

Unwin H, Mishra S, Bradley V, Gandy A, Mellan T, Coupland H, Ish-Horowicz J, Vollmer M, Whittaker C, Filippi S, Xi X, Monod M, Ratmann O, Hutchinson M, Valka F, Zhu H, Hawryluk I, Milton P, Ainslie K, Baguelin M, Boonyasiri A, Brazeau N, Cattarino L, Cucunuba Z, Cuomo-Dannenburg G, Dorigatti I, Eales O, Eaton J, van Elsland S, Fitzjohn R, Gaythorpe K, Green W, Hinsley W, Jeffrey B, Knock E, Laydon D, Lees J, Nedjati-Gilani G, Nouvellet P, Okell L, Parag K, Siveroni I, Thompson H, Walker P, Walters C, Watson O, Whittles L, Ghani A, Ferguson N, Riley S, Donnelly C, Bhatt S, Flaxman Set al., 2020, State-level tracking of COVID-19 in the United States, Nature Communications, Vol: 11, Pages: 1-9, ISSN: 2041-1723

As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly model the US epidemic at the state-level, using publicly available deathdata within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We use changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on therate of transmission of SARS-CoV-2. We estimate thatRtwas only below one in 23 states on 1st June. We also estimate that 3.7% [3.4%-4.0%] of the total population of the US had been infected, with wide variation between states, and approximately 0.01% of the population was infectious. We demonstrate good 3 week model forecasts of deaths with low error and good coverage of our credible intervals.

Journal article

Novitsky V, Zahralban-Steele M, Moyo S, Nkhisang T, Maruapula D, McLane MF, Leidner J, Bennett K, Consortium P, Wirth KE, Gaolathe T, Kadima E, Chakalisa U, Holme MP, Lockman S, Mmalane M, Makhema J, Gaseitsiwe S, DeGruttola V, Essex Met al., 2020, Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial, JOURNAL OF INFECTIOUS DISEASES, Vol: 222, Pages: 1670-1680, ISSN: 0022-1899

Journal article

Monod M, Blenkinsop A, Xi X, Hebert D, Bershan S, Tietze S, Bradley VC, Chen Y, Coupland H, Filippi S, Ish-Horowicz J, McManus M, Mellan T, Gandy A, Hutchinson M, T Unwin HJ, C Vollmer MA, Weber S, Zhu H, Bezancon A, Ferguson NM, Mishra S, Flaxman S, Bhatt S, Ratmann Oet al., 2020, Report 32: Age groups that sustain resurging COVID-19 epidemics in the United States

<jats:title>Summary</jats:title><jats:p>Following initial declines, in mid 2020, a resurgence in transmission of novel coronavirus disease (COVID-19) has occurred in the United States and parts of Europe. Despite the wide implementation of non-pharmaceutical interventions, it is still not known how they are impacted by changing contact patterns, age and other demographics. As COVID-19 disease control becomes more localised, understanding the age demographics driving transmission and how these impacts the loosening of interventions such as school reopening is crucial. Considering dynamics for the United States, we analyse aggregated, age-specific mobility trends from more than 10 million individuals and link these mechanistically to age-specific COVID-19 mortality data. In contrast to previous approaches, we link mobility to mortality via age specific contact patterns and use this rich relationship to reconstruct accurate transmission dynamics. Contrary to anecdotal evidence, we find little support for age-shifts in contact and transmission dynamics over time. We estimate that, until August, 63.4% [60.9%-65.5%] of SARS-CoV-2 infections in the United States originated from adults aged 20-49, while 1.2% [0.8%-1.8%] originated from children aged 0-9. In areas with continued, community-wide transmission, our transmission model predicts that re-opening kindergartens and elementary schools could facilitate spread and lead to additional COVID-19 attributable deaths over a 90-day period. These findings indicate that targeting interventions to adults aged 20-49 are an important consideration in halting resurgent epidemics and preventing COVID-19-attributable deaths when kindergartens and elementary schools reopen.</jats:p><jats:sec><jats:title>One sentence summary</jats:title><jats:p>Adults aged 20-49 are a main driver of the COVID-19 epidemic in the United States; yet, in areas with resurging epidemics, opening schools will lea

Journal article

Monod M, Blenkinsop A, Xi X, Herbert D, Bershan S, Tietze S, Bradley V, Chen Y, Coupland H, Filippi S, Ish-Horowicz J, McManus M, Mellan T, Gandy A, Hutchinson M, Unwin H, Vollmer M, Weber S, Zhu H, Bezancon A, Ferguson N, Mishra S, Flaxman S, Bhatt S, Ratmann O, Ainslie K, Baguelin M, Boonyasiri A, Boyd O, Cattarino L, Cooper L, Cucunuba Perez Z, Cuomo-Dannenburg G, Djaafara A, Dorigatti I, van Elsland S, Fitzjohn R, Gaythorpe K, Geidelberg L, Green W, Hamlet A, Jeffrey B, Knock E, Laydon D, Nedjati Gilani G, Nouvellet P, Parag K, Siveroni I, Thompson H, Verity R, Walters C, Donnelly C, Okell L, Bhatia S, Brazeau N, Eales O, Haw D, Imai N, Jauneikaite E, Lees J, Mousa A, Olivera Mesa D, Skarp J, Whittles Let al., 2020, Report 32: Targeting interventions to age groups that sustain COVID-19 transmission in the United States, Pages: 1-32

Following ini􀀂al declines, in mid 2020, a resurgence in transmission of novel coronavirus disease (COVID-19) has occurred in the United States and parts of Europe. Despite the wide implementa􀀂on of non-pharmaceu􀀂cal inter-ven􀀂ons, it is s􀀂ll not known how they are impacted by changing contact pa􀀁erns, age and other demographics. As COVID-19 disease control becomes more localised, understanding the age demographics driving transmission and how these impact the loosening of interven􀀂ons such as school reopening is crucial. Considering dynamics for the United States, we analyse aggregated, age-specific mobility trends from more than 10 million individuals and link these mechanis􀀂cally to age-specific COVID-19 mortality data. In contrast to previous approaches, we link mobility to mortality via age specific contact pa􀀁erns and use this rich rela􀀂onship to reconstruct accurate trans-mission dynamics. Contrary to anecdotal evidence, we find li􀀁le support for age-shi􀀃s in contact and transmission dynamics over 􀀂me. We es􀀂mate that, un􀀂l August, 63.4% [60.9%-65.5%] of SARS-CoV-2 infec􀀂ons in the United States originated from adults aged 20-49, while 1.2% [0.8%-1.8%] originated from children aged 0-9. In areas with con􀀂nued, community-wide transmission, our transmission model predicts that re-opening kindergartens and el-ementary schools could facilitate spread and lead to considerable excess COVID-19 a􀀁ributable deaths over a 90-day period. These findings indicate that targe􀀂ng interven􀀂ons to adults aged 20-49 are an important con-sidera􀀂on in hal􀀂ng resurgent epidemics, and preven􀀂ng COVID-19-a􀀁ributable deaths when kindergartens and elementary schools reopen.

Journal article

This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.

Request URL: http://wlsprd.imperial.ac.uk:80/respub/WEB-INF/jsp/search-html.jsp Request URI: /respub/WEB-INF/jsp/search-html.jsp Query String: respub-action=search.html&id=00459135&limit=30&person=true