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2. Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology

Author

Aguado, Julio, Amarilla, Alberto A., Taherian Fard, Atefeh, Albornoz, Eduardo A., Tyshkovskiy, Alexander, Schwabenland, Marius, Chaggar, Harman K., Modhiran, Naphak, Gómez-Inclán, Cecilia, Javed, Ibrahim, Baradar, Alireza A., Liang, Benjamin, Peng, Lianli, Dharmaratne, Malindrie, Pietrogrande, Giovanni, Padmanabhan, Pranesh, Freney, Morgan E., Parry, Rhys, Sng, Julian D. J., Isaacs, Ariel, Khromykh, Alexander A., Valenzuela Nieto, Guillermo, Rojas-Fernandez, Alejandro, Davis, Thomas P., Prinz, Marco, Bengsch, Bertram, Gladyshev, Vadim N., Woodruff, Trent M., Mar, Jessica C., Watterson, Daniel, and Wolvetang, Ernst J.

Published
2023
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3. SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike protein

Author

Albornoz, Eduardo A., Amarilla, Alberto A., Modhiran, Naphak, Parker, Sandra, Li, Xaria X., Wijesundara, Danushka K., Aguado, Julio, Zamora, Adriana Pliego, McMillan, Christopher L. D., Liang, Benjamin, Peng, Nias Y. G., Sng, Julian D. J., Saima, Fatema Tuj, Fung, Jenny N., Lee, John D., Paramitha, Devina, Parry, Rhys, Avumegah, Michael S., Isaacs, Ariel, Lo, Martin W., Miranda-Chacon, Zaray, Bradshaw, Daniella, Salinas-Rebolledo, Constanza, Rajapakse, Niwanthi W., Wolvetang, Ernst J., Munro, Trent P., Rojas-Fernandez, Alejandro, Young, Paul R., Stacey, Katryn J., Khromykh, Alexander A., Chappell, Keith J., Watterson, Daniel, and Woodruff, Trent M.

Published
2023
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4. In vivo inhibition of nuclear ACE2 translocation protects against SARS-CoV-2 replication and lung damage through epigenetic imprinting

Author

Tu, Wen Juan, Melino, Michelle, Dunn, Jenny, McCuaig, Robert D., Bielefeldt-Ohmann, Helle, Tsimbalyuk, Sofiya, Forwood, Jade K., Ahuja, Taniya, Vandermeide, John, Tan, Xiao, Tran, Minh, Nguyen, Quan, Zhang, Liang, Nam, Andy, Pan, Liuliu, Liang, Yan, Smith, Corey, Lineburg, Katie, Nguyen, Tam H., Sng, Julian D. J., Tong, Zhen Wei Marcus, Chew, Keng Yih, Short, Kirsty R., Le Grand, Roger, Seddiki, Nabila, and Rao, Sudha

Published
2023
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5. The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Published
2023
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6. A nanobody recognizes a unique conserved epitope and potently neutralizes SARS-CoV-2 omicron variants

Author

Modhiran, Naphak, Lauer, Simon Malte, Amarilla, Alberto A., Hewins, Peter, Lopes van den Broek, Sara Irene, Low, Yu Shang, Thakur, Nazia, Liang, Benjamin, Nieto, Guillermo Valenzuela, Jung, James, Paramitha, Devina, Isaacs, Ariel, Sng, Julian D.J., Song, David, Jørgensen, Jesper Tranekjær, Cheuquemilla, Yorka, Bürger, Jörg, Andersen, Ida Vang, Himelreichs, Johanna, Jara, Ronald, MacLoughlin, Ronan, Miranda-Chacon, Zaray, Chana-Cuevas, Pedro, Kramer, Vasko, Spahn, Christian, Mielke, Thorsten, Khromykh, Alexander A., Munro, Trent, Jones, Martina L., Young, Paul R., Chappell, Keith, Bailey, Dalan, Kjaer, Andreas, Herth, Matthias Manfred, Jurado, Kellie Ann, Schwefel, David, Rojas-Fernandez, Alejandro, and Watterson, Daniel

Published
2023
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11. A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses

Author

Amarilla, Alberto A., Sng, Julian D. J., Parry, Rhys, Deerain, Joshua M., Potter, James R., Setoh, Yin Xiang, Rawle, Daniel J., Le, Thuy T., Modhiran, Naphak, Wang, Xiaohui, Peng, Nias Y. G., Torres, Francisco J., Pyke, Alyssa, Harrison, Jessica J., Freney, Morgan E., Liang, Benjamin, McMillan, Christopher L. D., Cheung, Stacey T. M., Guevara, Darwin J. Da Costa, Hardy, Joshua M., Bettington, Mark, Muller, David A., Coulibaly, Fasséli, Moore, Frederick, Hall, Roy A., Young, Paul R., Mackenzie, Jason M., Hobson-Peters, Jody, Suhrbier, Andreas, Watterson, Daniel, and Khromykh, Alexander A.

Published
2021
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12. SARS-CoV-2 omicron BA.5 and XBB variants have increased neurotropic potential over BA.1 in K18-hACE2 mice and human brain organoids

Author

Stewart, Romal, primary, Yan, Kexin, additional, Ellis, Sevannah A., additional, Bishop, Cameron R., additional, Dumenil, Troy, additional, Tang, Bing, additional, Nguyen, Wilson, additional, Larcher, Thibaut, additional, Parry, Rhys, additional, Sng, Julian De Jun, additional, Khromykh, Alexander A., additional, Sullivan, Robert K. P., additional, Lor, Mary, additional, Meunier, Frédéric A., additional, Rawle, Daniel J., additional, and Suhrbier, Andreas, additional

Published
2023
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13. TMPRSS2 activation of Omicron lineage Spike glycoproteins is regulated by TMPRSS2 cleavage of ACE2

Author

Aggarwal, Anupriya, primary, Fichter, Christina, additional, Milogiannakis, Vanessa, additional, Akerman, Anouschka, additional, Ison, Timothy, additional, Ruiz Silva, Mariana, additional, Esneau, Camille, additional, Bartlett, Nathan, additional, Burrell, Louise, additional, Patel, Sheila, additional, Churchill, Melissa, additional, Angelovich, Thomas, additional, Parry, Rhys, additional, Sng, Julian D, additional, Neely, Greg G, additional, Moreno, Cesar L, additional, Loo, Lipin, additional, Kelleher, Anthony D, additional, Brilot, Fabienne, additional, Khromykh, Alexander, additional, and Turville, Stuart Grant, additional

Published
2023
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15. Elevated BMI reduces the humoral response to SARS‐CoV‐2 infection.

Author

Tong, Marcus ZW, Sng, Julian DJ, Carney, Meagan, Cooper, Lucy, Brown, Samuel, Lineburg, Katie E, Chew, Keng Yih, Collins, Neve, Ignacio, Kirsten, Airey, Megan, Burr, Lucy, Joyce, Briony A, Jayasinghe, Dhilshan, McMillan, Christopher LD, Muller, David A, Adhikari, Anurag, Gallo, Linda A, Dorey, Emily S, Barrett, Helen L, and Gras, Stephanie

Subjects
*HUMORAL immunity, *SARS-CoV-2, *B cells, *ANTIBODY titer, *BODY mass index
Abstract

Objective: Class III obesity (body mass index [BMI] ≥ 40 kg m−2) significantly impairs the immune response to SARS‐CoV‐2 vaccination. However, the effect of an elevated BMI (≥ 25 kg m−2) on humoral immunity to SARS‐CoV‐2 infection and COVID‐19 vaccination remains unclear. Methods: We collected blood samples from people who recovered from SARS‐CoV‐2 infection approximately 3 and 13 months of post‐infection (noting that these individuals were not exposed to SARS‐CoV‐2 or vaccinated in the interim). We also collected blood samples from people approximately 5 months of post‐second dose COVID‐19 vaccination (the majority of whom did not have a prior SARS‐CoV‐2 infection). We measured their humoral responses to SARS‐CoV‐2, grouping individuals based on a BMI greater or less than 25 kg m−2. Results: Here, we show that an increased BMI (≥ 25 kg m−2), when accounting for age and sex differences, is associated with reduced antibody responses after SARS‐CoV‐2 infection. At 3 months of post‐infection, an elevated BMI was associated with reduced antibody titres. At 13 months of post‐infection, an elevated BMI was associated with reduced antibody avidity and a reduced percentage of spike‐positive B cells. In contrast, no significant association was noted between a BMI ≥ 25 kg m−2 and humoral immunity to SARS‐CoV‐2 at 5 months of post‐secondary vaccination. Conclusions: Taken together, these data showed that elevated BMI is associated with an impaired humoral immune response to SARS‐CoV‐2 infection. The impairment of infection‐induced immunity in individuals with a BMI ≥ 25 kg m−2 suggests an added impetus for vaccination rather than relying on infection‐induced immunity. [ABSTRACT FROM AUTHOR]

Published
2023
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16. Obesity Is a Risk Factor for Severe Influenza Virus Infection and COVID-19 in Children.

Author

Noye, Ellesandra C, Bekkering, Siroon, Sng, Julian D J, Burgner, David, Longmore, Danielle K, and Short, Kirsty R

Subjects
IMMUNOGLOBULIN analysis, RISK assessment, IMMUNIZATION, DEATH, HOSPITAL care, INFLUENZA, SEVERITY of illness index, TREATMENT effectiveness, MULTISYSTEM inflammatory syndrome, CHILDHOOD obesity, COVID-19, DISEASE risk factors, DISEASE complications
Published
2025
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17. Additional file 13 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 13: Supplementary Table S11. Differentially expressed cytokine or cytokine related genes in infected avian endothelial cells.

Published
2023
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18. Additional file 4 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 4: Supplementary Table S2. BUSCO analysis of the final genomes.

Published
2023
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19. Additional file 5 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 5: Supplementary Table S3. CEGMA analysis of the final genomes.

Published
2023
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20. Additional file 7 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 7: Supplementary Table S5. List of genes known to affect plumage colour in birds.

Published
2023
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21. Additional file 2 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 2: Supplementary Table S1. Heterozygosity, QV and completeness values for swan genomes.

Published
2023
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22. Additional file 6 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 6: Supplementary Table S4. GO biological process annotation of inverted genes in the Mallard duck (relative to the black swan).

Published
2023
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23. Additional file 3 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 3: Online Methods.

Published
2023
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24. Additional file 8 of The swan genome and transcriptome, it is not all black and white

Author

Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, Challagulla, Arjun, Kraus, Robert, Mueller, Ralf C., Tong, Marcus Z. W., Hulme, Katina D., Bielefeldt-Ohmann, Helle, Steele, Lauren E., Wu, Melanie, Sng, Julian, Noye, Ellesandra, Bruxner, Timothy J., Au, Gough G., Lowther, Suzanne, Blommaert, Julie, Suh, Alexander, McCauley, Alexander J., Kaur, Parwinder, Dudchenko, Olga, Aiden, Erez, Fedrigo, Olivier, Formenti, Giulio, Mountcastle, Jacquelyn, Chow, William, Martin, Fergal J., Ogeh, Denye N., Thiaud-Nissen, Françoise, Howe, Kerstin, Tracey, Alan, Smith, Jacqueline, Kuo, Richard I., Renfree, Marilyn B., Kimura, Takashi, Sakoda, Yoshihiro, McDougall, Mathew, Spencer, Hamish G., Pyne, Michael, Tolf, Conny, Waldenström, Jonas, Jarvis, Erich D., Baker, Michelle L., Burt, David W., and Short, Kirsty R.

Abstract

Additional file 8: Supplementary Table S6. Immune gene families are contractive in black swans compared to mute swans. The number of genes in each immune gene sub-family identified is given in each column for the corresponding species.

Published
2023
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25. Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology

Author

Aguado, Julio, primary, Amarilla, Alberto A., additional, Taherian Fard, Atefeh, additional, Albornoz, Eduardo A., additional, Tyshkovskiy, Alexander, additional, Schwabenland, Marius, additional, Chaggar, Harman K., additional, Modhiran, Naphak, additional, Gómez-Inclán, Cecilia, additional, Javed, Ibrahim, additional, Baradar, Alireza A., additional, Liang, Benjamin, additional, Dharmaratne, Malindrie, additional, Pietrogrande, Giovanni, additional, Padmanabhan, Pranesh, additional, Freney, Morgan E., additional, Parry, Rhys, additional, Sng, Julian D.J., additional, Isaacs, Ariel, additional, Khromykh, Alexander A., additional, Rojas-Fernandez, Alejandro, additional, Davis, Thomas P., additional, Prinz, Marco, additional, Bengsch, Bertram, additional, Gladyshev, Vadim N., additional, Woodruff, Trent M., additional, Mar, Jessica C., additional, Watterson, Daniel, additional, and Wolvetang, Ernst J., additional

Published
2023
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26. Monoclonal Antibodies Specific for SARS-CoV-2 Spike Protein Suitable for Multiple Applications for Current Variants of Concern

Author

Morgan, Mahali S., primary, Yan, Kexin, additional, Le, Thuy T., additional, Johnston, Ryan A., additional, Amarilla, Alberto A., additional, Muller, David A., additional, McMillan, Christopher L. D., additional, Modhiran, Naphak, additional, Watterson, Daniel, additional, Potter, James R., additional, Sng, Julian D.J., additional, Lor, Mary, additional, Paramitha, Devina, additional, Isaacs, Ariel, additional, Khromykh, Alexander A., additional, Hall, Roy A., additional, Suhrbier, Andreas, additional, Rawle, Daniel J., additional, and Hobson-Peters, Jody, additional

Published
2022
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27. An alpaca-derived nanobody recognizes a unique conserved epitope and retains potent activity against the SARS-CoV-2 omicron variant

Author

Modhiran, Naphak, primary, Lauer, Simon Malte, additional, Amarilla, Alberto A, additional, Hewins, Peter, additional, van den Broek, Sara Irene Lopes, additional, Low, Yu Shang, additional, Thakur, Nazia, additional, Liang, Benjamin, additional, Nieto, Guillermo Valenzuela, additional, Jung, James, additional, Paramitha, Devina, additional, Isaacs, Ariel, additional, de Sng, Julian, additional, Song, David, additional, Jørgensen, Jesper Tranekjær, additional, Cheuquemilla, Yorka, additional, Bürger, Jörg, additional, Andersen, Ida Vang, additional, Himelreichs, Johanna, additional, Jara, Ronald, additional, MacLoughlin, Ronan, additional, Miranda-Chacon, Zaray, additional, Chana-Cuevas, Pedro, additional, Kramer, Vasko, additional, Spahn, Christian M.T., additional, Mielke, Thorsten, additional, Khromykh, Alexander A, additional, Munro, Trent, additional, Jones, Martina, additional, Young, Paul R, additional, Chappell, Keith, additional, Bailey, Dalan, additional, Kjaer, Andreas, additional, Herth, Matthias Manfred, additional, Jurado, Kellie Ann, additional, Schwefel, David, additional, Rojas-Fernandez, Alejandro, additional, and Watterson, Daniel, additional

Published
2022
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28. Increased neurovirulence of omicron BA.5 and XBB variants over BA.1 in K18-hACE2 mice and human brain organoids

Author

Stewart, Romal, primary, Yan, Kexin, additional, Ellis, Sevannah A., additional, Bishop, Cameron, additional, Dumenil, Troy, additional, Tang, Bing, additional, Nguyen, Wilson, additional, Larcher, Thibaut, additional, Parry, Rhys, additional, Jun Sng, Julian De, additional, Khromykh, Alexander A., additional, Sullivan, Robert K. P., additional, Lor, Mary, additional, Meunier, Frédéric A., additional, Rawle, Daniel J., additional, and Suhrbier, Andreas, additional

Published
2022
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29. Zika virus noncoding RNA cooperates with the viral protein NS5 to inhibit STAT1 phosphorylation and facilitate viral pathogenesis

Author

Slonchak, Andrii, primary, Wang, Xiaohui, additional, Aguado, Julio, additional, Sng, Julian D. J., additional, Chaggar, Harman, additional, Freney, Morgan E., additional, Yan, Kexin, additional, Torres, Francisco J., additional, Amarilla, Alberto A., additional, Balea, Rickyle, additional, Setoh, Yin Xiang, additional, Peng, Nias, additional, Watterson, Daniel, additional, Wolvetang, Ernst, additional, Suhrbier, Andreas, additional, and Khromykh, Alexander A., additional

Published
2022
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30. SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike protein

Author

Albornoz, Eduardo A., primary, Amarilla, Alberto A., additional, Modhiran, Naphak, additional, Parker, Sandra, additional, Li, Xaria X., additional, Wijesundara, Danushka K., additional, Aguado, Julio, additional, Zamora, Adriana Pliego, additional, McMillan, Christopher L. D., additional, Liang, Benjamin, additional, Peng, Nias Y. G., additional, Sng, Julian D. J., additional, Saima, Fatema Tuj, additional, Fung, Jenny N., additional, Lee, John D., additional, Paramitha, Devina, additional, Parry, Rhys, additional, Avumegah, Michael S., additional, Isaacs, Ariel, additional, Lo, Martin W., additional, Miranda-Chacon, Zaray, additional, Bradshaw, Daniella, additional, Salinas-Rebolledo, Constanza, additional, Rajapakse, Niwanthi W., additional, Wolvetang, Ernst J., additional, Munro, Trent P., additional, Rojas-Fernandez, Alejandro, additional, Young, Paul R., additional, Stacey, Katryn J., additional, Khromykh, Alexander A., additional, Chappell, Keith J., additional, Watterson, Daniel, additional, and Woodruff, Trent M., additional

Published
2022
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31. Ancestral SARS-CoV-2, but not Omicron, replicates less efficiently in primary pediatric nasal epithelial cells

Author

Zhu, Yanshan, primary, Chew, Keng Yih, additional, Wu, Melanie, additional, Karawita, Anjana C., additional, McCallum, Georgina, additional, Steele, Lauren E., additional, Yamamoto, Ayaho, additional, Labzin, Larisa I., additional, Yarlagadda, Tejasri, additional, Khromykh, Alexander A., additional, Wang, Xiaohui, additional, Sng, Julian D. J., additional, Stocks, Claudia J., additional, Xia, Yao, additional, Kollmann, Tobias R., additional, Martino, David, additional, Joensuu, Merja, additional, Meunier, Frédéric A., additional, Balistreri, Giuseppe, additional, Bielefeldt-Ohmann, Helle, additional, Bowen, Asha C., additional, Kicic, Anthony, additional, Sly, Peter D., additional, Spann, Kirsten M., additional, and Short, Kirsty R., additional

Published
2022
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32. Synthetic Heparan Sulfate Mimetic Pixatimod (PG545) Potently Inhibits SARS-CoV-2 by Disrupting the Spike-ACE2 Interaction

Author

Guimond, Scott E., Mycroft-West, Courtney J., Gandhi, Neha S., Tree, Julia A., Le, Thuy T., Spalluto, C. Mirella, Humbert, Maria V., Buttigieg, Karen R., Coombes, Naomi, Elmore, Michael J., Wand, Matthew, Nyström, Kristina, Said, Joanna, Setoh, Yin Xiang, Amarilla, Alberto A., Modhiran, Naphak, Sng, Julian D.J., Chhabra, Mohit, Young, Paul R., Rawle, Daniel J., Lima, Marcelo A., Yates, Edwin A., Karlsson, Richard, Miller, Rebecca L., Chen, Yen Hsi, Bagdonaite, Ieva, Yang, Zhang, Stewart, James, Nguyen, Dung, Laidlaw, Stephen, Hammond, Edward, Dredge, Keith, Wilkinson, Tom M.A., Watterson, Daniel, Khromykh, Alexander A., Suhrbier, Andreas, Carroll, Miles W., Trybala, Edward, Bergström, Tomas, Ferro, Vito, Skidmore, Mark A., Turnbull, Jeremy E., Guimond, Scott E., Mycroft-West, Courtney J., Gandhi, Neha S., Tree, Julia A., Le, Thuy T., Spalluto, C. Mirella, Humbert, Maria V., Buttigieg, Karen R., Coombes, Naomi, Elmore, Michael J., Wand, Matthew, Nyström, Kristina, Said, Joanna, Setoh, Yin Xiang, Amarilla, Alberto A., Modhiran, Naphak, Sng, Julian D.J., Chhabra, Mohit, Young, Paul R., Rawle, Daniel J., Lima, Marcelo A., Yates, Edwin A., Karlsson, Richard, Miller, Rebecca L., Chen, Yen Hsi, Bagdonaite, Ieva, Yang, Zhang, Stewart, James, Nguyen, Dung, Laidlaw, Stephen, Hammond, Edward, Dredge, Keith, Wilkinson, Tom M.A., Watterson, Daniel, Khromykh, Alexander A., Suhrbier, Andreas, Carroll, Miles W., Trybala, Edward, Bergström, Tomas, Ferro, Vito, Skidmore, Mark A., and Turnbull, Jeremy E.

Abstract

Heparan sulfate (HS) is a cell surface polysaccharide recently identified as a coreceptor with the ACE2 protein for the S1 spike protein on SARS-CoV-2 virus, providing a tractable new therapeutic target. Clinically used heparins demonstrate an inhibitory activity but have an anticoagulant activity and are supply-limited, necessitating alternative solutions. Here, we show that synthetic HS mimetic pixatimod (PG545), a cancer drug candidate, binds and destabilizes the SARS-CoV-2 spike protein receptor binding domain and directly inhibits its binding to ACE2, consistent with molecular modeling identification of multiple molecular contacts and overlapping pixatimod and ACE2 binding sites. Assays with multiple clinical isolates of SARS-CoV-2 virus show that pixatimod potently inhibits the infection of monkey Vero E6 cells and physiologically relevant human bronchial epithelial cells at safe therapeutic concentrations. Pixatimod also retained broad potency against variants of concern (VOC) including B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron). Furthermore, in a K18-hACE2 mouse model, pixatimod significantly reduced SARS-CoV-2 viral titers in the upper respiratory tract and virus-induced weight loss. This demonstration of potent anti-SARS-CoV-2 activity tolerant to emerging mutations establishes proof-of-concept for targeting the HS-Spike protein-ACE2 axis with synthetic HS mimetics and provides a strong rationale for clinical investigation of pixatimod as a potential multimodal therapeutic for COVID-19.

Published
2022

33. Ancestral SARS-CoV-2, but not Omicron, replicates less efficiently in primary pediatric nasal epithelial cells

Author

Zhu, Yanshan, Chew, Keng Yih, Wu, Melanie, Karawita, Anjana C., McCallum, Georgina, Steele, Lauren E., Yamamoto, Ayaho, Labzin, Larisa I., Yarlagadda, Tejasri, Khromykh, Alexander A., Wang, Xiaohui, Sng, Julian D. J., Stocks, Claudia J., Xia, Yao, Kollmann, Tobias R., Martino, David, Joensuu, Merja, Meunier, Frédéric A., Balistreri, Giuseppe, Bielefeldt-Ohmann, Helle, Bowen, Asha C., Kicic, Anthony, Sly, Peter D., Spann, Kirsten M., Short, Kirsty R., Zhu, Yanshan, Chew, Keng Yih, Wu, Melanie, Karawita, Anjana C., McCallum, Georgina, Steele, Lauren E., Yamamoto, Ayaho, Labzin, Larisa I., Yarlagadda, Tejasri, Khromykh, Alexander A., Wang, Xiaohui, Sng, Julian D. J., Stocks, Claudia J., Xia, Yao, Kollmann, Tobias R., Martino, David, Joensuu, Merja, Meunier, Frédéric A., Balistreri, Giuseppe, Bielefeldt-Ohmann, Helle, Bowen, Asha C., Kicic, Anthony, Sly, Peter D., Spann, Kirsten M., and Short, Kirsty R.

Abstract

Children typically experience more mild symptoms of Coronavirus Disease 2019 (COVID-19) when compared to adults. There is a strong body of evidence that children are also less susceptible to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection with the ancestral viral isolate. However, the emergence of SARS-CoV-2 variants of concern (VOCs) has been associated with an increased number of pediatric infections. Whether this is the result of widespread adult vaccination or fundamental changes in the biology of SARS-CoV-2 remain to be determined. Here, we use primary nasal epithelial cells (NECs) from children and adults, differentiated at an air-liquid interface to show that the ancestral SARS-CoV-2 replicates to significantly lower titers in the NECs of children compared to those of adults. This was associated with a heightened antiviral response to SARS-CoV-2 in the NECs of children. Importantly, the Delta variant also replicated to significantly lower titers in the NECs of children. This trend was markedly less pronounced in the case of Omicron. It is also striking to note that, at least in terms of viral RNA, Omicron replicated better in pediatric NECs compared to both Delta and the ancestral virus. Taken together, these data show that the nasal epithelium of children supports lower infection and replication of ancestral SARS-CoV-2, although this may be changing as the virus evolves.

Published
2022

35. The swan genome and transcriptome: its not all black and white

Author

Karawita, Anjana C., primary, Cheng, Yuanyuan, additional, Chew, Keng Yih, additional, Challgula, Arjun, additional, Kraus, Robert, additional, Mueller, Ralf C., additional, Tong, Marcus Z. W., additional, Hulme, Katina D., additional, Beielefeldt-Ohmann, Helle, additional, Steele, Lauren E., additional, Wu, Melanie, additional, Sng, Julian, additional, Noye, Ellesandra, additional, Bruxner, Timothy J., additional, Au, Gough G., additional, Lowther, Suzanne, additional, Blommaert, Julie, additional, Suh, Alexander, additional, McCauley, Alexander J., additional, Kaur, Parwinder, additional, Dudchenko, Olga, additional, Aiden, Erez, additional, Fedrigo, Olivier, additional, Formenti, Giulio, additional, Mountcastle, Jacquelyn, additional, Chow, William, additional, Martin, Fergal J., additional, Ogeh, Denye N., additional, Thiaud-Nissen, Françoise, additional, Howe, Kerstin, additional, Collins, Joanna, additional, Tracey, Alan, additional, Smith, Jacqueline, additional, Kuo, Richard I., additional, Renfree, Marilyn B., additional, Kimura, Takashi, additional, Sakoda, Yoshihiro, additional, McDougall, Mathew, additional, Spencer, Hamish G., additional, Pyne, Michael, additional, Tolf, Conny, additional, Waldenström, Jonas, additional, Jarvis, Erich D., additional, Baker, Michelle L., additional, Burt, David W., additional, and Short, Kirsty R., additional

Published
2022
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36. Synthetic Heparan Sulfate Mimetic Pixatimod (PG545) Potently Inhibits SARS-CoV-2 by Disrupting the Spike–ACE2 Interaction

Author

Guimond, Scott E., primary, Mycroft-West, Courtney J., additional, Gandhi, Neha S., additional, Tree, Julia A., additional, Le, Thuy T., additional, Spalluto, C. Mirella, additional, Humbert, Maria V., additional, Buttigieg, Karen R., additional, Coombes, Naomi, additional, Elmore, Michael J., additional, Wand, Matthew, additional, Nyström, Kristina, additional, Said, Joanna, additional, Setoh, Yin Xiang, additional, Amarilla, Alberto A., additional, Modhiran, Naphak, additional, Sng, Julian D. J., additional, Chhabra, Mohit, additional, Young, Paul R., additional, Rawle, Daniel J., additional, Lima, Marcelo A., additional, Yates, Edwin A., additional, Karlsson, Richard, additional, Miller, Rebecca L., additional, Chen, Yen-Hsi, additional, Bagdonaite, Ieva, additional, Yang, Zhang, additional, Stewart, James, additional, Nguyen, Dung, additional, Laidlaw, Stephen, additional, Hammond, Edward, additional, Dredge, Keith, additional, Wilkinson, Tom M. A., additional, Watterson, Daniel, additional, Khromykh, Alexander A., additional, Suhrbier, Andreas, additional, Carroll, Miles W., additional, Trybala, Edward, additional, Bergström, Tomas, additional, Ferro, Vito, additional, Skidmore, Mark A., additional, and Turnbull, Jeremy E., additional

Published
2022
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37. EDI in Singapore: emerging issues with sexual and gender minorities and people living with HIV

Author

Lim, Angeline Cuifang, Rajah, Jefferson K., Sng, Julian Wei Meng, and Kuan, Yee Han

Abstract

Diversity management had always been at the forefront of Singapore's social and economic policies. Over the last half a century, a slew of legislation, social and economic policies aimed at maintaining harmony and ensuring economic progress have successfully put Singapore on the world map as a global trading hub. Owing to Singapore's heritage as a migrant nation, much of the diversity management efforts in the past had focused on bases of diversity such as age, race, gender, religion. However, in recent years, there was much public discourse on the inclusion of gender and sexual minorities and people living with HIV, pushing for a greater need to address issues that have long been considered sensitive. This chapter spotlights the two issues against a backdrop of how diversity is managed in the Singapore context, and discusses two frameworks that may help shed more light on Singapore's approach to diversity management. acceptedVersion

Published
2022
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38. SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike-ACE2 receptor interaction

Author

Albornoz, Eduardo A, primary, Amarilla, Alberto A, additional, Modhiran, Naphak, additional, Parker, Sandra, additional, Li, Xaria X, additional, Wijesundara, Danushka K, additional, Pliego Zamora, Adriana, additional, McMillan, Christopher LD, additional, Liang, Benjamin, additional, Peng, Nias Y.G, additional, Sng, Julian D.J, additional, Tuj Saima, Fatema, additional, Paramitha, Devina, additional, Parry, Rhys, additional, Avumegah, Michael S, additional, Isaacs, Ariel, additional, Lo, Martin, additional, Miranda-Chacon, Zaray, additional, Bradshaw, Daniella, additional, Salinas-Rebolledo, Constanza, additional, Rajapakse, Niwanthi W, additional, Munro, Trent, additional, Rojas-Fernandez, Alejandro, additional, Young, Paul R, additional, Stacey, Katryn J, additional, Khromykh, Alexander A, additional, Chappell, Keith J, additional, Watterson, Daniel, additional, and Woodruff, Trent M, additional

Published
2022
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39. Monoclonal Antibodies Specific for SARS-CoV-2 Spike Protein Suitable for Multiple Applications for Current Variants of Concern.

Author

Morgan, Mahali S., Yan, Kexin, Le, Thuy T., Johnston, Ryan A., Amarilla, Alberto A., Muller, David A., McMillan, Christopher L. D., Modhiran, Naphak, Watterson, Daniel, Potter, James R., Sng, Julian D.J., Lor, Mary, Paramitha, Devina, Isaacs, Ariel, Khromykh, Alexander A., Hall, Roy A., Suhrbier, Andreas, Rawle, Daniel J., and Hobson-Peters, Jody

Subjects
MONOCLONAL antibodies, SARS-CoV-2, SARS-CoV-2 Omicron variant, COVID-19, COVID-19 pandemic
Abstract

The global coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spawned an ongoing demand for new research reagents and interventions. Herein we describe a panel of monoclonal antibodies raised against SARS-CoV-2. One antibody showed excellent utility for immunohistochemistry, clearly staining infected cells in formalin-fixed and paraffin embedded lungs and brains of mice infected with the original and the omicron variants of SARS-CoV-2. We demonstrate the reactivity to multiple variants of concern using ELISAs and describe the use of the antibodies in indirect immunofluorescence assays, Western blots, and rapid antigen tests. Finally, we illustrate the ability of two antibodies to reduce significantly viral tissue titers in K18-hACE2 transgenic mice infected with the original and an omicron isolate of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Published
2023
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40. Structural analysis of 3’UTRs in insect flaviviruses reveals novel determinant of sfRNA biogenesis and provides new insights into flavivirus evolution

Author

Slonchak, Andrii, primary, Parry, Rhys, additional, Pullinger, Brody, additional, Sng, Julian D.J., additional, Wang, Xiaohui, additional, Buck, Teresa F, additional, Torres, Francisco J, additional, Harrison, Jessica J, additional, Colmant, Agathe M G, additional, Hobson-Peters, Jody, additional, Hall, Roy A, additional, Tuplin, Andrew, additional, and Khromykh, Alexander A, additional

Published
2021
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41. Zika virus noncoding RNA cooperates with the viral protein NS5 to inhibit STAT1 phosphorylation and facilitate viral pathogenesis

Author

Slonchak, Andrii, primary, Wang, Xiaohui, additional, Chaggar, Harman, additional, Aguado, Julio, additional, Freney, Morgan, additional, Yan, Kexin, additional, Torres, Francisco J, additional, Amarilla, Alberto A, additional, Balea, Rickyle, additional, Sng, Julian D. J., additional, Setoh, Yin Xiang, additional, Peng, Nias, additional, Watterson, Daniel, additional, Wolvetang, Ernst, additional, Suhrbier, Andreas, additional, and Khromykh, Alexander A, additional

Published
2021
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42. Pediatric nasal epithelial cells are less permissive to SARS-CoV-2 replication compared to adult cells

Author

Zhu, Yanshan, primary, Chew, Keng Yih, additional, Wu, Melanie, additional, Karawita, Anjana C., additional, McCallum, Georgina, additional, Steele, Lauren E, additional, Yamamoto, Ayaho, additional, Labzin, Larisa L., additional, Yarlagadda, Tejasri, additional, Khromykh, Alexander A., additional, Wang, Xiaohui, additional, Sng, Julian, additional, Stocks, Claudia J., additional, Xia, Yao, additional, Kollmann, Tobias R., additional, Martino, David, additional, Joensuu, Merja, additional, Meunier, Frédéric A., additional, Balistreri, Giuseppe, additional, Bielefeldt-Ohmann, Helle, additional, Bowen, Asha C., additional, Kicic, Anthony, additional, Sly, Peter D., additional, Spann, Kirsten M., additional, and Short, Kirsty R., additional

Published
2021
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43. An Optimized High-Throughput Immuno-Plaque Assay for SARS-CoV-2

Author

Amarilla, Alberto A., primary, Modhiran, Naphak, additional, Setoh, Yin Xiang, additional, Peng, Nias Y. G., additional, Sng, Julian D. J., additional, Liang, Benjamin, additional, McMillan, Christopher L. D., additional, Freney, Morgan E., additional, Cheung, Stacey T. M., additional, Chappell, Keith J., additional, Khromykh, Alexander A., additional, Young, Paul R., additional, and Watterson, Daniel, additional

Published
2021
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44. Synthetic Heparan Sulfate Mimetic Pixatimod (PG545) Potently Inhibits SARS-CoV-2 By Disrupting The Spike-ACE2 interaction

Author

Guimond, Scott E., primary, Mycroft-West, Courtney J., additional, Gandhi, Neha S., additional, Tree, Julia A., additional, Le, Thuy T, additional, Spalluto, C. Mirella, additional, Humbert, Maria V., additional, Buttigieg, Karen R., additional, Coombes, Naomi, additional, Elmore, Michael J., additional, Nyström, Kristina, additional, Said, Joanna, additional, Setoh, Yin Xiang, additional, Amarilla, Alberto A., additional, Modhiran, Naphak, additional, Sng, Julian D.J., additional, Chhabra, Mohit, additional, Young, Paul R., additional, Lima, Marcelo A., additional, A.Yates, Edwin, additional, Karlsson, Richard, additional, Miller, Rebecca L., additional, Chen, Yen-Hsi, additional, Bagdonaite, Ieva, additional, Yang, Zhang, additional, Stewart, James, additional, Hammond, Edward, additional, Dredge, Keith, additional, Wilkinson, Tom M.A., additional, Watterson, Daniel, additional, Khromykh, Alexander A., additional, Suhrbier, Andreas, additional, Carroll, Miles W., additional, Trybala, Edward, additional, Bergström, Tomas, additional, Ferro, Vito, additional, Skidmore, Mark A., additional, and Turnbull, Jeremy E., additional

Published
2020
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45. High-Throughput Synthesis and Evaluation of Antiviral Copolymers for Enveloped Respiratory Viruses.

Author

Mengist HM, Denman P, Frost C, Sng JDJ, Logan S, Yarlagadda T, Spann KM, Barner L, Fairfull-Smith KE, Short KR, and Boase NR

Subjects
Humans, Animals, Rhinovirus drug effects, COVID-19 Drug Treatment, COVID-19 virology, Antiviral Agents pharmacology, Antiviral Agents chemistry, Antiviral Agents chemical synthesis, SARS-CoV-2 drug effects, Polymers chemistry, Polymers pharmacology, Polymers chemical synthesis, High-Throughput Screening Assays
Abstract

COVID-19 made apparent the devastating impact viral pandemics have had on global health and order. Development of broad-spectrum antivirals to provide early protection upon the inevitable emergence of new viral pandemics is critical. In this work, antiviral polymers are discovered using a combination of high-throughput polymer synthesis and antiviral screening, enabling diverse polymer compositions to be explored. Amphipathic polymers, with ionizable tertiary amine groups, are the most potent antivirals, effective against influenza virus and SARS-CoV-2, with minimal cytotoxicity. It is hypothesized that these polymers interact with the viral membrane as they showed no activity against a nonenveloped virus (rhinovirus). The switchable chemistry of the polymers during endosomal acidification was evaluated using lipid monolayers, indicating that a complex synergy between hydrophobicity and ionization drives polymer-membrane interactions. This new high-throughput methodology can be adapted to continue to engineer the potency of the lead candidates or develop antiviral polymers against other emerging viral classes.

Published
2024
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