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2,671 results on '"Holmes, Edward C."'

1. Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity

Author

Pan, Yuan-Fei, Zhao, Hailong, Gou, Qin-Yu, Shi, Pei-Bo, Tian, Jun-Hua, Feng, Yun, Li, Kun, Yang, Wei-Hong, Wu, De, Tang, Guangpeng, Zhang, Bing, Ren, Zirui, Peng, Shiqin, Luo, Geng-Yan, Le, Shi-Jia, Xin, Gen-Yang, Wang, Jing, Hou, Xin, Peng, Min-Wu, Kong, Jian-Bin, Chen, Xin-Xin, Yang, Chun-Hui, Mei, Shi-Qiang, Liao, Yu-Qi, Cheng, Jing-Xia, Wang, Juan, Chaolemen, Wu, Yu-Hui, Wang, Jian-Bo, An, Tongqing, Huang, Xinyi, Eden, John-Sebastian, Li, Jun, Guo, Deyin, Liang, Guodong, Jin, Xin, Holmes, Edward C., Li, Bo, Wang, Daxi, Li, Junhua, Wu, Wei-Chen, and Shi, Mang

Published
2024
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4. Rapid Epidemic Expansion of Chikungunya Virus East/Central/ South African Lineage, Paraguay

Author

Giovanetti, Marta, Vazquez, Cynthia, Lima, Mauricio, Castro, Emerson, Rojas, Analia, de la Fuente, Andrea Gomez, Aquino, Carolina, Cantero, Cesar, Fleitas, Fatima, Torales, Juan, Barrios, Julio, Ortega, Maria J., Gamarra, Maria L., Villalba, Shirley, Alfonzo, Tania, Xavier, Joilson, Adelino, Talita, Fritsch, Hegger, Iani, Felipe C.M., Pereira, Glauco C., de Oliveira, Carla, Schuab, Gabriel, Rodrigues, Evandra S., Kashima, Simone, Leite, Juliana, Gresh, Lionel, Franco, Leticia, Tegally, Houriiyah, Van Voorhis, Wesley C., Lessels, Richard, de Filippis, Ana Maria Bispo, Ojeda, Andrea, Sequera, Guillermo, Montoya, Romeo, Holmes, Edward C., de Oliveira, Tulio, Rico, Jairo M., Lourenco, Jose, Fonseca, Vagner, and Alcantara, Luiz C.J.

Subjects
Infants (Newborn) -- Diseases, Health, Pan American Health Organization
Abstract

Chikungunya is a mosquitoborne disease caused by the chikungunya virus (CHIKV), a single-stranded positive-sense RNA virus belonging to the family Togaviridae (1), which is transmitted to humans through the bite [...]

Published
2023
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11. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic

Author

Worobey, Michael, Levy, Joshua I, Serrano, Lorena Malpica, Crits-Christoph, Alexander, Pekar, Jonathan E, Goldstein, Stephen A, Rasmussen, Angela L, Kraemer, Moritz UG, Newman, Chris, Koopmans, Marion PG, Suchard, Marc A, Wertheim, Joel O, Lemey, Philippe, Robertson, David L, Garry, Robert F, Holmes, Edward C, Rambaut, Andrew, and Andersen, Kristian G

Subjects
Prevention, Emerging Infectious Diseases, Biodefense, Vaccine Related, Lung, Good Health and Well Being, Animals, COVID-19, China, Humans, Pandemics, SARS-CoV-2, Seafood, Viral Zoonoses, General Science & Technology
Abstract

Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2-susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.

Published
2022

12. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

Author

Pekar, Jonathan E, Magee, Andrew, Parker, Edyth, Moshiri, Niema, Izhikevich, Katherine, Havens, Jennifer L, Gangavarapu, Karthik, Malpica Serrano, Lorena Mariana, Crits-Christoph, Alexander, Matteson, Nathaniel L, Zeller, Mark, Levy, Joshua I, Wang, Jade C, Hughes, Scott, Lee, Jungmin, Park, Heedo, Park, Man-Seong, Ching Zi Yan, Katherine, Lin, Raymond Tzer Pin, Mat Isa, Mohd Noor, Noor, Yusuf Muhammad, Vasylyeva, Tetyana I, Garry, Robert F, Holmes, Edward C, Rambaut, Andrew, Suchard, Marc A, Andersen, Kristian G, Worobey, Michael, and Wertheim, Joel O

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Pneumonia, Biodefense, Lung, Vaccine Related, Emerging Infectious Diseases, Infectious Diseases, Prevention, Pneumonia & Influenza, Infection, Good Health and Well Being, Animals, COVID-19, Computer Simulation, Genetic Variation, Genomics, Humans, Molecular Epidemiology, Pandemics, Phylogeny, SARS-CoV-2, Viral Zoonoses, General Science & Technology
Abstract

Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B." Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.

Published
2022

17. The origins of SARS-CoV-2: A critical review

Author

Holmes, Edward C, Goldstein, Stephen A, Rasmussen, Angela L, Robertson, David L, Crits-Christoph, Alexander, Wertheim, Joel O, Anthony, Simon J, Barclay, Wendy S, Boni, Maciej F, Doherty, Peter C, Farrar, Jeremy, Geoghegan, Jemma L, Jiang, Xiaowei, Leibowitz, Julian L, Neil, Stuart JD, Skern, Tim, Weiss, Susan R, Worobey, Michael, Andersen, Kristian G, Garry, Robert F, and Rambaut, Andrew

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Pneumonia, Emerging Infectious Diseases, Biodefense, Vaccine Related, Infectious Diseases, Prevention, Pneumonia & Influenza, Lung, Good Health and Well Being, Animals, Biological Evolution, COVID-19, Humans, Laboratories, SARS-CoV-2, Zoonoses, evolution, origins, zoonosis, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.

Published
2021

21. Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus

Author

Wierenga, Janelle R., Grimwood, Rebecca M., Taylor, Harry S., Hunter, Stuart, Argilla, Lisa S., Webster, Trudi, Lim, Lauren, French, Rebecca, Schultz, Hendrik, Jorge, Fátima, Bostina, Mihnea, Burga, Laura, Swindells-Wallace, Puawai, Holmes, Edward C., McInnes, Kate, Morgan, Kerri J., and Geoghegan, Jemma L.

Published
2023
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25. Feline Calicivirus Virulent Systemic Disease: Clinical Epidemiology, Analysis of Viral Isolates and In Vitro Efficacy of Novel Antivirals in Australian Outbreaks

Author

Bordicchia, Matteo, Fumian, Tulio Machado, Van Brussel, Kate, Russo, Alice G, Carrai, Maura, Le, Shi-Jia, Pesavento, Patricia A, Holmes, Edward C, Martella, Vito, White, Peter, Beatty, Julia A, Shi, Mang, and Barrs, Vanessa R

Subjects
Microbiology, Biological Sciences, Infection, Good Health and Well Being, Animals, Antiviral Agents, Australia, Caliciviridae Infections, Calicivirus, Feline, Capsid, Cat Diseases, Cats, Cytidine, Disease Outbreaks, Female, Male, Metagenome, Nitro Compounds, Phylogeny, Thiazoles, Caliciviridae, Vesivirus, nitazoxanide, '-C-methylcytidine, NITD-008, 2′-C-methylcytidine
Abstract

Feline calicivirus (FCV) causes upper respiratory tract disease (URTD) and sporadic outbreaks of virulent systemic disease (FCV-VSD). The basis for the increased pathogenicity of FCV-VSD viruses is incompletely understood, and antivirals for FCV-VSD have yet to be developed. We investigated the clinicoepidemiology and viral features of three FCV-VSD outbreaks in Australia and evaluated the in vitro efficacy of nitazoxanide (NTZ), 2'-C-methylcytidine (2CMC) and NITD-008 against FCV-VSD viruses. Overall mortality among 23 cases of FCV-VSD was 39%. Metagenomic sequencing identified five genetically distinct FCV lineages within the three outbreaks, all seemingly evolving in situ in Australia. Notably, no mutations that clearly distinguished FCV-URTD from FCV-VSD phenotypes were identified. One FCV-URTD strain likely originated from a recombination event. Analysis of seven amino-acid residues from the hypervariable E region of the capsid in the cultured viruses did not support the contention that properties of these residues can reliably differentiate between the two pathotypes. On plaque reduction assays, dose-response inhibition of FCV-VSD was obtained with all antivirals at low micromolar concentrations; NTZ EC50, 0.4-0.6 µM, TI = 21; 2CMC EC50, 2.7-5.3 µM, TI > 18; NITD-008, 0.5 to 0.9 µM, TI > 111. Investigation of these antivirals for the treatment of FCV-VSD is warranted.

Published
2021

27. Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

Author

Giovanetti, Marta, Slavov, Svetoslav Nanev, Fonseca, Vagner, Wilkinson, Eduan, Tegally, Houriiyah, Patané, José Salvatore Leister, Viala, Vincent Louis, San, Emmanuel James, Rodrigues, Evandra Strazza, Santos, Elaine Vieira, Aburjaile, Flavia, Xavier, Joilson, Fritsch, Hegger, Adelino, Talita Emile Ribeiro, Pereira, Felicidade, Leal, Arabela, Iani, Felipe Campos de Melo, de Carvalho Pereira, Glauco, Vazquez, Cynthia, Sanabria, Gladys Mercedes Estigarribia, Oliveira, Elaine Cristina de, Demarchi, Luiz, Croda, Julio, dos Santos Bezerra, Rafael, Paola Oliveira de Lima, Loyze, Martins, Antonio Jorge, Renata dos Santos Barros, Claudia, Marqueze, Elaine Cristina, de Souza Todao Bernardino, Jardelina, Moretti, Debora Botequio, Brassaloti, Ricardo Augusto, de Lello Rocha Campos Cassano, Raquel, Mariani, Pilar Drummond Sampaio Corrêa, Kitajima, João Paulo, Santos, Bibiana, Proto-Siqueira, Rodrigo, Cantarelli, Vlademir Vicente, Tosta, Stephane, Nardy, Vanessa Brandão, Reboredo de Oliveira da Silva, Luciana, Gómez, Marcela Kelly Astete, Lima, Jaqueline Gomes, Ribeiro, Adriana Aparecida, Guimarães, Natália Rocha, Watanabe, Luiz Takao, Barbosa Da Silva, Luana, da Silva Ferreira, Raquel, da Penha, Mara Patricia F., Ortega, María José, de la Fuente, Andrea Gómez, Villalba, Shirley, Torales, Juan, Gamarra, María Liz, Aquino, Carolina, Figueredo, Gloria Patricia Martínez, Fava, Wellington Santos, Motta-Castro, Ana Rita C., Venturini, James, do Vale Leone de Oliveira, Sandra Maria, Gonçalves, Crhistinne Cavalheiro Maymone, do Carmo Debur Rossa, Maria, Becker, Guilherme Nardi, Giacomini, Mayra Presibella, Marques, Nelson Quallio, Riediger, Irina Nastassja, Raboni, Sonia, Mattoso, Gabriela, Cataneo, Allan D., Zanluca, Camila, Duarte dos Santos, Claudia N., Assato, Patricia Akemi, Allan da Silva da Costa, Felipe, Poleti, Mirele Daiana, Lesbon, Jessika Cristina Chagas, Mattos, Elisangela Chicaroni, Banho, Cecilia Artico, Sacchetto, Lívia, Moraes, Marília Mazzi, Grotto, Rejane Maria Tommasini, Souza-Neto, Jayme A., Nogueira, Maurício Lacerda, Fukumasu, Heidge, Coutinho, Luiz Lehmann, Calado, Rodrigo Tocantins, Neto, Raul Machado, Bispo de Filippis, Ana Maria, Venancio da Cunha, Rivaldo, Freitas, Carla, Peterka, Cassio Roberto Leonel, de Fátima Rangel Fernandes, Cássia, Navegantes, Wildo, do Carmo Said, Rodrigo Fabiano, Campelo de A e Melo, Carlos F., Almiron, Maria, Lourenço, José, de Oliveira, Tulio, Holmes, Edward C., Haddad, Ricardo, Sampaio, Sandra Coccuzzo, Elias, Maria Carolina, Kashima, Simone, Junior de Alcantara, Luiz Carlos, and Covas, Dimas Tadeu

Published
2022
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34. LucaOne: Generalized Biological Foundation Model with Unified Nucleic Acid and Protein Language

Author

He, Yong, primary, Fang, Pan, additional, Shan, Yongtao, additional, Pan, Yuanfei, additional, Wei, Yanhong, additional, Chen, Yichang, additional, Chen, Yihao, additional, Liu, Yi, additional, Zeng, Zhenyu, additional, Zhou, Zhan, additional, Zhu, Feng, additional, Holmes, Edward C., additional, Ye, Jieping, additional, Li, Jun, additional, Shu, Yuelong, additional, Shi, Mang, additional, and Li, Zhaorong, additional

Published
2024
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36. Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease

Author

Wu, Wei-Chen, primary, Pan, Yuan-Fei, additional, Zhou, Wu-Di, additional, Liao, Yu-Qi, additional, Peng, Min-Wu, additional, Luo, Geng-Yan, additional, Xin, Gen-Yang, additional, Peng, Ya-Ni, additional, An, Tongqing, additional, Li, Bo, additional, Luo, Huanle, additional, Barrs, Vanessa R., additional, Beatty, Julia A., additional, Holmes, Edward C., additional, Zhao, Wenjing, additional, and Shu, Yuelong, additional

Published
2024
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38. Off-season RSV epidemics in Australia after easing of COVID-19 restrictions

Author

Eden, John-Sebastian, Sikazwe, Chisha, Xie, Ruopeng, Deng, Yi-Mo, Sullivan, Sheena G., Michie, Alice, Levy, Avram, Cutmore, Elena, Blyth, Christopher C., Britton, Philip N., Crawford, Nigel, Dong, Xiaomin, Dwyer, Dominic E., Edwards, Kimberly M., Horsburgh, Bethany A., Foley, David, Kennedy, Karina, Minney-Smith, Cara, Speers, David, Tulloch, Rachel L., Holmes, Edward C., Dhanasekaran, Vijaykrishna, Smith, David W., Kok, Jen, and Barr, Ian G.

Published
2022
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40. Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

Author

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., and Sintchenko, Vitali

Published
2022
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45. Surveillance of Rodent Pests for SARS-CoV-2 and Other Coronaviruses, Hong Kong

Author

Miot, Elliott F., Worthington, Brian M., Ng, Kar Hon, Lataillade, Lucy de Guilhem de, Pierce, Mac P., Liao, Yunshi, Ko, Ronald, Shum, Marcus H., Cheung, William Y., Holmes, Edward C., Leung, Kathy S., Zhu, Huachen, Poon, Leo L., Peiris, J.S. Malik, Guan, Yi, Leung, Gabriel M., Wu, Joseph T., and Lam, Tommy T.

Subjects
Pests -- Statistics -- Health aspects, Rodents -- Statistics -- Health aspects, Disease transmission -- Risk factors, Animals as carriers of disease -- Statistics -- Health aspects, Health
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in Wuhan, China, in late 2019 (1) and soon spread globally. Although its zoonotic origin remains unclear, animal species potentially [...]

Published
2022

47. A ~40-kb flavi-like virus does not encode a known error-correcting mechanism.

Author

Petrone, Mary E., Grove, Joe, Mélade, Julien, Mifsud, Jonathon C. O., Parry, Rhys H., Marzinelli, Ezequiel M., and Holmes, Edward C.

Subjects
GENOME size, VIRAL genomes, RNA viruses, NIDOVIRUSES, NUCLEIC acids
Abstract

It is commonly held that there is a fundamental relationship between genome size and error rate, manifest as a notional "error threshold" that sets an upper limit on genome sizes. The genome sizes of RNA viruses, which have intrinsically high mutation rates due to a lack of mechanisms for error correction, must therefore be small to avoid accumulating an excessive number of deleterious mutations that will ultimately lead to population extinction. The proposed exceptions to this evolutionary rule are RNA viruses from the order Nidovirales (such as coronaviruses) that encode error-correcting exonucleases, enabling them to reach genome lengths greater than 40 kb. The recent discovery of large-genome flavi-like viruses (Flaviviridae), which comprise genomes up to 27 kb in length yet seemingly do not encode exonuclease domains, has led to the proposal that a proofreading mechanism is required to facilitate the expansion of nonsegmented RNA virus genomes above 30 kb. Herein, we describe a ~40 kb flavi-like virus identified in a Haliclona sponge metatranscriptome that does not encode a known exonuclease. Structural analysis revealed that this virus may have instead captured cellular domains associated with nucleic acid metabolism that have not been previously found in RNA viruses. Phylogenetic inference placed this virus as a divergent pesti-like lineage, such that we have provisionally termed it "Maximus pesti-like virus." This virus represents an instance of a flavi-like virus achieving a genome size comparable to that of the Nidovirales and demonstrates that RNA viruses have evolved multiple solutions to overcome the error threshold. [ABSTRACT FROM AUTHOR]

Published
2024
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48. Transcriptome Analysis and In Situ Hybridization for FcaGHV1 in Feline Lymphoma.

Author

Aghazadeh, Mahdis, Shi, Mang, Pesavento, Patricia A, Durham, Amy C, Polley, Tamsen, Donahoe, Shannon L, Troyer, Ryan M, Barrs, Vanessa R, Holmes, Edward C, and Beatty, Julia A

Subjects
Animals, Cats, Gammaherpesvirinae, Herpesviridae Infections, Lymphoma, Cat Diseases, In Situ Hybridization, Gene Expression Profiling, Reverse Transcriptase Polymerase Chain Reaction, High-Throughput Nucleotide Sequencing, B-cell, T-cell, cancer, domestic cat, felid, gammaherpesvirus, immunodeficiency, lymphoma, lymphomagenesis, oncogenic, transcriptome, virus, Microbiology
Abstract

Lymphoma is one of the most common malignancies in domestic cats. The lymphomagenic potential of Felis catus gammaherpesvirus 1 (FcaGHV1), a common infection in domestic cats, is unknown. In other species, including humans, cellular transformation by gammaherpesviruses is typically mediated by viral genes expressed during latency. We analysed tumour RNA, from diffuse large B-cell lymphomas (DLBCL) appearing in cats coinfected with FcaGHV1 and feline immunodeficiency virus (FIV) (n = 10), by high throughput transcriptome sequencing and reverse transcription PCR. A limited repertoire of FcaGHV transcripts was identified in five tumors, including homologs of oncogenic latency-associated transcripts, latency-associated nuclear antigen (LANA, ORF73) and vFLIP (F7), lytic genes (ORF50, ORF6, ORF59, F10), and an ORF unique to FcaGHV1, F20. In situ hybridization of FIV-associated DLBCLs (n = 9), post-transplant lymphomas (n = 6) and high-grade B and T-cell intestinal lymphomas (n = 8) identified a single case in which FcaGHV1 nucleic acid was detectable. These results demonstrate that FcaGHV1 transcripts can be detected in some FIV-associated lymphomas, but at low copy number, precluding assessment of a potential role for FcaGHV1 in lymphomagenesis. Future investigation of the FcaGHV1 transcriptome in clinical samples might employ viral enrichment and greater sequencing depth to enhance the retrieval of viral reads. Our results suggest prioritization of a subset of intestinal T-cell tumors, large granular lymphocyte lymphoma, for study.

Published
2018

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