Browsing by author "Holmes, Edward C."
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Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Rambaut, Andrew; Holmes, Edward C.; O’Toole, Áine; Hill, Verity; McCrone, John T.; Ruis, Christopher; du Plessis, Louis; Pybus, Oliver G.Published 2021An Addendum to this paper has been published: https://doi.org/10.1038/s41564-021-00872-5.Article -
After the pandemic: perspectives on the future trajectory of COVID-19. [Review]
Telenti, Amalio; Arvin, Ann; Corey, Lawrence; Corti, Davide; Diamond, Michael S; Garcia-Sastre, Adolfo; Garry, Robert F; Holmes, Edward C.; Pang, Phil; Virgin, Herbert WPublished 2021There is a realistic expectation that the global effort in vaccination will bring the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic under control. Nonetheless, uncertainties remain about the type ...Article -
Assessment of Coronavirus Disease 2019 Intervention Strategies in the Nordic Countries Using Genomic Epidemiology
Duchene, Sebastian; Featherstone, Leo; Freiesleben de Blasio, Birgitte; Holmes, Edward C.; Bohlin, Jon; Pettersson, John H OPublished 2022We explored how the duration, size, and number of virus transmission clusters, defined as country-specific monophyletic groups in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) phylogenetic tree, differed ...Article -
Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology
Duchene, Sebastian; Featherstone, Leo; de Blasio, Birgitte Freiesleben; Holmes, Edward C.; Bohlin, Jon; Pettersson, John H.-O.Published 2021Abstract The Nordic countries, defined here as Norway, Sweden, Denmark, Finland and Iceland, are known for their comparable demographics and political systems. Since these countries implemented different COVID-19 intervention ...Preprint -
Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool
O'Toole, A'ine; Scher, Emily; Underwood, Anthony; Jackson, Ben; Hill, Verity; McCrone, John T; Colquhoun, Rachel; Ruis, Chris; Abu-Dahab, Khalil; Taylor, Ben; Yeats, Corin; Du Plessis, Louis; Maloney, Daniel; Medd, Nathan; Attwood, Stephen W; Aanensen, David M; Holmes, Edward C.; Pybus, Oliver G; Rambaut, AndrewPublished 2021The response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards the 'real-time' generation and ...Article -
Author Correction: A new coronavirus associated with human respiratory disease in China
Wu, Fan; Zhao, Su; Yu, Bin; Chen, Yan-Mei; Wang, Wen; Song, Zhi-Gang; Hu, Yi; Tao, Zhao-Wu; Tian, Jun-Hua; Pei, Yuan-Yuan; Yuan, Ming-Li; Zhang, Yu-Ling; Dai, Fa-Hui; Liu, Yi; Wang, Qi-Min; Zheng, Jiao-Jiao; Xu, Lin; Holmes, Edward C.; Zhang, Yong-ZhenPublished 2020Article -
Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain
Benfield, Camilla To; MacKenzie, Farrell; Ritzefeld, Markus; Mazzon, Michela; Weston, Stuart; Tate, Edward W; Teo, Boon Han; Smith, Sarah E; Kellam, Paul; Holmes, Edward C.; Marsh, MarkPublished 2020Host interferon-induced transmembrane proteins (IFITMs) are broad-spectrum antiviral restriction factors. Of these, IFITM3 potently inhibits viruses that enter cells through acidic endosomes, many of which are zoonotic and ...Article -
Bioinformatics resources for SARS-CoV-2 discovery and surveillance.
Hu, Tao; Li, Juan; Zhou, Hong; Li, Cixiu; Holmes, Edward C.; Shi, WeifengPublished 2021In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and readily available bioinformatics pipelines. In ...Article -
Blood molecular markers associated with COVID-19 immunopathology and multi?organ damage
Chen, Yan‐Mei; Zheng, Yuanting; Yu, Ying; Wang, Yunzhi; Huang, Qingxia; Qian, Feng; Sun, Lei; Song, Zhi‐Gang; Chen, Ziyin; Feng, Jinwen; An, Yanpeng; Yang, Jingcheng; Su, Zhenqiang; Sun, Shanyue; Dai, Fahui; Chen, Qinsheng; Lu, Qinwei; Li, Pengcheng; Ling, Yun; Yang, Zhong; Tang, Huiru; Shi, Leming; Jin, Li; Holmes, Edward C.; Ding, Chen; Zhu, Tong‐Yu; Zhang, Yong‐ZhenPublished 2020COVID-19 is characterised by dysregulated immune responses, metabolic dysfunction and adverse effects on the function of multiple organs. To understand host responses to COVID-19 pathophysiology, we combined transcriptomics, ...Article -
Co-infecting pathogens can contribute to inflammatory responses and severe symptoms in COVID-19
Chen, Liping; Shen, Lihan; Wu, Weichen; Guan, Wenda; Zhou, Jinchao; Luo, Gengyan; Chen, Qimin; Zhou, Hongxia; Deng, Zhenxuan; Chen, Yaoqing; Zhao, Wenjing; Jin, Wenxiang; Qiu, Minshan; Zheng, Qianwei; Wang, Yutao; Liu, Chen; Bai, Xiangxiang; Guo, Deyin; Holmes, Edward C.; Zhong, Nanshan; Shi, Mang; Yang, ZifengPublished 2022Background: The current COVID-19 pandemic is posing a major challenge to public health on a global scale. While it is generally believed that severe COVID-19 results from over-expression of inflammatory mediators (i.e., a ...Article -
Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance
Rockett, Rebecca J.; Draper, Jenny; Gall, Mailie; Sim, Eby M.; Arnott, Alicia; Agius, Jessica E.; Johnson-Mackinnon, Jessica; Fong, Winkie; Martinez, Elena; Drew, Alexander P.; Lee, Clement; Ngo, Christine; Ramsperger, Marc; Ginn, Andrew N.; Wang, Qinning; Fennell, Michael; Ko, Danny; Hueston, Linda; Kairaitis, Lukas; Holmes, Edward C.; O’Sullivan, Matthew N.; Chen, Sharon C.-A.; Kok, Jen; Dwyer, Dominic E.; Sintchenko, VitaliPublished 2022Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their ...Article -
Co-infection with SARS-COV-2 Omicron and Delta Variants Revealed by Genomic Surveillance
Rockett, Rebecca J; Draper, Jenny; Gall, Mailie; Sim, Eby M; Arnott, Alicia; Agius, Jessica E; Johnson-Mackinnon, Jessica; Martinez, Elena; Drew, Alexander P; Lee, Clement; Ngo, Christine; Ramsperger, Marc; Ginn, Andrew N; Wang, Qinning; Fennell, Michael; Ko, Danny; Huston, Linda; Kairaitis, Lukas; Holmes, Edward C.; O'Sullivan, Matthew N; Chen, Sharon C-A; Kok, Jen; Dwyer, Dominic E; Sintchenko, VitaliPublished 2022We identified the co-infection of the SARS-CoV-2 Omicron and Delta variants in two epidemiologically unrelated patients with chronic kidney disease requiring haemodialysis. Both SARS-CoV-2 variants were co-circulating ...Preprint -
Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China
Wu, Fan; Zhao, Su; Yu, Bin; Chen, Yan-Mei; Wang, Wen; Hu, Yi; Song, Zhi-Gang; Tao, Zhao-Wu; Tian, Jun-Hua; Pei, Yuan-Yuan; Yuan, Ming-Li; Zhang, Yu-Ling; Dai, Fa-Hui; Liu, Yi; Wang, Qi-Min; Zheng, Jiao-Jiao; Xu, Lin; Holmes, Edward C.; Zhang, Yong-ZhenPublished 2020Emerging and re-emerging infectious diseases, such as SARS, MERS, Zika and highly pathogenic influenza present a major threat to public health1–3. Despite intense research effort, how, when and where novel diseases appear ...Preprint -
COVID-19 - lessons for zoonotic disease
Holmes, Edward C.Published 2022Disease emergence is driven by human-animal contact in a global viral ecosystem.Article -
COVID-19 Futures: A Framework for Exploring Medium and Long-Term Impacts
Bedford, Juliet; Berglof, Erik; Buckee, Caroline; Farrar, Jeremy; Grenfell, Bryan; Holmes, Edward C.; Metcalf, C. Jessica E.; Sridhar, Devi; Thompson, BethPublished 2020Background: Considering the possible trajectories of the COVID-19 pandemic is important to inform both short- and long-term responses and to prepare for pandemics of the future. We describe a framework to explore four ...Preprint -
Dengue Virus in Sub-tropical Northern and Central Viet Nam: Population Immunity and Climate Shape Patterns of Viral Invasion and Maintenance
Rabaa, Maia A.; Simmons, Cameron P.; Fox, Annette; Le, Mai Quynh; Nguyen, Thuy Thi Thu; Le, Hai Yen; Gibbons, Robert V.; Holmes, Edward C.; Aaskov, John G.Published 2013-12-05Dengue virus transmission occurs in both epidemic and endemic cycles across tropical and sub-tropical regions of the world. Incidence is particularly high in much of Southeast Asia, where hyperendemic transmission plagues ...Open AccessArticle -
Diversity and circulation of Jingmen tick virus in ticks and mammals
Guo, Jing-Jing; Lin, Xian-Dan; Chen, Yan-Mei; Hao, Zong-Yu; Wang, Zhao-Xiao; Yu, Zhu-Mei; Lu, Miao; Li, Kun; Qin, Xin-Cheng; Wang, Wen; Holmes, Edward C.; Hou, Wei; Zhang, Yong-ZhenPublished 2020Since its initial identification in ticks in 2010, Jingmen tick virus (JMTV) has been described in cattle, rodents and primates. To better understand the diversity, evolution and transmission of JMTV, we sampled 215 ticks, ...Article -
Diversity and evolution of the animal virome
Harvey, Erin; Holmes, Edward C.Published 2022The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other ...Article -
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Rambaut, Andrew; Holmes, Edward C.; O’Toole, Áine; Hill, Verity; McCrone, John T.; Ruis, Christopher; du Plessis, Louis; Pybus, Oliver G.Published 2020The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of ...Article -
A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology
Rambaut, Andrew; Holmes, Edward C.; Hill, Verity; OToole, Aine; McCrone, John; Ruis, Chris; du Plessis, Louis; Pybus, OliverPublished 2020The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, associated with severe pneumonia disease (COVID-19), has resulted in the generation of thousands of virus genome sequences. The rate of genome generation ...Preprint
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