Edward C Holmes

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2023
Publications (10 Years): 177

Top Venues

University of Sydney

University of Cambridge (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Sydney Oct 1o 2012

Australia

Professor :: School of Biological Sciences and Sydney Medical School

Education History

University of Cambridge

United Kingdom

PHD :: Department of Zoology

Publications

Katherine Eaton, Leo Featherstone, Sebastián Duchêne, Ann G Carmichael, Nükhet Varlık, G Brian Golding, Edward C Holmes, Hendrik N Poinar
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis. Communications biology 6 (1) (2023)
Katherine Eaton, Leo Featherstone, Sebastián Duchêne, Ann G Carmichael, Nükhet Varlık, G Brian Golding, Edward C Holmes, Hendrik N Poinar
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis. Communications biology 6 (1) (2023)
Rachel L Tulloch, Karan Kim, Chisha T Sikazwe, Alice Michie, Rebecca Burrell, Edward C Holmes, Dominic E Dwyer, Philip N Britton, Jen Kok, John-Sebastian Eden
RAPID prep : A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples. Viruses 15 (4) (2023)
Brian R Wasik, Evin Rothschild, Ian E H Voorhees, Stephanie E Reedy, Pablo Ramiro Murcia, Nicola Pusterla, Thomas M Chambers, Laura B Goodman, Edward C Holmes, James C Kile, Colin R Parrish
Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus evolution 9 (2) (2023)
Rebecca K French, Sandra H Anderson, Kristal E Cain, Terry C Greene, Maria Minor, Colin M Miskelly, José M Montoya, Michelle Wille, Chris G Muller, Michael W Taylor, Andrew Digby, null null, Edward C Holmes
Host phylogeny shapes viral transmission networks in an island ecosystem. Nature ecology & evolution (2023)
Vincenzo A Costa, David R Bellwood, Jonathon C O Mifsud, Kate Van Brussel, Jemma L Geoghegan, Edward C Holmes, Erin Harvey
Limited cross-species virus transmission in a spatially restricted coral reef fish community. Virus evolution 9 (1) (2023)
Alexander Crits-Christoph, Joshua I Levy, Jonathan E Pekar, Stephen A Goldstein, Reema Singh, Zach Hensel, Karthik Gangavarapu, Matthew B Rogers, Niema Moshiri, Robert F Garry, Edward C Holmes, Marion P G Koopmans, Philippe Lemey, Saskia V Popescu, Andrew Rambaut, David L Robertson, Marc A Suchard, Joel O Wertheim, Angela L Rasmussen, Kristian G Andersen, Michael Worobey, Florence Débarre
Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. bioRxiv : the preprint server for biology (2023)
Mary E Petrone, Edward C Holmes, Erin Harvey
Through an ecological lens: An ecosystem-based approach to zoonotic risk assessment: An ecosystem-based approach to zoonotic risk assessment. EMBO reports 24 (2) (2023)
Katherine Eaton, Leo Featherstone, Sebastián Duchêne, Ann G Carmichael, Nükhet Varlık, G Brian Golding, Edward C Holmes, Hendrik N Poinar
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis. Communications biology 6 (1) (2023)
Mary E Petrone, Edward C Holmes, Erin Harvey
Through an ecological lens: An ecosystem-based approach to zoonotic risk assessment: An ecosystem-based approach to zoonotic risk assessment. EMBO reports (2023)
Mary E Petrone, Edward C Holmes, Erin Harvey
Through an ecological lens: An ecosystem-based approach to zoonotic risk assessment: An ecosystem-based approach to zoonotic risk assessment. EMBO reports 24 (2) (2023)
Robert A López-Astacio, Oluwafemi F Adu, Daniel J Goetschius, Hyunwook Lee, Wendy S Weichert, Brian R Wasik, Simon P Frueh, Brynn K Alford, Ian E H Voorhees, Joseph F Flint, Sarah Saddoris, Laura B Goodman, Edward C Holmes, Susan L Hafenstein, Colin R Parrish
Viral Capsid, Antibody, and Receptor Interactions: Experimental Analysis of the Antibody Escape Evolution of Canine Parvovirus. Journal of virology (2023)
Michelle Wille, Simeon Lisovski, David Roshier, Marta Ferenczi, Bethany J Hoye, Trent Leen, Simone Warner, Ron A M Fouchier, Aeron C Hurt, Edward C Holmes, Marcel Klaassen
Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proceedings. Biological sciences 290 (1991) (2023)
Wan-Ting He, Dongyan Li, Guy Baele, Jin Zhao, Zhiwen Jiang, Xiang Ji, Michael Veit, Marc A Suchard, Edward C Holmes, Philippe Lemey, Maciej F Boni, Shuo Su
Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype. Virus evolution 9 (2) (2023)
Mary E Petrone, Edward C Holmes, Erin Harvey
Through an ecological lens: An ecosystem-based approach to zoonotic risk assessment: An ecosystem-based approach to zoonotic risk assessment. EMBO reports 24 (2) (2023)
Erin Harvey, Jonathon C O Mifsud, Edward C Holmes, Jackie E Mahar
Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids). Virus evolution 9 (2) (2023)
Mary E Petrone, Edward C Holmes, Erin Harvey
Through an ecological lens: An ecosystem-based approach to zoonotic risk assessment: An ecosystem-based approach to zoonotic risk assessment. EMBO reports 24 (2) (2023)
Rachel L Tulloch, Karan Kim, Chisha T Sikazwe, Alice Michie, Rebecca Burrell, Edward C Holmes, Dominic E Dwyer, Philip N Britton, Jen Kok, John-Sebastian Eden
RAPID prep : A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples. Viruses 15 (4) (2023)
Jing Wang, Yuan-Fei Pan, Li-Fen Yang, Wei-Hong Yang, Kexin Lv, Chu-Ming Luo, Juan Wang, Guo-Peng Kuang, Wei-Chen Wu, Qin-Yu Gou, Gen-Yang Xin, Bo Li, Huan-le Luo, Shoudeng Chen, Yue-Long Shu, Deyin Guo, Zi-Hou Gao, Guodong Liang, Jun Li, Yao-Qing Chen, Edward C Holmes, Yun Feng, Mang Shi
Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nature communications 14 (1) (2023)
Michelle Wille, Simeon Lisovski, David Roshier, Marta Ferenczi, Bethany J Hoye, Trent Leen, Simone Warner, Ron A M Fouchier, Aeron C Hurt, Edward C Holmes, Marcel Klaassen
Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proceedings. Biological sciences 290 (1991) (2023)
Callum Le Lay, Joshua N Hamm, Timothy J Williams, Mang Shi, Ricardo Cavicchioli, Edward C Holmes
Viral community composition of hypersaline lakes. Virus evolution 9 (2) (2023)
Rachel L Tulloch, Karan Kim, Chisha T Sikazwe, Alice Michie, Rebecca Burrell, Edward C Holmes, Dominic E Dwyer, Philip N Britton, Jen Kok, John-Sebastian Eden
RAPID prep : A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples. Viruses 15 (4) (2023)
Vincenzo A Costa, David R Bellwood, Jonathon C O Mifsud, Kate Van Brussel, Jemma L Geoghegan, Edward C Holmes, Erin Harvey
Limited cross-species virus transmission in a spatially restricted coral reef fish community. Virus evolution 9 (1) (2023)
Michelle Wille, Simeon Lisovski, David Roshier, Marta Ferenczi, Bethany J Hoye, Trent Leen, Simone Warner, Ron A M Fouchier, Aeron C Hurt, Edward C Holmes, Marcel Klaassen
Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proceedings. Biological sciences 290 (1991) (2023)
Katherine Eaton, Leo Featherstone, Sebastián Duchêne, Ann G Carmichael, Nükhet Varlık, G Brian Golding, Edward C Holmes, Hendrik N Poinar
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis. Communications biology 6 (1) (2023)
Marta Giovanetti, Francesco Pinotti, Camila Zanluca, Vagner Fonseca, Taishi Nakase, Andrea Cristine Koishi, Marcel Tscha, Guilherme Soares, Gisiane Gruber Dorl, Antônio Ernesto M L Marques, Renato Sousa, Talita Émile Ribeiro Adelino, Joilson Xavier, Carla Oliveira, Sandro Patroca, Natalia Rocha Guimaraes, Hegger Fritsch, Maria Angélica Monteiro de Mello Mares-Guia, Flavia Levy, Pedro Henrique Passos, Vinicius Leme da Silva, Luiz Augusto Pereira, Ana Flávia Mendonça, Isabel Luana de Macêdo, Davi Emanuel Ribeiro de Sousa, Gabriela Rodrigues de Toledo Costa, Marcio Botelho de Castro, Miguel de Souza Andrade, Filipe Vieira Santos de Abreu, Fabrício Souza Campos, Felipe Campos de Melo Iani, Maira Alves Pereira, Karina Ribeiro Leite Jardim Cavalcante, André Ricardo Ribas Freitas, Carlos Frederico Campelo de Albuquerque E Melo, Eduardo Marques Macário, Marlei Pickler Debiasi Dos Anjos, Rosane Campanher Ramos, Aline Alves Scarpellini Campos, Adriano Pinter, Marcia Chame, Livia Abdalla, Irina Nastassja Riediger, Sérvio Pontes Ribeiro, Ana I Bento, Tulio de Oliveira, Carla Freitas, Noely Fabiana Oliveira de Moura, Allison Fabri, Cintia Damasceno Dos Santos Rodrigues, Carolina Cardoso Dos Santos, Marco Antonio Barreto de Almeida, Edmilson Dos Santos, Jáder da Cruz Cardoso, Douglas Adriano Augusto, Eduardo Krempser, Luis Filipe Mucci, Renata Rispoli Gatti, Sabrina Fernandes Cardoso, João Augusto Brancher Fuck, Maria Goretti David Lopes, Ivana Lucia Belmonte, Gabriela Mayoral Pedroso da Silva, Maiane Regina Ferreira Soares, Marilia de Melo Santos de Castilhos, Joseana Cardoso de Souza E Silva, Alceu Bisetto Junior, Emanuelle Gemin Pouzato, Laurina Setsuko Tanabe, Daniele Akemi Arita, Ricardo Matsuo, Josiane Dos Santos Raymundo, Paula Cristina Linder Silva, Ana Santana Araújo Ferreira Silva, Sandro Patroca da Silva, Glauco Carvalho, Rodrigo Guerino Stabeli, Wildo Navegantes, Luciano Andrade Moreira, Alvaro Gil A Ferreira, Guilherme Garcia Pinheiro, Bruno Tardelli Diniz Nunes, Daniele Barbosa de Almeida Medeiros, Ana Cecília Ribeiro Cruz, Rivaldo Venâncio da Cunha, Wesley C Van Voorhis, Ana Maria Bispo de Filippis, Maria Almiron, Edward C Holmes, Daniel Garkauskas Ramos, Alessandro Pecego Martins Romano, Paul S Wikramaratna, Luiz Carlos Junior Alcantara, Claudia N Duarte Dos Santos
Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil. Science advances 9 (35) (2023)
Michelle Wille, Simeon Lisovski, David Roshier, Marta Ferenczi, Bethany J Hoye, Trent Leen, Simone Warner, Ron A M Fouchier, Aeron C Hurt, Edward C Holmes, Marcel Klaassen
Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proceedings. Biological sciences 290 (1991) (2023)
Mary E Petrone, Rhys Parry, Jonathon C O Mifsud, Kate Van Brussel, Ian Vorhees, Zoe T Richards, Edward C Holmes
Evidence for an ancient aquatic origin of the RNA viral order Articulavirales . Proceedings of the National Academy of Sciences of the United States of America 120 (45) (2023)
Robert A López-Astacio, Oluwafemi F Adu, Daniel J Goetschius, Hyunwook Lee, Wendy S Weichert, Brian R Wasik, Simon P Frueh, Brynn K Alford, Ian E H Voorhees, Joseph F Flint, Sarah Saddoris, Laura B Goodman, Edward C Holmes, Susan L Hafenstein, Colin R Parrish
Viral capsid, antibody, and receptor interactions: experimental analysis of the antibody escape evolution of canine parvovirus. bioRxiv : the preprint server for biology (2023)
Michelle Wille, Simeon Lisovski, David Roshier, Marta Ferenczi, Bethany J Hoye, Trent Leen, Simone Warner, Ron A M Fouchier, Aeron C Hurt, Edward C Holmes, Marcel Klaassen
Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proceedings. Biological sciences 290 (1991) (2023)
Peiwen Chen, Ziying Jin, Liuxia Peng, Zuoyi Zheng, Yiu-Man Cheung, Jing Guan, Liming Chen, Yiteng Huang, Xiaohui Fan, Zengfeng Zhang, Dongmei Shi, Jin Xie, Rirong Chen, Boheng Xiao, Chun Hung Yip, David K Smith, Wenshan Hong, Yongmei Liu, Lifeng Li, Jia Wang, Edward C Holmes, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan
Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health. Journal of virology (2023)
Cixiu Li, Shuqi Liu, Hong Zhou, Wei Zhu, Mingxue Cui, Juan Li, Jiao Wang, Jiangyun Liu, Jin Zhu, Weiping Li, Yuhai Bi, Michael J Carr, Edward C Holmes, Wei-Feng Shi
Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome. Microbiology spectrum (2023)
Rachel L Tulloch, Karan Kim, Chisha T Sikazwe, Alice Michie, Rebecca Burrell, Edward C Holmes, Dominic E Dwyer, Philip N Britton, Jen Kok, John-Sebastian Eden
RAPID prep : A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples. Viruses 15 (4) (2023)
Mary E Petrone, Carolina Lucas, Bridget Menasche, Mallery I Breban, Inci Yildirim, Melissa Campbell, Saad B Omer, Edward C Holmes, Albert I Ko, Nathan D Grubaugh, Akiko Iwasaki, Craig B Wilen, Chantal B F Vogels, Joseph R Fauver
Non-systematic reporting biases of the SARS-CoV-2 variant Mu could impact our understanding of the epidemiological dynamics of emerging variants. Genome biology and evolution (2023)
Katherine Eaton, Leo Featherstone, Sebastián Duchêne, Ann G Carmichael, Nükhet Varlık, G Brian Golding, Edward C Holmes, Hendrik N Poinar
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis. Communications biology 6 (1) (2023)
Michelle Wille, Simeon Lisovski, David Roshier, Marta Ferenczi, Bethany J Hoye, Trent Leen, Simone Warner, Ron A M Fouchier, Aeron C Hurt, Edward C Holmes, Marcel Klaassen
Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proceedings. Biological sciences 290 (1991) (2023)
Justine Charon, Jan P Buchmann, Sabrina Sadiq, Edward C Holmes
RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data. Virus evolution 8 (2) (2022)
Soufien Sghaier, Corinne Sailleau, Maurilia Marcacci, Sarah Thabet, Valentina Curini, Thameur Ben Hassine, Liana Teodori, Ottavio Portanti, Salah Hammami, Lucija Jurisic, Spedicato Massimo, Lydie Postic, Ines Gazani, Raja Ben Osman, Stephan Zientara, Emmanuel Bréard, Paolo Calistri, Juergen A Richt, Edward C Holmes, Giovanni Savini, Francesca Di Giallonardo, Alessio Lorusso
Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses 15 (1) (2022)
Justine Charon, Tim Kahlke, Michaela E Larsson, Raffaela Abbriano, Audrey Commault, Joel Burke, Peter Ralph, Edward C Holmes
Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures. Journal of virology 96 (20) (2022)
Soufien Sghaier, Corinne Sailleau, Maurilia Marcacci, Sarah Thabet, Valentina Curini, Thameur Ben Hassine, Liana Teodori, Ottavio Portanti, Salah Hammami, Lucija Jurisic, Spedicato Massimo, Lydie Postic, Ines Gazani, Raja Ben Osman, Stephan Zientara, Emmanuel Bréard, Paolo Calistri, Juergen A Richt, Edward C Holmes, Giovanni Savini, Francesca Di Giallonardo, Alessio Lorusso
Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses 15 (1) (2022)
Yan-Mei Chen, Sabrina Sadiq, Jun-Hua Tian, Xiao Chen, Xian-Dan Lin, Jin-Jin Shen, Hao Chen, Zong-Yu Hao, Michelle Wille, Zhuo-Cheng Zhou, Jun Wu, Feng Li, Hong-Wei Wang, Wei-Di Yang, Qi-Yi Xu, Wen Wang, Wen-Hua Gao, Edward C Holmes, Yong-Zhen Zhang
RNA viromes from terrestrial sites across China expand environmental viral diversity. Nature microbiology 7 (8) (2022)
Sabrina Sadiq, Yan-Mei Chen, Yong-Zhen Zhang, Edward C Holmes
Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota . Virus evolution 8 (1) (2022)
Benjamin J Perry, Mitra Mohamadi Darestani, Motia Gulshan Ara, Amélie Hoste, Jennifer M Jandt, Ludovic Dutoit, Edward C Holmes, Travis Ingram, Jemma L Geoghegan
Viromes of Freshwater Fish with Lacustrine and Diadromous Life Histories Differ in Composition. Viruses 14 (2) (2022)
Jonathon C O Mifsud, Vincenzo A Costa, Mary E Petrone, Ezequiel M Marzinelli, Edward C Holmes, Erin Harvey
Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus evolution 9 (1) (2022)
Soufien Sghaier, Corinne Sailleau, Maurilia Marcacci, Sarah Thabet, Valentina Curini, Thameur Ben Hassine, Liana Teodori, Ottavio Portanti, Salah Hammami, Lucija Jurisic, Spedicato Massimo, Lydie Postic, Ines Gazani, Raja Ben Osman, Stephan Zientara, Emmanuel Bréard, Paolo Calistri, Juergen A Richt, Edward C Holmes, Giovanni Savini, Francesca Di Giallonardo, Alessio Lorusso
Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses 15 (1) (2022)
Michael Worobey, Joshua I Levy, Lorena Mariana Malpica Serrano, Alexander Crits-Christoph, Jonathan E Pekar, Stephen A Goldstein, Angela L Rasmussen, Moritz U G Kraemer, Chris Newman, Marion P G Koopmans, Marc A Suchard, Joel O Wertheim, Philippe Lemey, David L Robertson, Robert F Garry, Edward C Holmes, Andrew Rambaut, Kristian G Andersen
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science (New York, N.Y.) 377 (6609) (2022)
Peter J Kerr, Isabella M Cattadori, Derek Sim, June Liu, Edward C Holmes, Andrew F Read
Divergent Evolutionary Pathways of Myxoma Virus in Australia: Virulence Phenotypes in Susceptible and Partially Resistant Rabbits Indicate Possible Selection for Transmissibility. Journal of virology 96 (20) (2022)
Justine Charon, Jan P Buchmann, Sabrina Sadiq, Edward C Holmes
RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data. Virus evolution 8 (2) (2022)
Soufien Sghaier, Corinne Sailleau, Maurilia Marcacci, Sarah Thabet, Valentina Curini, Thameur Ben Hassine, Liana Teodori, Ottavio Portanti, Salah Hammami, Lucija Jurisic, Spedicato Massimo, Lydie Postic, Ines Gazani, Raja Ben Osman, Stephan Zientara, Emmanuel Bréard, Paolo Calistri, Juergen A Richt, Edward C Holmes, Giovanni Savini, Francesca Di Giallonardo, Alessio Lorusso
Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses 15 (1) (2022)
Rebecca J Rockett, Jenny Draper, Mailie Gall, Eby M Sim, Alicia Arnott, Jessica E Agius, Jessica Johnson-Mackinnon, Winkie Fong, Elena Martinez, Alexander P Drew, Clement Lee, Christine Ngo, Marc Ramsperger, Andrew N Ginn, Qinning Wang, Michael Fennell, Danny Ko, Linda Hueston, Lukas Kairaitis, Edward C Holmes, Matthew V N O'Sullivan, Sharon C-A Chen, Jen Kok, Dominic E Dwyer, Vitali Sintchenko
Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance. Nature communications 13 (1) (2022)
Marta Giovanetti, Svetoslav Nanev Slavov, Vagner Fonseca, Eduan Wilkinson, Houriiyah Tegally, José Salvatore Leister Patané, Vincent Louis Viala, James Emmanuel San, Evandra Strazza Rodrigues, Elaine Vieira Santos, Flávia Figueira Aburjaile, Joilson Xavier, Hegger Fritsch, Talita Émile Ribeiro Adelino, Felicidade Pereira, Arabela Leal, Felipe Campos de Melo Iani, Glauco de Carvalho Pereira, Cynthia Vazquez, Gladys Mercedes Estigarribia Sanabria, Elaine Cristina de Oliveira, Luiz Henrique Ferraz Demarchi, Julio Henrique Rosa Croda, Rafael Dos Santos Bezerra, Loyze Paola Oliveira de Lima, Antonio Jorge Martins, Claudia Renata Dos Santos Barros, Elaine Cristina Marqueze, Jardelina de Souza Todao Bernardino, Debora Botequio Moretti, Ricardo Augusto Brassaloti, Raquel de Lello Rocha Campos Cassano, Pilar Drummond Sampaio Corrêa Mariani, João Paulo Kitajima, Bibiana Santos, Rodrigo Proto-Siqueira, Vlademir Vicente Cantarelli, Stephane Tosta, Vanessa Brandão Nardy, Luciana Reboredo de Oliveira da Silva, Marcela Kelly Astete Gómez, Jaqueline Gomes Lima, Adriana Aparecida Ribeiro, Natália Rocha Guimarães, Luiz Takao Watanabe, Luana Barbosa Da Silva, Raquel da Silva Ferreira, Mara Patricia F da Penha, María José Ortega, Andrea Gómez de la Fuente, Shirley Villalba, Juan Torales, María Liz Gamarra, Carolina Aquino, Gloria Patricia Martínez Figueredo, Wellington Santos Fava, Ana Rita C Motta-Castro, James Venturini, Sandra Maria do Vale Leone de Oliveira, Crhistinne Cavalheiro Maymone Gonçalves, Maria do Carmo Debur Rossa, Guilherme Nardi Becker, Mayra Presibella Giacomini, Nelson Quallio Marques, Irina Nastassja Riediger, Sonia Maria Raboni, Gabriela Mattoso, Allan D Cataneo, Camila Zanluca, Claudia N Duarte Dos Santos, Patricia Akemi Assato, Felipe Allan da Silva da Costa, Mirele Daiana Poleti, Jessika Cristina Chagas Lesbon, Elisangela Chicaroni Mattos, Cecilia Artico Banho, Lívia Sacchetto, Marília Mazzi Moraes, Rejane Maria Tommasini Grotto, Jayme A Souza-Neto, Mauricio Lacerda Nogueira, Heidge Fukumasu, Luiz Lehmann Coutinho, Rodrigo Tocantins Calado, Raul Machado Neto, Ana Maria Bispo de Filippis, Rivaldo Venancio da Cunha, Carla Freitas, Cassio Roberto Leonel Peterka, Cássia de Fátima Rangel Fernandes, Wildo Navegantes de Araújo, Rodrigo Fabiano do Carmo Said, Carlos Frederico Campelo de Albuquerque E Melo, Maria Almiron, Paul S Wikramaratna, Tulio de Oliveira, Edward C Holmes, Ricardo Haddad, Sandra Coccuzzo Sampaio, Maria Carolina Elias, Simone Kashima, Luiz Carlos Junior Alcantara, Dimas Tadeu Covas
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nature microbiology 7 (9) (2022)
Xiuwan Wang, Maura Carrai, Kate Van Brussel, Shuo Feng, Edward C Holmes, Mang Shi, Edward C Holmes, Jun Li, Vanessa R D Barrs
Low Intrahost and Interhost Genetic Diversity of Carnivore Protoparvovirus 1 in Domestic Cats during a Feline Panleukopenia Outbreak. Viruses 14 (7) (2022)
Erin Harvey, Edward C Holmes
Diversity and evolution of the animal virome. Nature reviews. Microbiology 20 (6) (2022)
Jonathan E Pekar, Andrew F Magee, Edyth Parker, Niema Moshiri, Katherine Izhikevich, Jennifer L Havens, Karthik Gangavarapu, Lorena Mariana Malpica Serrano, Alexander Crits-Christoph, Nathaniel L Matteson, Mark Zeller, Joshua I Levy, Jade C Wang, Scott Hughes, Jungmin Lee, Heedo Park, Man-Seong Park, Katherine Ching Zi Yan, Raymond Tzer Pin Lin, Mohd Noor Mat Isa, Yusuf Muhammad Noor, Tetyana I Vasylyeva, Robert F Garry, Edward C Holmes, Andrew Rambaut, Marc A Suchard, Kristian G Andersen, Michael Worobey, Joel O Wertheim
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science (New York, N.Y.) 377 (6609) (2022)
Jonathon C O Mifsud, Rachael V Gallagher, Edward C Holmes, Jemma L Geoghegan
Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom. Journal of virology (2022)
John-Sebastian Eden, Chisha Sikazwe, Ruopeng Xie, Yi-Mo Deng, Sheena G Sullivan, Alice Michie, Avram Levy, Elena Cutmore, Christopher C Blyth, Philip N Britton, Nigel Crawford, Xiaomin Dong, Dominic E Dwyer, Kimberly M Edwards, Bethany A Horsburgh, David Anthony Foley, Karina Kennedy, Cara Minney-Smith, David Speers, Rachel L Tulloch, Edward C Holmes, Vijaykrishna Dhanasekaran, David W Smith, Jen Kok, Ian G Barr, null null
Off-season RSV epidemics in Australia after easing of COVID-19 restrictions. Nature communications 13 (1) (2022)
Jonathon C O Mifsud, Vincenzo A Costa, Mary E Petrone, Ezequiel M Marzinelli, Edward C Holmes, Erin Harvey
Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus evolution 9 (1) (2022)
Rebecca K French, Zoë L Stone, Kevin A Parker, Edward C Holmes
Novel viral and microbial species in a translocated Toutouwai (Petroica longipes) population from Aotearoa/New Zealand. One health outlook 4 (1) (2022)
Soufien Sghaier, Corinne Sailleau, Maurilia Marcacci, Sarah Thabet, Valentina Curini, Thameur Ben Hassine, Liana Teodori, Ottavio Portanti, Salah Hammami, Lucija Jurisic, Spedicato Massimo, Lydie Postic, Ines Gazani, Raja Ben Osman, Stephan Zientara, Emmanuel Bréard, Paolo Calistri, Juergen A Richt, Edward C Holmes, Giovanni Savini, Francesca Di Giallonardo, Alessio Lorusso
Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses 15 (1) (2022)
Mang Shi, Su Zhao, Bin Yu, Wei-Chen Wu, Yi Hu, Jun-Hua Tian, Wen Yin, Fang Ni, Hong-Ling Hu, Shuang Geng, Li Tan, Ying Peng, Zhi-Gang Song, Wen Wang, Yan-Mei Chen, Edward C Holmes, Yong-Zhen Zhang
Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China. PLoS pathogens 18 (2) (2022)
Vincenzo A Costa, Jemma L Geoghegan, Edward C Holmes, Erin Harvey
Genetic Reassortment between Endemic and Introduced Macrobrachium rosenbergii Nodaviruses in the Murray-Darling Basin, Australia. Viruses 14 (10) (2022)
Yun Feng, Qin-Yu Gou, Wei-Hong Yang, Wei-Chen Wu, Juan Wang, Edward C Holmes, Guodong Liang, Mang Shi
A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes. Virus evolution 8 (1) (2022)
Rebecca K French, Antoine Filion, Chris N Niebuhr, Edward C Holmes
Metatranscriptomic Comparison of Viromes in Endemic and Introduced Passerines in New Zealand. Viruses 14 (7) (2022)
Allison K Miller, Jonathon C O Mifsud, Vincenzo A Costa, Rebecca M Grimwood, Jane Kitson, Cindy Baker, Cara L Brosnahan, Anjali Pande, Edward C Holmes, Neil J Gemmell, Jemma L Geoghegan
Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae. Virus evolution 7 (2) (2021)
Matteo Bordicchia, Tulio Machado Fumian, Kate Van Brussel, Alice G Russo, Maura Carrai, Shi-Jia Le, Patricia A Pesavento, Edward C Holmes, Vito Martella, Peter A White, Edward C Holmes, Mang Shi, Vanessa R D Barrs
Feline Calicivirus Virulent Systemic Disease: Clinical Epidemiology, Analysis of Viral Isolates and In Vitro Efficacy of Novel Antivirals in Australian Outbreaks. Viruses 13 (10) (2021)
Chadi M Saad-Roy, Sinead E Morris, Charlotte Jessica E Metcalf, Michael Joseph Mina, Rachel E Baker, Jeremy J Farrar, Edward C Holmes, Oliver George Pybus, Andrea L Graham, Simon Asher Levin, Bryan T Grenfell, Caroline E Wagner
Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes. Science (New York, N.Y.) 372 (6540) (2021)
Frank Konings, Mark D Perkins, Jens H Kuhn, Mark J Pallen, Erik J Alm, Brett N Archer, Amal Barakat, Trevor Bedford, Jinal N Bhiman, Leon Caly, Lisa L Carter, Anne Cullinane, Tulio de Oliveira, Julian Druce, Ihab El Masry, Roger Evans, George F Gao, Alexander E Gorbalenya, Esther Hamblion, Belinda L Herring, Emma Hodcroft, Edward C Holmes, Manish Kakkar, Shagun Khare, Marion P G Koopmans, Bette Korber, Juliana Leite, Duncan MacCannell, Marco Marklewitz, Sebastian Maurer-Stroh, Jairo Andres Mendez Rico, Vincent J Munster, Richard A Neher, Bas Oude Munnink, Boris I Pavlin, Joseph S Malik Peiris, Leo L M Poon, Oliver George Pybus, Andrew Rambaut, Paola Cristina Resende Silva, Lorenzo Subissi, Volker Thiel, Suxiang Tong, Sylvie van der Werf, Anne von Gottberg, John Ziebuhr, Maria D Van Kerkhove
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nature microbiology 6 (7) (2021)
Edward C Holmes, Aeron C Hurt, Zuzana Dobbie, Barry Clinch, John S Oxford, Pedro A Piedra
Understanding the Impact of Resistance to Influenza Antivirals. Clinical microbiology reviews 34 (2) (2021)
Vincenzo A Costa, Jonathon C O Mifsud, Dean Gilligan, Jane E Williamson, Edward C Holmes, Jemma L Geoghegan
Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia. Virus evolution 7 (1) (2021)
Jemma L Geoghegan, Francesca Di Giallonardo, Michelle Wille, Ayda Susana Ortiz-Baez, Vincenzo A Costa, Timothy M Ghaly, Jonathon C O Mifsud, Olivia M H Turnbull, David R Bellwood, Jane E Williamson, Edward C Holmes
Virome composition in marine fish revealed by meta-transcriptomics. Virus evolution 7 (1) (2021)
Francesca Di Giallonardo, Ilaria Puglia, Valentina Curini, Cesare Camma, Iolanda Mangone, Paolo Calistri, Joanna C A Cobbin, Edward C Holmes, Alessio Lorusso
Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy. Viruses 13 (5) (2021)
Ashleigh F Porter, Joanna Cobbin, Ci-Xiu Li, John-Sebastian Eden, Edward C Holmes
Metagenomic Identification of Viral Sequences in Laboratory Reagents. Viruses 13 (11) (2021)
Michelle Wille, Jemma L Geoghegan, Edward C Holmes
How accurately can we assess zoonotic risk? PLoS biology 19 (4) (2021)
Rebecca M Grimwood, Edward C Holmes, Jemma L Geoghegan
A Novel Rubi-Like Virus in the Pacific Electric Ray (Tetronarce californica) Reveals the Complex Evolutionary History of the Matonaviridae. Viruses 13 (4) (2021)
Karen N Barnard, Brian R Wasik, Brynn K Alford, Jessica J Hayward, Wendy S Weichert, Ian E H Voorhees, Edward C Holmes, Colin R Parrish
Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors. Journal of evolutionary biology (2021)
Áine Niamh O'Toole, Emily Scher, Anthony Underwood, Benjamin C Jackson, Verity Hill, John T McCrone, Rachel Colquhoun, Chris Ruis, Khalil Abu-Dahab, Ben Taylor, Corin Yeats, Louis du Plessis, Daniel Maloney, Nathan C Medd, Stephen W Attwood, David M Aanensen, Edward C Holmes, Oliver George Pybus, Andrew Rambaut
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus evolution 7 (2) (2021)
Amalio Telenti, Ann M Arvin, Lawrence Corey, Davide Corti, Michael S. Diamond, Adolfo García-Sastre, Robert F Garry, Edward C Holmes, Phillip S Pang, Herbert W Virgin
After the pandemic: perspectives on the future trajectory of COVID-19. Nature 596 (7873) (2021)
Andrew Rambaut, Edward C Holmes, Áine Niamh O'Toole, Verity Hill, John T McCrone, Christopher Ruis, Louis du Plessis, Oliver George Pybus
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature microbiology 6 (3) (2021)
Caroline E Wagner, Chadi M Saad-Roy, Sinead E Morris, Rachel E Baker, Michael Joseph Mina, Jeremy J Farrar, Edward C Holmes, Oliver George Pybus, Andrea L Graham, Ezekiel J Emanuel, Simon Asher Levin, Charlotte Jessica E Metcalf, Bryan T Grenfell
Vaccine nationalism and the dynamics and control of SARS-CoV-2. Science (New York, N.Y.) 373 (6562) (2021)
Talita Émile Ribeiro Adelino, Marta Giovanetti, Vagner Fonseca, Joilson Xavier, Álvaro Salgado de Abreu, Valdinete Alves do Nascimento, Luiz Henrique Ferraz Demarchi, Marluce Aparecida Assunção Oliveira, Vinícius Lemes da Silva, Arabela Leal E Silva de Mello, Gabriel Muricy Cunha, Roselene Hans Santos, Elaine Cristina de Oliveira, Jorge Antônio Chamon Júnior, Felipe Campos de Melo Iani, Ana Maria Bispo de Filippis, André Luiz de Abreu, Ronaldo de Jesus, Carlos Frederico Campelo de Albuquerque, Jairo Mendez Rico, Rodrigo Fabiano do Carmo Said, Joscélio Aguiar Silva, Noely Fabiana Oliveira de Moura, Priscila Leite, Livia Carla Vinhal Frutuoso, Simone Kashima Haddad, Alexander Martínez, Fernanda Khouri Barreto, Cynthia Carolina Vazquez, Rivaldo Venâncio da Cunha, Emerson Luiz Lima Araújo, Stephane Fraga de Oliveira Tosta, Allison de Araújo Fabri, Flávia Löwen Levy Chalhoub, Poliana da Silva Lemos, Fernanda de Bruycker-Nogueira, Gislene Garcia de Castro Lichs, Marina Castilhos Souza Umaki Zardin, Fátima María Cardozo Segovia, Crhistinne Cavalheiro Maymone Gonçalves, Zoraida Del Carmen Fernandez Grillo, Svetoslav Nanev Slavov, Luiz Augusto Pereira, Ana Flávia Mendonça, Felicidade Mota Pereira, Jurandy Júnior Ferraz de Magalhães, Agenor de Castro Moreira Dos Santos Júnior, Maricélia Maia de Lima, Rita Maria Ribeiro Nogueira, Aristóteles Góes-Neto, Vasco Ariston de Carvalho Azevedo, Dario Brock Ramalho, Wanderson Kleber de Oliveira, Eduardo Marques Macario, Arnaldo Correia de Medeiros, Victor Pimentel, null null, Edward C Holmes, Tulio de Oliveira, Paul S Wikramaratna, Luiz Carlos Junior Alcantara
Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil. Nature communications 12 (1) (2021)
Jackie E Mahar, Maria Jenckel, Nina Huang, Elena Smertina, Edward C Holmes, Tanja Strive, Robyn N Hall
Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses. Virus evolution 7 (2) (2021)
Michelle Wille, Erin Harvey, Mang Shi, Daniel Gonzalez-Acuña, Edward C Holmes, Aeron C Hurt
Sustained RNA virome diversity in Antarctic penguins and their ticks. The ISME journal 14 (7) (2020)
Timothy E Schlub, Edward C Holmes
Properties and abundance of overlapping genes in viruses. Virus evolution 6 (1) (2020)
Callum Le Lay, Mang Shi, Aleš Buček, Thomas Bourguignon, Nathan Lo, Edward C Holmes
Unmapped RNA Virus Diversity in Termites and their Symbionts. Viruses 12 (10) (2020)
Jana Batovska, Jan P Buchmann, Edward C Holmes, Stacey E Lynch
Coding-Complete Genome Sequence of Yada Yada Virus, a Novel Alphavirus Detected in Australian Mosquitoes. Microbiology resource announcements 9 (2) (2020)
Wei-Shan Chang, Ci-Xiu Li, Jane Hall, John-Sebastian Eden, Timothy H Hyndman, Edward C Holmes, Karrie Rose
Meta-Transcriptomic Discovery of a Divergent Circovirus and a Chaphamaparvovirus in Captive Reptiles with Proliferative Respiratory Syndrome. Viruses 12 (10) (2020)
Leo L M Poon, Timothy Song, David E Wentworth, Edward C Holmes, Benjamin D Greenbaum, Joseph S M Peiris, Benjamin John Cowling, Elodie Ghedin
Reply to 'Reconciling disparate estimates of viral genetic diversity during human influenza infections'. Nature genetics 51 (9) (2020)
Jing-Jing Guo, Xian-Dan Lin, Yan-Mei Chen, Zong-Yu Hao, Zhao-Xiao Wang, Zhu-Mei Yu, Miao Lu, Kun Li, Xin-Cheng Qin, Wen Wang, Edward C Holmes, Wei Hou, Yong-Zhen Zhang
Diversity and circulation of Jingmen tick virus in ticks and mammals. Virus evolution 6 (2) (2020)
Jackie E Mahar, Mang Shi, Robyn N Hall, Tanja Strive, Edward C Holmes
Comparative Analysis of RNA Virome Composition in Rabbits and Associated Ectoparasites. Journal of virology 94 (11) (2020)
Ci-Xiu Li, Wei Li, Jun Zhou, Bing Zhang, Yan Feng, Chang-Ping Xu, Yi-Yu Lu, Edward C Holmes, Mang Shi
High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection. Scientific reports 10 (1) (2020)
Mohammad Alfelali, Elizabeth A Haworth, Osamah Barasheed, Al-Mamoon Badahdah, Hamid Bokhary, Mohamed Tashani, Mohammad I Azeem, Jen Kok, Janette Taylor, Elizabeth H Barnes, Haitham El Bashir, Gulam Khandaker, Edward C Holmes, Dominic E Dwyer, Leon G Heron, Godwin J Wilson, Robert Booy, Harunor Rashid, null null
Facemask against viral respiratory infections among Hajj pilgrims: A challenging cluster-randomized trial. PloS one 15 (10) (2020)
Nathan D Grubaugh, Mary E Petrone, Edward C Holmes
We shouldn't worry when a virus mutates during disease outbreaks. Nature microbiology 5 (4) (2020)
Rebecca J Rockett, Alicia Arnott, Connie Lam, Rosemarie Sadsad, Verlaine J Timms, Karen-Ann Gray, John-Sebastian Eden, Sheryl Le Chang, Mailie L Gall, Jenny L Draper, Eby M Sim, Nathan L Bachmann, Ian Carter, Kerri Basile, Roy Byun, Matthew V N O'Sullivan, Sharon C-A Chen, Susan Maddocks, Tania C Sorrell, Dominic E Dwyer, Edward C Holmes, Jen Kok, Mikhail Prokopenko, Vitali Sintchenko
Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nature medicine 26 (9) (2020)
Wen-Hua Gao, Xian-Dan Lin, Yan-Mei Chen, Chun-Gang Xie, Zhi-Zhou Tan, Jia-Jun Zhou, Shuai Chen, Edward C Holmes, Yong-Zhen Zhang
Newly identified viral genomes in pangolins with fatal disease. Virus evolution 6 (1) (2020)
Wen Wang, Xian-Dan Lin, Hai-Lin Zhang, Miao-Ruo Wang, Xiao-Qing Guan, Edward C Holmes, Yong-Zhen Zhang
Extensive genetic diversity and host range of rodent-borne coronaviruses. Virus evolution 6 (2) (2020)
Kristian G Andersen, Andrew Rambaut, W Ian Lipkin, Edward C Holmes, Robert F Garry
The proximal origin of SARS-CoV-2. Nature medicine 26 (4) (2020)
Rhys Parry, Michelle Wille, Olivia M H Turnbull, Jemma L Geoghegan, Edward C Holmes
Divergent Influenza-Like Viruses of Amphibians and Fish Support an Ancient Evolutionary Association. Viruses 12 (9) (2020)
Francesca Di Giallonardo, Sebastián Duchêne, Ilaria Puglia, Valentina Curini, Francesca Profeta, Cesare Camma, Maurilia Marcacci, Paolo Calistri, Edward C Holmes, Alessio Lorusso
Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy. Viruses 12 (12) (2020)
Jemma L Geoghegan, Xiaoyun Ren, Matthew Storey, James Hadfield, Lauren Jelley, Sarah Jefferies, Jill Sherwood, Shevaun Paine, Q Sue Huang, Jordan Douglas, Fábio K Mendes, Andrew A Sporle, Michael G Baker, David R Murdoch, Nigel P French, Colin R Simpson, David Welch, Alexei J Drummond, Edward C Holmes, Sebastián Duchêne, Joep de Ligt
Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nature communications 11 (1) (2020)
Olivia M H Turnbull, Ayda Susana Ortiz-Baez, John-Sebastian Eden, Mang Shi, Jane E Williamson, Troy F Gaston, Yong-Zhen Zhang, Edward C Holmes, Jemma L Geoghegan
Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish. Viruses 12 (11) (2020)

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Edward C Holmes