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1. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Author

Faria, Nuno R, Mellan, Thomas A, Whittaker, Charles, Claro, Ingra M, Candido, Darlan da S, Mishra, Swapnil, Crispim, Myuki AE, Sales, Flavia CS, Hawryluk, Iwona, McCrone, John T, Hulswit, Ruben JG, Franco, Lucas AM, Ramundo, Mariana S, de Jesus, Jaqueline G, Andrade, Pamela S, Coletti, Thais M, Ferreira, Giulia M, Silva, Camila AM, Manuli, Erika R, Pereira, Rafael HM, Peixoto, Pedro S, Kraemer, Moritz UG, Gaburo, Nelson, Camilo, Cecilia da C, Hoeltgebaum, Henrique, Souza, William M, Rocha, Esmenia C, de Souza, Leandro M, de Pinho, Mariana C, Araujo, Leonardo JT, Malta, Frederico SV, de Lima, Aline B, Silva, Joice do P, Zauli, Danielle AG, Ferreira, Alessandro C de S, Schnekenberg, Ricardo P, Laydon, Daniel J, Walker, Patrick GT, Schlüter, Hannah M, Dos Santos, Ana LP, Vidal, Maria S, Del Caro, Valentina S, Filho, Rosinaldo MF, Dos Santos, Helem M, Aguiar, Renato S, Proença-Modena, José L, Nelson, Bruce, Hay, James A, Monod, Mélodie, Miscouridou, Xenia, Coupland, Helen, Sonabend, Raphael, Vollmer, Michaela, Gandy, Axel, Prete, Carlos A, Nascimento, Vitor H, Suchard, Marc A, Bowden, Thomas A, Pond, Sergei LK, Wu, Chieh-Hsi, Ratmann, Oliver, Ferguson, Neil M, Dye, Christopher, Loman, Nick J, Lemey, Philippe, Rambaut, Andrew, Fraiji, Nelson A, Carvalho, Maria do PSS, Pybus, Oliver G, Flaxman, Seth, Bhatt, Samir, and Sabino, Ester C

Subjects
Human Genome, Immunization, Pneumonia & Influenza, Lung, Prevention, Genetics, Vaccine Related, Biotechnology, Pneumonia, Emerging Infectious Diseases, Biodefense, Infectious Diseases, Infection, Good Health and Well Being, Angiotensin-Converting Enzyme 2, Brazil, COVID-19, Communicable Diseases, Emerging, Epidemiological Monitoring, Genome, Viral, Genomics, Humans, Models, Theoretical, Molecular Epidemiology, Mutation, Protein Binding, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Viral Load, General Science & Technology
Abstract

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

Published
2021

2. SAT-409 Whole-genome hepatitis B virus sequencing at low viral loads from serum and dried blood spot using a multiplexed tiled amplicon approach

Author

Lumley, Sheila, primary, Kent, Christopher, additional, Wilkinson, Samuel, additional, Morgan, Camille, additional, Waddilove, Elizabeth, additional, Delphin, Marion, additional, Airey, George, additional, Campbell, James, additional, De Lara, Catherine, additional, Martin, Jacqueline, additional, Ngimbi, Patrick, additional, Parr, Jonathan B., additional, Thompson, Peyton, additional, Barnes, Eleanor, additional, Ansari, Azim, additional, Loman, Nick, additional, Quick, Josh, additional, and Matthews, Philippa C, additional

Published
2024
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3. WED-469 Investigating household hepatitis B transmission using whole-genome sequencing and serological analysis in Kinshasa Province, Democratic Republic of Congo

Author

Morgan, Camille, primary, Ngimbi, Patrick, additional, Ntambua, Sarah, additional, Matondo, Jolie, additional, Mavinga, Jeansy, additional, Tukebana, Bienvenu, additional, Tabala, Martine, additional, Mbonze, Nana, additional, Kashamuka, Melchior, additional, James, Linda, additional, Anderson, Mark, additional, Cloherty, Gavin, additional, Hennelly, Chris, additional, Quick, Josh, additional, Loman, Nick, additional, Kent, Christopher, additional, Wilkinson, Samuel, additional, Waddilove, Elizabeth, additional, Delphin, Marion, additional, Airey, George, additional, Lumley, Sheila, additional, Matthews, Philippa C, additional, Yotebieng, Marcel, additional, Mampunza, Samuel, additional, Parr, Jonathan B., additional, and Thompson, Peyton, additional

Published
2024
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4. Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity

Author

Butera, Yvan, Mukantwari, Enatha, Artesi, Maria, Umuringa, Jeanne d’arc, O’Toole, Áine Niamh, Hill, Verity, Rooke, Stefan, Hong, Samuel Leandro, Dellicour, Simon, Majyambere, Onesphore, Bontems, Sebastien, Boujemla, Bouchra, Quick, Josh, Resende, Paola Cristina, Loman, Nick, Umumararungu, Esperance, Kabanda, Alice, Murindahabi, Marylin Milumbu, Tuyisenge, Patrick, Gashegu, Misbah, Rwabihama, Jean Paul, Sindayiheba, Reuben, Gikic, Djordje, Souopgui, Jacob, Ndifon, Wilfred, Rutayisire, Robert, Gatare, Swaibu, Mpunga, Tharcisse, Ngamije, Daniel, Bours, Vincent, Rambaut, Andrew, Nsanzimana, Sabin, Baele, Guy, Durkin, Keith, Mutesa, Leon, and Rujeni, Nadine

Published
2021
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5. Your letters.

Author

Eades, Alwyn, Hinwood, Jon, Edge, Sam, Pallen, Mark, Parker, Aimee, Loman, Nick, Walker, Alan, Stock, Bob, Bullimore, Blaise, Giles, Alan, Kvaalen, Eric, Glover, Bryn, Malzeard, Kirkby, and Fenton, James

Subjects
COMMON sense, ATOMIC nucleus, COOLING towers, EVAPORATIVE cooling, ELECTRIC charge
Abstract

The article from New Scientist features a collection of letters discussing various topics. These include the concept of common sense, the absence of a brain microbiome, the benefits of growing one's own produce, factors contributing to increased rainfall in cities, the need for clarity in physics terminology, potential solutions for keeping the International Space Station in orbit, speculation on the existence of black holes before the big bang, concerns about artificial food production, and a correction regarding a photo caption. The letters come from contributors in the US, Australia, the UK, and France, offering diverse perspectives on scientific and societal issues. [Extracted from the article]

Published
2024

6. Genomics-informed outbreak investigations of SARS-CoV-2 using civet

Author

O'Toole, Áine, Hill, Verity, Jackson, Ben, Dewar, Rebecca, Sahadeo, Nikita, Colquhoun, Rachel, Rooke, Stefan, McCrone, JT, Duggan, Kate, McHugh, Martin P, Nicholls, Samuel M, Poplawski, Radoslaw, COVID-19 Genomics UK (COG-UK) Consortium, COVID-19 Impact Project (Trinidad & Tobago Group), Aanensen, David, Holden, Matt, Connor, Tom, Loman, Nick, Goodfellow, Ian, Carrington, Christine VF, Templeton, Kate, Rambaut, Andrew, O'Toole, Áine [0000-0001-8083-474X], Jackson, Ben [0000-0002-9981-0649], Colquhoun, Rachel [0000-0002-5577-9897], McCrone, J T [0000-0002-9846-8917], Duggan, Kate [0000-0002-6709-4983], McHugh, Martin P [0000-0002-0370-3700], Nicholls, Samuel M [0000-0003-4081-065X], Poplawski, Radoslaw [0000-0002-9594-085X], Carrington, Christine V F [0000-0001-6533-9302], Apollo - University of Cambridge Repository, McCrone, JT [0000-0002-9846-8917], Carrington, Christine VF [0000-0001-6533-9302], University of St Andrews. School of Medicine, and University of St Andrews. Infection and Global Health Division

Subjects
MCC, SDG 3 - Good Health and Well-being, COVID-19 Genomics UK (COG-UK) Consortium, RA Public aspects of medicine, COVID-19, 3rd-DAS, COVID-19 Impact Project (Trinidad & Tobago Group), NIS, RA
Abstract

Funder: Trinidad and Tobago - UWI Research Development Impact Fund, The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.

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

Author

McCrone, John J.T., Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben B.C., Inward, Rhys, Bhatt, Samir, Volz, Erik, Ruis, Christopher, Dellicour, Simon, Baele, Guy, Zarebski, Alexander Eugene, Sadilek, Adam, Wu, Neo, Schneider, Aaron, Ji, Xiang, Raghwani, Jayna, Jackson, Ben, Colquhoun, Rachel, O’Toole, Áine Niamh, Peacock, Thomas T.P., Twohig, Kate, Thelwall, Simon, Dabrera, Gavin, Myers, Richard, Faria, Nuno Rodrigues, Huber, Carmen, Bogoch, Isaac Israel, Khan, Kamran, du Plessis, Louis, Barrett, Jeffrey Carl, Aanensen, David Michael, Barclay, Wendy W.S., Chand, Meera, Connor, Thomas, Loman, Nick, Suchard, Marc M.A., Pybus, Oliver George, Rambaut, Andrew, Kraemer, Moritz U G, McCrone, John J.T., Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben B.C., Inward, Rhys, Bhatt, Samir, Volz, Erik, Ruis, Christopher, Dellicour, Simon, Baele, Guy, Zarebski, Alexander Eugene, Sadilek, Adam, Wu, Neo, Schneider, Aaron, Ji, Xiang, Raghwani, Jayna, Jackson, Ben, Colquhoun, Rachel, O’Toole, Áine Niamh, Peacock, Thomas T.P., Twohig, Kate, Thelwall, Simon, Dabrera, Gavin, Myers, Richard, Faria, Nuno Rodrigues, Huber, Carmen, Bogoch, Isaac Israel, Khan, Kamran, du Plessis, Louis, Barrett, Jeffrey Carl, Aanensen, David Michael, Barclay, Wendy W.S., Chand, Meera, Connor, Thomas, Loman, Nick, Suchard, Marc M.A., Pybus, Oliver George, 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)., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2022

13. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Author

Faria, Nuno R., Mellan, Thomas A., Whittaker, Charles, Claro, Ingra M., Candido, Darlan da S., Mishra, Swapnil, Crispim, Myuki A. E., Sales, Flavia C., Hawryluk, Iwona, McCrone, John T., Hulswit, Ruben J. G., Franco, Lucas A. M., Ramundo, Mariana S., de Jesus, Jaqueline G., Andrade, Pamela S., Coletti, Thais M., Ferreira, Giulia M., Silva, Camila A. M., Manuli, Erika R., Pereira, Rafael H. M., Peixoto, Pedro S., Kraemer, Moritz U., Gaburo, Nelson, Camilo, Cecilia da C., Hoeltgebaum, Henrique, Souza, William M., Rocha, Esmenia C., de Souza, Leandro M., de Pinho, Mariana C., Araujo, Leonardo J. T., Malta, Frederico S., de Lima, Aline B., Silva, Joice do P., Zauli, Danielle A. G., Ferreira, Alessandro C. de S., Schnekenberg, Ricardo P., Laydon, Daniel J., Walker, Patrick G. T., Schlueter, Hannah M., dos Santos, Ana L. P., Vidal, Maria S., Del Caro, Valentina S., Filho, Rosinaldo M. F., dos Santos, Helem M., Aguiar, Renato S., Proenca-Modena, Jose L. P., Nelson, Bruce, Hay, James A., Monod, Melodie, Miscouridou, Xenia, Coupland, Helen, Sonabend, Raphael, Vollmer, Michaela, Gandy, Axel, Prete, Carlos A., Nascimento, Vitor H., Suchard, Marc A., Bowden, Thomas A., Pond, Sergei L. K., Wu, Chieh-Hsi, Ratmann, Oliver, Ferguson, Neil M., Dye, Christopher, Loman, Nick J., Lemey, Philippe, Rambaut, Andrew, Fraiji, Nelson A., Carvalho, Maria do P. S. S., Pybus, Oliver G., Flaxman, Seth, Bhatt, Samir, Sabino, Ester C., Faria, Nuno R., Mellan, Thomas A., Whittaker, Charles, Claro, Ingra M., Candido, Darlan da S., Mishra, Swapnil, Crispim, Myuki A. E., Sales, Flavia C., Hawryluk, Iwona, McCrone, John T., Hulswit, Ruben J. G., Franco, Lucas A. M., Ramundo, Mariana S., de Jesus, Jaqueline G., Andrade, Pamela S., Coletti, Thais M., Ferreira, Giulia M., Silva, Camila A. M., Manuli, Erika R., Pereira, Rafael H. M., Peixoto, Pedro S., Kraemer, Moritz U., Gaburo, Nelson, Camilo, Cecilia da C., Hoeltgebaum, Henrique, Souza, William M., Rocha, Esmenia C., de Souza, Leandro M., de Pinho, Mariana C., Araujo, Leonardo J. T., Malta, Frederico S., de Lima, Aline B., Silva, Joice do P., Zauli, Danielle A. G., Ferreira, Alessandro C. de S., Schnekenberg, Ricardo P., Laydon, Daniel J., Walker, Patrick G. T., Schlueter, Hannah M., dos Santos, Ana L. P., Vidal, Maria S., Del Caro, Valentina S., Filho, Rosinaldo M. F., dos Santos, Helem M., Aguiar, Renato S., Proenca-Modena, Jose L. P., Nelson, Bruce, Hay, James A., Monod, Melodie, Miscouridou, Xenia, Coupland, Helen, Sonabend, Raphael, Vollmer, Michaela, Gandy, Axel, Prete, Carlos A., Nascimento, Vitor H., Suchard, Marc A., Bowden, Thomas A., Pond, Sergei L. K., Wu, Chieh-Hsi, Ratmann, Oliver, Ferguson, Neil M., Dye, Christopher, Loman, Nick J., Lemey, Philippe, Rambaut, Andrew, Fraiji, Nelson A., Carvalho, Maria do P. S. S., Pybus, Oliver G., Flaxman, Seth, Bhatt, Samir, and Sabino, Ester C.

Abstract

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

Published
2021

14. Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Author

Kraemer, Moritz U G, Hill, Verity, Ruis, Christopher, Dellicour, Simon, Bajaj, Sumali, McCrone, John J.T., Baele, Guy, Parag, Kris K.V., Battle, Anya Lindström, Gutierrez, Bernardo, Jackson, Ben, Colquhoun, Rachel, O'Toole, Áine, Klein, Brennan, Vespignani, Alessandro, Volz, Erik, Faria, Nuno Rodrigues, Aanensen, David Michael, Loman, Nick, du Plessis, Louis, Cauchemez, Simon, Rambaut, Andrew, Scarpino, Samuel, Pybus, Oliver George, Kraemer, Moritz U G, Hill, Verity, Ruis, Christopher, Dellicour, Simon, Bajaj, Sumali, McCrone, John J.T., Baele, Guy, Parag, Kris K.V., Battle, Anya Lindström, Gutierrez, Bernardo, Jackson, Ben, Colquhoun, Rachel, O'Toole, Áine, Klein, Brennan, Vespignani, Alessandro, Volz, Erik, Faria, Nuno Rodrigues, Aanensen, David Michael, Loman, Nick, du Plessis, Louis, Cauchemez, Simon, Rambaut, Andrew, Scarpino, Samuel, and Pybus, Oliver George

Abstract

Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2021

16. Genomic Sequencing of SARS-CoV-2 in Rwanda: evolution and regional dynamics

Author

Butera, Yvan, primary, Mukantwari, Enatha, additional, Artesi, Maria, additional, D’Arc Umuringa, Jeanne, additional, O’Toole, Áine Niamh, additional, Hill, Verity, additional, Rooke, Stefan, additional, Hong, Samuel Leandro, additional, Dellicour, Simon, additional, Majyambere, Onesphore, additional, Bontems, Sebastien, additional, Boujemla, Bouchra, additional, Quick, Josh, additional, Resende, Paola Cristina, additional, Loman, Nick, additional, Umumararungu, Esperance, additional, Kabanda, Alice, additional, Murindahabi, Marylin Milumbu, additional, Tuyisenge, Patrick, additional, Gashegu, Misbah, additional, Rwabihama, Jean Paul, additional, Sindayiheba, Reuben, additional, Gikic, Djordje, additional, Souopgui, Jacob, additional, Ndifon, Wilfred, additional, Rutayisire, Robert, additional, Gatare, Swaibu, additional, Mpunga, Tharcisse, additional, Ngamije, Daniel, additional, Bours, Vincent, additional, Rambaut, Andrew, additional, Nsanzimana, Sabin, additional, Baele, Guy, additional, Durkin, Keith, additional, Mutesa, Leon, additional, and Rujeni, Nadine, additional

Published
2021
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17. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

Author

Faria, Nuno R., primary, Mellan, Thomas A., additional, Whittaker, Charles, additional, Claro, Ingra M., additional, Candido, Darlan da S., additional, Mishra, Swapnil, additional, Crispim, Myuki A. E., additional, Sales, Flavia C., additional, Hawryluk, Iwona, additional, McCrone, John T., additional, Hulswit, Ruben J. G., additional, Franco, Lucas A. M., additional, Ramundo, Mariana S., additional, de Jesus, Jaqueline G., additional, Andrade, Pamela S., additional, Coletti, Thais M., additional, Ferreira, Giulia M., additional, Silva, Camila A. M., additional, Manuli, Erika R., additional, Pereira, Rafael H. M., additional, Peixoto, Pedro S., additional, Kraemer, Moritz U., additional, Gaburo, Nelson, additional, Camilo, Cecilia da C., additional, Hoeltgebaum, Henrique, additional, Souza, William M., additional, Rocha, Esmenia C., additional, de Souza, Leandro M., additional, de Pinho, Mariana C., additional, Araujo, Leonardo J. T, additional, Malta, Frederico S. V., additional, de Lima, Aline B., additional, Silva, Joice do P., additional, Zauli, Danielle A. G., additional, Ferreira, Alessandro C. de S., additional, Schnekenberg, Ricardo P, additional, Laydon, Daniel J., additional, Walker, Patrick G. T., additional, Schlüter, Hannah M., additional, dos Santos, Ana L. P., additional, Vidal, Maria S., additional, Del Caro, Valentina S., additional, Filho, Rosinaldo M. F., additional, dos Santos, Helem M., additional, Aguiar, Renato S., additional, Modena, José L. P., additional, Nelson, Bruce, additional, Hay, James A., additional, Monod, Melodie, additional, Miscouridou, Xenia, additional, Coupland, Helen, additional, Sonabend, Raphael, additional, Vollmer, Michaela, additional, Gandy, Axel, additional, Suchard, Marc A., additional, Bowden, Thomas A., additional, Pond, Sergei L. K., additional, Wu, Chieh-Hsi, additional, Ratmann, Oliver, additional, Ferguson, Neil M., additional, Dye, Christopher, additional, Loman, Nick J., additional, Lemey, Philippe, additional, Rambaut, Andrew, additional, Fraiji, Nelson A., additional, Carvalho, Maria do P. S. S., additional, Pybus, Oliver G., additional, Flaxman, Seth, additional, Bhatt, Samir, additional, and Sabino, Ester C., additional

Published
2021
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18. Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

Author

Lauring, Adam S., Hill, Sarah C., de Souza, Renato, Thézé, Julien, Claro, Ingra, Aguiar, Renato S., Abade, Leandro, Santos, Fabiana C. P., Cunha, Mariana S., Nogueira, Juliana S., Salles, Flavia C. S., Rocco, Iray M., Maeda, Adriana Y., Vasami, Fernanda G. S., du Plessis, Louis, Silveira, Paola P., de Jesus, Jaqueline G., Quick, Joshua, Fernandes, Natália C. C. A., Guerra, Juliana M., Réssio, Rodrigo A., Giovanetti, Marta, Alcantara, Luiz C. J., Cirqueira, Cinthya S., Díaz-Delgado, Josué, Macedo, Fernando L. L., Timenetsky, Maria do Carmo S. T., de Paula, Regiane, Spinola, Roberta, Telles de Deus, Juliana, Mucci, Luís F., Tubaki, Rosa Maria, de Menezes, Regiane M. T., Ramos, Patrícia L., de Abreu, Andre L., Cruz, Laura N., Loman, Nick, Dellicour, Simon, Pybus, Oliver G., Sabino, Ester C., and Faria, Nuno R.

Subjects
parasitic diseases, geographic locations
Abstract

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.

Published
2020

19. Evolution and epidemic spread of SARS-CoV-2 in Brazil

Author

Candido, Darlan S, Claro, Ingra M, de Jesus, Jaqueline G, Souza, William M, Moreira, Filipe RR, Dellicour, Simon, Mellan, Thomas A, du Plessis, Louis, Pereira, Rafael HM, Sales, Flavia CS, Manuli, Erika R, Thézé, Julien, Almeida, Luiz, Menezes, Mariane T, Voloch, Carolina M, Fumagalli, Marcilio J, Coletti, Thaís M, da Silva, Camila AM, Ramundo, Mariana S, Amorim, Mariene R, Hoeltgebaum, Henrique H, Mishra, Swapnil, Gill, Mandev S, Carvalho, Luiz M, Buss, Lewis F, Prete, Carlos A, Ashworth, Jordan, Nakaya, Helder I, Peixoto, Pedro S, Brady, Oliver J, Nicholls, Samuel M, Tanuri, Amilcar, Rossi, Átila D, Braga, Carlos KV, Gerber, Alexandra L, de C Guimarães, Ana Paula, Gaburo, Nelson, Alencar, Cecila Salete, Ferreira, Alessandro CS, Lima, Cristiano X, Levi, José Eduardo, Granato, Celso, Ferreira, Giulia M, Francisco, Ronaldo S, Granja, Fabiana, Garcia, Marcia T, Moretti, Maria Luiza, Perroud, Mauricio W, Castiñeiras, Terezinha MPP, Lazari, Carolina S, Hill, Sarah C, de Souza Santos, Andreza Aruska, Simeoni, Camila L, Forato, Julia, Sposito, Andrei C, Schreiber, Angelica Z, Santos, Magnun NN, de Sá, Camila Zolini, Souza, Renan P, Resende-Moreira, Luciana C, Teixeira, Mauro M, Hubner, Josy, Leme, Patricia AF, Moreira, Rennan G, Nogueira, Maurício L, Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics an, Ferguson, Neil M, Costa, Silvia F, Proenca-Modena, José Luiz, Vasconcelos, Ana Tereza R, Bhatt, Samir, Lemey, Philippe, Wu, Chieh-Hsi, Rambaut, Andrew, Loman, Nick J, Aguiar, Renato S, Pybus, Oliver G, Sabino, Ester C, and Faria, Nuno Rodrigues

Abstract

Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.

Published
2020

20. Genomic surveillance of Yellow fever virus epizootic in São Paulo, Brazil, 2016-2018

Author

Hill, Sarah Catherine, de Souza, Renato, Thézé, Julien, Claro, Ingra Morales, Aguiar, Renato Santana, Abade, Leandro, Santos, Fabiana Cristina Pereira Dos F.C.P., Cunha, Mariana Sequetin, Nogueira, Juliana Silva, Salles, Flavia F.C.S., Rocco, Iray Maria, Maeda, Adriana Yurika, Vasami, Fernanda Gisele Silva, du Plessis, Louis, Silveira, Paola Paz, de Jesus, Jaqueline Goes, Quick, Joshua, Fernandes, Natália N.C.C.A., Guerra, Juliana Mariotti, Réssio, Rodrigo Albergaria, Giovanetti, Marta, Alcantara, Luiz Carlos L.C.J., Cirqueira, Cinthya Dos Santos C.S., Díaz-Delgado, Josué, Macedo, Fernando Luiz Lima, Timenetsky, Maria Do Carmo Sampaio Tavares Timenetsky M.d.C.S.T., de Paula, Regiane, Spinola, Roberta, Telles de Deus, Juliana, Mucci, Luís Filipe, Tubaki, Rosa Maria, de Menezes, Regiane María Tironi, Ramos, Patrícia Locosque, de Abreu, André Luiz, Cruz, Laura Nogueira, Loman, Nick, Dellicour, Simon, Pybus, Oliver George, Sabino, Ester Cerdeira, Faria, Nuno Rodrigues, Hill, Sarah Catherine, de Souza, Renato, Thézé, Julien, Claro, Ingra Morales, Aguiar, Renato Santana, Abade, Leandro, Santos, Fabiana Cristina Pereira Dos F.C.P., Cunha, Mariana Sequetin, Nogueira, Juliana Silva, Salles, Flavia F.C.S., Rocco, Iray Maria, Maeda, Adriana Yurika, Vasami, Fernanda Gisele Silva, du Plessis, Louis, Silveira, Paola Paz, de Jesus, Jaqueline Goes, Quick, Joshua, Fernandes, Natália N.C.C.A., Guerra, Juliana Mariotti, Réssio, Rodrigo Albergaria, Giovanetti, Marta, Alcantara, Luiz Carlos L.C.J., Cirqueira, Cinthya Dos Santos C.S., Díaz-Delgado, Josué, Macedo, Fernando Luiz Lima, Timenetsky, Maria Do Carmo Sampaio Tavares Timenetsky M.d.C.S.T., de Paula, Regiane, Spinola, Roberta, Telles de Deus, Juliana, Mucci, Luís Filipe, Tubaki, Rosa Maria, de Menezes, Regiane María Tironi, Ramos, Patrícia Locosque, de Abreu, André Luiz, Cruz, Laura Nogueira, Loman, Nick, Dellicour, Simon, Pybus, Oliver George, Sabino, Ester Cerdeira, and Faria, Nuno Rodrigues

Abstract

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2020

24. Successful treatment of COVID-19 with remdesivir in the absence of humoral immunity

Author

Buckland, Matthew S, primary, Galloway, James, additional, Fhogartaig, Caoimhe Nic, additional, Meredith, Luke, additional, Provine, Nicholas M., additional, Bloor, Stuart, additional, Ogbe, Ane, additional, Zelek, Wioleta M., additional, Smielewska, Anna, additional, Yakovleva, Anna, additional, Mann, Tiffeney, additional, Bergamaschi, Laura, additional, Turner, Lorinda, additional, Mescia, Frederica, additional, Toonen, Erik J.M., additional, Hackstein, Carl-Philipp, additional, Akther, Hossain Delowar, additional, Vieira, Vinicius Adriano, additional, Ceron-Gutierrez, Lourdes, additional, Periselneris, Jimstan, additional, Kiani-Alikhan, Sorena, additional, Grigoriadou, Sofia, additional, Vaghela, Devan, additional, Lear, Sara E., additional, Torok, Estee, additional, Hamilton, William L., additional, Quick, Josh, additional, Stockton, Joanne, additional, Nelson, Peter, additional, Hunter, Michael, additional, Coulter, Tanya I, additional, Devlin, Lisa, additional, Bradley, John, additional, Smith, Ken, additional, Ouwehand, Willem, additional, Estcourt, Lise, additional, Simmonds, Heli Harvala, additional, Roberts, Dave, additional, Wilkinson, Ian, additional, Screaton, Nick, additional, Loman, Nick, additional, Lyons, Paul, additional, Doffinger, Rainer, additional, Morgan, Paul, additional, Goodfellow, Ian, additional, Klenerman, Paul, additional, Lehner, Paul, additional, Matheson, Nick, additional, and Thaventhiran, James, additional

Published
2020
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25. Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2

Author

Liu, Zhe, primary, Zheng, Huanying, additional, Lin, Huifang, additional, Li, Mingyue, additional, Yuan, Runyu, additional, Peng, Jinju, additional, Xiong, Qianling, additional, Sun, Jiufeng, additional, Li, Baisheng, additional, Wu, Jie, additional, Yi, Lina, additional, Peng, Xiaofang, additional, Zhang, Huan, additional, Zhang, Wei, additional, Hulswit, Ruben J. G., additional, Loman, Nick, additional, Rambaut, Andrew, additional, Ke, Changwen, additional, Bowden, Thomas A., additional, Pybus, Oliver G., additional, and Lu, Jing, additional

Published
2020
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26. Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

Author

Hill, Sarah C., primary, de Souza, Renato, additional, Thézé, Julien, additional, Claro, Ingra, additional, Aguiar, Renato S., additional, Abade, Leandro, additional, Santos, Fabiana C. P., additional, Cunha, Mariana S., additional, Nogueira, Juliana S., additional, Salles, Flavia C. S., additional, Rocco, Iray M., additional, Maeda, Adriana Y., additional, Vasami, Fernanda G. S., additional, du Plessis, Louis, additional, Silveira, Paola P., additional, de Jesus, Jaqueline G., additional, Quick, Joshua, additional, Fernandes, Natália C. C. A., additional, Guerra, Juliana M., additional, Réssio, Rodrigo A., additional, Giovanetti, Marta, additional, Alcantara, Luiz C. J., additional, Cirqueira, Cinthya S., additional, Díaz-Delgado, Josué, additional, Macedo, Fernando L. L., additional, Timenetsky, Maria do Carmo S. T., additional, de Paula, Regiane, additional, Spinola, Roberta, additional, Telles de Deus, Juliana, additional, Mucci, Luís F., additional, Tubaki, Rosa Maria, additional, de Menezes, Regiane M. T., additional, Ramos, Patrícia L., additional, de Abreu, Andre L., additional, Cruz, Laura N., additional, Loman, Nick, additional, Dellicour, Simon, additional, Pybus, Oliver G., additional, Sabino, Ester C., additional, and Faria, Nuno R., additional

Published
2020
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27. Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

Author

Lu, Jing, primary, du Plessis, Louis, additional, Liu, Zhe, additional, Hill, Verity, additional, Kang, Min, additional, Lin, Huifang, additional, Sun, Jiufeng, additional, François, Sarah, additional, Kraemer, Moritz U.G., additional, Faria, Nuno R., additional, McCrone, John T., additional, Peng, Jinju, additional, Xiong, Qianling, additional, Yuan, Runyu, additional, Zeng, Lilian, additional, Zhou, Pingping, additional, Liang, Chumin, additional, Yi, Lina, additional, Liu, Jun, additional, Xiao, Jianpeng, additional, Hu, Jianxiong, additional, Liu, Tao, additional, Ma, Wenjun, additional, Li, Wei, additional, Su, Juan, additional, Zheng, Huanying, additional, Peng, Bo, additional, Fang, Shisong, additional, Su, Wenzhe, additional, Li, Kuibiao, additional, Sun, Ruilin, additional, Bai, Ru, additional, Tang, Xi, additional, Liang, Minfeng, additional, Quick, Josh, additional, Song, Tie, additional, Rambaut, Andrew, additional, Loman, Nick, additional, Raghwani, Jayna, additional, Pybus, Oliver G., additional, and Ke, Changwen, additional

Published
2020
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29. Identification of a common deletion in the spike protein of SARS-CoV-2

Author

Liu, Zhe, primary, Zheng, Huanying, additional, Yuan, Runyu, additional, Li, Mingyue, additional, Lin, Huifang, additional, Peng, Jingju, additional, Xiong, Qianlin, additional, Sun, Jiufeng, additional, Li, Baisheng, additional, Wu, Jie, additional, Hulswit, Ruben J.G., additional, Bowden, Thomas A., additional, Rambaut, Andrew, additional, Loman, Nick, additional, Pybus, Oliver G, additional, Ke, Changwen, additional, and Lu, Jing, additional

Published
2020
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30. Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019

Author

de Jesus, Jaqueline Goes, primary, Dutra, Karina Rocha, additional, Sales, Flavia Cristina da Silva, additional, Claro, Ingra Morales, additional, Terzian, Ana Carolina, additional, Candido, Darlan da Silva, additional, Hill, Sarah C, additional, Thézé, Julien, additional, Torres, Celeste, additional, D’Agostini, Tatiana Lang, additional, Felix, Alvina Clara, additional, Reis, Andreia F Negri, additional, Alcantara, Luiz Carlos Junior, additional, de Abreu, André L, additional, Croda, Júlio HR, additional, de Oliveira, Wanderson K, additional, de Filipis, Ana Maria Bispo, additional, Camis, Maria do Carmo Rodrigues dos Santos, additional, Romano, Camila Malta, additional, Loman, Nick J, additional, Pybus, Oliver G, additional, Sabino, Ester Cerdeira, additional, Nogueira, Mauricio L, additional, and Faria, Nuno Rodrigues, additional

Published
2020
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31. Early identification of dengue virus lineage replacement in Brazil using portable genomic surveillance

Author

de Jesus, Jaqueline Goes, primary, Dutra, Karina Rocha, additional, da Silva Salles, Flavia Cristina, additional, Claro, Ingra Morales, additional, Terzian, Ana Carolina, additional, da Silva Candido, Darlan, additional, Hill, Sarah C., additional, Thézé, Julien, additional, D’Agostini, Tatiana Lang, additional, Felix, Alvina Clara, additional, Negri Reis, Andreia F., additional, Alcantara, Luiz Carlos Junior, additional, Abreu, André L., additional, Croda, Júlio H. R., additional, de Oliveira, Wanderson K., additional, de Filipis, Ana Maria Bispo, additional, dos Santos Camis, Maria do Carmo Rodrigues, additional, Romano, Camila Malta, additional, Loman, Nick J., additional, Pybus, Oliver G., additional, Sabino, Ester Cerdeira, additional, Nogueira, Mauricio L., additional, and Faria, Nuno Rodrigues, additional

Published
2019
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34. The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically linked kindred

Author

Ijaz, Umer Zeeshan, Quince, Christopher, Hanske, Laura, Loman, Nick, Calus, Szymon T., Bertz, Martin, Edwards, Christine A., Gaya, Daniel R., Hansen, Richard, McGrogan, Paraic, Russell, Richard K., and Gerasimidis, Konstantinos

Abstract

Background/Aims:\ud \ud Studying the gut microbiota in unaffected relatives of people with Crohn’s disease (CD) may advance our understanding of the role of bacteria in disease aetiology.\ud Methods:\ud \ud Faecal microbiota composition (16S rRNA gene sequencing), genetic functional capacity (shotgun metagenomics) and faecal short chain fatty acids (SCFA) were compared in unaffected adult relatives of CD children (CDR, n = 17) and adult healthy controls, unrelated to CD patients (HUC, n = 14). The microbiota characteristics of 19 CD children were used as a benchmark of CD ‘dysbiosis’.\ud Results:\ud \ud The CDR microbiota was less diverse (p = 0.044) than that of the HUC group. Local contribution of β-diversity analysis showed no difference in community structure between the CDR and HUC groups. Twenty one of 1,243 (1.8%) operational taxonomic units discriminated CDR from HUC. The metagenomic functional capacity (p = 0.207) and SCFA concentration or pattern were similar between CDR and HUC (p>0.05 for all SCFA). None of the KEGG metabolic pathways were different between these two groups. Both of these groups (HUC and CDR) had a higher microbiota α-diversity (CDR, p = 0.026 and HUC, p

Published
2017

35. Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015

Author

Pini, Alessandro, primary, Zomahoun, Delayo, additional, Duraffour, Sophie, additional, Derrough, Tarik, additional, Charles, Myrna, additional, Quick, Joshua, additional, Loman, Nick, additional, Cowley, Lauren, additional, Leno, Mamadou, additional, Ouedraogo, Nobila, additional, Thiam, Oumou, additional, Hernández-Romieu, Alfonso, additional, Iko, Annie, additional, Keita, Halimatou, additional, Konate, Djiba, additional, Soumah, Aboubacar Aboubak, additional, Bouchouar, Etran, additional, Ileka-Priouzeau, Samuel, additional, Keita, Sakoba, additional, Diallo, Boubacar, additional, Cisse, Fode, additional, Jansa, Josep, additional, Carroll, Miles, additional, Günther, Stephan, additional, Severi, Ettore, additional, and Formenty, Pierre, additional

Published
2018
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36. ABPHM15 EtherPad Archive

Author

Gardy, Jennifer, Loman, Nick, Underwood, Anthony, Schaik, Willem Van, Connor, Tom, Seemann, Torsten, Lipsitch, Marc, Robinson, Esther, and Ashton, Phil

Abstract

An archived record of the EtherPad collaborative notes document from Applied Bioinformatics for Public Health Microbiology conference, held 6-8 May, 2015 at the Wellcome Trust Sanger Centre, Cambridge, UK. Live EtherPad at https://etherpad.mozilla.org/rxHOz9HvDr

Published
2015
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37. Extensive modulation of the fecal metagenome in children With Crohn’s disease during exclusive enteral nutrition

Author

Quince, Christopher, Ijaz, Umer Zeeshan, Loman, Nick, Eren, A. Murat, Saulnier, Delphine, Russell, Julie, Haig, Sarah J., Calus, Szymon T., Quick, Joshua, Barclay, Andrew H., Bertz, Martin, Blaut, Michael, Hansen, Richard, McGrogan, Paraic, Russell, Richard K., Edwards, Christine A., Gerasimidis, Konstantinos, Quince, Christopher, Ijaz, Umer Zeeshan, Loman, Nick, Eren, A. Murat, Saulnier, Delphine, Russell, Julie, Haig, Sarah J., Calus, Szymon T., Quick, Joshua, Barclay, Andrew H., Bertz, Martin, Blaut, Michael, Hansen, Richard, McGrogan, Paraic, Russell, Richard K., Edwards, Christine A., and Gerasimidis, Konstantinos

Abstract

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in American Journal of Gastroenterology 110 (2015): 1718–1729, doi:10.1038/ajg.2015.357., Exploring associations between the gut microbiota and colonic inflammation and assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into the microbial origins of Crohn’s disease (CD). Fecal samples (n=117) were collected from 23 CD and 21 healthy children. From CD children fecal samples were collected before, during EEN, and when patients returned to their habitual diets. Microbiota composition and functional capacity were characterized using sequencing of the 16S rRNA gene and shotgun metagenomics. Microbial diversity was lower in CD than controls before EEN (P=0.006); differences were observed in 36 genera, 141 operational taxonomic units (OTUs), and 44 oligotypes. During EEN, the microbial diversity of CD children further decreased, and the community structure became even more dissimilar than that of controls. Every 10 days on EEN, 0.6 genus diversity equivalents were lost; 34 genera decreased and one increased during EEN. Fecal calprotectin correlated with 35 OTUs, 14 of which accounted for 78% of its variation. OTUs that correlated positively or negatively with calprotectin decreased during EEN. The microbiota of CD patients had a broader functional capacity than healthy controls, but diversity decreased with EEN. Genes involved in membrane transport, sulfur reduction, and nutrient biosynthesis differed between patients and controls. The abundance of genes involved in biotin (P=0.005) and thiamine biosynthesis decreased (P=0.017), whereas those involved in spermidine/putrescine biosynthesis (P=0.031), or the shikimate pathway (P=0.058), increased during EEN. Disease improvement following treatment with EEN is associated with extensive modulation of the gut microbiome., The IBD team at Royal Hospital for Children, Glasgow, is supported by the Catherine McEwan Foundation and the Yorkhill IBD fund.

Published
2016

39. Voices of biotech

Author

Amit, Ido, primary, Baker, David, additional, Barker, Roger, additional, Berger, Bonnie, additional, Bertozzi, Carolyn, additional, Bhatia, Sangeeta, additional, Biffi, Alessandra, additional, Demichelis, Francesca, additional, Doudna, Jennifer, additional, Dowdy, Steven F, additional, Endy, Drew, additional, Helmstaedter, Moritz, additional, Junca, Howard, additional, June, Carl, additional, Kamb, Sasha, additional, Khvorova, Anastasia, additional, Kim, Dae-hyeong, additional, Kim, Jin-Soo, additional, Krishnan, Yamuna, additional, Lakadamyali, Melike, additional, Lappalainen, Tuuli, additional, Lewin, Sharon, additional, Liao, James, additional, Loman, Nick, additional, Lundberg, Emma, additional, Lynd, Lee, additional, Martin, Cathie, additional, Mellman, Ira, additional, Miyawaki, Atsushi, additional, Mummery, Christine, additional, Nelson, Karen, additional, Paz, Jeanne, additional, Peralta-Yahya, Pamela, additional, Picotti, Paola, additional, Polyak, Kornelia, additional, Prather, Kristala, additional, Qin, Jun, additional, Quake, Stephen, additional, Regev, Aviv, additional, Rogers, John A, additional, Shetty, Reshma, additional, Sommer, Morten, additional, Stevens, Molly, additional, Stolovitzky, Gustavo, additional, Takahashi, Masayo, additional, Tang, Fuchou, additional, Teichmann, Sarah, additional, Torres-Padilla, Maria-Elena, additional, Tripathi, Leena, additional, Vemula, Praveen, additional, Verdine, Greg, additional, Vollmer, Frank, additional, Wang, Jun, additional, Ying, Jackie Y, additional, Zhang, Feng, additional, and Zhang, Tian, additional

Published
2016
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40. Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition

Author

Quince, Christopher, primary, Ijaz, Umer Zeeshan, additional, Loman, Nick, additional, Eren, Murat A, additional, Saulnier, Delphine, additional, Russell, Julie, additional, Haig, Sarah J, additional, Calus, Szymon T, additional, Quick, Joshua, additional, Barclay, Andrew, additional, Bertz, Martin, additional, Blaut, Michael, additional, Hansen, Richard, additional, McGrogan, Paraic, additional, Russell, Richard K, additional, Edwards, Christine A, additional, and Gerasimidis, Konstantinos, additional

Published
2015
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42. Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015.

Author

Fini, Alessandro, Zomahoun, Delayo, Duraffour, Sophie, Derrough, Tarik, Charles, Myrna, Quick, Joshua, Loman, Nick, Cowley, Lauren, Leno, Mamadou, Ouedraogo, Nobila, Thiam, Oumou, Hernández-Romieu, Alfonso, Iko, Annie, Halimatou Keita, Konate, Djiba, Soumah, Aboubacar Aboubak, Bouchouar, Etran, Ileka-Friouzeau, Samuel, Keita, Sakoba, and Diallo, Boubacar

Published
2018
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44. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

Author

Freschi, Luca, primary, Jeukens, Julie, additional, Kukavica-Ibrulj, Irena, additional, Boyle, Brian, additional, Dupont, Marie-Josée, additional, Laroche, Jérôme, additional, Larose, Stéphane, additional, Maaroufi, Halim, additional, Fothergill, Joanne L., additional, Moore, Matthew, additional, Winsor, Geoffrey L., additional, Aaron, Shawn D., additional, Barbeau, Jean, additional, Bell, Scott C., additional, Burns, Jane L., additional, Camara, Miguel, additional, Cantin, André, additional, Charette, Steve J., additional, Dewar, Ken, additional, Déziel, Éric, additional, Grimwood, Keith, additional, Hancock, Robert E. W., additional, Harrison, Joe J., additional, Heeb, Stephan, additional, Jelsbak, Lars, additional, Jia, Baofeng, additional, Kenna, Dervla T., additional, Kidd, Timothy J., additional, Klockgether, Jens, additional, Lam, Joseph S., additional, Lamont, Iain L., additional, Lewenza, Shawn, additional, Loman, Nick, additional, Malouin, François, additional, Manos, Jim, additional, McArthur, Andrew G., additional, McKeown, Josie, additional, Milot, Julie, additional, Naghra, Hardeep, additional, Nguyen, Dao, additional, Pereira, Sheldon K., additional, Perron, Gabriel G., additional, Pirnay, Jean-Paul, additional, Rainey, Paul B., additional, Rousseau, Simon, additional, Santos, Pedro M., additional, Stephenson, Anne, additional, Taylor, Véronique, additional, Turton, Jane F., additional, Waglechner, Nicholas, additional, Williams, Paul, additional, Thrane, Sandra W., additional, Wright, Gerard D., additional, Brinkman, Fiona S. L., additional, Tucker, Nicholas P., additional, Tümmler, Burkhard, additional, Winstanley, Craig, additional, and Levesque, Roger C., additional

Published
2015
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47. Role of Faecalibacterium prausnitzii in Crohnʼs Disease

Author

Gerasimidis, Konstantinos, primary, Russell, Richard, additional, Hansen, Richard, additional, Quince, Christopher, additional, Loman, Nick, additional, Bertz, Martin, additional, Hanske, Laura, additional, Blaut, Michael, additional, McGrogan, Paraic, additional, and Edwards, Christine A., additional

Published
2014
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50. Extreme genetic fragility of the HIV-1 capsid

Author

Rihn, Suzannah, primary, Wilson, Sam, additional, Loman, Nick, additional, Alim, Mudathir, additional, Bakker, Saskia, additional, Bhella, David, additional, Rixon, Frazer, additional, and Bieniasz, Paul, additional

Published
2013
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