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Novel Epidemic Metrics to Communicate Outbreak Risk at the Municipality Level: Dengue and Zika in the Dominican Republic.

Rhys Kingston, Isobel Routledge, Samir Bhatt, Leigh R Bowman,

Arboviruses remain a significant cause of morbidity, mortality and economic cost across the global human population. Epidemics of arboviral disease, such as Zika and dengue, also cause significant disruption to health services at local and national levels. This study examined 2014-2016 Zika and dengue epidemic data at the sub-national level ... Read more >>

Viruses (Viruses)
[2022, 14(1):]

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Purifying selection determines the short-term time dependency of evolutionary rates in SARS-CoV-2 and pH1N1 influenza.

Mahan Ghafari, Louis du Plessis, Jayna Raghwani, Samir Bhatt, Bo Xu, Oliver G Pybus, Aris Katzourakis,

High throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Crucially, there is ... Read more >>

Mol Biol Evol (Molecular biology and evolution)
[2022, :]

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Context-specific emergence and growth of the SARS-CoV-2 Delta variant

Moritz Kraemer, John McCrone, Verity Hill, Sumali Bajaj, Rosario Evans-Pena, Ben Lambert, Rhys Inward, Samir Bhatt, Erik Volz, Christopher Ruis, Simon Dellicour, Guy Baele, Alexander Zarebski, Adam Sadilek, Neo Wu, Aaron Schneider, Xiang Ji, Jayna Raghwani, Ben Jackson, Rachel Colquhoun, Aine O'Toole, Thomas Peacock, Kate Twohig, Simon Thelwall, Gavin Dabrera, Richard Meyers, Nuno Faria, Carmen Huber, Kamran Khan, Isaac Bogoch, Louis Plessis, Jeffrey Barrett, David Aanensen, Wendy Barclay, Meera Chand, Thomas Connor, Nicholas Loman, Marc Suchard, Oliver Pybus, Andrew Rambaut,

The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases. The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 Delta genomes from England in combination ... Read more >>

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Context-specific emergence and growth of the SARS-CoV-2 Delta variant

John McCrone, Verity Hill, Sumali Bajaj, Rosario Evans Pena, Ben Lambert, Rhys Inward, Samir Bhatt, Erik Volz, Christopher Ruis, Simon Dellicour, Guy Baele, Alexander Zarebski, Adam Sadilek, Neo Wu, Aaron Schneider, Xiang Ji, Jayna Raghwani, Ben Jackson, Rachel Colquhoun, Áine O’Toole, Thomas Peacock, Kate Twohig, Simon Thelwall, Gavin Dabrera, Richard Myers, Nuno Faria, Carmen Huber, Isaac Bogoch, Kamran Khan, Louis du Plessis, Jeffrey Barrett, David Aanensen, Wendy Barclay, Meera Chand, Thomas Connor, Nicholas Loman, Marc Suchard, Oliver Pybus, Andrew Rambaut, Moritz U.G. Kraemer, ,

<h4>Summary</h4> The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases 1–3 . The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions 4,5 . Here we analyse 52,992 Delta ... Read more >>

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Track Omicron's spread with molecular data.

Lesley Scott, Nei-Yuan Hsiao, Sikhuline Moyo, Lavanya Singh, Houriiyah Tegally, Graeme Dor, Piet Maes, Oliver G Pybus, Moritz U G Kraemer, Elizaveta Semenova, Samir Bhatt, Seth Flaxman, Nuno R Faria, Tulio de Oliveira,

[Figure: see text]. ... Read more >>

Science (Science (New York, N.Y.))
[2021, 374(6574):1454-1455]

Cited: 1 time

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Report 46: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

Andrea Brizzi, Charles Whittaker, Luciana Servo, Iwona Hawryluk, Carlos Prete, William de Souza, Renato Aguiar, Leonardo Araujo, Leonardo Bastos, Alexandra Blenkinsop, Lewis Buss, Darlan Candido, Marcia Castro, Silvia Costa, Julio Croda, Andreza Aruska de Souza Santos, Christopher Dye, Seth Flaxman, Paula Fonseca, Victor Geddes, Bernardo Gutierrez, Philippe Lemey, Anna Levin, Thomas Mellan, Diego Bonfim, Xenia Miscouridou, Swapnil Mishra, Mélodie Monod, Filipe Moreira, Bruce Nelson, Rafael Pereira, Otavio Ranzani, Ricardo Schnekenberg, Elizaveta Semenova, Raphael Sonnabend, Renan Souza, Xiaoyue Xi, Ester Sabino, Nuno Faria, Samir Bhatt, Oliver Ratmann,

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 ... Read more >>

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Vaccinating adolescents against SARS-CoV-2 in England: a risk-benefit analysis.

Deepti Gurdasani, Samir Bhatt, Anthony Costello, Spiros Denaxas, Seth Flaxman, Trisha Greenhalgh, Stephen Griffin, Zoë Hyde, Aris Katzourakis, Martin McKee, Susan Michie, Oliver Ratmann, Stephen Reicher, Gabriel Scally, Christopher Tomlinson, Christian Yates, Hisham Ziauddeen, Christina Pagel,

<h4>Objective</h4>To offer a quantitative risk-benefit analysis of two doses of SARS-CoV-2 vaccination among adolescents in England.<h4>Setting</h4>England.<h4>Design</h4>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 ... Read more >>

J R Soc Med (Journal of the Royal Society of Medicine)
[2021, 114(11):513-524]

Cited: 2 times

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Quantifying changes in vaccine coverage in mainstream media as a result of COVID-19 outbreak

Bente Christensen, Daniel Laydon, Tadeusz Chelkowski, Dariusz Jemielniak, Michaela Vollmer, Samir Bhatt, Konrad Krawczyk,

<h4>Background</h4> Achieving vaccine-derived herd immunity depends on public acceptance of vaccination, which in turn relies on people’s understanding of its risks and benefits. The fundamental objective of public health messaging on vaccines is therefore the clear and concise communication of often complex information, and increasingly the countering of misinformation. The ... Read more >>

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Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe.

Mrinank Sharma, Sören Mindermann, Charlie Rogers-Smith, Gavin Leech, Benedict Snodin, Janvi Ahuja, Jonas B Sandbrink, Joshua Teperowski Monrad, George Altman, Gurpreet Dhaliwal, Lukas Finnveden, Alexander John Norman, Sebastian B Oehm, Julia Fabienne Sandkühler, Laurence Aitchison, Tomáš Gavenčiak, Thomas Mellan, Jan Kulveit, Leonid Chindelevitch, Seth Flaxman, Yarin Gal, Swapnil Mishra, Samir Bhatt, Jan Markus Brauner,

European governments use non-pharmaceutical interventions (NPIs) to control resurging waves of COVID-19. However, they only have outdated estimates for how effective individual NPIs were in the first wave. We estimate the effectiveness of 17 NPIs in Europe's second wave from subnational case and death data by introducing a flexible hierarchical ... Read more >>

Nat Commun (Nature communications)
[2021, 12(1):5820]

Cited: 2 times

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Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.

Mahesh S Dhar, Robin Marwal, Radhakrishnan Vs, Kalaiarasan Ponnusamy, Bani Jolly, Rahul C Bhoyar, Viren Sardana, Salwa Naushin, Mercy Rophina, Thomas A Mellan, Swapnil Mishra, Charles Whittaker, Saman Fatihi, Meena Datta, Priyanka Singh, Uma Sharma, Rajat Ujjainiya, Nitin Bhatheja, Mohit Kumar Divakar, Manoj K Singh, Mohamed Imran, Vigneshwar Senthivel, Ranjeet Maurya, Neha Jha, Priyanka Mehta, Vivekanand A, Pooja Sharma, Arvinden Vr, Urmila Chaudhary, Namita Soni, Lipi Thukral, Seth Flaxman, Samir Bhatt, Rajesh Pandey, Debasis Dash, Mohammed Faruq, Hemlata Lall, Hema Gogia, Preeti Madan, Sanket Kulkarni, Himanshu Chauhan, Shantanu Sengupta, Sandhya Kabra, , Ravindra K Gupta, Sujeet K Singh, Anurag Agrawal, Partha Rakshit, Vinay Nandicoori, Karthik Bharadwaj Tallapaka, Divya Tej Sowpati, K Thangaraj, Murali Dharan Bashyam, Ashwin Dalal, Sridhar Sivasubbu, Vinod Scaria, Ajay Parida, Sunil K Raghav, Punit Prasad, Apurva Sarin, Satyajit Mayor, Uma Ramakrishnan, Dasaradhi Palakodeti, Aswin Sai Narain Seshasayee, Manoj Bhat, Yogesh Shouche, Ajay Pillai, Tanzin Dikid, Saumitra Das, Arindam Maitra, Sreedhar Chinnaswamy, Nidhan Kumar Biswas, Anita Sudhir Desai, Chitra Pattabiraman, M V Manjunatha, Reeta S Mani, Gautam Arunachal Udupi, Priya Abraham, Potdar Varsha Atul, Sarah S Cherian,

[Figure: see text]. ... Read more >>

Science (Science (New York, N.Y.))
[2021, 374(6570):995-999]

Cited: 30 times

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Global disparities in SARS-CoV-2 genomic surveillance

Anderson Brito, Elizaveta Semenova, Gytis Dudas, Gabriel Hassler, Chaney Kalinich, Moritz U.G. Kraemer, Joses Ho, Houriiyah Tegally, George Githinji, Charles Agoti, Lucy Matkin, Charles Whittaker, Benjamin Howden, Vitali Sintchenko, Neta Zuckerman, Orna Mor, Heather Blankenship, Tulio de Oliveira, Raymond Lin, Marilda Mendonça Siqueira, Paola Cristina Resende, Ana Tereza Vasconcelos, Fernando Spilki, Renato Santana Aguiar, Ivailo Alexiev, Ivan Ivanov, Ivva Philipova, Christine Carrington, Nikita Sahadeo, Céline Gurry, Sebastian Maurer-Stroh, Dhamari Naidoo, Karin von Eije, Mark Perkins, Maria van Kerkhove, Sarah Hill, Ester Sabino, Oliver Pybus, Christopher Dye, Samir Bhatt, Seth Flaxman, Marc Suchard, Nathan Grubaugh, Guy Baele, Nuno Faria, , , , ,

Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in ... Read more >>

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The impact of the COVID-19 pandemic on patterns of attendance at emergency departments in two large London hospitals: an observational study.

Michaela A C Vollmer, Sreejith Radhakrishnan, Mara D Kont, Seth Flaxman, Samir Bhatt, Ceire Costelloe, Kate Honeyford, Paul Aylin, Graham Cooke, Julian Redhead, Alison Sanders, Helen Mangan, Peter J White, Neil Ferguson, Katharina Hauck, Shevanthi Nayagam, Pablo N Perez-Guzman,

<h4>Background</h4>Hospitals in England have undergone considerable change to address the surge in demand imposed by the COVID-19 pandemic. The impact of this on emergency department (ED) attendances is unknown, especially for non-COVID-19 related emergencies.<h4>Methods</h4>This analysis is an observational study of ED attendances at the Imperial College Healthcare NHS Trust (ICHNT). ... Read more >>

BMC Health Serv Res (BMC health services research)
[2021, 21(1):1008]

Cited: 1 time

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The association between mechanical ventilator compatible bed occupancy and mortality risk in intensive care patients with COVID-19: a national retrospective cohort study.

Harrison Wilde, Thomas Mellan, Iwona Hawryluk, John M Dennis, Spiros Denaxas, Christina Pagel, Andrew Duncan, Samir Bhatt, Seth Flaxman, Bilal A Mateen, Sebastian J Vollmer,

<h4>Background</h4>The literature paints a complex picture of the association between mortality risk and ICU strain. In this study, we sought to determine if there is an association between mortality risk in intensive care units (ICU) and occupancy of beds compatible with mechanical ventilation, as a proxy for strain.<h4>Methods</h4>A national retrospective ... Read more >>

BMC Med (BMC medicine)
[2021, 19(1):213]

Cited: 3 times

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Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England.

Swapnil Mishra, Sören Mindermann, Mrinank Sharma, Charles Whittaker, Thomas A Mellan, Thomas Wilton, Dimitra Klapsa, Ryan Mate, Martin Fritzsche, Maria Zambon, Janvi Ahuja, Adam Howes, Xenia Miscouridou, Guy P Nason, Oliver Ratmann, Elizaveta Semenova, Gavin Leech, Julia Fabienne Sandkühler, Charlie Rogers-Smith, Michaela Vollmer, H Juliette T Unwin, Yarin Gal, Meera Chand, Axel Gandy, Javier Martin, Erik Volz, Neil M Ferguson, Samir Bhatt, Jan M Brauner, Seth Flaxman, ,

<h4>Background</h4>Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) 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 and how ... Read more >>

EClinicalMedicine (EClinicalMedicine)
[2021, 39:101064]

Cited: 14 times

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Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling.

Swapnil Mishra, James A Scott, Daniel J Laydon, Seth Flaxman, Axel Gandy, Thomas A Mellan, H Juliette T Unwin, Michaela Vollmer, Helen Coupland, Oliver Ratmann, Melodie Monod, Harrison H Zhu, Anne Cori, Katy A M Gaythorpe, Lilith K Whittles, Charles Whittaker, Christl A Donnelly, Neil M Ferguson, Samir Bhatt,

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 ... Read more >>

Sci Rep (Scientific reports)
[2021, 11(1):16342]

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Correction: Quantifying Online News Media Coverage of the COVID-19 Pandemic: Text Mining Study and Resource.

Konrad Krawczyk, Tadeusz Chelkowski, Daniel J Laydon, Swapnil Mishra, Denise Xifara, Benjamin Gibert, Seth Flaxman, Thomas Mellan, Veit Schwämmle, Richard Röttger, Johannes T Hadsund, Samir Bhatt,

[This corrects the article DOI: 10.2196/28253.]. ... Read more >>

J Med Internet Res (Journal of medical Internet research)
[2021, 23(7):e31544]

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Is the cure really worse than the disease? The health impacts of lockdowns during COVID-19.

Gideon Meyerowitz-Katz, Samir Bhatt, Oliver Ratmann, Jan Markus Brauner, Seth Flaxman, Swapnil Mishra, Mrinank Sharma, Sören Mindermann, Valerie Bradley, Michaela Vollmer, Lea Merone, Gavin Yamey,

BMJ Glob Health (BMJ global health)
[2021, 6(8):]

Cited: 4 times

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Purifying selection determines the short-term time dependency of evolutionary rates in SARS-CoV-2 and pH1N1 influenza

Mahan Ghafari, Louis du Plessis, Jayna Raghwani, Samir Bhatt, Bo Xu, Oliver Pybus, Aris Katzourakis,

High throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Here, we characterise ... Read more >>

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Mass mask-wearing notably reduces COVID-19 transmission

Gavin Leech, Charlie Rogers-Smith, Jonas Sandbrink, Benedict Snodin, Robert Zinkov, Benjamin Rader, John Brownstein, Yarin Gal, Samir Bhatt, Mrinank Sharma, Sören Mindermann, Jan Brauner, Laurence Aitchison,

<h4>ABSTRACT</h4> Mask-wearing has been a controversial measure to control the COVID-19 pandemic. While masks are known to substantially reduce disease transmission in healthcare settings [1–3], studies in community settings report inconsistent results [4–6]. Investigating the inconsistency within epidemiological studies, we find that a commonly used proxy, government mask mandates, does ... Read more >>

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Global minimum estimates of children affected by COVID-19-associated orphanhood and deaths of caregivers: a modelling study.

Susan D Hillis, H Juliette T Unwin, Yu Chen, Lucie Cluver, Lorraine Sherr, Philip S Goldman, Oliver Ratmann, Christl A Donnelly, Samir Bhatt, Andrés Villaveces, Alexander Butchart, Gretchen Bachman, Laura Rawlings, Phil Green, Charles A Nelson, Seth Flaxman,

<h4>Background</h4>The COVID-19 pandemic priorities have 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 institutionalisation. We provide estimates for the magnitude of this problem resulting from ... Read more >>

Lancet (Lancet (London, England))
[2021, 398(10298):391-402]

Cited: 14 times

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Maps and metrics of insecticide-treated net access, use, and nets-per-capita in Africa from 2000-2020.

Amelia Bertozzi-Villa, Caitlin A Bever, Hannah Koenker, Daniel J Weiss, Camilo Vargas-Ruiz, Anita K Nandi, Harry S Gibson, Joseph Harris, Katherine E Battle, Susan F Rumisha, Suzanne Keddie, Punam Amratia, Rohan Arambepola, Ewan Cameron, Elisabeth G Chestnutt, Emma L Collins, Justin Millar, Swapnil Mishra, Jennifer Rozier, Tasmin Symons, Katherine A Twohig, T Deirdre Hollingsworth, Peter W Gething, Samir Bhatt,

Insecticide-treated nets (ITNs) are one of the most widespread and impactful malaria interventions in Africa, yet a spatially-resolved time series of ITN coverage has never been published. Using data from multiple sources, we generate high-resolution maps of ITN access, use, and nets-per-capita annually from 2000 to 2020 across the 40 ... Read more >>

Nat Commun (Nature communications)
[2021, 12(1):3589]

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Resurgence of SARS-CoV-2 in India: Potential role of the B.1.617.2 (Delta) variant and delayed interventions

Maxwell Salvatore, Rupam Bhattacharyya, Soumik Purkayastha, Lauren Zimmermann, Debashree Ray, Aditi Hazra, Michael Kleinsasser, Thomas Mellan, Charlie Whittaker, Seth Flaxman, Samir Bhatt, Swapnil Mishra, Bhramar Mukherjee,

India has seen a surge of SARS-CoV-2 infections and deaths in early part of 2021, despite having controlled the epidemic during 2020. Building on a two-strain, semi-mechanistic model that synthesizes mortality and genomic data, we find evidence that altered epidemiological properties of B.1.617.2 (Delta) variant play an important role in ... Read more >>

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Inference of malaria reproduction numbers in three elimination settings by combining temporal data and distance metrics.

Isobel Routledge, H Juliette T Unwin, Samir Bhatt,

Individual-level geographic information about malaria cases, such as the GPS coordinates of residence or health facility, is often collected as part of surveillance in near-elimination settings, but could be more effectively utilised to infer transmission dynamics, in conjunction with additional information such as symptom onset time and genetic distance. However, ... Read more >>

Sci Rep (Scientific reports)
[2021, 11(1):14495]

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Regularised B-splines projected Gaussian Process priors to estimate the age profile of COVID-19 deaths before and after vaccine roll-out

Mélodie Monod, Alexandra Blenkinsop, Andrea Brizzi, Yu Chen, Vidoushee Jogarah, Yuanrong Wang, Seth Flaxman, Samir Bhatt, Oliver Ratmann,

The COVID-19 pandemic has caused severe public health consequences in the United States. The United States began a vaccination campaign at the end of 2020 targeting primarily elderly residents before extending access to younger individuals. With both COVID-19 infection fatality ratios and vaccine uptake being heterogeneous across ages, an important ... Read more >>

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Gaussian Process Nowcasting: Application to COVID-19 Mortality Reporting

Iwona Hawryluk, Henrique Hoeltgebaum, Swapnil Mishra, Xenia Miscouridou, Ricardo Schnekenberg, Charles Whittaker, Michaela Vollmer, Seth Flaxman, Samir Bhatt, Thomas Mellan,

Updating observations of a signal due to the delays in the measurement process is a common problem in signal processing, with prominent examples in a wide range of fields. An important example of this problem is the nowcasting of COVID-19 mortality: given a stream of reported counts of daily deaths, ... Read more >>

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