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1. Author Correction: Higher Delta variant-specific neutralizing antibodies prevented infection in close contacts vaccinated with ancestral mRNA vaccines during the SARS-CoV-2 Delta wave

Author

Goh, Yun Shan, Fong, Siew-Wai, Tay, Matthew Zirui, Rouers, Angeline, Chang, Zi Wei, Chavatte, Jean-Marc, Hor, Pei Xiang, Loh, Chiew Yee, Huang, Yuling, Tan, Yong Jie, Wang, Bei, Ngoh, Eve Zi Xian, Mohd Salleh, Siti Nazihah, Lee, Raphael Tze Chuen, Lim, Georgina, Maurer-Stroh, Sebastian, Wang, Cheng-I, Leo, Yee‐Sin, Lin, Raymond T. P., Lam, Meng Chon, Lye, David C., Young, Barnaby Edward, Ng, Lisa F. P., and Renia, Laurent

Published
2024
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2. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.

Author

Latif, Alaa, Mullen, Julia, Alkuzweny, Manar, Hufbauer, Emory, Tsueng, Ginger, Haag, Emily, Zeller, Mark, Aceves, Christine, Zaiets, Karina, Cano, Marco, Zhou, Xinghua, Qian, Zhongchao, Sattler, Rachel, Matteson, Nathaniel, Levy, Joshua, Lee, Raphael, Freitas, Lucas, Maurer-Stroh, Sebastian, Wu, Chunlei, Su, Andrew, Andersen, Kristian, Hughes, Laura, Suchard, Marc, and Gangavarapu, Karthik

Subjects
Humans, SARS-CoV-2, COVID-19, Genomics, Disease Outbreaks, Mutation
Abstract

In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info , a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales.

Published
2023

3. Inhibition of SARS-CoV-2 growth in the lungs of mice by a peptide-conjugated morpholino oligomer targeting viral RNA

Author

Sakai, Alexandra, Singh, Gagandeep, Khoshbakht, Mahsa, Bittner, Scott, Löhr, Christiane V., Diaz-Tapia, Randy, Warang, Prajakta, White, Kris, Luo, Luke Le, Tolbert, Blanton, Blanco, Mario, Chow, Amy, Guttman, Mitchell, Li, Cuiping, Bao, Yiming, Ho, Joses, Maurer-Stroh, Sebastian, Chatterjee, Arnab, Chanda, Sumit, García-Sastre, Adolfo, Schotsaert, Michael, Teijaro, John R., Moulton, Hong M., and Stein, David A.

Published
2024
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4. Higher Delta variant-specific neutralizing antibodies prevented infection in close contacts vaccinated with ancestral mRNA vaccines during the SARS-CoV-2 Delta wave

Author

Goh, Yun Shan, Fong, Siew-Wai, Tay, Matthew Zirui, Rouers, Angeline, Chang, Zi Wei, Chavatte, Jean-Marc, Hor, Pei Xiang, Loh, Chiew Yee, Huang, Yuling, Tan, Yong Jie, Wang, Bei, Ngoh, Eve Zi Xian, Mohd Salleh, Siti Nazihah, Lee, Raphael Tze Chuen, Lim, Georgina, Maurer-Stroh, Sebastian, Wang, Cheng-I, Leo, Yee‐Sin, Lin, Raymond T. P., Lam, Meng Chon, Lye, David C., Young, Barnaby Edward, Ng, Lisa F. P., and Renia, Laurent

Published
2023
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5. Global disparities in SARS-CoV-2 genomic surveillance

Author

Brito, Anderson F, Semenova, Elizaveta, Dudas, Gytis, Hassler, Gabriel W, Kalinich, Chaney C, Kraemer, Moritz UG, Ho, Joses, Tegally, Houriiyah, Githinji, George, Agoti, Charles N, Matkin, Lucy E, Whittaker, Charles, Howden, Benjamin P, Sintchenko, Vitali, Zuckerman, Neta S, Mor, Orna, Blankenship, Heather M, de Oliveira, Tulio, Lin, Raymond TP, Siqueira, Marilda Mendonça, Resende, Paola Cristina, Vasconcelos, Ana Tereza R, Spilki, Fernando R, Aguiar, Renato Santana, Alexiev, Ivailo, Ivanov, Ivan N, Philipova, Ivva, Carrington, Christine VF, Sahadeo, Nikita SD, Branda, Ben, Gurry, Céline, Maurer-Stroh, Sebastian, Naidoo, Dhamari, von Eije, Karin J, Perkins, Mark D, van Kerkhove, Maria, Hill, Sarah C, Sabino, Ester C, Pybus, Oliver G, Dye, Christopher, Bhatt, Samir, Flaxman, Seth, Suchard, Marc A, Grubaugh, Nathan D, Baele, Guy, and Faria, Nuno R

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Health Sciences, Prevention, Human Genome, Biodefense, Vaccine Related, Immunization, Emerging Infectious Diseases, Genetics, Infection, Good Health and Well Being, Humans, SARS-CoV-2, Genome, Viral, COVID-19, Pandemics, Genomics, Bulgarian SARS-CoV-2 sequencing group, Communicable Diseases Genomics Network, COVID-19 Impact Project, Danish Covid-19 Genome Consortium, Fiocruz COVID-19 Genomic Surveillance Network, GISAID core curation team, Network for Genomic Surveillance in South Africa, Swiss SARS-CoV-2 Sequencing Consortium
Abstract

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time

Published
2022

6. Monkeypox Virus Infection in 2 Female Travelers Returning to Vietnam from Dubai, United Arab Emirates, 2022

Author

Dung, Nguyen Thanh, Hung, Le Manh, Hoa, Huynh Thi Thuy, Nga, Le Hong, Hong, Nguyen Thi Thu, Thuong, Tang Chi, Ngoc, Nghiem My, Ny, Nguyen Thi Han, Quy, Vo Truong, Thoa, Vu Thi Kim, Thanh, Nguyen Thi, Tho, Phan Vinh, Toan, Le Mau, Quang, Vo Minh, Man, Dinh Nguyen Huy, Phat, Nguyen Tan, Phuong, Tran Thi Lan, Tam, Tran Thi Thanh, Thoa, Pham Thi Ngoc, Tam, Nguyen Hong, Lan, Truong Thi Thanh, Thanh, Tran Tan, Maurer-Stroh, Sebastian, Khanh, Le Thuy Thuy, Yen, Lam Minh, Hung, Nguyen Huu, Thwaites, Guy, Tung, Nguyen Le Nhu, Thwaites, Louise, Chau, Nguyen Van Vinh, Anh, Nguyen To, and Van Tan, Le

Subjects
Human monkeypox -- Case studies, Travelers -- Case studies, Disease transmission -- Case studies, Health
Abstract

By January 12, 2023, more than 84,500 mpox cases and 80 deaths had been reported from 110 countries because of an ongoing multicountry outbreak (1). Cases from Europe and Americas [...]

Published
2023
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7. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations

Author

Gangavarapu, Karthik, Latif, Alaa Abdel, Mullen, Julia L., Alkuzweny, Manar, Hufbauer, Emory, Tsueng, Ginger, Haag, Emily, Zeller, Mark, Aceves, Christine M., Zaiets, Karina, Cano, Marco, Zhou, Xinghua, Qian, Zhongchao, Sattler, Rachel, Matteson, Nathaniel L., Levy, Joshua I., Lee, Raphael T. C., Freitas, Lucas, Maurer-Stroh, Sebastian, Suchard, Marc A., Wu, Chunlei, Su, Andrew I., Andersen, Kristian G., and Hughes, Laura D.

Published
2023
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8. The Singapore National Precision Medicine Strategy

Author

Wong, Eleanor, Bertin, Nicolas, Hebrard, Maxime, Tirado-Magallanes, Roberto, Bellis, Claire, Lim, Weng Khong, Chua, Chee Yong, Tong, Philomena Mei Lin, Chua, Raymond, Mak, Kenneth, Lim, Tit Meng, Cheong, Wei Yang, Thien, Kwee Eng, Goh, Khean Teik, Chai, Jin-Fang, Lee, Jimmy, Sung, Joseph Jao-Yiu, Wong, Tien Yin, Chin, Calvin Woon Loong, Gluckman, Peter D., Goh, Liuh Ling, Ban, Kenneth Hon Kim, Tan, Tin Wee, Sim, Xueling, Cheng, Ching-Yu, Davila, Sonia, Karnani, Neerja, Leong, Khai Pang, Liu, Jianjun, Prabhakar, Shyam, Maurer-Stroh, Sebastian, Verma, Chandra Shekhar, Krishnaswamy, Pavitra, Goh, Rick Siow Mong, Chia, Irenaeus, Ho, Clarissa, Low, Doreen, Virabhak, Suchin, Yong, Jacklyn, Zheng, Weiling, Seow, Shih Wee, Seck, Yee Kwang, Koh, Mingshi, Chambers, John C., Tai, E. Shyong, and Tan, Patrick

Published
2023
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9. Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia

Author

Asarnow, Daniel, Wang, Bei, Lee, Wen-Hsin, Hu, Yuanyu, Huang, Ching-Wen, Faust, Bryan, Ng, Patricia Miang Lon, Ngoh, Eve Zi Xian, Bohn, Markus, Bulkley, David, Pizzorno, Andrés, Ary, Beatrice, Tan, Hwee Ching, Lee, Chia Yin, Minhat, Rabiatul Adawiyah, Terrier, Olivier, Soh, Mun Kuen, Teo, Frannie Jiuyi, Yeap, Yvonne Yee Chin, Seah, Shirley Gek Kheng, Chan, Conrad En Zuo, Connelly, Emily, Young, Nicholas J, Maurer-Stroh, Sebastian, Renia, Laurent, Hanson, Brendon John, Rosa-Calatrava, Manuel, Manglik, Aashish, Cheng, Yifan, Craik, Charles S, and Wang, Cheng-I

Subjects
Vaccine Related, Pneumonia, Infectious Diseases, Pneumonia & Influenza, Prevention, Biodefense, Lung, Emerging Infectious Diseases, Aetiology, 2.1 Biological and endogenous factors, Infection, Good Health and Well Being, Angiotensin-Converting Enzyme 2, Animals, Antibodies, Neutralizing, Antigen-Antibody Complex, Binding Sites, CHO Cells, COVID-19, Cricetinae, Cricetulus, Cryoelectron Microscopy, Giant Cells, Humans, Membrane Fusion, Peptide Library, Protein Binding, Protein Domains, Protein Structure, Quaternary, SARS-CoV-2, Spike Glycoprotein, Coronavirus, SARS-CoV, Spike protein, coronavirus, phage display, receptor binding domain, recombinant monoclonal antibody, syncytia, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by binding of the viral Spike protein to host receptor angiotensin-converting enzyme 2 (ACE2), followed by fusion of viral and host membranes. Although antibodies that block this interaction are in emergency use as early coronavirus disease 2019 (COVID-19) therapies, the precise determinants of neutralization potency remain unknown. We discovered a series of antibodies that potently block ACE2 binding but exhibit divergent neutralization efficacy against the live virus. Strikingly, these neutralizing antibodies can inhibit or enhance Spike-mediated membrane fusion and formation of syncytia, which are associated with chronic tissue damage in individuals with COVID-19. As revealed by cryoelectron microscopy, multiple structures of Spike-antibody complexes have distinct binding modes that not only block ACE2 binding but also alter the Spike protein conformational cycle triggered by ACE2 binding. We show that stabilization of different Spike conformations leads to modulation of Spike-mediated membrane fusion with profound implications for COVID-19 pathology and immunity.

Published
2021

10. Intense interseasonal influenza outbreaks, Australia, 2018/19.

Author

Barr, Ian, Deng, Yi, Grau, Miguel, Han, Alvin, Gilmour, Robin, Irwin, Melissa, Markey, Peter, Freeman, Kevin, Higgins, Geoff, Turra, Mark, Komadina, Naomi, Peck, Heidi, Booy, Robert, Maurer-Stroh, Sebastian, Dhanasekaran, Vijaykrishna, and Sullivan, Sheena

Subjects
Australia, human, influenza, seasonality, Adolescent, Adult, Aged, Australia, Child, Child, Preschool, Disease Notification, Disease Outbreaks, Female, Hemagglutinins, Viral, Humans, Infant, Influenza A virus, Influenza B virus, Influenza, Human, Male, Middle Aged, New South Wales, Phylogeny, Population Surveillance, Seasons, Sentinel Surveillance
Abstract

BackgroundInterseasonal influenza outbreaks are not unusual in countries with temperate climates and well-defined influenza seasons. Usually, these are small and diminish before the main influenza season begins. However, the 2018/19 summer-autumn interseasonal influenza period in Australia saw unprecedented large and widespread influenza outbreaks.AimOur objective was to determine the extent of the intense 2018/19 interseasonal influenza outbreaks in Australia epidemiologically and examine the genetic, antigenic and structural properties of the viruses responsible for these outbreaks.MethodsThis observational study combined the epidemiological and virological surveillance data obtained from the Australian Government Department of Health, the New South Wales Ministry of Health, sentinel outpatient surveillance, public health laboratories and data generated by the World Health Organization Collaborating Centre for Reference and Research on Influenza in Melbourne and the Singapore Agency for Science, Technology and Research.ResultsThere was a record number of laboratory-confirmed influenza cases during the interseasonal period November 2018 to May 2019 (n= 85,286; 5 times the previous 3-year average) and also more institutional outbreaks, hospitalisations and deaths, than what is normally seen.ConclusionsThe unusually large interseasonal influenza outbreaks in 2018/19 followed a mild 2018 influenza season and resulted in a very early start to the 2019 influenza season across Australia. The reasons for this unusual event have yet to be fully elucidated but are likely to be a complex mix of climatic, virological and host immunity-related factors. These outbreaks reinforce the need for year-round surveillance of influenza, even in temperate climates with strong seasonality patterns.

Published
2019

12. Impact of Delta Variant and Vaccination on SARS-CoV-2 Secondary Attack Rate Among Household Close Contacts

Author

Ng, Oon Tek, Koh, Vanessa, Chiew, Calvin J, Marimuthu, Kalisvar, Thevasagayam, Natascha May, Mak, Tze Minn, Chua, Joon Kiat, Ong, Shannen Si Hui, Lim, Yong Kai, Ferdous, Zannatul, Johari, Alifa Khairunnisa bte, Chen, Mark I-Cheng, Maurer-Stroh, Sebastian, Cui, Lin, Lin, Raymond Tzer Pin, Tan, Kelvin Bryan, Cook, Alex R, Leo, Prof. Yee-Sin, and Lee, Prof. Vernon JM

Published
2021
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15. Plasmodium vivax binds host CD98hc (SLC3A2) to enter immature red blood cells

Author

Malleret, Benoît, El Sahili, Abbas, Tay, Matthew Zirui, Carissimo, Guillaume, Ong, Alice Soh Meoy, Novera, Wisna, Lin, Jianqing, Suwanarusk, Rossarin, Kosaisavee, Varakorn, Chu, Trang T. T., Sinha, Ameya, Howland, Shanshan Wu, Fan, Yiping, Gruszczyk, Jakub, Tham, Wai-Hong, Colin, Yves, Maurer-Stroh, Sebastian, Snounou, Georges, Ng, Lisa F. P., Chan, Jerry Kok Yen, Chacko, Ann-Marie, Lescar, Julien, Chandramohanadas, Rajesh, Nosten, François, Russell, Bruce, and Rénia, Laurent

Published
2021
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17. Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study

Author

Young, Barnaby E, Wei, Wycliffe E, Fong, Siew-Wai, Mak, Tze-Minn, Anderson, Danielle E, Chan, Yi-Hao, Pung, Rachael, Heng, Cheryl SY, Ang, Li Wei, Zheng, Adrian Kang Eng, Lee, Bernett, Kalimuddin, Shirin, Pada, Surinder, Tambyah, Paul A, Parthasarathy, Purnima, Tan, Seow Yen, Sun, Louisa, Smith, Gavin JD, Lin, Raymond Tzer Pin, Leo, Yee-Sin, Renia, Laurent, Wang, Lin-Fa, Ng, Lisa FP, Maurer-Stroh, Sebastian, Lye, David Chien, and Lee, Vernon J

Published
2021
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18. Viral factors in influenza pandemic risk assessment.

Author

Lipsitch, Marc, Barclay, Wendy, Raman, Rahul, Russell, Charles J, Belser, Jessica A, Cobey, Sarah, Kasson, Peter M, Lloyd-Smith, James O, Maurer-Stroh, Sebastian, Riley, Steven, Beauchemin, Catherine Aa, Bedford, Trevor, Friedrich, Thomas C, Handel, Andreas, Herfst, Sander, Murcia, Pablo R, Roche, Benjamin, Wilke, Claus O, and Russell, Colin A

Subjects
Animals, Humans, Influenza A virus, Zoonoses, RNA Replicase, Hemagglutinin Glycoproteins, Influenza Virus, Virulence Factors, Risk Assessment, Influenza, Human, Pandemics, Epidemiological Monitoring, epidemiology, global health, human, infectious disease, influenza A, microbiology, pandemic, risk prediction, virus, Hemagglutinin Glycoproteins, Influenza Virus, Influenza, Human, Biochemistry and Cell Biology
Abstract

The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus. The goal would be to use genetic sequence and/or biological assays of viral traits to identify those non-human influenza viruses with the greatest risk of evolving into pandemic threats, and/or to understand drivers of such evolution, to prioritize pandemic prevention or response measures. We describe such efforts, identify progress and ongoing challenges, and discuss three specific traits of influenza viruses (hemagglutinin receptor binding specificity, hemagglutinin pH of activation, and polymerase complex efficiency) that contribute to pandemic risk.

Published
2016

21. SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

Author

Konings, Frank, Perkins, Mark D., Kuhn, Jens H., Pallen, Mark J., Alm, Erik J., Archer, Brett N., Barakat, Amal, Bedford, Trevor, Bhiman, Jinal N., Caly, Leon, Carter, Lisa L., Cullinane, Anne, de Oliveira, Tulio, Druce, Julian, El Masry, Ihab, Evans, Roger, Gao, George F., Gorbalenya, Alexander E., Hamblion, Esther, Herring, Belinda L., Hodcroft, Emma, Holmes, Edward C., Kakkar, Manish, Khare, Shagun, Koopmans, Marion P. G., Korber, Bette, Leite, Juliana, MacCannell, Duncan, Marklewitz, Marco, Maurer-Stroh, Sebastian, Rico, Jairo Andres Mendez, Munster, Vincent J., Neher, Richard, Munnink, Bas Oude, Pavlin, Boris I., Peiris, Malik, Poon, Leo, Pybus, Oliver, Rambaut, Andrew, Resende, Paola, Subissi, Lorenzo, Thiel, Volker, Tong, Suxiang, van der Werf, Sylvie, von Gottberg, Anne, Ziebuhr, John, and Van Kerkhove, Maria D.

Published
2021
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25. Knockout of the non-essential gene SUGCT creates diet-linked, age-related microbiome disbalance with a diabetes-like metabolic syndrome phenotype

Author

Niska-Blakie, Joanna, Gopinathan, Lakshmi, Low, Kia Ngee, Kien, Yang Lay, Goh, Christine M. F., Caldez, Matias J., Pfeiffenberger, Elisabeth, Jones, Oliver S., Ong, Chee Bing, Kurochkin, Igor V., Coppola, Vincenzo, Tessarollo, Lino, Choi, Hyungwon, Kanagasundaram, Yoganathan, Eisenhaber, Frank, Maurer-Stroh, Sebastian, and Kaldis, Philipp

Published
2020
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26. Imprinting of IgA responses in previously infected individuals receiving bivalent mRNA vaccines (WT and BA.4/BA.5 or WT and BA.1)

Author

Goh, Yun Shan, Fong, Siew‐Wai, Hor, Pei Xiang, Loh, Chiew Yee, Tay, Matthew Zirui, Wang, Bei, Salleh, Siti Nazihah Mohd, Ngoh, Eve Zi Xian, Lee, Raphael Tze Chuen, Poh, Xuan Ying, Lee, I. Russel, Rao, Suma, Chia, Po Ying, Maurer-Stroh, Sebastian, Wang, Cheng-I, Leo, Yee‐Sin, Lye, David C., Young, Barnaby Edward, Ng, Lisa F.P., and Renia, Laurent

Published
2024
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27. Improving pandemic influenza risk assessment.

Author

Russell, Colin A, Kasson, Peter M, Donis, Ruben O, Riley, Steven, Dunbar, John, Rambaut, Andrew, Asher, Jason, Burke, Stephen, Davis, C Todd, Garten, Rebecca J, Gnanakaran, Sandrasegaram, Hay, Simon I, Herfst, Sander, Lewis, Nicola S, Lloyd-Smith, James O, Macken, Catherine A, Maurer-Stroh, Sebastian, Neuhaus, Elizabeth, Parrish, Colin R, Pepin, Kim M, Shepard, Samuel S, Smith, David L, Suarez, David L, Trock, Susan C, Widdowson, Marc-Alain, George, Dylan B, Lipsitch, Marc, and Bloom, Jesse D

Subjects
Humans, Influenza A virus, Risk Assessment, Public Health, Base Sequence, Geography, Models, Biological, Influenza, Human, Biological Evolution, Pandemics, Epidemiological Monitoring, emergence, evolutionary biology, genomics, human, infectious disease, influenza, microbiology, pandemic, viruses, Models, Biological, Influenza, Human, Biochemistry and Cell Biology
Abstract

Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response.

Published
2014

31. Positive‐strand RNA viruses—a Keystone Symposia report

Author

Cable, Jennifer, Denison, Mark R., Kielian, Margaret, Jackson, William T., Bartenschlager, Ralf, Ahola, Tero, Mukhopadhyay, Suchetana, Fremont, Daved H., Kuhn, Richard J., Shannon, Ashleigh, Frazier, Meredith N., Yuen, Kwok-Yung, Coyne, Carolyn B., Wolthers, Katja C., Ming, Guo-Li, Guenther, Camy S., Moshiri, Jasmine, Best, Sonja M., Schoggins, John W., Jurado, Kellie Ann, Ebel, Gregory D., Schäfer, Alexandra, Ng, Lisa F. P., Kikkert, Marjolein, Sette, Alessandro, Harris, Eva, Wing, Peter A. C., Eggenberger, Julie, Krishnamurthy, Siddharth R., Mah, Marcus G., Meganck, Rita M., Chung, Donghoon, Maurer-Stroh, Sebastian, Andino, Raul, Korber, Bette, Perlman, Stanley, Shi, Pei-Yong, Bárcena, Montserrat, Aicher, Sophie-Marie, Vu, Michelle N., Kenney, Devin J., Lindenbach, Brett D., Nishida, Yukiko, Rénia, Laurent, Williams, Evan P., Medical Microbiology and Infection Prevention, and AII - Infectious diseases

Subjects
RNA virus, flavivirus, History and Philosophy of Science, enterovirus, SARS-CoV-2, General Neuroscience, coronavirus, alphavirus, General Biochemistry, Genetics and Molecular Biology
Abstract

Positive-strand RNA viruses have been the cause of several recent outbreaks and epidemics, including the Zika virus epidemic in 2015, the SARS outbreak in 2003, and the ongoing SARS-CoV-2 pandemic. On June 18-22, 2022, researchers focusing on positive-strand RNA viruses met for the Keystone Symposium "Positive-Strand RNA Viruses" to share the latest research in molecular and cell biology, virology, immunology, vaccinology, and antiviral drug development. This report presents concise summaries of the scientific discussions at the symposium.

Published
2023

32. Genome-Wide Analysis of Protein-Coding Variants in Leprosy

Author

Liu, Hong, Wang, Zhenzhen, Li, Yi, Yu, Gongqi, Fu, Xi’an, Wang, Chuan, Liu, Wenting, Yu, Yongxiang, Bao, Fangfang, Irwanto, Astrid, Liu, Jian, Chu, Tongsheng, Andiappan, Anand Kumar, Maurer-Stroh, Sebastian, Limviphuvadh, Vachiranee, Wang, Honglei, Mi, Zihao, Sun, Yonghu, Sun, Lele, Wang, Ling, Wang, Chaolong, You, Jiabao, Li, Jinghui, Foo, Jia Nee, Liany, Herty, Meah, Wee Yang, Niu, Guiye, Yue, Zhenhua, Zhao, Qing, Wang, Na, Yu, Meiwen, Yu, Wenjun, Cheng, Xiujun, Khor, Chiea Chuen, Sim, Kar Seng, Aung, Tin, Wang, Ningli, Wang, Deyun, Shi, Li, Ning, Yong, Zheng, Zhongyi, Yang, Rongde, Li, Jinlan, Yang, Jun, Yan, Liangbin, Shen, Jianping, Zhang, Guocheng, Chen, Shumin, Liu, Jianjun, and Zhang, Furen

Published
2017
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34. Outbreak of Zika virus infection in Singapore: an epidemiological, entomological, virological, and clinical analysis

Author

Ho, Zheng Jie Marc, Hapuarachchi, Hapuarachchige Chanditha, Barkham, Timothy, Chow, Angela, Ng, Lee Ching, Lee, Jian Ming Vernon, Leo, Yee Sin, Prem, Kiesha, Lim, Yue Hui Georgina, de Sessions, Paola F, Rabaa, Maia A, Chong, Chee Seng, Tan, Cheong Huat, Rajarethinam, Jayanthi, Tan, Junhao, Anderson, Danielle E, Ong, Xinmei, Cook, Alex R, Chong, Chia Yin, Hsu, Li Yang, Yap, Grace, Lai, Yee Ling, Chawla, Tanu, Pan, Louise, Sim, Shuzhen, Chen, I-Cheng Mark, Thoon, Koh Cheng, Yung, Chee Fu, Li, Jia Hui, Ng, Hee Ling Deborah, Nandar, Khine, Ooi, Peng Lim, Lin, Raymond Tzer Pin, Aw, Pauline, Uehara, Anna, Pratim De, Partha, Soon, Wendy, Hibberd, Martin Lloyd, Ng, Huck Hui, Maurer-Stroh, Sebastian, and Sessions, October M

Published
2017
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36. Artificial intelligence innovation in healthcare: Relevance of reporting guidelines for clinical translation from bench to bedside

Author

Teo, Zhen Ling, primary, Kwee, Ann, additional, Lim, John CW, additional, Lam, Carolyn SP, additional, Ho, Dean, additional, Maurer-Stroh, Sebastian, additional, Su, Yi, additional, Chesterman, Simon, additional, Chen, Tsuhan, additional, Tan, Chorh Chuan, additional, Wong, Tien Yin, additional, Ngiam, Kee Yuan, additional, Tan, Cher Heng, additional, Soon, Danny, additional, Choong, May Ling, additional, Chua, Raymond, additional, Wong, Sutowo, additional, Lim, Colin, additional, Cheong, Wei Yang, additional, and Ting, Daniel SW, additional

Published
2023
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37. Erratum to “Impact of delta variant and vaccination on SARS-CoV-2 secondary attack rate among household close contacts” [The Lancet Regional Health – Western Pacific 17 (2021) 100299]

Author

Ng, Oon Tek, primary, Koh, Vanessa, additional, Chiew, Calvin J., additional, Marimuthu, Kalisvar, additional, Thevasagayam, Natascha May, additional, Mak, Tze Minn, additional, Chua, Joon Kiat, additional, Hui Ong, Shannen Si, additional, Lim, Yong Kai, additional, Ferdous, Zannatul, additional, Khairunnisa bte Johari, Alifa, additional, I-Cheng Chen, Mark, additional, Maurer-Stroh, Sebastian, additional, Cui, Lin, additional, Pin Lin, Raymond Tzer, additional, Tan, Kelvin Bryan, additional, Cook, Alex R., additional, Leo, Prof. Yee-Sin, additional, and Lee, Prof. Vernon J.M., additional

Published
2023
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38. Heterologous mRNA vaccine boosters induce a stronger and longer-lasting antibody response against Omicron XBB variant

Author

Tay, Matthew Zirui, primary, Goh, Yun Shan, additional, Fong, Siew-Wai, additional, Chang, Zi Wei, additional, Rouers, Angeline, additional, Wong, Nathan, additional, Torres-Ruesta, Anthony, additional, Huang, Yuling, additional, Selvam, Sooriya Kannan, additional, Hor, Pei Xiang, additional, Loh, Chiew Yee, additional, Wang, Bei, additional, Mohd Salleh, Siti Nazihah, additional, Ngoh, Eve Zi Xian, additional, Lee, Raphael Tze Chuen, additional, Neo, Vanessa, additional, Kam, Isaac Kai Jie, additional, Poh, Xuan Ying, additional, Rao, Suma, additional, Chia, Po Ying, additional, Ong, Sean W.X., additional, Lee, Tau Hong, additional, Lim, Clarissa, additional, Teo, Jefanie, additional, Maurer-Stroh, Sebastian, additional, Wang, Cheng-I, additional, Leo, Yee-Sin, additional, Lin, Raymond Tzer Pin, additional, Lye, David C., additional, Young, Barnaby Edward, additional, Ng, Lisa F.P., additional, and Renia, Laurent, additional

Published
2023
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39. Directed Evolution and Predictive Modelling of Galactose Oxidase towards Bulky Benzylic and Unactivated Secondary Alcohols

Author

Yeo, Wan Lin, primary, Tay, Dillon W. P., additional, Miyajima, Jhoann M.T., additional, Supekar, Shreyas, additional, Teh, Tong Mei, additional, Xu, Jin, additional, Tan, Yee Ling, additional, See, Jie Yang, additional, Fan, Hao, additional, Maurer-Stroh, Sebastian, additional, Lim, Yee Hwee, additional, and Ang, Ee Lui, additional

Published
2023
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45. Genomic landscape of drug binding and pharmacogenetic variation across diverse populations using SNPdrug3D

Author

Maurer-Stroh, Sebastian, primary, Malik, Ashar, additional, Kenanov, Dimitar, additional, Chong, Cheng-Shoong, additional, Ozturk, Mert Burak, additional, Hebrard, Maxime, additional, Ho, Ying Swan, additional, Wang, Zhenxun, additional, Limviphuvadh, Vachiranee, additional, Miyajima, Jhoann, additional, Magallanes, Roberto, additional, Sim, Xueling, additional, Chai, Jin Fang, additional, Davila, Sonia, additional, Yeo, Khung Keong, additional, Leong, Khai Pang, additional, Goh, Liuh Ling, additional, Karnani, Neerja, additional, Eriksson, Johan Gunnar, additional, Cheng, Ching-Yu, additional, Wong, Tien, additional, Loh, Marie, additional, Dalan, Rinkoo, additional, Khor, Chiea Chuen, additional, Chew, Guo-Liang, additional, Lim, Weng Khong, additional, Ngeow, Joanne, additional, Chambers, John, additional, Tai, E Shyong, additional, Bertin, Nicolas, additional, Tan, Chris Soon Heng, additional, Koh, Judice, additional, Tan, Patrick, additional, and Verma, Chandra, additional

Published
2023
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48. Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses/Analyse systematique des similarites proteiques entre le virus Zika et d'autres virus transmis par des arthropodes/Analisis sistematico de la identidad proteica entre el virus de Zika y otros virus trasmitidos por artropodos

Author

Chang, Hsiao-Han, Huber, Roland G., Bond, Peter J., Grad, Yonatan H., Camerini, David, Maurer-Stroh, Sebastian, and Lipsitch, Marc

Subjects
United States. National Center for Biotechnology Information -- Analysis, Yellow fever -- Analysis -- Health aspects, Amino acids -- Usage -- Analysis -- Health aspects, Zika virus -- Analysis -- Health aspects, Encephalitis -- Analysis -- Health aspects, Health
Abstract

Objective To analyse the proportions of protein identity between Zika virus and dengue, Japanese encephalitis, yellow fever, West Nile and chikungunya viruses as well as polymorphism between different Zika virus strains. Methods We used published protein sequences for the Zika virus and obtained protein sequences for the other viruses from the National Center for Biotechnology Information (NCBI) protein database or the NCBI virus variation resource. We used BLASTP to find regions of identity between viruses. We quantified the identity between the Zika virus and each of the other viruses, as well as within-Zika virus polymorphism for all amino acid k-mers across the proteome, with k ranging from 6 to 100. We assessed accessibility of protein fragments by calculating the solvent accessible surface area for the envelope and nonstructural-1 (NS1) proteins. Findings In total, we identified 294 Zika virus protein fragments with both low proportion of identity with other viruses and low levels of polymorphisms among Zika virus strains. The list includes protein fragments from all Zika virus proteins, except NS3. NS4A has the highest number (190 k-mers) of protein fragments on the list. Conclusion We provide a candidate list of protein fragments that could be used when developing a sensitive and specific serological test to detect previous Zika virus infections. Objectif Analyser les pourcentages de similarite protelque entre le virus Zika et les virus de la dengue, de l'encephalite japonaise, de la fievre jaune, du Nil occidental et du chikungunya, ainsi que le polymorphisme entre differentes souches du virus Zika. Methodes Nous avons utilise les sequences proteiques publiees du virus Zika et avons obtenu les sequences proteiques des autres virus dans la banque proteique du National Center for Biotechnology Information (NCBI) ou dans la base de donnees Virus Variation du NCBI. Nous avons utilise BLASTP pour identifier les regions de similarite entre les virus. Nous avons quantine la similarite entre le virus Zika et chacun des autres virus ainsi que le polymorphisme du virus Zika pour tous les k-mers d'acldes amines, dans tout le proteome, avec k allant de 6 a 100. Nous avons etudie l'accessibilite des fragments proteiques en calculant la surface accessible au solvant pour les proteines d'enveloppe et non structurale-1 (NS1). Resultats Au total, nous avons identifie 294 fragments proteiques du virus Zika qui presentent a la fois un faible degre de similarite avec les autres virus et un faible degre de polymorphisme entre les souches du virus Zika. Notre liste comprend des fragments proteiques issus de toutes les proteines du virus Zika, a l'exception de la proteine NS3. Le plus grand nombre defragments proteiques de notre liste (190 k-mers) correspond a la proteine NS4A. Conclusion Nous proposons une liste de fragments proteiques candidats, qui pourraient etre utilises pour concevolr un test serologique sensible et specifique pour depister les infections anterieures par le virus Zika. Objective Analizar las proporciones de Identidad proteica entre el virus de Zika y los virus del dengue, la encefalitis japonesa, la fiebre amarilla, el Nilo Occidental y el chikungunya, asi como el polimorfismo entre las distintas cepas del virus de Zika. Metodos Se utilizaron secuencias de proteinas publicadas para el virus de Zika y secuencias de proteinas obtenidas para los otros virus de la base de datos de proteinas del Centro Nacional para la Informacion Biotecnologica (NCBI) o la fuente de informacion sobre la variacion de virus del NCBI. Se utilizo el programa BLASTP para encontrar regiones de identidad entre los virus. Se cuantifico la identidad entre el virus de Zika y cada uno de los otros virus, asi como el polimorfismo del virus de Zika para todos los k-mers de aminoacidos a traves del proteoma, con una variacion de k de 6 a 100. Se evaluo la accesibilidad de los fragmentos proteicos calculando la superficie accesible solvente para las proteinas de envoltura y no estructurales 1 (NS1). Resultados En total, se identificaron 294 fragmentos proteicos del virus de Zika con una proporcion escasa de identidad con otros virus y con niveles bajos de polimorfismos entre las distintas cepas del virus de Zika. En la lista se incluyen fragmentos proteicos de todas las proteinas del virus de Zika, salvo la NS3. La NS4A cuenta con el mayor numero (190 k-mers) de fragmentos proteicos de la lista. Conclusion Se proporciono una lista de posibles fragmentos proteicos que podrian utilizarse para desarrollar una prueba serologica sensible y especifica para detectar infecciones del virus de Zika anteriores., Introduction Monitoring the geographic and the demographic distribution of people infected with Zika virus is important for informing decision-makers and researchers during the ongoing epidemic. Health officials also need further [...]

Published
2017
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50. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus [perspective]

Author

Happi, Christian, Adetifa, Ifedayo, Mbala, Placide, Njouom, Richard, Nakoune, Emmanuel, Happi, Anise, Ndodo, Nnaemeka, Ayansola, Oyeronke, Mboowa, Gerald, Bedford, Trevor, Neher, Richard A, Roemer, Cornelius, Hodcroft, Emma, Tegally, Houriiyah, O'Toole, Áine, Rambaut, Andrew, Pybus, Oliver, Kraemer, Moritz U G, Wilkinson, Eduan, Isidro, Joana, Borges, Vítor, Pinto, Miguel, Gomes, João Paulo, Freitas, Lucas, Resende, Paola C, Lee, Raphael T C, Maurer-Stroh, Sebastian, Baxter, Cheryl, Lessells, Richard, Ogwell, Ahmed E, Kebede, Yenew, Tessema, Sofonias K, and de Oliveira, Tulio

Subjects
360 Social problems & social services, 610 Medicine & health
Abstract

We propose a novel, non-discriminatory classification of monkeypox virus. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomics surveillance.

Published
2022

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