38 results on '"Laydon, D"'
Search Results
2. Author Correction: Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’ (Nature, (2020), 584, 7821, (425-429), 10.1038/s41586-020-2488-1)
- Author
-
Lavezzo, E., Franchin, E., Ciavarella, C., Cuomo-Dannenburg, G., Barzon, L., Del Vecchio, C., Rossi, L., Manganelli, R., Loregian, A., Navarin, N., Abate, D., Sciro, M., Merigliano, S., De Canale, E., Vanuzzo, M. C., Besutti, V., Saluzzo, F., Onelia, F., Pacenti, M., Parisi, S. G., Carretta, G., Donato, D., Flor, L., Cocchio, S., Masi, G., Sperduti, A., Cattarino, L., Salvador, R., Nicoletti, M., Caldart, F., Castelli, G., Nieddu, E., Labella, B., Fava, L., Drigo, M., Gaythorpe, K. A. M., Ainslie, K. E. C., Baguelin, M., Bhatt, S., Boonyasiri, A., Boyd, O., Coupland, H. L., Cucunuba, Z., Djafaara, B. A., van Elsland, S. L., Fitzjohn, R., Flaxman, S., Green, W. D., Hallett, T., Hamlet, A., Haw, D., Imai, N., Jeffrey, B., Knock, E., Laydon, D. J., Mellan, T., Mishra, S., Nedjati-Gilani, G., Nouvellet, P., Okell, L. C., Parag, K. V., Riley, S., Thompson, H. A., Unwin, H. J. T., Verity, R., Vollmer, M. A. C., Walker, P. G. T., Walters, C. E., Wang, H., Wang, Y., Watson, O. J., Whittaker, C., Whittles, L. K., Xi, X., Brazzale, A. R., Toppo, S., Trevisan, M., Baldo, V., Donnelly, C. A., Ferguson, N. M., Dorigatti, I., and Crisanti, A.
- Published
- 2021
3. Report 41: The 2020 SARS-CoV-2 epidemic in England: key epidemiological drivers and impact of interventions
- Author
-
Knock, E, Whittles, L, Lees, J, Perez Guzman, P, Verity, R, Fitzjohn, R, Gaythorpe, K, Imai, N, Hinsley, W, Okell, L, Rosello, A, Kantas, N, Walters, C, Bhatia, S, Watson, O, Whittaker, C, Cattarino, L, Boonyasiri, A, Djaafara, A, Fraser, K, Fu, H, Wang, H, Xi, X, Donnelly, C, Jauneikaite, E, Laydon, D, White, P, Ghani, A, Ferguson, N, Cori, A, Baguelin, M, and Medical Research Council (MRC)
- Subjects
Coronavirus ,England ,COVID19 ,COVID-19 ,United Kingdom ,Real Time Modelling - Abstract
England has been severely affected by COVID-19. We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional 2020 surveillance data. Only national lockdown brought the reproduction number below 1 consistently; introduced one week earlier in the first wave it could have reduced mortality by 23,300 deaths on average. The mean infection fatality ratio was initially ~1.3% across all regions except London and halved following clinical care improvements. The infection fatality ratio was two-fold lower throughout in London, even when adjusting for demographics. The infection fatality ratio in care homes was 2.5-times that in the elderly in the community. Population-level infection-induced immunity in England is still far from herd immunity, with regional mean cumulative attack rates ranging between 4.4% and 15.8%.
- Published
- 2020
- Full Text
- View/download PDF
4. Report 33: Modelling the allocation and impact of a COVID-19 vaccine
- Author
-
Hogan, A, Winskill, P, Watson, O, Walker, P, Whittaker, C, Baguelin, M, Haw, D, Lochen, A, Gaythorpe, K, Ainslie, K, Bhatt, S, Boonyasiri, A, Boyd, O, Brazeau, N, Cattarino, L, Charles, G, Cooper, L, Coupland, H, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Donnelly, C, Dorigatti, I, Eales, O, Van Elsland, S, Ferreira Do Nascimento, F, Fitzjohn, R, Flaxman, S, Green, W, Hallett, T, Hamlet, A, Hinsley, W, Imai, N, Jauneikaite, E, Jeffrey, B, Knock, E, Laydon, D, Lees, J, Mellan, T, Mishra, S, Nedjati Gilani, G, Nouvellet, P, Ower, A, Parag, K, Ragonnet-Cronin, M, Siveroni, I, Skarp, J, Thompson, H, Unwin, H, Verity, R, Vollmer, M, Volz, E, Walters, C, Wang, H, Wang, Y, Whittles, L, Xi, X, Muhib, F, Smith, P, Hauck, K, Ferguson, N, Ghani, A, Medical Research Council (MRC), and Abdul Latif Jameel Foundation
- Subjects
Coronavirus ,COVID19 ,COVID-19 ,Vaccine - Abstract
Several SARS-CoV-2 vaccine candidates are now in late-stage trials, with efficacy and safety results expected by the end of 2020. Even under optimistic scenarios for manufacture and delivery, the doses available in 2021 are likely to be limited. Here we identify optimal vaccine allocation strategies within and between countries to maximise health (avert deaths) under constraints on dose supply. We extended an existing mathematical model of SARS-CoV-2 transmission across different country settings to model the public health impact of potential vaccines, using a range of target product profiles developed by the World Health Organization. We show that as supply increases, vaccines that reduce or block infection – and thus transmission – in addition to preventing disease have a greater impact than those that prevent disease alone, due to the indirect protection provided to high-risk groups. We further demonstrate that the health impact of vaccination will depend on the cumulative infection incidence in the population when vaccination begins, the duration of any naturally acquired immunity, the likely trajectory of the epidemic in 2021 and the level of healthcare available to effectively treat those with disease. Within a country, we find that for a limited supply (doses for
- Published
- 2020
5. Report 32: Targeting interventions to age groups that sustain COVID-19 transmission in the United States
- Author
-
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, L, Medical Research Council (MRC), and Abdul Latif Jameel Foundation
- Subjects
Coronavirus ,COVID19 ,COVID-19 ,USA - Abstract
Following inial 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 implementaon of non-pharmaceucal inter-venons, it is sll not known how they are impacted by changing contact paerns, 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 intervenons 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 mechaniscally to age-specific COVID-19 mortality data. In contrast to previous approaches, we link mobility to mortality via age specific contact paerns and use this rich relaonship to reconstruct accurate trans-mission dynamics. Contrary to anecdotal evidence, we find lile support for age-shis in contact and transmission dynamics over me. We esmate that, unl August, 63.4% [60.9%-65.5%] of SARS-CoV-2 infecons 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 connued, 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 aributable deaths over a 90-day period. These findings indicate that targeng intervenons to adults aged 20-49 are an important con-sideraon in halng resurgent epidemics, and prevenng COVID-19-aributable deaths when kindergartens and elementary schools reopen.
- Published
- 2020
- Full Text
- View/download PDF
6. Report 31: Estimating the burden of COVID-19 in Damascus, Syria: an analysis of novel data sources to infer mortality under-ascertainment
- Author
-
Van Elsland, S, Watson, O, Alhaffar, M, Mehchy, Z, Whittaker, C, Akil, Z, Ainslie, K, Baguelin, M, Bhatt, S, Boonyasiri, A, Boyd, O, Brazeau, N, Cattarino, L, Charles, G, Ciavarella, C, Cooper, L, Coupland, H, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Djaafara, A, Donnelly, C, Dorigatti, I, Eales, O, Nascimento, F, Fitzjohn, R, Flaxman, S, Forna, A, Fu, H, Gaythorpe, K, Green, W, Hamlet, A, Hauck, K, Haw, D, Hayes, S, Hinsley, W, Imai, N, Jeffrey, B, Johnson, R, Jorgensen, D, Knock, E, Laydon, D, Lees, J, Mellan, T, Mishra, S, Nedjati Gilani, G, Nouvellet, P, Okell, L, Olivera Mesa, D, Pons Salort, M, Ragonnet-Cronin, M, Siveroni, I, Stopard, I, Thompson, H, Unwin, H, Verity, R, Vollmer, M, Volz, E, Walters, C, Wang, H, Wang, Y, Whittles, L, Winskill, P, Xi, X, Ferguson, N, Beals, E, Walker, P, Anonymous Authors, Medical Research Council (MRC), and Abdul Latif Jameel Foundation
- Subjects
Coronavirus ,Syria ,COVID19 ,COVID-19 - Abstract
The COVID-19 pandemic has resulted in substantial mortality worldwide. However, to date, countries in the Middle East and Africa have reported substantially lower mortality rates than in Europe and the Americas. One hypothesis is that these countries have been ‘spared’, but another is that deaths have been under-ascertained (deaths that have been unreported due to any number of reasons, for instance due to limited testing capacity). However, the scale of under-ascertainment is difficult to assess with currently available data. In this analysis, we estimate the potential under-ascertainment of COVID-19 mortality in Damascus, Syria, where all-cause mortality data has been reported between 25th July and 1st August. We fit a mathematical model of COVID-19 transmission to reported COVID-19 deaths in Damascus since the beginning of the pandemic and compare the model-predicted deaths to reported excess deaths. Exploring a range of different assumptions about under-ascertainment, we estimate that only 1.25% of deaths (sensitivity range 1% - 3%) due to COVID-19 are reported in Damascus. Accounting for under-ascertainment also corroborates local reports of exceeded hospital bed capacity. To validate the epidemic dynamics inferred, we leverage community-uploaded obituary certificates as an alternative data source, which confirms extensive mortality under-ascertainment in Damascus between July and August. This level of under-ascertainment suggests that Damascus is at a much later stage in its epidemic than suggested by surveillance reports, which have repo. We estimate that 4,340 (95% CI: 3,250 - 5,540) deaths due to COVID-19 in Damascus may have been missed as of 2nd September 2020. Given that Damascus is likely to have the most robust surveillance in Syria, these findings suggest that other regions of the country could have experienced similar or worse mortality rates due to COVID-19.
- Published
- 2020
7. Report 30: The COVID-19 epidemic trends and control measures in mainland China
- Author
-
Fu, H, Xi, X, Wang, H, Boonyasiri, A, Wang, Y, Hinsley, W, Fraser, K, McCabe, R, Olivera Mesa, D, Skarp, J, Ledda, A, Dewe, T, Dighe, A, Winskill, P, Van Elsland, S, Ainslie, K, Baguelin, M, Bhatt, S, Boyd, O, Brazeau, N, Cattarino, L, Charles, G, Coupland, H, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Donnelly, C, Dorigatti, I, Green, W, Hamlet, A, Hauck, K, Haw, D, Jeffrey, B, Laydon, D, Lees, J, Mellan, T, Mishra, S, Nedjati Gilani, G, Nouvellet, P, Okell, L, Parag, K, Ragonnet-Cronin, M, Riley, S, Schmit, N, Thompson, H, Unwin, H, Verity, R, Vollmer, M, Volz, E, Walker, P, Walters, C, Watson, O, Whittaker, C, Whittles, L, Imai, N, Bhatia, S, Ferguson, N, and Medical Research Council (MRC)
- Subjects
Coronavirus ,China ,COVID19 ,COVID-19 - Published
- 2020
8. Potential impact of the COVID-19 pandemic on HIV, TB and malaria in low- and middle-income countries: a modelling study
- Author
-
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, T, Medical Research Council (MRC), Bill & Melinda Gates Foundation, Wellcome Trust, Imperial College Healthcare NHS Trust- BRC Funding, The Academy of Medical Sciences, National Institute for Health Research, Imperial College LOndon, Medical Research Council, and The Royal Society
- Subjects
Pneumonia, Viral ,Humans ,Tuberculosis ,HIV Infections ,Models, Theoretical ,Coronavirus Infections ,Developing Countries ,Pandemics ,Health Services Accessibility ,Malaria ,0605 Microbiology ,1117 Public Health and Health Services - Abstract
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
- Published
- 2020
9. Estimating the number of undetected COVID-19 cases among travellers from mainland China
- Author
-
Bhatia, S, Imai, N, Cuomo-Dannenburg, G, Baguelin, M, Boonyasiri, A, Cori, A, Cucunuba Perez, Z, Dorigatti, I, Fitzjohn, R, Fu, H, Gaythorpe, K, Ghani, A, Hamlet, A, Hinsley, W, Laydon, D, Nedjati Gilani, G, Okell, L, Riley, S, Thompson, H, Van Elsland, S, Volz, E, Wang, H, Wang, Y, Whittaker, C, Xi, X, Donnelly, CA, Ferguson, NM, and Medical Research Council (MRC)
- Abstract
Background: Since the start of the COVID-19 epidemic in late 2019, there have been more than 152 affected regions and countries with over 110,000 confirmed cases outside mainland China. Methods: We analysed COVID-19 cases among travellers from mainland China to different regions and countries, comparing the region- and country-specific rates of detected and confirmed cases per flight volume to estimate the relative sensitivity of surveillance in different regions and countries. Results: Although travel restrictions from Wuhan City and other cities across China may have reduced the absolute number of travellers to and from China, we estimated that more than two thirds (70%, 95% CI: 54% - 80%, compared to Singapore; 75%, 95% CI: 66% - 82%, compared to multiple countries) of cases exported from mainland China have remained undetected. Conclusions: These undetected cases potentially resulted in multiple chains of human-to-human transmission outside mainland China.
- Published
- 2020
10. Report 26: Reduction in mobility and COVID-19 transmission
- Author
-
Nouvellet, P, Bhatia, S, Cori, A, Ainslie, K, Baguelin, M, Bhatt, S, Boonyasiri, A, Brazeau, N, Cattarino, L, Cooper, L, Coupland, H, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Dighe, A, Djaafara, A, Dorigatti, I, Eales, O, Van Elsland, S, Nscimento, F, Fitzjohn, R, Gaythorpe, K, Geidelberg, L, Grassly, N, Green, W, Hamlet, A, Hauck, K, Hinsley, W, Imai, N, Jeffrey, B, Knock, E, Laydon, D, Lees, J, Mangal, T, Mellan, T, Nedjati Gilani, G, Parag, K, Pons Salort, M, Ragonnet-Cronin, M, Riley, S, Unwin, H, Verity, R, Vollmer, M, Volz, E, Walker, P, Walters, C, Wang, H, Watson, O, Whittaker, C, Whittles, L, Xi, X, Ferguson, N, Donnelly, C, and Medical Research Council (MRC)
- Subjects
Mobility ,COVID19 ,Transmissibility ,COVID-19 - Abstract
In response to the COVID-19 pandemic, countries have sought to control transmission of SARS-CoV-2 by restricting population movement through social distancing interventions, reducing the number of contacts. Mobility data represent an important proxy measure of social distancing. Here, we develop a framework to infer the relationship between mobility and the key measure of population-level disease transmission, the reproduction number (R). The framework is applied to 53 countries with sustained SARS-CoV-2 transmission based on two distinct country-specific automated measures of human mobility, Apple and Google mobility data. For both datasets, the relationship between mobility and transmission was consistent within and across countries and explained more than 85% of the variance in the observed variation in transmissibility. We quantified country-specific mobility thresholds defined as the reduction in mobility necessary to expect a decline in new infections (R
- Published
- 2020
11. Report 23: State-level tracking of COVID-19 in the United States
- Author
-
Unwin, H, Mishra, S, Bradley, VC, Gandy, A, Vollmer, M, Mellan, T, Coupland, H, Ainslie, K, Whittaker, C, Ish-Horowicz, J, Filippi, S, Xi, X, Monod, M, Ratmann, O, Hutchinson, M, Valka, F, Zhu, H, Hawryluk, I, Milton, P, Baguelin, M, Boonyasiri, A, Brazeau, N, Cattarino, L, Charles, G, Cooper, L, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Djaafara, A, Dorigatti, I, Eales, O, Eaton, J, Van Elsland, S, Fitzjohn, R, Gaythorpe, K, Green, W, Hallett, T, Hinsley, W, Imai, N, Jeffrey, B, Knock, E, Laydon, D, Lees, J, Nedjati Gilani, G, Nouvellet, P, Okell, L, Ower, A, Parag, K, Siveroni, I, Thompson, H, Verity, R, Walker, P, Walters, C, Wang, Y, Watson, O, Whittles, L, Ghani, A, Ferguson, N, Riley, S, Donnelly, C, Bhatt, S, Flaxman, S, and Medical Research Council (MRC)
- Subjects
Coronavirus ,COVID19 ,COVID-19 ,United States - Abstract
our estimates show that the percentage of individuals that have been infected is 4.1% [3.7%-4.5%], with wide variation between states. For all states, even for the worst affected states, we estimate that less than a quarter of the population has been infected; in New York, for example, we estimate that 16.6% [12.8%-21.6%] of individuals have been infected to date. Our attack rates for New York are in line with those from recent serological studies [1] broadly supporting our choice of infection fatality rate. There is variation in the initial reproduction number, which is likely due to a range of factors; we find a strong association between the initial reproduction number with both population density (measured at the state level) and the chronological date when 10 cumulative deaths occurred (a crude estimate of the date of locally sustained transmission). Our estimates suggest that the epidemic is not under control in much of the US: as of 17 May 2020 the reproduction number is above the critical threshold (1.0) in 24 [95% CI: 20-30] states. Higher reproduction numbers are geographically clustered in the South and Midwest, where epidemics are still developing, while we estimate lower reproduction numbers in states that have already suffered high COVID-19 mortality (such as the Northeast). These estimates suggest that caution must be taken in loosening current restrictions if effective additional measures are not put in place. We predict that increased mobility following relaxation of social distancing will lead to resurgence of transmission, keeping all else constant. We predict that deaths over the next two-month period could exceed current cumulative deaths by greater than two-fold, if the relationship between mobility and transmission remains unchanged. Our results suggest that factors modulating transmission such as rapid testing, contact tracing and behavioural precautions are crucial to offset the rise of transmission associated with loosening of social distancing. Overall, we show that while all US states have substantially reduced their reproduction numbers, there is little evidence that any states are approaching herd immunity and thus the epidemic is close to over in any state.
- Published
- 2020
- Full Text
- View/download PDF
12. Report 22: Equity in response to the COVID-19 pandemic: an assessment of the direct and indirect impacts on disadvantaged and vulnerable populations in low- and lower middle-income countries
- Author
-
Winskill, P, Whittaker, C, Walker, P, Watson, O, Laydon, D, Imai, N, Cuomo-Dannenburg, G, Ainslie, K, Baguelin, M, Bhatt, S, Boonyasiri, A, Cattarino, L, Ciavarella, C, Cooper, L, Coupland, H, Cucunuba Perez, Z, Van Elsland, S, Fitzjohn, R, Flaxman, S, Gaythorpe, K, Green, W, Hallett, T, Hamlet, A, Hinsley, W, Knock, E, Lees, J, Mellan, T, Mishra, S, Nedjati Gilani, G, Nouvellet, P, Okell, L, Parag, K, Thompson, H, Unwin, H, Wang, Y, Whittles, L, Xi, X, Ferguson, N, Donnelly, C, Ghani, A, and Medical Research Council (MRC)
- Subjects
Coronavirus ,COVID19 ,COVID-19 ,Equity - Abstract
The impact of the COVID-19 pandemic in low-income settings is likely to be more severe due to limited healthcare capacity. Within these settings, however, there exists unfair or avoidable differences in health among different groups in society – health inequities – that mean that some groups are particularly at risk from the negative direct and indirect consequences of COVID-19. The structural determinants of these are often reflected in differences by income strata, with the poorest populations having limited access to preventative measures such as handwashing. Their more fragile income status will also mean that they are likely to be employed in occupations that are not amenable to social-distancing measures, thereby further reducing their ability to protect themselves from infection. Furthermore, these populations may also lack access to timely healthcare on becoming ill. We explore these relationships by using large-scale household surveys to quantify the differences in handwashing access, occupation and hospital access with respect to wealth status in low-income settings. We use a COVID-19 transmission model to demonstrate the impact of these differences. Our results demonstrate clear trends that the probability of death from COVID-19 increases with increasing poverty. On average, we estimate a 32.0% (2.5th-97.5th centile 8.0%-72.5%) increase in the probability of death in the poorest quintile compared to the wealthiest quintile from these three factors alone. We further explore how risk mediators and the indirect impacts of COVID-19 may also hit these same disadvantaged and vulnerable the hardest. We find that larger, inter-generational households that may hamper efforts to protect the elderly if social distancing are associated with lower-income countries and, within LMICs, lower wealth status. Poorer populations are also more susceptible to food security issues - with these populations having the highest levels under-nourishment whilst also being most dependent on their own food production. We show that timing of the COVID-19 epidemic in low-resource settings has the potential to interrupt planting and harvesting seasons for staple crops, thereby accentuating this vulnerability. These enhanced risks and key vulnerabilities – alongside the broader concerns surrounding displaced or conflict-affected populations - demonstrate the challenges that the most marginalised populations face during the ongoing COVID-19 pandemic.
- Published
- 2020
- Full Text
- View/download PDF
13. Report 21: Estimating COVID-19 cases and reproduction number in Brazil
- Author
-
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, S, and Medical Research Council (MRC)
- Subjects
Coronavirus ,0303 health sciences ,03 medical and health sciences ,0302 clinical medicine ,COVID19 ,COVID-19 ,030212 general & internal medicine ,Brazil ,3. Good health ,030304 developmental biology - Abstract
Brazil is an epicentre for COVID-19 in Latin America. In this report we describe the Brazilian epidemic using 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 we therefore limit our analysis to 16 states that have experienced a total of more than fifty deaths. The distribution 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, we estimate 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 (a measure of transmission intensity) at the start of the epidemic meant that an infected individual would infect 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 the reproduction number remains above 1. A reproduction number above 1 means that the epidemic is not 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 reproduction number below 1. While the Brazilian epidemic is still relatively nascent on a national scale, our results suggest that further action is needed to limit spread and prevent health system overload.
- Published
- 2020
14. Report 20: A sub-national analysis of the rate of transmission of Covid-19 in Italy
- Author
-
Vollmer, M, Mishra, S, Unwin, H, Gandy, A, Melan, T, Bradley, V, Zhu, H, Coupland, H, Hawryluk, I, Hutchinson, M, Ratmann, O, Monod, M, Walker, P, Whittaker, C, Cattarino, L, Ciavarella, C, Cilloni, L, 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, Ghani, A, Riley, S, Okell, L, Donnelly, C, Ferguson, N, Dorigatti, I, Flaxman, S, Bhatt, S, and Medical Research Council (MRC)
- Subjects
Coronavirus ,Italy ,COVID19 ,Lockdown ,COVID-19 ,Transmission - Abstract
Italy was the first European country to experience sustained local transmission of COVID-19. As of 1st May 2020, the Italian health authorities reported 28; 238 deaths nationally. To control the epidemic, the Italian government implemented a suite of non-pharmaceutical interventions (NPIs), including school and university closures, social distancing and full lockdown involving banning of public gatherings and non essential movement. In this report, we model the effect of NPIs on transmission using data on average mobility. We estimate that the average reproduction number (a measure of transmission intensity) is currently below one for all Italian regions, and significantly so for the majority of the regions. Despite the large number of deaths, the proportion of population that has been infected by SARS-CoV-2 (the attack rate) is far from the herd immunity threshold in all Italian regions, with the highest attack rate observed in Lombardy (13.18% [10.66%-16.70%]). Italy is set to relax the currently implemented NPIs from 4th May 2020. Given the control achieved by NPIs, we consider three scenarios for the next 8 weeks: a scenario in which mobility remains the same as during the lockdown, a scenario in which mobility returns to pre-lockdown levels by 20%, and a scenario in which mobility returns to pre-lockdown levels by 40%. The scenarios explored assume that mobility is scaled evenly across all dimensions, that behaviour stays the same as before NPIs were implemented, that no pharmaceutical interventions are introduced, and it does not include transmission reduction from contact tracing, testing and the isolation of confirmed or suspected cases. We find that, in the absence of additional interventions, even a 20% return to pre-lockdown mobility could lead to a resurgence in the number of deaths far greater than experienced in the current wave in several regions. Future increases in the number of deaths will lag behind the increase in transmission intensity and so a second wave will not be immediately apparent from just monitoring of the daily number of deaths. Our results suggest that SARS-CoV-2 transmission as well as mobility should be closely monitored in the next weeks and months. To compensate for the increase in mobility that will occur due to the relaxation of the currently implemented NPIs, enhanced community surveillance including swab testing, contact tracing and the early isolation of infections are of paramount importance to reduce the risk of resurgence in transmission.
- Published
- 2020
- Full Text
- View/download PDF
15. Report 19: The potential impact of the COVID-19 epidemic on HIV, TB and malaria in low- and middle-income countries
- Author
-
Hogan, A, Jewell, B, Sherrard-Smith, E, Vesga, J, Watson, O, Whittaker, C, Hamlet, A, Smith, J, Ainslie, K, Baguelin, M, Bhatt, S, Boonyasiri, A, Brazeau, N, Cattarino, L, Charles, G, Cooper, L, Coupland, H, Cuomo-Dannenburg, G, Dighe, A, Djaafara, A, Donnelly, C, Dorigatti, I, Eaton, J, Van Elsland, S, Fitzjohn, R, Fu, H, Gaythorpe, K, Green, W, Haw, D, Hayes, S, Hinsley, W, Imai, N, Knock, E, Laydon, D, Lees, J, Mangal, T, Mellan, T, Mishra, S, Nedjati Gilani, G, Nouvellet, P, Okell, L, Ower, A, Parag, K, Pickles, M, Stopard, I, Thompson, H, Unwin, H, Verity, R, Vollmer, M, Walters, C, Wang, H, Wang, Y, Whittles, L, Winskill, P, Xi, X, Ferguson, N, Churcher, T, Arinaminpathy, N, Ghani, A, Walker, P, Hallett, T, and Medical Research Council (MRC)
- Abstract
COVID-19 has the potential to cause disruptions to health services in different ways; through the health system becoming overwhelmed with COVID-19 patients, through the intervention used to slow transmission of COVID-19 inhibiting access to preventative interventions and services, and through supplies of medicine being interrupted. We aim to quantify the extent to which such disruptions in services for HIV, TB and malaria in high burden low- and middle-income countries could lead to additional loss of life. In high burden settings, HIV, TB and malaria related deaths over 5 years may be increased by up to 10%, 20% and 36%, respectively, compared to if there were no COVID-19 epidemic. We estimate the greatest impact on HIV to be from interruption to ART, which may occur during a period of high or extremely 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 a long period of COVID-19 suppression interventions; for malaria, we estimate that the greatest impact could come from reduced prevention activities including interruption of planned net campaigns, through all phases of the COVID-19 epidemic. In high burden settings, the impact of each type of disruption could be significant and lead to a 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. Maintaining the most critical prevention activities and healthcare services for HIV, TB and malaria could significantly reduce the overall impact of the COVID-19 epidemic.
- Published
- 2020
- Full Text
- View/download PDF
16. Report 16: Role of testing in COVID-19 control
- Author
-
Grassly, N, Pons Salort, M, Parker, E, White, P, Ainslie, K, Baguelin, M, Bhatt, S, Boonyasiri, A, Boyd, O, Brazeau, N, Cattarino, L, Ciavarella, C, Cooper, L, Coupland, H, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Dighe, A, Djaafara, A, Donnelly, C, Dorigatti, I, Van Elsland, S, Ferreira Do Nascimento, F, Fitzjohn, R, Fu, H, Gaythorpe, K, Geidelberg, L, Green, W, Hallett, T, Hamlet, A, Hayes, S, Hinsley, W, Imai, N, Jorgensen, D, Knock, E, Laydon, D, Lees, J, Mangal, T, Mellan, T, Mishra, S, Nedjati Gilani, G, Nouvellet, P, Okell, L, Ower, A, Parag, K, Pickles, M, Ragonnet-Cronin, M, Stopard, I, Thompson, H, Unwin, H, Verity, R, Vollmer, M, Volz, E, Walker, P, Walters, C, Wang, H, Wang, Y, Watson, O, Whittaker, C, Whittles, L, Winskill, P, Xi, X, Ferguson, N, and Medical Research Council (MRC)
- Subjects
Coronavirus ,COVID19 ,Testing ,COVID-19 - Abstract
The World Health Organization has called for increased molecular testing in response to the COVID-19 pandemic, but different countries have taken very different approaches. We used a simple mathematical model to investigate the potential effectiveness of alternative testing strategies for COVID-19 control. Weekly screening of healthcare workers (HCWs) and other at-risk groups using PCR or point-of-care tests for infection irrespective of symptoms is estimated to reduce their contribution to transmission by 25-33%, on top of reductions achieved by self-isolation following symptoms. Widespread PCR testing in the general population is unlikely to limit transmission more than contact-tracing and quarantine based on symptoms alone, but could allow earlier release of contacts from quarantine. Immunity passports based on tests for antibody or infection could support return to work but face significant technical, legal and ethical challenges. Testing is essential for pandemic surveillance but its direct contribution to the prevention of transmission is likely to be limited to patients, HCWs and other high-risk groups.
- Published
- 2020
17. Report 13: Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in 11 European countries
- Author
-
Flaxman, S, Mishra, S, Gandy, A, Unwin, H, Coupland, H, Mellan, T, Zhu, H, Berah, T, Eaton, J, Perez Guzman, P, Schmit, N, Cilloni, L, Ainslie, K, Baguelin, M, Blake, I, Boonyasiri, A, Boyd, O, Cattarino, L, Ciavarella, C, Cooper, L, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Dighe, A, Djaafara, A, Dorigatti, I, Van Elsland, S, Fitzjohn, R, Fu, H, Gaythorpe, K, Geidelberg, L, Grassly, N, Green, W, Hallett, T, Hamlet, A, Hinsley, W, Jeffrey, B, Jorgensen, D, Knock, E, Laydon, D, Nedjati Gilani, G, Nouvellet, P, Parag, K, Siveroni, I, Thompson, H, Verity, R, Volz, E, Walters, C, Wang, H, Wang, Y, Watson, O, Winskill, P, Xi, X, Whittaker, C, Walker, P, Ghani, A, Donnelly, C, Riley, S, Okell, L, Vollmer, M, Ferguson, N, Bhatt, S, Medical Research Council (MRC), and The Royal Society
- Subjects
Europe ,COVID19 ,Non-pharmaceutical Interventions ,Pneumonia, Viral ,Coronavirus Infections ,CoronaVirus - Abstract
Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe is now experiencing large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, widescale social distancing including local and national lockdowns. In this report, we use a semi-mechanistic Bayesian hierarchical model to attempt to infer the impact of these interventions across 11 European countries. Our methods assume that changes in the reproductive number – a measure of transmission - are an immediate response to these interventions being implemented rather than broader gradual changes in behaviour. Our model estimates these changes by calculating backwards from the deaths observed over time to estimate transmission that occurred several weeks prior, allowing for the time lag between infection and death. One of the key assumptions of the model is that each intervention has the same effect on the reproduction number across countries and over time. This allows us to leverage a greater amount of data across Europe to estimate these effects. It also means that our results are driven strongly by the data from countries with more advanced epidemics, and earlier interventions, such as Italy and Spain. We find that the slowing growth in daily reported deaths in Italy is consistent with a significant impact of interventions implemented several weeks earlier. In Italy, we estimate that the effective reproduction number, Rt, dropped to close to 1 around the time of lockdown (11th March), although with a high level of uncertainty. Overall, we estimate that countries have managed to reduce their reproduction number. Our estimates have wide credible intervals and contain 1 for countries that have implemented all interventions considered in our analysis. This means that the reproduction number may be above or below this value. With current interventions remaining in place to at least the end of March, we estimate that interventions across all 11 countries will have averted 59,000 deaths up to 31 March [95% credible interval 21,000-120,000]. Many more deaths will be averted through ensuring that interventions remain in place until transmission drops to low levels. We estimate that, across all 11 countries between 7 and 43 million individuals have been infected with SARS-CoV-2 up to 28th March, representing between 1.88% and 11.43% of the population. The proportion of the population infected to date – the attack rate - is estimated to be highest in Spain followed by Italy and lowest in Germany and Norway, reflecting the relative stages of the epidemics. Given the lag of 2-3 weeks between when transmission changes occur and when their impact can be observed in trends in mortality, for most of the countries considered here it remains too early to be certain that recent interventions have been effective. If interventions in countries at earlier stages of their epidemic, such as Germany or the UK, are more or less effective than they were in the countries with advanced epidemics, on which our estimates are largely based, or if interventions have improved or worsened over time, then our estimates of the reproduction number and deaths averted would change accordingly. It is therefore critical that the current interventions remain in place and trends in cases and deaths are closely monitored in the coming days and weeks to provide reassurance that transmission of SARS-Cov-2 is slowing.
- Published
- 2020
18. Report 12: The global impact of COVID-19 and strategies for mitigation and suppression
- Author
-
Walker, P, Whittaker, C, Watson, O, Baguelin, M, Ainslie, K, Bhatia, S, Bhatt, S, Boonyasiri, A, Boyd, O, Cattarino, L, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Dighe, A, Donnelly, C, Dorigatti, I, Van Elsland, S, Fitzjohn, R, Flaxman, S, Fu, H, Gaythorpe, K, Geidelberg, L, Grassly, N, Green, W, Hamlet, A, Hauck, K, Haw, D, Hayes, S, Hinsley, W, Imai, N, Jorgensen, D, Knock, E, Laydon, D, Mishra, S, Nedjati Gilani, G, Okell, L, Riley, S, Thompson, H, Unwin, H, Verity, R, Vollmer, M, Walters, C, Wang, H, Wang, Y, Winskill, P, Xi, X, Ferguson, N, Ghani, A, Medical Research Council (MRC), and The Royal Society
- Subjects
Coronavirus ,COVID19 ,Global Burden - Abstract
The world faces a severe and acute public health emergency due to the ongoing COVID-19 global pandemic. How individual countries respond in the coming weeks will be critical in influencing the trajectory of national epidemics. Here we combine data on age-specific contact patterns and COVID-19 severity to project the health impact of the pandemic in 202 countries. We compare predicted mortality impacts in the absence of interventions or spontaneous social distancing with what might be achieved with policies aimed at mitigating or suppressing transmission. Our estimates of mortality and healthcare demand are based on data from China and high-income countries; differences in underlying health conditions and healthcare system capacity will likely result in different patterns in low income settings. We estimate that in the absence of interventions, COVID-19 would have resulted in 7.0 billion infections and 40 million deaths globally this year. Mitigation strategies focussing on shielding the elderly (60% reduction in social contacts) and slowing but not interrupting transmission (40% reduction in social contacts for wider population) could reduce this burden by half, saving 20 million lives, but we predict that even in this scenario, health systems in all countries will be quickly overwhelmed. This effect is likely to be most severe in lower income settings where capacity is lowest: our mitigated scenarios lead to peak demand for critical care beds in a typical low-income setting outstripping supply by a factor of 25, in contrast to a typical high-income setting where this factor is 7. As a result, we anticipate that the true burden in low income settings pursuing mitigation strategies could be substantially higher than reflected in these estimates. Our analysis therefore suggests that healthcare demand can only be kept within manageable levels through the rapid adoption of public health measures (including testing and isolation of cases and wider social distancing measures) to suppress transmission, similar to those being adopted in many countries at the current time. If a suppression strategy is implemented early (at 0.2 deaths per 100,000 population per week) and sustained, then 38.7 million lives could be saved whilst if it is initiated when death numbers are higher (1.6 deaths per 100,000 population per week) then 30.7 million lives could be saved. Delays in implementing strategies to suppress transmission will lead to worse outcomes and fewer lives saved. We do not consider the wider social and economic costs of suppression, which will be high and may be disproportionately so in lower income settings. Moreover, suppression strategies will need to be maintained in some manner until vaccines or effective treatments become available to avoid the risk of later epidemics. Our analysis highlights the challenging decisions faced by all governments in the coming weeks and months, but demonstrates the extent to which rapid, decisive and collective action now could save millions of lives.
- Published
- 2020
- Full Text
- View/download PDF
19. Report 11: Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment
- Author
-
Ainslie, K, Walters, C, Fu, H, Bhatia, S, Wang, H, Baguelin, M, Bhatt, S, Boonyasiri, A, Boyd, O, Cattarino, L, Ciavarella, C, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Dighe, A, Dorigatti, I, Van Elsland, S, Fitzjohn, R, Gaythorpe, K, Geidelberg, L, Ghani, A, Green, W, Hamlet, A, Hauck, K, Hinsley, W, Imai, N, Jorgensen, D, Knock, E, Laydon, D, Nedjati Gilani, G, Okell, L, Siveroni, I, Thompson, H, Unwin, H, Verity, R, Vollmer, M, Walker, P, Wang, Y, Watson, O, Whittaker, C, Winskill, P, Xi, X, Donnelly, C, Ferguson, N, Riley, S, Medical Research Council (MRC), and The Royal Society
- Subjects
Coronavirus ,COVID19 ,Containment ,Social Distancing - Abstract
The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. As of 20 March 2020, over 254,000 cases and 10,000 deaths had been reported worldwide. The outbreak began in the Chinese city of Wuhan in December 2019. In response to the fast-growing epidemic, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. At the peak of the outbreak in China (early February), there were between 2,000 and 4,000 new confirmed cases per day. For the first time since the outbreak began there have been no new confirmed cases caused by local transmission in China reported for five consecutive days up to 23 March 2020. This is an indication that the social distancing measures enacted in China have led to control of COVID-19 in China. These interventions have also impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic is not yet clear. Here, we estimate transmissibility from reported cases and compare those estimates with daily data on within-city movement, as a proxy for economic activity. Initially, within-city movement and transmission were very strongly correlated in the 5 provinces most affected by the epidemic and Beijing. However, that correlation is no longer apparent even though within-city movement has started to increase. A similar analysis for Hong Kong shows that intermediate levels of local activity can be maintained while avoiding a large outbreak. These results do not preclude future epidemics in China, nor do they allow us to estimate the maximum proportion of previous within-city activity that will be recovered in the medium term. However, they do suggest that after very intense social distancing which resulted in containment, China has successfully exited their stringent social distancing policy to some degree. Globally, China is at a more advanced stage of the pandemic. Policies implemented to reduce the spread of COVID-19 in China and the exiting strategies that followed can inform decision making processes for countries once containment is achieved.
- Published
- 2020
- Full Text
- View/download PDF
20. Report 9: Impact of non-pharmaceutical interventions (NPIs) to reduce COVID19 mortality and healthcare demand
- Author
-
Ferguson, N, Laydon, D, Nedjati Gilani, G, Imai, N, Ainslie, K, Baguelin, M, Bhatia, S, Boonyasiri, A, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Dighe, A, Dorigatti, I, Fu, H, Gaythorpe, K, Green, W, Hamlet, A, Hinsley, W, Okell, L, Van Elsland, S, Thompson, H, Verity, R, Volz, E, Wang, H, Wang, Y, Walker, P, Walters, C, Winskill, P, Whittaker, C, Donnelly, C, Riley, S, Ghani, A, Medical Research Council (MRC), and The Royal Society
- Subjects
Coronavirus ,COVID19 ,Non-pharmaceutical interventions ,healthcare demand ,Mortality - Abstract
The global impact of COVID-19 has been profound, and the public health threat it represents is the most serious seen in a respiratory virus since the 1918 H1N1 influenza pandemic. Here we present the results of epidemiological modelling which has informed policymaking in the UK and other countries in recent weeks. In the absence of a COVID-19 vaccine, we assess the potential role of a number of public health measures – so-called non-pharmaceutical interventions (NPIs) – aimed at reducing contact rates in the population and thereby reducing transmission of the virus. In the results presented here, we apply a previously published microsimulation model to two countries: the UK (Great Britain specifically) and the US. We conclude that the effectiveness of any one intervention in isolation is likely to be limited, requiring multiple interventions to be combined to have a substantial impact on transmission. Two fundamental strategies are possible: (a) mitigation, which focuses on slowing but not necessarily stopping epidemic spread – reducing peak healthcare demand while protecting those most at risk of severe disease from infection, and (b) suppression, which aims to reverse epidemic growth, reducing case numbers to low levels and maintaining that situation indefinitely. Each policy has major challenges. We find that that optimal mitigation policies (combining home isolation of suspect cases, home quarantine of those living in the same household as suspect cases, and social distancing of the elderly and others at most risk of severe disease) might reduce peak healthcare demand by 2/3 and deaths by half. However, the resulting mitigated epidemic would still likely result in hundreds of thousands of deaths and health systems (most notably intensive care units) being overwhelmed many times over. For countries able to achieve it, this leaves suppression as the preferred policy option. We show that in the UK and US context, suppression will minimally require a combination of social distancing of the entire population, home isolation of cases and household quarantine of their family members. This may need to be supplemented by school and university closures, though it should be recognised that such closures may have negative impacts on health systems due to increased absenteeism. The major challenge of suppression is that this type of intensive intervention package – or something equivalently effective at reducing transmission – will need to be maintained until a vaccine becomes available (potentially 18 months or more) – given that we predict that transmission will quickly rebound if interventions are relaxed. We show that intermittent social distancing – triggered by trends in disease surveillance – may allow interventions to be relaxed temporarily in relative short time windows, but measures will need to be reintroduced if or when case numbers rebound. Last, while experience in China and now South Korea show that suppression is possible in the short term, it remains to be seen whether it is possible long-term, and whether the social and economic costs of the interventions adopted thus far can be reduced.
- Published
- 2020
- Full Text
- View/download PDF
21. Report 8: Symptom progression of COVID-19
- Author
-
Gaythorpe, K, Imai, N, Cuomo-Dannenburg, G, Baguelin, M, Bhatia, S, Boonyasiri, A, Cori, A, Cucunuba Perez, Z, Dighe, A, Dorigatti, I, Fitzjohn, R, Fu, H, Green, W, Griffin, J, Hamlet, A, Hinsley, W, Hong, N, Kwun, M, Laydon, D, Nedjati Gilani, G, Okell, L, Riley, S, Thompson, H, Van Elsland, S, Verity, R, Volz, E, Walker, P, Wang, H, Wang, Y, Walters, C, Whittaker, C, Winskill, P, Xi, X, Donnelly, C, Ghani, A, Ferguson, N, Medical Research Council (MRC), and The Royal Society
- Subjects
Coronavirus ,COVID19 ,Symptom - Abstract
The COVID-19 epidemic was declared a Public Health Emergency of International Concern (PHEIC) by WHO on 30th January 2020 [1]. As of 8 March 2020, over 107,000 cases had been reported. Here, we use published and preprint studies of clinical characteristics of cases in mainland China as well as case studies of individuals from Hong Kong, Japan, Singapore and South Korea to examine the proportional occurrence of symptoms and the progression of symptoms through time. We find that in mainland China, where specific symptoms or disease presentation are reported, pneumonia is the most frequently mentioned, see figure 1. We found a more varied spectrum of severity in cases outside mainland China. In Hong Kong, Japan, Singapore and South Korea, fever was the most frequently reported symptom. In this latter group, presentation with pneumonia is not reported as frequently although it is more common in individuals over 60 years old. The average time from reported onset of first symptoms to the occurrence of specific symptoms or disease presentation, such as pneumonia or the use of mechanical ventilation, varied substantially. The average time to presentation with pneumonia is 5.88 days, and may be linked to testing at hospitalisation; fever is often reported at onset (where the mean time to develop fever is 0.77 days).
- Published
- 2020
- Full Text
- View/download PDF
22. Report 7: Estimating infection prevalence in Wuhan City from repatriation flights
- Author
-
Thompson, H, Imai, N, Dighe, A, Baguelin, M, Bhatia, S, Boonyasiri, A, Cori, A, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Dorigatti, I, Fitzjohn, R, Fu, H, Gaythorpe, K, Ghani, A, Green, W, Hamlet, A, Hinsley, W, Laydon, D, Nedjati Gilani, G, Okell, L, Riley, S, Van Elsland, S, Volz, E, Wang, H, Yuanrong, W, Whittaker, C, Xi, X, Donnelly, C, Ferguson, N, and Medical Research Council (MRC)
- Subjects
Coronavirus ,Prevalence ,COVID-19 ,Repatriation flights ,health care economics and organizations - Abstract
Since the end of January 2020, in response to the growing COVID-19 epidemic, 55 countries have repatriated over 8000 citizens from Wuhan City, China. In addition to quarantine measures for returning citizens, many countries implemented PCR screening to test for infection regardless of symptoms. These flights therefore give estimates of infection prevalence in Wuhan over time. Between 30th January and 1st February (close to the peak of the epidemic in Wuhan), infection prevalence was 0.87% (95% CI: 0.32% - 1.89%). As countries now start to repatriate citizens from Iran and northern Italy, information from repatriated citizens could help inform the level of response necessary to help control the outbreaks unfolding in newly affected areas.
- Published
- 2020
23. Report 6: Relative sensitivity of international surveillance
- Author
-
Bhatia, S, Imai, N, Cuomo-Dannenburg, G, Baguelin, M, Boonyasiri, A, Cori, A, Cucunuba Perez, Z, Dorigatti, I, Fitzjohn, R, Fu, H, Gaythorpe, K, Ghani, A, Hamlet, A, Hinsley, W, Laydon, D, Nedjati Gilani, G, Thompson, H, Okell, L, Riley, S, Van Elsland, S, Volz, E, Wang, H, Wang, Y, Whittaker, C, Xi, X, Donnelly, C, Ferguson, N, and Medical Research Council (MRC)
- Subjects
Surveillance ,COVID-19 - Abstract
Since the start of the COVID-19 epidemic in late 2019, there are now 29 affected countries with over 1000 confirmed cases outside of mainland China. In previous reports, we estimated the likely epidemic size in Wuhan City based on air traffic volumes and the number of detected cases internationally. Here we analysed COVID-19 cases exported from mainland China to different regions and countries, comparing the country-specific rates of detected and confirmed cases per flight volume to estimate the relative sensitivity of surveillance in different countries. Although travel restrictions from Wuhan City and other cities across China may have reduced the absolute number of travellers to and from China, we estimated that about two thirds of COVID-19 cases exported from mainland China have remained undetected worldwide, potentially resulting in multiple chains of as yet undetected human-to-human transmission outside mainland China.
- Published
- 2020
24. Report 5: Phylogenetic analysis of SARS-CoV-2
- Author
-
Volz, E, Baguelin, M, Bhatia, S, Boonyasiri, A, Cori, A, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Donnelly, C, Dorigatti, I, Fitzjohn, R, Fu, H, Gaythorpe, K, Ghani, A, Hamlet, A, Hinsley, W, Imai, N, Laydon, D, Nedjati Gilani, G, Okell, L, Riley, S, Van Elsland, S, Wang, H, Wang, Y, Xi, X, Ferguson, N, Medical Research Council (MRC), and The Royal Society
- Subjects
Phylogenetics ,COVID-19 - Abstract
Genetic diversity of SARS-CoV-2 (formerly 2019-nCoV), the virus which causes COVID-19, provides information about epidemic origins and the rate of epidemic growth. By analysing 53 SARS-CoV-2 whole genome sequences collected up to February 3, 2020, we find a strong association between the time of sample collection and accumulation of genetic diversity. Bayesian and maximum likelihood phylogenetic methods indicate that the virus was introduced into the human population in early December and has an epidemic doubling time of approximately seven days. Phylodynamic modelling provides an estimate of epidemic size through time. Precise estimates of epidemic size are not possible with current genetic data, but our analyses indicate evidence of substantial heterogeneity in the number of secondary infections caused by each case, as indicated by a high level of over-dispersion in the reproduction number. Larger numbers of more systematically sampled sequences – particularly from across China – will allow phylogenetic estimates of epidemic size and growth rate to be substantially refined.
- Published
- 2020
- Full Text
- View/download PDF
25. Report 4: Severity of 2019-novel coronavirus (nCoV)
- Author
-
Dorigatti, I, Okell, L, Cori, A, Imai, N, Baguelin, M, Bhatia, S, Boonyasiri, A, Cucunuba Perez, Z, Cuomo-Dannenburg, G, Fitzjohn, R, Fu, H, Gaythorpe, K, Hamlet, A, Hinsley, W, Hong, N, Kwun, M, Laydon, D, Nedjati Gilani, G, Riley, S, Van Elsland, S, Volz, E, Wang, H, Walters, C, Xi, X, Donnelly, C, Ghani, A, Ferguson, N, Medical Research Council (MRC), and The Royal Society
- Subjects
CFR ,COVID-19 ,Severity - Abstract
We present case fatality ratio (CFR) estimates for three strata of 2019-nCoV infections. For cases detected in Hubei, we estimate the CFR to be 18% (95% credible interval: 11%-81%). For cases detected in travellers outside mainland China, we obtain central estimates of the CFR in the range 1.2-5.6% depending on the statistical methods, with substantial uncertainty around these central values. Using estimates of underlying infection prevalence in Wuhan at the end of January derived from testing of passengers on repatriation flights to Japan and Germany, we adjusted the estimates of CFR from either the early epidemic in Hubei Province, or from cases reported outside mainland China, to obtain estimates of the overall CFR in all infections (asymptomatic or symptomatic) of approximately 1% (95% confidence interval 0.5%-4%). It is important to note that the differences in these estimates does not reflect underlying differences in disease severity between countries. CFRs seen in individual countries will vary depending on the sensitivity of different surveillance systems to detect cases of differing levels of severity and the clinical care offered to severely ill cases. All CFR estimates should be viewed cautiously at the current time as the sensitivity of surveillance of both deaths and cases in mainland China is unclear. Furthermore, all estimates rely on limited data on the typical time intervals from symptom onset to death or recovery which influences the CFR estimates.
- Published
- 2020
26. Rapid dissemination of human T-lymphotropic virus type 1 during primary infection in transplant recipients
- Author
-
Cook, LBM, Melamed, A, Demontis, MA, Laydon, D, Martin, F, Fox, J, Tosswill, J, De Freitas, D, Price, A, Medcalf, J, Neuberger, J, Bangham, C, Taylor, G, Bloodwise, and Medical Research Council (MRC)
- Subjects
Virology ,1103 Clinical Sciences - Published
- 2015
27. Pre-morbid human T-lymphotropic virus type I proviral load, rather than percentage of abnormal lymphocytes, is associated with an increased risk of aggressive adult T-cell leukemia/lymphoma
- Author
-
Hodson, A., primary, Laydon, D. J., additional, Bain, B. J., additional, Fields, P. A., additional, and Taylor, G. P., additional
- Published
- 2012
- Full Text
- View/download PDF
28. Quantifying Online News Media Coverage of the COVID-19 Pandemic: Text Mining Study and Resource
- Author
-
Krawczyk, Konrad, Chelkowski, Tadeusz, Laydon, Daniel J, Mishra, Swapnil, Xifara, Denise, Flaxman, Seth, Mellan, Thomas, Schwämmle, Veit, Röttger, Richard, Hadsund, Johannes T, and Bhatt, Samir
- Subjects
Computer applications to medicine. Medical informatics ,R858-859.7 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundBefore the advent of an effective vaccine, nonpharmaceutical interventions, such as mask-wearing, social distancing, and lockdowns, have been the primary measures to combat the COVID-19 pandemic. Such measures are highly effective when there is high population-wide adherence, which requires information on current risks posed by the pandemic alongside a clear exposition of the rules and guidelines in place. ObjectiveHere we analyzed online news media coverage of COVID-19. We quantified the total volume of COVID-19 articles, their sentiment polarization, and leading subtopics to act as a reference to inform future communication strategies. MethodsWe collected 26 million news articles from the front pages of 172 major online news sources in 11 countries (available online at SciRide). Using topic detection, we identified COVID-19–related content to quantify the proportion of total coverage the pandemic received in 2020. The sentiment analysis tool Vader was employed to stratify the emotional polarity of COVID-19 reporting. Further topic detection and sentiment analysis was performed on COVID-19 coverage to reveal the leading themes in pandemic reporting and their respective emotional polarizations. ResultsWe found that COVID-19 coverage accounted for approximately 25.3% of all front-page online news articles between January and October 2020. Sentiment analysis of English-language sources revealed that overall COVID-19 coverage was not exclusively negatively polarized, suggesting wide heterogeneous reporting of the pandemic. Within this heterogenous coverage, 16% of COVID-19 news articles (or 4% of all English-language articles) can be classified as highly negatively polarized, citing issues such as death, fear, or crisis. ConclusionsThe goal of COVID-19 public health communication is to increase understanding of distancing rules and to maximize the impact of governmental policy. The extent to which the quantity and quality of information from different communication channels (eg, social media, government pages, and news) influence public understanding of public health measures remains to be established. Here we conclude that a quarter of all reporting in 2020 covered COVID-19, which is indicative of information overload. In this capacity, our data and analysis form a quantitative basis for informing health communication strategies along traditional news media channels to minimize the risks of COVID-19 while vaccination is rolled out.
- Published
- 2021
- Full Text
- View/download PDF
29. HTLV-1 drives vigorous clonal expansion of infected CD8+ T cells in natural infection
- Author
-
Bangham, CRM, Melamed, A, Laydon, D, Al Khatib, H, Rowan, A, and Taylor, G
- Subjects
Infectious Diseases ,HTLV-1 ,viruses ,hemic and lymphatic diseases ,Virology ,Latency ,Integration ,Cytotoxic T cells ,Human retroviral infection ,Clonality - Full Text
- View/download PDF
30. Clonality, latency and integration of HTLV-1 in vivo
- Author
-
Charles Bangham, Cook L, Laydon D, Asquith B, and Melamed A
31. Quantifying Changes in Vaccine Coverage in Mainstream Media as a Result of the COVID-19 Outbreak: Text Mining Study.
- Author
-
Christensen B, Laydon D, Chelkowski T, Jemielniak D, Vollmer M, Bhatt S, and Krawczyk K
- Abstract
Background: Achieving herd immunity through vaccination depends upon the public's acceptance, which in turn relies on their understanding of its risks and benefits. The fundamental objective of public health messaging on vaccines is therefore the clear communication of often complex information and, increasingly, the countering of misinformation. The primary outlet shaping public understanding is mainstream online news media, where coverage of COVID-19 vaccines was widespread., Objective: We used text-mining analysis on the front pages of mainstream online news to quantify the volume and sentiment polarization of vaccine coverage., Methods: We analyzed 28 million articles from 172 major news sources across 11 countries between July 2015 and April 2021. We employed keyword-based frequency analysis to estimate the proportion of overall articles devoted to vaccines. We performed topic detection using BERTopic and named entity recognition to identify the leading subjects and actors mentioned in the context of vaccines. We used the Vader Python module to perform sentiment polarization quantification of all collated English-language articles., Results: The proportion of front-page articles mentioning vaccines increased from 0.1% to 4% with the outbreak of COVID-19. The number of negatively polarized articles increased from 6698 in 2015-2019 to 28,552 in 2020-2021. However, overall vaccine coverage before the COVID-19 pandemic was slightly negatively polarized (57% negative), whereas coverage during the pandemic was positively polarized (38% negative)., Conclusions: Throughout the pandemic, vaccines have risen from a marginal to a widely discussed topic on the front pages of major news outlets. Mainstream online media has been positively polarized toward vaccines, compared with mainly negative prepandemic vaccine news. However, the pandemic was accompanied by an order-of-magnitude increase in vaccine news that, due to low prepandemic frequency, may contribute to a perceived negative sentiment. These results highlight important interactions between the volume of news and overall polarization. To the best of our knowledge, our work is the first systematic text mining study of front-page vaccine news headlines in the context of COVID-19., Competing Interests: Conflicts of Interest: None declared., (©Bente Christensen, Daniel Laydon, Tadeusz Chelkowski, Dariusz Jemielniak, Michaela Vollmer, Samir Bhatt, Konrad Krawczyk. Originally published in JMIR Infodemiology (https://infodemiology.jmir.org), 20.09.2022.)
- Published
- 2022
- Full Text
- View/download PDF
32. Estimating the number of undetected COVID-19 cases among travellers from mainland China.
- Author
-
Bhatia S, Imai N, Cuomo-Dannenburg G, Baguelin M, Boonyasiri A, Cori A, Cucunubá Z, Dorigatti I, FitzJohn R, Fu H, Gaythorpe K, Ghani A, Hamlet A, Hinsley W, Laydon D, Nedjati-Gilani G, Okell L, Riley S, Thompson H, van Elsland S, Volz E, Wang H, Wang Y, Whittaker C, Xi X, Donnelly CA, and Ferguson NM
- Abstract
Background: As of August 2021, every region of the world has been affected by the COVID-19 pandemic, with more than 196,000,000 cases worldwide. Methods: We analysed COVID-19 cases among travellers from mainland China to different regions and countries, comparing the region- and country-specific rates of detected and confirmed cases per flight volume to estimate the relative sensitivity of surveillance in different regions and countries. Results: Although travel restrictions from Wuhan City and other cities across China may have reduced the absolute number of travellers to and from China, we estimated that up to 70% (95% CI: 54% - 80%) of imported cases could remain undetected relative to the sensitivity of surveillance in Singapore. The percentage of undetected imported cases rises to 75% (95% CI 66% - 82%) when comparing to the surveillance sensitivity in multiple countries. Conclusions: Our analysis shows that a large number of COVID-19 cases remain undetected across the world. These undetected cases potentially resulted in multiple chains of human-to-human transmission outside mainland China., Competing Interests: No competing interests were disclosed., (Copyright: © 2021 Bhatia S et al.)
- Published
- 2021
- Full Text
- View/download PDF
33. Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment.
- Author
-
Ainslie KEC, Walters CE, Fu H, Bhatia S, Wang H, Xi X, Baguelin M, Bhatt S, Boonyasiri A, Boyd O, Cattarino L, Ciavarella C, Cucunuba Z, Cuomo-Dannenburg G, Dighe A, Dorigatti I, van Elsland SL, FitzJohn R, Gaythorpe K, Ghani AC, Green W, Hamlet A, Hinsley W, Imai N, Jorgensen D, Knock E, Laydon D, Nedjati-Gilani G, Okell LC, Siveroni I, Thompson HA, Unwin HJT, Verity R, Vollmer M, Walker PGT, Wang Y, Watson OJ, Whittaker C, Winskill P, Donnelly CA, Ferguson NM, and Riley S
- Abstract
Background : The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods : Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results : Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Ainslie KEC et al.)
- Published
- 2020
- Full Text
- View/download PDF
34. The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries.
- Author
-
Walker PGT, Whittaker C, Watson OJ, Baguelin M, Winskill P, Hamlet A, Djafaara BA, Cucunubá Z, Olivera Mesa D, Green W, Thompson H, Nayagam S, Ainslie KEC, Bhatia S, Bhatt S, Boonyasiri A, Boyd O, Brazeau NF, Cattarino L, Cuomo-Dannenburg G, Dighe A, Donnelly CA, Dorigatti I, van Elsland SL, FitzJohn R, Fu H, Gaythorpe KAM, Geidelberg L, Grassly N, Haw D, Hayes S, Hinsley W, Imai N, Jorgensen D, Knock E, Laydon D, Mishra S, Nedjati-Gilani G, Okell LC, Unwin HJ, Verity R, Vollmer M, Walters CE, Wang H, Wang Y, Xi X, Lalloo DG, Ferguson NM, and Ghani AC
- Subjects
- COVID-19, Coronavirus Infections transmission, Humans, Patient Acceptance of Health Care, Pneumonia, Viral transmission, Public Health, Coronavirus Infections epidemiology, Coronavirus Infections prevention & control, Developing Countries, Global Health, Pandemics prevention & control, Pneumonia, Viral epidemiology, Pneumonia, Viral prevention & control, Poverty
- Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic poses a severe threat to public health worldwide. We combine data on demography, contact patterns, disease severity, and health care capacity and quality to understand its impact and inform strategies for its control. Younger populations in lower-income countries may reduce overall risk, but limited health system capacity coupled with closer intergenerational contact largely negates this benefit. Mitigation strategies that slow but do not interrupt transmission will still lead to COVID-19 epidemics rapidly overwhelming health systems, with substantial excess deaths in lower-income countries resulting from the poorer health care available. Of countries that have undertaken suppression to date, lower-income countries have acted earlier. However, this will need to be maintained or triggered more frequently in these settings to keep below available health capacity, with associated detrimental consequences for the wider health, well-being, and economies of these countries., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
- Published
- 2020
- Full Text
- View/download PDF
35. Estimating the number of undetected COVID-19 cases among travellers from mainland China.
- Author
-
Bhatia S, Imai N, Cuomo-Dannenburg G, Baguelin M, Boonyasiri A, Cori A, Cucunubá Z, Dorigatti I, FitzJohn R, Fu H, Gaythorpe K, Ghani A, Hamlet A, Hinsley W, Laydon D, Nedjati-Gilani G, Okell L, Riley S, Thompson H, van Elsland S, Volz E, Wang H, Wang Y, Whittaker C, Xi X, Donnelly CA, and Ferguson NM
- Abstract
Background: Since the start of the COVID-19 epidemic in late 2019, there have been more than 152 affected regions and countries with over 110,000 confirmed cases outside mainland China. Methods: We analysed COVID-19 cases among travellers from mainland China to different regions and countries, comparing the region- and country-specific rates of detected and confirmed cases per flight volume to estimate the relative sensitivity of surveillance in different regions and countries. Results: Although travel restrictions from Wuhan City and other cities across China may have reduced the absolute number of travellers to and from China, we estimated that more than two thirds (70%, 95% CI: 54% - 80%, compared to Singapore; 75%, 95% CI: 66% - 82%, compared to multiple countries) of cases exported from mainland China have remained undetected. Conclusions: These undetected cases potentially resulted in multiple chains of human-to-human transmission outside mainland China., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Bhatia S et al.)
- Published
- 2020
- Full Text
- View/download PDF
36. Estimates of the severity of coronavirus disease 2019: a model-based analysis.
- Author
-
Verity R, Okell LC, Dorigatti I, Winskill P, Whittaker C, Imai N, Cuomo-Dannenburg G, Thompson H, Walker PGT, Fu H, Dighe A, Griffin JT, Baguelin M, Bhatia S, Boonyasiri A, Cori A, Cucunubá Z, FitzJohn R, Gaythorpe K, Green W, Hamlet A, Hinsley W, Laydon D, Nedjati-Gilani G, Riley S, van Elsland S, Volz E, Wang H, Wang Y, Xi X, Donnelly CA, Ghani AC, and Ferguson NM
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Betacoronavirus, COVID-19, Child, Child, Preschool, China epidemiology, Hospitalization statistics & numerical data, Humans, Incidence, Infant, Infant, Newborn, Middle Aged, Models, Statistical, SARS-CoV-2, Young Adult, Coronavirus Infections mortality, Pandemics statistics & numerical data, Pneumonia, Viral mortality
- Abstract
Background: In the face of rapidly changing data, a range of case fatality ratio estimates for coronavirus disease 2019 (COVID-19) have been produced that differ substantially in magnitude. We aimed to provide robust estimates, accounting for censoring and ascertainment biases., Methods: We collected individual-case data for patients who died from COVID-19 in Hubei, mainland China (reported by national and provincial health commissions to Feb 8, 2020), and for cases outside of mainland China (from government or ministry of health websites and media reports for 37 countries, as well as Hong Kong and Macau, until Feb 25, 2020). These individual-case data were used to estimate the time between onset of symptoms and outcome (death or discharge from hospital). We next obtained age-stratified estimates of the case fatality ratio by relating the aggregate distribution of cases to the observed cumulative deaths in China, assuming a constant attack rate by age and adjusting for demography and age-based and location-based under-ascertainment. We also estimated the case fatality ratio from individual line-list data on 1334 cases identified outside of mainland China. Using data on the prevalence of PCR-confirmed cases in international residents repatriated from China, we obtained age-stratified estimates of the infection fatality ratio. Furthermore, data on age-stratified severity in a subset of 3665 cases from China were used to estimate the proportion of infected individuals who are likely to require hospitalisation., Findings: Using data on 24 deaths that occurred in mainland China and 165 recoveries outside of China, we estimated the mean duration from onset of symptoms to death to be 17·8 days (95% credible interval [CrI] 16·9-19·2) and to hospital discharge to be 24·7 days (22·9-28·1). In all laboratory confirmed and clinically diagnosed cases from mainland China (n=70 117), we estimated a crude case fatality ratio (adjusted for censoring) of 3·67% (95% CrI 3·56-3·80). However, after further adjusting for demography and under-ascertainment, we obtained a best estimate of the case fatality ratio in China of 1·38% (1·23-1·53), with substantially higher ratios in older age groups (0·32% [0·27-0·38] in those aged <60 years vs 6·4% [5·7-7·2] in those aged ≥60 years), up to 13·4% (11·2-15·9) in those aged 80 years or older. Estimates of case fatality ratio from international cases stratified by age were consistent with those from China (parametric estimate 1·4% [0·4-3·5] in those aged <60 years [n=360] and 4·5% [1·8-11·1] in those aged ≥60 years [n=151]). Our estimated overall infection fatality ratio for China was 0·66% (0·39-1·33), with an increasing profile with age. Similarly, estimates of the proportion of infected individuals likely to be hospitalised increased with age up to a maximum of 18·4% (11·0-37·6) in those aged 80 years or older., Interpretation: These early estimates give an indication of the fatality ratio across the spectrum of COVID-19 disease and show a strong age gradient in risk of death., Funding: UK Medical Research Council., (Copyright © 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
37. Lifelong Socio Economic Position and biomarkers of later life health: testing the contribution of competing hypotheses.
- Author
-
Ploubidis GB, Benova L, Grundy E, Laydon D, and DeStavola B
- Subjects
- Adult, Age Factors, Aged, Aged, 80 and over, Biomarkers, England epidemiology, Female, Fibrinogen analysis, Health Status Disparities, Humans, Longitudinal Studies, Male, Middle Aged, Risk Factors, Sex Factors, Socioeconomic Factors, Aging physiology, Health Status
- Abstract
The relative contribution of early or later life Socio Economic Position (SEP) to later life health is not fully understood and there are alternative hypotheses about the pathways through which they may influence health. We used data from the English Longitudinal Study of Ageing with a formal approach for the identification of mediating factors in order to investigate alternative hypotheses about life course influences on biomarkers of later life health. We found that early life SEP predicts physical health at least 65 years later. However, a more complicated pattern of associations than that implied by previous findings was also observed. Age group specific effects emerged, with current SEP dominating the effect on later life physical health and fibrinogen levels in participants under 65, while early life SEP had a more prominent role in explaining inequalities in physical health for men and women over 75. We extend previous findings on mid adulthood and early old age, to old age and the beginnings of late old age. The complexity of our findings highlights the need for further research on the mechanisms that underlie the association between SEP and later life health., (Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
38. The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemia/lymphoma.
- Author
-
Cook LB, Melamed A, Niederer H, Valganon M, Laydon D, Foroni L, Taylor GP, Matsuoka M, and Bangham CR
- Subjects
- Adult, Animals, Binding Sites genetics, Cell Line, Chromosome Mapping, Clone Cells metabolism, Clone Cells virology, Cohort Studies, Gene Expression, Gene Ontology, Gene Products, tax genetics, Genome, Human genetics, HTLV-I Infections virology, Host-Pathogen Interactions genetics, Human T-lymphotropic virus 1 physiology, Humans, Leukemia-Lymphoma, Adult T-Cell virology, Rats, T-Lymphocytes metabolism, T-Lymphocytes pathology, T-Lymphocytes virology, Terminal Repeat Sequences genetics, HTLV-I Infections genetics, Human T-lymphotropic virus 1 genetics, Leukemia-Lymphoma, Adult T-Cell genetics, Proviruses genetics, Virus Integration genetics
- Abstract
Adult T-cell leukemia/lymphoma (ATL) occurs in ∼5% of human T-lymphotropic virus type 1 (HTLV-1)-infected individuals and is conventionally thought to be a monoclonal disease in which a single HTLV-1(+) T-cell clone progressively outcompetes others and undergoes malignant transformation. Here, using a sensitive high-throughput method, we quantified clonality in 197 ATL cases, identified genomic characteristics of the proviral integration sites in malignant and nonmalignant clones, and investigated the proviral features (genomic structure and 5' long terminal repeat methylation) that determine its capacity to express the HTLV-1 oncoprotein Tax. Of the dominant, presumed malignant clones, 91% contained a single provirus. The genomic characteristics of the integration sites in the ATL clones resembled those of the frequent low-abundance clones (present in both ATL cases and carriers) and not those of the intermediate-abundance clones observed in 24% of ATL cases, suggesting that oligoclonal proliferation per se does not cause malignant transformation. Gene ontology analysis revealed an association in 6% of cases between ATL and integration near host genes in 3 functional categories, including genes previously implicated in hematologic malignancies. In all cases of HTLV-1 infection, regardless of ATL, there was evidence of preferential survival of the provirus in vivo in acrocentric chromosomes (13, 14, 15, 21, and 22)., (© 2014 by The American Society of Hematology.)
- Published
- 2014
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.