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38 results on '"Zarebski, Alexander E."'

1. Investigation of P. Vivax Elimination via Mass Drug Administration

Author

Anwar, Md Nurul, McCaw, James M., Zarebski, Alexander E., Hickson, Roslyn I., and Flegg, Jennifer A.

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Plasmodium vivax is the most geographically widespread malaria parasite due to its ability to remain dormant (as a hypnozoite) in the human liver and subsequently reactivate. Given the majority of P. vivax infections are due to hypnozoite reactivation, targeting the hypnozoite reservoir with a radical cure is crucial for achieving P. vivax elimination. Stochastic effects can strongly influence dynamics when disease prevalence is low or when the population size is small. Hence, it is important to account for this when modelling malaria elimination.cWe use a stochastic multiscale model of P. vivax transmission to study the impacts of multiple rounds of mass drug administration (MDA) with a radical cure, accounting for superinfection and hypnozoite dynamics. Our results indicate multiple rounds of MDA with a high-efficacy drug are needed to achieve a substantial probability of elimination. This work has the potential to help guide P. vivax elimination strategies by quantifying elimination probabilities for an MDA approach.

Published
2024
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2. A hybrid framework for compartmental models enabling simulation-based inference

Author

Germano, Domenic P. J., Zarebski, Alexander E., Hautphenne, Sophie, Moss, Robert, Flegg, Jennifer A., and Flegg, Mark B.

Subjects
Quantitative Biology - Populations and Evolution, Mathematics - Dynamical Systems
Abstract

Multi-scale systems often exhibit stochastic and deterministic dynamics. Capturing these aspects in a compartmental model is challenging. Notably, low occupancy compartments exhibit stochastic dynamics and high occupancy compartments exhibit deterministic dynamics. Failing to account for stochasticity in small populations can produce 'atto-foxes', e.g. in the Lotka-Volterra ordinary differential equation (ODE) model. This limitation becomes problematic when studying extinction of species or the clearance of infection, but it can be resolved by using discrete stochastic models e.g. continuous time Markov chains (CTMCs). Unfortunately, simulating CTMCs is infeasible for most realistic populations. We develop a novel mathematical framework, to couple continuous ODEs and discrete CTMCs: 'Jump-Switch-Flow' (JSF). In this framework populations can reach extinct states ("absorbing states"), thereby resolving atto-fox-type problems. JSF has the desired behaviours of exact CTMC simulation, but is substantially faster than existing alternatives. JSF's utility for simulation-based inference, particularly multi-scale problems, is demonstrated by several case-studies. In a simulation study, we demonstrate how JSF can enable a more nuanced analysis of the efficacy of public health interventions. We also carry out a novel analysis of longitudinal within-host data from SARS-CoV-2 infections to quantify the timing of viral clearance. JSF offers a novel approach to compartmental model development and simulation.

Published
2024

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

Author

McCrone, John T, Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben C, Inward, Rhys, Bhatt, Samir, Volz, Erik, Ruis, Christopher, Dellicour, Simon, Baele, Guy, Zarebski, Alexander E, Sadilek, Adam, Wu, Neo, Schneider, Aaron, Ji, Xiang, Raghwani, Jayna, Jackson, Ben, Colquhoun, Rachel, O’Toole, Áine, Peacock, Thomas P, Twohig, Kate, Thelwall, Simon, Dabrera, Gavin, Myers, Richard, Faria, Nuno R, Huber, Carmen, Bogoch, Isaac I, Khan, Kamran, du Plessis, Louis, Barrett, Jeffrey C, Aanensen, David M, Barclay, Wendy S, Chand, Meera, Connor, Thomas, Loman, Nicholas J, Suchard, Marc A, Pybus, Oliver G, Rambaut, Andrew, and Kraemer, Moritz UG

Subjects
Emerging Infectious Diseases, Infectious Diseases, Good Health and Well Being, COVID-19, Cities, Contact Tracing, England, Genome, Viral, Humans, Quarantine, SARS-CoV-2, Travel, COVID-19 Genomics UK (COG-UK) Consortium, General Science & Technology
Abstract

The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).

Published
2022

5. Epidemiological data from the COVID-19 outbreak, real-time case information.

Author

Xu, Bo, Gutierrez, Bernardo, Mekaru, Sumiko, Sewalk, Kara, Goodwin, Lauren, Loskill, Alyssa, Cohn, Emily L, Hswen, Yulin, Hill, Sarah C, Cobo, Maria M, Zarebski, Alexander E, Li, Sabrina, Wu, Chieh-Hsi, Hulland, Erin, Morgan, Julia D, Wang, Lin, O'Brien, Katelynn, Scarpino, Samuel V, Brownstein, John S, Pybus, Oliver G, Pigott, David M, and Kraemer, Moritz UG

Subjects
Humans, Pneumonia, Viral, Coronavirus Infections, Public Health, Geography, China, Epidemics, Pandemics, Geographic Mapping, Betacoronavirus, Pneumonia, Viral
Abstract

Cases of a novel coronavirus were first reported in Wuhan, Hubei province, China, in December 2019 and have since spread across the world. Epidemiological studies have indicated human-to-human transmission in China and elsewhere. To aid the analysis and tracking of the COVID-19 epidemic we collected and curated individual-level data from national, provincial, and municipal health reports, as well as additional information from online reports. All data are geo-coded and, where available, include symptoms, key dates (date of onset, admission, and confirmation), and travel history. The generation of detailed, real-time, and robust data for emerging disease outbreaks is important and can help to generate robust evidence that will support and inform public health decision making.

Published
2020

8. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Author

Viana, Raquel, Moyo, Sikhulile, Amoako, Daniel G., Tegally, Houriiyah, Scheepers, Cathrine, Althaus, Christian L., Anyaneji, Ugochukwu J., Bester, Phillip A., Boni, Maciej F., Chand, Mohammed, Choga, Wonderful T., Colquhoun, Rachel, Davids, Michaela, Deforche, Koen, Doolabh, Deelan, du Plessis, Louis, Engelbrecht, Susan, Everatt, Josie, Giandhari, Jennifer, Giovanetti, Marta, Hardie, Diana, Hill, Verity, Hsiao, Nei-Yuan, Iranzadeh, Arash, Ismail, Arshad, Joseph, Charity, Joseph, Rageema, Koopile, Legodile, Kosakovsky Pond, Sergei L., Kraemer, Moritz U. G., Kuate-Lere, Lesego, Laguda-Akingba, Oluwakemi, Lesetedi-Mafoko, Onalethatha, Lessells, Richard J., Lockman, Shahin, Lucaci, Alexander G., Maharaj, Arisha, Mahlangu, Boitshoko, Maponga, Tongai, Mahlakwane, Kamela, Makatini, Zinhle, Marais, Gert, Maruapula, Dorcas, Masupu, Kereng, Matshaba, Mogomotsi, Mayaphi, Simnikiwe, Mbhele, Nokuzola, Mbulawa, Mpaphi B., Mendes, Adriano, Mlisana, Koleka, Mnguni, Anele, Mohale, Thabo, Moir, Monika, Moruisi, Kgomotso, Mosepele, Mosepele, Motsatsi, Gerald, Motswaledi, Modisa S., Mphoyakgosi, Thongbotho, Msomi, Nokukhanya, Mwangi, Peter N., Naidoo, Yeshnee, Ntuli, Noxolo, Nyaga, Martin, Olubayo, Lucier, Pillay, Sureshnee, Radibe, Botshelo, Ramphal, Yajna, Ramphal, Upasana, San, James E., Scott, Lesley, Shapiro, Roger, Singh, Lavanya, Smith-Lawrence, Pamela, Stevens, Wendy, Strydom, Amy, Subramoney, Kathleen, Tebeila, Naume, Tshiabuila, Derek, Tsui, Joseph, van Wyk, Stephanie, Weaver, Steven, Wibmer, Constantinos K., Wilkinson, Eduan, Wolter, Nicole, Zarebski, Alexander E., Zuze, Boitumelo, Goedhals, Dominique, Preiser, Wolfgang, Treurnicht, Florette, Venter, Marietje, Williamson, Carolyn, Pybus, Oliver G., Bhiman, Jinal, Glass, Allison, Martin, Darren P., Rambaut, Andrew, Gaseitsiwe, Simani, von Gottberg, Anne, and de Oliveira, Tulio

Published
2022
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10. Influencing public health policy with data-informed mathematical models of infectious diseases: Recent developments and new challenges

Author

Alahmadi, Amani, Belet, Sarah, Black, Andrew, Cromer, Deborah, Flegg, Jennifer A., House, Thomas, Jayasundara, Pavithra, Keith, Jonathan M., McCaw, James M., Moss, Robert, Ross, Joshua V., Shearer, Freya M., Tun, Sai Thein Than, Walker, Camelia R., White, Lisa, Whyte, Jason M., Yan, Ada W.C., and Zarebski, Alexander E.

Published
2020
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12. Crowding and the shape of COVID-19 epidemics

Author

Rader, Benjamin, Scarpino, Samuel V., Nande, Anjalika, Hill, Alison L., Adlam, Ben, Reiner, Robert C., Pigott, David M., Gutierrez, Bernardo, Zarebski, Alexander E., Shrestha, Munik, Brownstein, John S., Castro, Marcia C., Dye, Christopher, Tian, Huaiyu, Pybus, Oliver G., and Kraemer, Moritz U. G.

Published
2020
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14. Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil

Author

de Souza, William Marciel, Buss, Lewis Fletcher, Candido, Darlan da Silva, Carrera, Jean-Paul, Li, Sabrina, Zarebski, Alexander E., Pereira, Rafael Henrique Moraes, Prete, Jr, Carlos A., de Souza-Santos, Andreza Aruska, Parag, Kris V., Belotti, Maria Carolina T. D., Vincenti-Gonzalez, Maria F., Messina, Janey, da Silva Sales, Flavia Cristina, Andrade, Pamela dos Santos, Nascimento, Vítor Heloiz, Ghilardi, Fabio, Abade, Leandro, Gutierrez, Bernardo, Kraemer, Moritz U. G., Braga, Carlos K. V., Aguiar, Renato Santana, Alexander, Neal, Mayaud, Philippe, Brady, Oliver J., Marcilio, Izabel, Gouveia, Nelson, Li, Guangdi, Tami, Adriana, de Oliveira, Silvano Barbosa, Porto, Victor Bertollo Gomes, Ganem, Fabiana, de Almeida, Walquiria Aparecida Ferreira, Fantinato, Francieli Fontana Sutile Tardetti, Macário, Eduardo Marques, de Oliveira, Wanderson Kleber, Nogueira, Mauricio L., Pybus, Oliver G., Wu, Chieh-Hsi, Croda, Julio, Sabino, Ester C., and Faria, Nuno Rodrigues

Published
2020
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18. Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1.

Author

Tsui, Joseph L.-H., McCrone, John T., Lambert, Ben, Bajaj, Sumali, Inward, Rhys P. D., Bosetti, Paolo, Evans Pena, Rosario, Tegally, Houriiyah, Hill, Verity, Zarebski, Alexander E., Peacock, Thomas P., Luyang Liu, Neo Wu, Davis, Megan, Bogoch, Isaac I., Khan, Kamran, Kall, Meaghan, Abdul Aziz, Nurin Iwani Binti, Colquhoun, Rachel, and O’Toole, Áine

Published
2023
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19. Climate and land-use shape the spread of zoonotic yellow fever virus

Author

Hill, Sarah C., primary, Dellicour, Simon, additional, Claro, Ingra M., additional, Sequeira, Patricia C., additional, Adelino, Talita, additional, Thézé, Julien, additional, Wu, Chieh-Hsi, additional, Rebello Moreira, Filipe Romero, additional, Giovanetti, Marta, additional, Li, Sabrina L., additional, de Jesus, Jaqueline G., additional, Colón-González, Felipe J., additional, Chamberlain, Heather R., additional, Pannell, Oliver, additional, Tejedor-Garavito, Natalia, additional, de Bruycker-Nogueira, Fernanda, additional, Fabri, Allison A., additional, Angélica Mares-Guia, Maria, additional, Xavier, Joilson, additional, Zarebski, Alexander E., additional, Hamlet, Arran, additional, Mureb Sallum, Maria Anice, additional, da Costa, Antonio C., additional, Manuli, Erika R., additional, Levin, Anna S., additional, Mucci, Luís Filipe, additional, Tubaki, Rosa Maria, additional, de Menezes, Regiane Maria Tironi, additional, de Deus, Juliana Telles, additional, Spinola, Roberta, additional, Saad, Leila, additional, Kallas, Esper G., additional, Wint, G.R. William, additional, Peixoto, Pedro S., additional, de Souza Santos, Andreza Aruska, additional, Messina, Jane P., additional, Brady, Oliver J., additional, Tatem, Andrew J., additional, Suchard, Marc A., additional, Mendez-Rico, Jairo A., additional, Abreu, André, additional, Aguiar, Renato Santana, additional, Pybus, Oliver G., additional, Baele, Guy, additional, Lemey, Philippe, additional, Iani, Felipe, additional, Cunha, Mariana S., additional, de Filippis, Ana M. Bispo, additional, Sabino, Ester C., additional, and Faria, Nuno R., additional

Published
2022
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20. Context-specific emergence and growth of the SARS-CoV-2 Delta variant

Author

McCrone, John T., Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben C., Inward, Rhys, Bhatt, Samir, Volz, Erik, Ruis, Christopher, Dellicour, Simon, Baele, Guy, Zarebski, Alexander E., Sadilek, Adam, Wu, Neo, Schneider, Aaron, Ji, Xiang, Raghwani, Jayna, Jackson, Ben, Colquhoun, Rachel, O’Toole, Áine, Peacock, Thomas P., Twohig, Kate, Thelwall, Simon, Dabrera, Gavin, Myers, Richard, Faria, Nuno R., Huber, Carmen, Bogoch, Isaac I., Khan, Kamran, du Plessis, Louis, Barrett, Jeffrey C., Aanensen, David M., Barclay, Wendy S., Chand, Meera, Connor, Thomas, Loman, Nicholas J., Suchard, Marc A., Pybus, Oliver G., Rambaut, Andrew, Kraemer, Moritz U.G., McCrone, John T., Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben C., Inward, Rhys, Bhatt, Samir, Volz, Erik, Ruis, Christopher, Dellicour, Simon, Baele, Guy, Zarebski, Alexander E., Sadilek, Adam, Wu, Neo, Schneider, Aaron, Ji, Xiang, Raghwani, Jayna, Jackson, Ben, Colquhoun, Rachel, O’Toole, Áine, Peacock, Thomas P., Twohig, Kate, Thelwall, Simon, Dabrera, Gavin, Myers, Richard, Faria, Nuno R., Huber, Carmen, Bogoch, Isaac I., Khan, Kamran, du Plessis, Louis, Barrett, Jeffrey C., Aanensen, David M., Barclay, Wendy S., Chand, Meera, Connor, Thomas, Loman, Nicholas J., Suchard, Marc A., Pybus, Oliver G., Rambaut, Andrew, and Kraemer, Moritz U.G.

Abstract

The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing—and not the number of importations—were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).

Published
2022

24. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Author

Viana, Raquel, primary, Moyo, Sikhulile, additional, Amoako, Daniel G, additional, Tegally, Houriiyah, additional, Scheepers, Cathrine, additional, Althaus, Christian L, additional, Anyaneji, Ugochukwu J, additional, Bester, Phillip A, additional, Boni, Maciej F, additional, Chand, Mohammed, additional, Choga, Wonderful T, additional, Colquhoun, Rachel, additional, Davids, Michaela, additional, Deforche, Koen, additional, Doolabh, Deelan, additional, Engelbrecht, Susan, additional, Everatt, Josie, additional, Giandhari, Jennifer, additional, Giovanetti, Marta, additional, Hardie, Diana, additional, Hill, Verity, additional, Hsiao, Nei-Yuan, additional, Iranzadeh, Arash, additional, Ismail, Arshad, additional, Joseph, Charity, additional, Joseph, Rageema, additional, Koopile, Legodile, additional, Pond, Sergei L Kosakovsky, additional, Kraemer, Moritz UG, additional, Kuate-Lere, Lesego, additional, Laguda-Akingba, Oluwakemi, additional, Lesetedi-Mafoko, Onalethatha, additional, Lessells, Richard J, additional, Lockman, Shahin, additional, Lucaci, Alexander G, additional, Maharaj, Arisha, additional, Mahlangu, Boitshoko, additional, Maponga, Tongai, additional, Mahlakwane, Kamela, additional, Makatini, Zinhle, additional, Marais, Gert, additional, Maruapula, Dorcas, additional, Masupu, Kereng, additional, Matshaba, Mogomotsi, additional, Mayaphi, Simnikiwe, additional, Mbhele, Nokuzola, additional, Mbulawa, Mpaphi B, additional, Mendes, Adriano, additional, Mlisana, Koleka, additional, Mnguni, Anele, additional, Mohale, Thabo, additional, Moir, Monika, additional, Moruisi, Kgomotso, additional, Mosepele, Mosepele, additional, Motsatsi, Gerald, additional, Motswaledi, Modisa S, additional, Mphoyakgosi, Thongbotho, additional, Msomi, Nokukhanya, additional, Mwangi, Peter N, additional, Naidoo, Yeshnee, additional, Ntuli, Noxolo, additional, Nyaga, Martin, additional, Olubayo, Lucier, additional, Pillay, Sureshnee, additional, Radibe, Botshelo, additional, Ramphal, Yajna, additional, Ramphal, Upasana, additional, San, James E, additional, Scott, Lesley, additional, Shapiro, Roger, additional, Singh, Lavanya, additional, Smith-Lawrence, Pamela, additional, Stevens, Wendy, additional, Strydom, Amy, additional, Subramoney, Kathleen, additional, Tebeila, Naume, additional, Tshiabuila, Derek, additional, Tsui, Joseph, additional, van Wyk, Stephanie, additional, Weaver, Steven, additional, Wibmer, Constantinos K, additional, Wilkinson, Eduan, additional, Wolter, Nicole, additional, Zarebski, Alexander E, additional, Zuze, Boitumelo, additional, Goedhals, Dominique, additional, Preiser, Wolfgang, additional, Treurnicht, Florette, additional, Venter, Marietje, additional, Williamson, Carolyn, additional, Pybus, Oliver G, additional, Bhiman, Jinal, additional, Glass, Allison, additional, Martin, Darren P, additional, Rambaut, Andrew, additional, Gaseitsiwe, Simani, additional, von Gottberg, Anne, additional, and de Oliveira, Tulio, additional

Published
2021
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25. Investigation of P. vivax elimination via mass drug administration: A simulation study.

Author

Anwar, Md Nurul, McCaw, James M., Zarebski, Alexander E., Hickson, Roslyn I., and Flegg, Jennifer A.

Abstract

Plasmodium vivax is the most geographically widespread malaria parasite. P. vivax has the ability to remain dormant (as a hypnozoite) in the human liver and subsequently reactivate, which makes control efforts more difficult. Given the majority of P. vivax infections are due to hypnozoite reactivation, targeting the hypnozoite reservoir with a radical cure is crucial for achieving P. vivax elimination. Stochastic effects can strongly influence dynamics when disease prevalence is low or when the population size is small. Hence, it is important to account for this when modelling malaria elimination. We use a stochastic multiscale model of P. vivax transmission to study the impacts of multiple rounds of mass drug administration (MDA) with a radical cure, accounting for superinfection and hypnozoite dynamics. Our results indicate multiple rounds of MDA with a high-efficacy drug are needed to achieve a substantial probability of elimination. This work has the potential to help guide P. vivax elimination strategies by quantifying elimination probabilities for an MDA approach. [ABSTRACT FROM AUTHOR]

Published
2024
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26. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Author

du Plessis, Louis, McCrone, John T., Zarebski, Alexander E., Hill, Verity, Ruis, Christopher, Gutierrez, Bernardo, Raghwani, Jayna, Ashworth, Jordan, Colquhoun, Rachel, Connor, Thomas R., Faria, Nuno R., Jackson, Ben, Loman, Nicholas J., O’Toole, Áine, Nicholls, Samuel M., Parag, Kris V., Scher, Emily, Vasylyeva, Tetyana I., Volz, Erik M., Watts, Alexander, Bogoch, Isaac I., Khan, Kamran, Aanensen, David M., Kraemer, Moritz U. G., Rambaut, Andrew, Pybus, Oliver G., COVID-19 Genomics UK (COG-UK) Consortium, Bashton, Matthew, Smith, Darren, Young, Greg, and Nelson, Andrew

Subjects
Lineage (genetic), Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Genome, Viral, Biology, Genome, Virus, law.invention, 03 medical and health sciences, 0302 clinical medicine, Communicable Diseases, Imported, Phylogenetics, law, Humans, 030212 general & internal medicine, Epidemics, Phylogeny, 030304 developmental biology, Chain of Infection, Travel, 0303 health sciences, Multidisciplinary, Phylogenetic tree, SARS-CoV-2, COVID-19, C700, United Kingdom, Transmission (mechanics), Evolutionary biology, Communicable Disease Control
Abstract

Lineage dynamics The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. The United Kingdom has contributed more than 26,000 sequences to this effort. This volume of data allowed du Plessis et al. to develop a detailed picture of the influxes of virus reaching U.K. shores as the pandemic developed during the first months of 2020 (see the Perspective by Nelson). Before lockdown, high travel volumes and few restrictions on international travel allowed more than 1000 lineages to become established. This accelerated local epidemic growth and exceeded contact tracing capacity. The authors were able to quantify the abundance, size distribution, and spatial range of the lineages that were transmitted. Transmission was highly heterogeneous, favoring some lineages that became widespread and subsequently harder to eliminate. This dire history indicates that rapid or even preemptive responses should have been used as they were elsewhere where containment was successful. Science , this issue p. 708 ; see also p. 680

Published
2021

27. Higher risk of death from COVID-19 in low-income and non-White populations of São Paulo, Brazil

Author

Li, Sabrina L, primary, Pereira, Rafael H M, additional, Prete Jr, Carlos A, additional, Zarebski, Alexander E, additional, Emanuel, Lucas, additional, Alves, Pedro J H, additional, Peixoto, Pedro S, additional, Braga, Carlos K V, additional, de Souza Santos, Andreza Aruska, additional, de Souza, William M, additional, Barbosa, Rogerio J, additional, Buss, Lewis F, additional, Mendrone, Alfredo, additional, de Almeida-Neto, Cesar, additional, Ferreira, Suzete C, additional, Salles, Nanci A, additional, Marcilio, Izabel, additional, Wu, Chieh-Hsi, additional, Gouveia, Nelson, additional, Nascimento, Vitor H, additional, Sabino, Ester C, additional, Faria, Nuno R, additional, and Messina, Jane P, additional

Published
2021
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28. Social and racial inequalities in COVID-19 risk of hospitalisation and death across São Paulo state, Brazil

Author

Li, Sabrina L, primary, Pereira, Rafael H M, additional, Prete, Carlos A, additional, Zarebski, Alexander E, additional, Emanuel, Lucas, additional, Alves, Pedro JH, additional, Peixoto, Pedro S, additional, Braga, Carlos KV, additional, de Souza Santos, Andreza A, additional, de Souza, William M, additional, Barbosa, Rogerio J, additional, Buss, Lewis F, additional, Mendrone, Alfredo, additional, de Almeida-Neto, Cesar, additional, Ferreira, Suzete C, additional, Salles, Nanci A, additional, Marcilio, Izabel, additional, Wu, Chieh-Hsi, additional, Gouveia, Nelson, additional, Nascimento, Vitor H, additional, Sabino, Ester C, additional, Faria, Nuno R, additional, and Messina, Jane P, additional

Published
2020
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30. Epidemiological and clinical characteristics of the early phase of the COVID-19 epidemic in Brazil

Author

de Souza, William Marciel, primary, Buss, Lewis Fletcher, additional, Candido, Darlan da Silva, additional, Carrera, Jean-Paul, additional, Li, Sabrina, additional, Zarebski, Alexander E., additional, Vincenti-Gonzalez, Maria F., additional, Messina, Janey, additional, Silva Sales, Flavia Cristina da, additional, Santos Andrade, Pamela dos, additional, Prete, Carlos A., additional, Nascimento, Vítor Heloiz, additional, Ghilardi, Fabio, additional, Moraes Pereira, Rafael Henrique, additional, Souza Santos, Andreza Aruska de, additional, Abade, Leandro, additional, Gutierrez, Bernardo, additional, Kraemer, Moritz U. G., additional, Aguiar, Renato Santana, additional, Alexander, Neal, additional, Mayaud, Philippe, additional, Brady, Oliver J., additional, de Souza, Izabel Oliva Marcilio, additional, Gouveia, Nelson, additional, Li, Guangdi, additional, Tami, Adriana, additional, de Oliveira, Silvano Barbosa, additional, Gomes Porto, Victor Bertollo, additional, Ganem, Fabiana, additional, de Almeida, Walquiria Aparecida Ferreira, additional, Tardetti Fantinato, Francieli Fontana Sutile, additional, Macário, Eduardo Marques, additional, de Oliveira, Wanderson Kleber, additional, Pybus, Oliver G., additional, Wu, Chieh-Hsi, additional, Croda, Julio, additional, Sabino, Ester C., additional, and Faria, Nuno Rodrigues, additional

Published
2020
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31. Methodology, Acknowledgments, Quantification of beads and lipids inside macrophages and Derivation and analysis of a coagulation-fragmentation model of substance accumulation in macrophages from Efferocytosis perpetuates substance accumulation inside macrophage populations

Author

Ford, Hugh Z., Zeboudj, Lynda, Purvis, Gareth S. D., Bokum, Annemieke Ten, Zarebski, Alexander E., Bull, Joshua A., Byrne, Helen M., Myerscough, Mary R., and Greaves, David R.

Abstract

Supplementary Material

Published
2019
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35. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

Author

Plessis, Louis du, McCrone, John T., Zarebski, Alexander E., Hill, Verity, Ruis, Christopher, Gutierrez, Bernardo, Raghwani, Jayna, Ashworth, Jordan, Colquhoun, Rachel, Connor, Thomas R., Faria, Nuno R., Jackson, Ben, Loman, Nicholas J., O’Toole, Áine, Nicholls, Samuel M., Parag, Kris V., Scher, Emily, Vasylyeva, Tetyana I., Volz, Erik M., and Watts, Alexander

Published
2021
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37. Context-specific emergence and growth of the SARS-CoV-2 Delta variant.

Author

McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, and Kraemer MUG

Abstract

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 genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Delta's nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Delta's invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.

Published
2021
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38. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

Author

du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, and Pybus OG

Subjects
COVID-19 prevention & control, COVID-19 transmission, Chain of Infection, Communicable Disease Control, Communicable Diseases, Imported epidemiology, Communicable Diseases, Imported virology, Epidemics, Humans, Phylogeny, Travel, United Kingdom epidemiology, COVID-19 epidemiology, COVID-19 virology, Genome, Viral, SARS-CoV-2 genetics
Abstract

The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Published
2021
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