Alexander Khromykh has PhD degree in Molecular Virology. He worked as Postdoctoral Fellow at the University of Ottawa in Canada. He then joined Sir Albert Sakzewski Virus Research Centre in Brisbane and became a laboratory Head in 2001. He moved his laboratory to St Luica campus in 2005 to take an appointment with the School of Chemistry and Molecular Biosciences (SCMB). He was the founding Director of the SCMB’s Centre for Infectious Disease Research and is currently the Deputy Director of the Australian Infectious Diseases Research Centre. He is also the Director of Centre of Excellence and a member of COVID-19 and Zika virus Task Forces in the Global Virus Network.
The main areas of research of the group are molecular virology, viral pathogenesis, and virus-host interactions. The viruses studied in the group are pathogenic RNA viruses, viruses such as West Nile virus, Zika virus, and SARS-CoV-2 virus. The goal of the research is to determine the mechanisms by which these viruses cause disease in the hosts and to identify viral and host factors determining the outcome of infection. The group uses a range of classical and more modern approaches including molecular manipulations with viral infectious cDNA clones and replicons, transient and stable expression of viral proteins and noncoding RNAs, viral replication and virulence assays, deep mutational scanning, mass spectrometry, next generation sequencing, siRNA knockdowns, and knockout cells and mice. Together, these approaches allow the group to perform detailed analysis of the effects of changes in the viral and host genomes that are likely to have a profound impact on virus replication and pathogenesis. The obtained knowldge is also applied to develop novel vaccine platforms and test antivirals.
Journal Article: Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology
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. ... Wolvetang, Ernst J. (2023). Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology. Nature Aging, 1-15. doi: 10.1038/s43587-023-00519-6
Journal Article: A nanobody recognizes a unique conserved epitope and potently neutralizes against the SARS-CoV-2 omicron variants
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 M. T., Mielke, Thorsten, Khromykh, Alexander A., Munro, Trent, Jones, Martina L. ... Watterson, Daniel (2023). A nanobody recognizes a unique conserved epitope and potently neutralizes against the SARS-CoV-2 omicron variants. iScience, 26 (7) 107085, 107085. doi: 10.1016/j.isci.2023.107085
Journal Article: Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2
Shaker, Mohammed R., Slonchak, Andrii, Al-mhanawi, Bahaa, Morrison, Sean D., Sng, Julian D. J., Cooper-White, Justin, Khromykh, Alexander A. and Wolvetang, Ernst J. (2023). Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2. bioRxiv. doi: 10.1101/2023.06.12.544552
Predicting and preparing for the unfolding evolution of SARS-CoV-2
(2022–2025) NHMRC IDEAS Grants
How the synergy between flavivirus protein and noncoding RNA defeats antiviral response
(2022–2024) NHMRC IDEAS Grants
Chimeric insect-specific viruses as novel vaccines for mosquito-borne diseases
(2020–2023) NHMRC Development Grant
Uncovering host determinants of Zika virus replication using an in vivo and in vitro RNAi screening approach
(2023) Doctor Philosophy
Cooperation between sfRNA and non-structural protein NS5 for flavivirus immune evasion
Doctor Philosophy
Uncovering molecular determinants in ZIKV-NS5 related to replication, virulence, and transmissibility
(2022) Doctor Philosophy
Cooperation between sfRNA and non-structural protein NS5 for flavivirus immune evasion
This Earmarked Scholarship project is aligned with a recently awarded Category 1 research grant. It offers you the opportunity to work with leading researchers and contribute to large projects of national significance.
Flaviviruses are important human pathogens that include West Nile, Dengue, Zika, Yellow fever virus and other viruses. They have a unique ability to produce viral noncoding RNA from their 3' untranslated region by hijacking host exoribonuclease. This RNA, termed subgenomic flaviviral RNA (sfRNA), accumulates in infected cells in high abundance and facilitates viral pathogenesis by supressing antiviral response. However, the molecular mechanism that determines this activity is not fully elucidated. Recently we have discovered that sfRNA of Zika virus executes this function in cooperation with the viral protein NS5. We found that sfRNA binds to and stabilises NS5, allowing this protein to inhibit phosphorylation of transcriptional factor STAT1, a key mediator of antiviral signalling.
This project is aimed to uncover how sfRNA binding effects NS5 conformation and its ability to inhibit STAT1 phosphorylation by identifying interacting sites in both molecules, characterising structural changes in NS5 caused by sfRNA binding and creating mutant viruses incapable of sfRNA-NS5 interactions. It will also investigate whether this mechanism is conserved between all flaviviruses.
The successful candidate will have an opportunity to join one of the leading flavivirus laboratories and work in the dynamic team of internationally recognised experts at the forefront of flavivirus research. He/she will obtain experience in the wide range of classical and modern research techniques such as cryo-electron microscopy, next generation sequencing, generation of mutant viruses, immunofluorescent virus detection, quantitative PCR, Northern blotting, electrophoretic mobility shift assay, etc. He/she will have an opportunity to communicate their research at the national and international conferences and publish in the leading academic journals.
Predicting and preparing for the unfolding evolution of SARS-CoV-2
This Earmarked Scholarship project is aligned with a recently awarded Category 1 research grant. It offers you the opportunity to work with leading researchers and contribute to large projects of national significance.
SARS-CoV-2 is the cause of current COVID-19 pandemic which has already infected >270 million people and killed >5 million of them. Currently deployed and future vaccines are likely to significantly decrease the burden of pandemic, however, new viral variants are emerging that are less susceptible to vaccine-induced immunity. Hence, deeper understanding of what drives viral evolution under the pressure of vaccine-induced immune responses is needed to predict and prepare for the emergence of future variants and inform development of more effective vaccines. The project will employ deep mutational scanning methodology to identify changes in the viral spike protein responsible for altered susceptibility to vaccine-induced antibodies. The implications of identified changes on the properties of spike protein and susceptibility to vaccine-induced antibodies will be investigated using structural analysis and various functional assays. The findings will be critical for predicting viral changes that are likely to emerge in the landscape of vaccinations and provide invaluable information for pre-emptive development of vaccines that will be able to minimise future emergence of vaccine-resistant variants.
Flavivirus replication and assembly
Roby, Justin A., Funk, Anneke and Khromykh, Alexander A. (2012). Flavivirus replication and assembly. Molecular virology and control of flaviviruses. (pp. 21-49) edited by Pei-Yong Shi. Norfolk, United Kingdom: Caister Academic Press.
Nucleic acid-based infectious and pseudoinfectious flavivirus vaccines
Roby, Justin A., Hall, Roy A. and Khromykh, Alexander A. (2011). Nucleic acid-based infectious and pseudoinfectious flavivirus vaccines. Replicating vaccines : A new generation. (pp. 299-320) edited by Philip R. Dormitzer, Christian W. Mandl and Rino Rappuoli. Basel, Switzerland: Springer. doi: 10.1007/978-3-0346-0277-8_13
Vaccine development against West Nile Virus
Khromykh, Alexander A., Chang, David C. and Hall, Roy A. (2009). Vaccine development against West Nile Virus. West Nile Encephalitis Virus Infection: Viral Pathogenesis and the Host Immune Response. (pp. 427-451) edited by Diamond, Michael S.. New York: Springer Science + Business Media. doi: 10.1007/978-0-387-79840-0_20
Kunjin RNA replication and applications of Kunjin replicons
Westaway, E. G., Mackenzie, J. M. and Khromykh, A. A. (2003). Kunjin RNA replication and applications of Kunjin replicons. The Flaviviruses: Structure, replication and evolution. (pp. 100-140) edited by Thomas J. Chambers, Thomas P. Monath, Karl Maramorosch, Aaron J. Shatkin and Frederick A. Murphy. San Diego: Academic Press Inc. doi: 10.1016/S0065-3527(03)59004-2
Replication and gene function in Kunjin virus
Westaway, E. G., Mackenzie, J. M. and Khromykh, A. A. (2002). Replication and gene function in Kunjin virus. Japanese Encephalitis and West Nile Viruses. (pp. 323-352) edited by J. S. Mackenzie, A. D. T. Barrett and V. Deubel. Berlin: Springer.
Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology
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. ... Wolvetang, Ernst J. (2023). Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology. Nature Aging, 1-15. doi: 10.1038/s43587-023-00519-6
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 M. T., Mielke, Thorsten, Khromykh, Alexander A., Munro, Trent, Jones, Martina L. ... Watterson, Daniel (2023). A nanobody recognizes a unique conserved epitope and potently neutralizes against the SARS-CoV-2 omicron variants. iScience, 26 (7) 107085, 107085. doi: 10.1016/j.isci.2023.107085
Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2
Shaker, Mohammed R., Slonchak, Andrii, Al-mhanawi, Bahaa, Morrison, Sean D., Sng, Julian D. J., Cooper-White, Justin, Khromykh, Alexander A. and Wolvetang, Ernst J. (2023). Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2. bioRxiv. doi: 10.1101/2023.06.12.544552
Slonchak, Andrii, Chaggar, Harman, Aguado, Julio, Wolvetang, Ernst and Khromykh, Alexander A. (2023). Noncoding RNA of Zika virus affects interplay between Wnt-signaling and pro-apoptotic pathways in the developing brain tissue. Viruses, 15 (5) 1062, 1062. doi: 10.3390/v15051062
Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”
Speck, Peter, Mackenzie, Jason, Bull, Rowena A., Slobedman, Barry, Drummer, Heidi, Fraser, Johanna, Herrero, Lara, Helbig, Karla, Londrigan, Sarah, Moseley, Gregory, Prow, Natalie, Hansman, Grant, Edwards, Robert, Ahlenstiel, Chantelle, Abendroth, Allison, Tscharke, David, Hobson-Peters, Jody, Kriiger-Loterio, Robson, Parry, Rhys, Marsh, Glenn, Harding, Emma, Jacques, David A., Gartner, Matthew J., Lee, Wen Shi, McAuley, Julie, Vaz, Paola, Sainsbury, Frank, Tate, Michelle D., Sinclair, Jane ... Young, Paul (2023). Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”. Journal of Virology, 97 (5), e0045123. doi: 10.1128/jvi.00451-23
Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”
Speck, Peter, Mackenzie, Jason, Bull, Rowena A., Slobedman, Barry, Drummer, Heidi, Fraser, Johanna, Herrero, Lara, Helbig, Karla, Londrigan, Sarah, Moseley, Gregory, Prow, Natalie, Hansman, Grant, Edwards, Robert, Ahlenstiel, Chantelle, Abendroth, Allison, Tscharke, David, Hobson-Peters, Jody, Kriiger-Loterio, Robson, Parry, Rhys, Marsh, Glenn, Harding, Emma, Jacques, David A., Gartner, Matthew J., Lee, Wen Shi, McAuley, Julie, Vaz, Paola, Sainsbury, Frank, Tate, Michelle D., Sinclair, Jane ... Young, Paul (2023). Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”. mBio, 14 (3), e0081523. doi: 10.1128/mbio.00815-23
Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”
Speck, Peter, Mackenzie, Jason, Bull, Rowena A., Slobedman, Barry, Drummer, Heidi, Fraser, Johanna, Herrero, Lara, Helbig, Karla, Londrigan, Sarah, Moseley, Gregory, Prow, Natalie, Hansman, Grant, Edwards, Robert, Ahlenstiel, Chantelle, Abendroth, Allison, Tscharke, David, Hobson-Peters, Jody, Kriiger-Loterio, Robson, Parry, Rhys, Marsh, Glenn, Harding, Emma, Jacques, David A., Gartner, Matthew J., Lee, Wen Shi, McAuley, Julie, Vaz, Paola, Sainsbury, Frank, Tate, Michelle D., Sinclair, Jane ... Young, Paul (2023). Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”. mSphere, 8 (3), e0016523. doi: 10.1128/msphere.00165-23
Hobson‐Peters, Jody, Amarilla, Alberto A., Rustanti, Lina, Marks, Denese C., Roulis, Eileen, Khromykh, Alexander A., Modhiran, Naphak, Watterson, Daniel, Reichenberg, Stefan, Tolksdorf, Frank, Sumian, Chryslain, Seltsam, Axel, Gravemann, Ute and Faddy, Helen M. (2023). Inactivation of SARS‐CoV ‐2 infectivity in platelet concentrates or plasma following treatment with ultraviolet C light or with methylene blue combined with visible light. Transfusion, 63 (2), 288-293. doi: 10.1111/trf.17238
GPR183 antagonism reduces macrophage infiltration in influenza and SARS-CoV-2 infection
Foo, Cheng Xiang, Bartlett, Stacey, Chew, Keng Yih, Ngo, Minh Dao, Bielefeldt-Ohmann, Helle, Jayakody Arachchige, Buddhika, Matthews, Benjamin, Reed, Sarah, Wang, Ran, Smith, Christian, Sweet, Matthew J., Burr, Lucy, Bisht, Kavita, Shatunova, Svetlana, Sinclair, Jane E., Parry, Rhys, Yang, Yuanhao, Lévesque, Jean-Pierre, Khromykh, Alexander, Rosenkilde, Mette Marie, Short, Kirsty R. and Ronacher, Katharina (2023). GPR183 antagonism reduces macrophage infiltration in influenza and SARS-CoV-2 infection. European Respiratory Journal, 61 (3) 2201306, 1-15. doi: 10.1183/13993003.01306-2022
SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike protein
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. ... Woodruff, Trent M. (2023). SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike protein. Molecular Psychiatry, 28 (7), 2878-2893. doi: 10.1038/s41380-022-01831-0
Statement in Support of: “Virology under the Microscope-a Call for Rational Discourse”
Speck, Peter, Mackenzie, Jason, Bull, Rowena A., Slobedman, Barry, Drummer, Heidi, Fraser, Johanna, Herrero, Lara, Helbig, Karla, Londrigan, Sarah, Moseley, Gregory, Prow, Natalie, Hansman, Grant, Edwards, Robert, Ahlenstiel, Chantelle, Abendroth, Allison, Tscharke, David, Hobson-Peters, Jody, Kriiger-Loterio, Robson, Parry, Rhys, Marsh, Glenn, Harding, Emma, Jacques, David A., Gartner, Matthew J., Lee, Wen Shi, McAuley, Julie, Vaz, Paola, Sainsbury, Frank, Tate, Michelle D., Sinclair, Jane ... Young, Paul (2023). Statement in Support of: “Virology under the Microscope-a Call for Rational Discourse”. Journal of Virology, 97 (5). doi: 10.1128/jvi.00451-23
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 (2022). Monoclonal antibodies specific for SARS-CoV-2 spike protein suitable for multiple applications for current variants of concern. Viruses, 15 (1) 139, 1-18. doi: 10.3390/v15010139
Slonchak, Andrii, Wang, Xiaohui, Aguado, Julio, Sng, Julian D. J., Chaggar, Harman, Freney, Morgan E., Yan, Kexin, Torres, Francisco J., Amarilla, Alberto A., Balea, Rickyle, Setoh, Yin Xiang, Peng, Nias, Watterson, Daniel, Wolvetang, Ernst, Suhrbier, Andreas and Khromykh, Alexander A. (2022). Zika virus noncoding RNA cooperates with the viral protein NS5 to inhibit STAT1 phosphorylation and facilitate viral pathogenesis. Science Advances, 8 (48) eadd8095, eadd8095. doi: 10.1126/sciadv.add8095
McMillan, Christopher L.D., Amarilla, Alberto A., Modhiran, Naphak, Choo, Jovin J.Y., Azuar, Armira, Honeyman, Kate E., Khromykh, Alexander A., Young, Paul R., Watterson, Daniel and Muller, David A. (2022). Skin-patch delivered subunit vaccine induces broadly neutralising antibodies against SARS-CoV-2 variants of concern. Vaccine, 40 (34), 4929-4932. doi: 10.1016/j.vaccine.2022.07.013
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. (2022). Ancestral SARS-CoV-2, but not Omicron, replicates less efficiently in primary pediatric nasal epithelial cells. PLoS Biology, 20 (8) e3001728, 1-19. doi: 10.1371/journal.pbio.3001728
SARS-CoV-2 triggers complement activation through interactions with heparan sulfate
Lo, Martin W., Amarilla, Alberto A., Lee, John D., Albornoz, Eduardo A., Modhiran, Naphak, Clark, Richard J., Ferro, Vito, Chhabra, Mohit, Khromykh, Alexander A., Watterson, Daniel and Woodruff, Trent M. (2022). SARS-CoV-2 triggers complement activation through interactions with heparan sulfate. Clinical and Translational Immunology, 11 (8) e1413, e1413. doi: 10.1002/cti2.1413
Reporter flaviviruses as tools to demonstrate homologous and heterologous superinfection exclusion
Torres, Francisco J., Parry, Rhys, Hugo, Leon E. , Slonchak, Andrii , Newton, Natalee D. , Vet, Laura J. , Modhiran, Naphak, Pullinger, Brody , Wang, Xiaohui , Potter, James , Winterford, Clay , Hobson-Peters, Jody , Hall, Roy A. and Khromykh, Alexander A. (2022). Reporter flaviviruses as tools to demonstrate homologous and heterologous superinfection exclusion. Viruses, 14 (7) 1501, 1501. doi: 10.3390/v14071501
Peng, Nias Y. G., Amarilla, Alberto A., Hugo, Leon E., Modhiran, Naphak, Sng, Julian D. J., Slonchak, Andrii, Watterson, Daniel, Setoh, Yin Xiang and Khromykh, Alexander A. (2022). The distinguishing NS5-M114V mutation in American Zika virus isolates has negligible impacts on virus replication and transmission potential. PLoS Neglected Tropical Diseases, 16 (5) e0010426, 1-17. doi: 10.1371/journal.pntd.0010426
Shalash, Ahmed O., Azuar, Armira, Madge, Harrison Y. R., Modhiran, Naphak, Amarilla, Alberto A., Liang, Benjamin, Khromykh, Alexander A., Hussein, Waleed M., Chappell, Keith J., Watterson, Daniel, Young, Paul R., Skwarczynski, Mariusz and Toth, Istvan (2022). Peptide-based vaccine against SARS-CoV-2: peptide antigen discovery and screening of adjuvant systems. Pharmaceutics, 14 (4) 856, 856. doi: 10.3390/pharmaceutics14040856
Dermal delivery of a SARS-CoV-2 subunit vaccine induces immunogenicity against variants of concern
McMillan, Christopher L. D., Azuar, Armira, Choo, Jovin J. Y., Modhiran, Naphak, Amarilla, Alberto A., Isaacs, Ariel, Honeyman, Kate E., Cheung, Stacey T. M., Liang, Benjamin, Wurm, Maria J., Pino, Paco, Kint, Joeri, Fernando, Germain J. P., Landsberg, Michael J., Khromykh, Alexander A., Hobson-Peters, Jody, Watterson, Daniel, Young, Paul R. and Muller, David A. (2022). Dermal delivery of a SARS-CoV-2 subunit vaccine induces immunogenicity against variants of concern. Vaccines, 10 (4) 578, 578. doi: 10.3390/vaccines10040578
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 ... Turnbull, Jeremy E. (2022). Synthetic heparan sulfate mimetic pixatimod (PG545) potently inhibits SARS-CoV-2 by disrupting the spike–ACE2 interaction. ACS Central Science, 8 (5) acscentsci.1c01293, 527-545. doi: 10.1021/acscentsci.1c01293
Slonchak, Andrii, Parry, Rhys, Pullinger, Brody, Sng, Julian D. J., Wang, Xiaohui, Buck, Teresa F., Torres, Francisco J., Harrison, Jessica J., Colmant, Agathe M. G., Hobson-Peters, Jody, Hall, Roy A., Tuplin, Andrew and Khromykh, Alexander A. (2022). Structural analysis of 3’UTRs in insect flaviviruses reveals novel determinants of sfRNA biogenesis and provides new insights into flavivirus evolution. Nature Communications, 13 (1) 1279, 1-16. doi: 10.1038/s41467-022-28977-3
Gestuveo, Rommel J., Parry, Rhys, Dickson, Laura B., Lequime, Sebastian, Sreenu, Vattipally B., Arnold, Matthew J., Khromykh, Alexander A., Schnettler, Esther, Lambrechts, Louis, Varjak, Margus and Kohl, Alain (2022). Mutational analysis of Aedes aegypti Dicer 2 provides insights into the biogenesis of antiviral exogenous small interfering RNAs. PLOS Pathogens, 18 (1) e1010202, 1-29. doi: 10.1371/journal.ppat.1010202
Shalash, Ahmed O., Azuar, Armira, Madge, Harrison Y. R., Modhiran, Naphak, Amarilla, Alberto A., Liang, Benjamin, Khromykh, Alexander A., Watterson, Daniel, Young, Paul R., Toth, Istvan and Skwarczynski, Mariusz (2021). Detection and quantification of SARS-CoV-2 receptor binding domain neutralization by a sensitive competitive ELISA assay. Vaccines, 9 (12) 1493, 1-21. doi: 10.3390/vaccines9121493
Valenzuela Nieto, Guillermo, Jara, Ronald, Watterson, Daniel, Modhiran, Naphak, Amarilla, Alberto A., Himelreichs, Johanna, Khromykh, Alexander A., Salinas-Rebolledo, Constanza, Pinto, Teresa, Cheuquemilla, Yorka, Margolles, Yago, López González del Rey, Natalia, Miranda-Chacon, Zaray, Cuevas, Alexei, Berking, Anne, Deride, Camila, González-Moraga, Sebastián, Mancilla, Héctor, Maturana, Daniel, Langer, Andreas, Toledo, Juan Pablo, Müller, Ananda, Uberti, Benjamín, Krall, Paola, Ehrenfeld, Pamela, Blesa, Javier, Chana-Cuevas, Pedro, Rehren, German, Schwefel, David ... Rojas-Fernandez, Alejandro (2021). Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody. Scientific Reports, 11 (1) 3318, 3318. doi: 10.1038/s41598-021-82833-w
Complete protection by a single-dose skin patch–delivered SARS-CoV-2 spike vaccine
McMillan, Christopher L. D., Choo, Jovin J. Y., Idris, Adi, Supramaniam, Aroon, Modhiran, Naphak, Amarilla, Alberto A., Isaacs, Ariel, Cheung, Stacey T. M., Liang, Benjamin, Bielefeldt-Ohmann, Helle, Azuar, Armira, Acharya, Dhruba, Kelly, Gabrielle, Fernando, Germain J. P., Landsberg, Michael J., Khromykh, Alexander A., Watterson, Daniel, Young, Paul R., McMillan, Nigel A. J. and Muller, David A. (2021). Complete protection by a single-dose skin patch–delivered SARS-CoV-2 spike vaccine. Science Advances, 7 (44) eabj8065, eabj8065. doi: 10.1126/sciadv.abj8065
No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing
Smits, Nathan, Rasmussen, Jay, Bodea, Gabriela O., Amarilla, Alberto A., Gerdes, Patricia, Sanchez-Luque, Francisco J., Ajjikuttira, Prabha, Modhiran, Naphak, Liang, Benjamin, Faivre, Jamila, Deveson, Ira W., Khromykh, Alexander A., Watterson, Daniel, Ewing, Adam D. and Faulkner, Geoffrey J. (2021). No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. Cell Reports, 36 (7) 109530, 109530. doi: 10.1016/j.celrep.2021.109530
Nakayama, Eri, Kato, Fumihiro, Tajima, Shigeru, Ogawa, Shinya, Yan, Kexin, Takahashi, Kenta, Sato, Yuko, Suzuki, Tadaki, Kawai, Yasuhiro, Inagaki, Takuya, Taniguchi, Satoshi, Le, Thuy T., Tang, Bing, Prow, Natalie A., Uda, Akihiko, Maeki, Takahiro, Lim, Chang-Kweng, Khromykh, Alexander A., Suhrbier, Andreas and Saijo, Masayuki (2021). Neuroinvasiveness of the MR766 strain of Zika virus in IFNAR-/- mice maps to prM residues conserved amongst African genotype viruses. PLoS Pathogens , 17 (7) e1009788, 1-39. doi: 10.1371/journal.ppat.1009788
Jansen van Vuren, Petrus , Parry, Rhys, Khromykh, Alexander A. and Paweska, Janusz T. (2021). A 1958 isolate of Kedougou Virus (KEDV) from Ndumu, South Africa, expands the geographic and temporal range of KEDV in Africa. Viruses, 13 (7) 1368, 1368. doi: 10.3390/v13071368
A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses
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A broadly protective antibody that targets the flavivirus NS1 protein
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Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes
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Contemporary anti-Ebola drug discovery approaches and platforms
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Subgenomic flaviviral RNAs: what do we know after the first decade of research
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Fetal brain infection is not a unique characteristic of Brazilian Zika viruses
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Characterization of recombinant Flaviviridae viruses possessing a small reporter-tag
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Cell fusing agent virus and dengue virus mutually interact in Aedes aegypti cell lines
Zhang, Guangmei, Asad, Sultan, Khromykh, Alexander A. and Asgari, Sassan (2017). Cell fusing agent virus and dengue virus mutually interact in Aedes aegypti cell lines. Scientific Reports, 7 (1) 6935, 6935.1-6935.8. doi: 10.1038/s41598-017-07279-5
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Genetic characterization of Cacipacoré virus from ticks collected in São Paulo State, Brazil
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Pyankov, Oleg V., Setoh, Yin Xiang, Bodnev, Sergey A., Edmonds, Judith H., Pyankova, Olga G., Pyankov, Stepan A., Pali, Gabor, Belford, Shane, Lu, Louis, La, Mylinh, Lovrecz, George, Volchkova, Valentina A., Chappell, Keith J., Watterson, Daniel, Marsh, Glenn, Young, Paul R., Agafonov, Alexander A., Farmer, Jillann F., Volchkov, Victor E., Suhrbier, Andreas and Khromykh, Alexander A. (2017). Successful post-exposure prophylaxis of Ebola infected non-human primates using Ebola glycoprotein-specific equine IgG. Scientific Reports, 7 (1) 41537, 41537. doi: 10.1038/srep41537
Pliego Zamora, Adriana, Edmonds, Judith H., Reynolds, Maxwell J., Khromykh, Alexander A. and Ralph, Stephen J. (2016). The in vitro and in vivo antiviral properties of combined monoterpene alcohols against West Nile virus infection. Virology, 495, 18-32. doi: 10.1016/j.virol.2016.04.021
Virulence and evolution of West Nile Virus, Australia, 1960-2012
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Slonchak, Andrii, Shannon, Rory P, Pali, Gabor and Khromykh, Alexander A (2016). Human miRNA miR-532-5p exhibits antiviral activity against West Nile virus via suppression of host genes SESTD1 and TAB3 required for virus replication. Journal of Virology, 90 (5), 2388-2402. doi: 10.1128/JVI.02608-15
Functional non-coding RNAs derived from the flavivirus 3' untranslated region
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Young, Lucy B., Melian, Ezequiel Balmori, Setoh, Yin Xiang, Young, Paul R. and Khromykh, Alexander A. (2015). Last 20 aa of the West Nile virus NS1' protein are responsible for its retention in cells and the formation of unique heat-stable dimers.. Journal of General Virology, 96 (5), 1042-1054. doi: 10.1099/vir.0.000053
O'Brien, Caitlin A., Hobson-Peters, Jody, Yam, Alice Wei Yee, Colmant, Agathe M. G., McLean, Breeanna J., Prow, Natalie A., Watterson, Daniel, Hall-Mendelin, Sonja, Warrilow, David, Ng, Mah-Lee, Khromykh, Alexander A. and Hall, Roy A. (2015). Viral RNA intermediates as targets for detection and discovery of novel and emerging mosquito-borne viruses. PLoS Neglected Tropical Diseases, 9 (3) e0003629, 1-27. doi: 10.1371/journal.pntd.0003629
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Rawle, Daniel J., Setoh, Yin Xiang, Edmonds, Judith H. and Khromykh, Alexander A. (2015). Comparison of attenuated and virulent West Nile virus strains in human monocyte-derived dendritic cells as a model of initial human infection. Virology Journal, 12 (1) 46, 46.1-46.5. doi: 10.1186/s12985-015-0279-3
Post-translational regulation and modifications of flavivirus structural proteins
Roby, Justin A., Setoh, Yin Xiang, Hall, Roy A. and Khromykh, Alexander A. (2015). Post-translational regulation and modifications of flavivirus structural proteins. Journal of General Virology, 96 (7), 1551-1569. doi: 10.1099/vir.0.000097
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Multiple immune factors are involved in controlling acute and chronic chikungunya virus infection
Poo, Yee Suan, Rudd, Penny A., Gardner, Joy, Wilson, Jane A. C., Larcher, Thibaut, Colle, Marie-Anne, Le, Thuy T., Nakaya, Helder I., Warrilow, David, Allcock, Richard, Bielefeldt-Ohmann, Helle, Schroder, Wayne A., Khromykh, Alexander A., Lopez, Jose A. and Suhrbier, Andreas (2014). Multiple immune factors are involved in controlling acute and chronic chikungunya virus infection. PLoS Neglected Tropical Diseases, 8 (12) e3354, 1-15. doi: 10.1371/journal.pntd.0003354
Melian, Ezequiel Balmori, Hall-Mendelin, Sonja, Du, Fangyao, Owens, Nick, Bosco-Lauth, Angela M., Nagasaki, Tomoko, Rudd, Stephen, Brault, Aaron C., Bowen, Richard A., Hall, Roy A., van den Hurk, Andrew F. and Khromykh, Alexander A. (2014). Programmed ribosomal frameshift alters expression of West Nile virus genes and facilitates virus replication in birds and mosquitoes. PLoS Pathogens, 10 (11), e1004447.1-e1004447.18. doi: 10.1371/journal.ppat.1004447
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Slonchak, Andrii, Hussain, Mazhar, Torres Morales, Shessy, Asgari, Sassan and Khromykh, Alexander (2014). Expression of mosquito microRNA aae-miR-2940-5p is down-regulated in response to West Nile Virus infection to restrict viral replication. Journal of Virology, 88 (15), 8457-8467. doi: 10.1128/JVI.00317-14
Mayoral, Jamie G., Etebari, Kayvan, Hussain, Mazhar, Khromykh, Alexander A. and Asgari, Sassan (2014). Wolbachia infection modifies the profile, shuttling and structure of MicroRNAs in a mosquito cell line. PLoS One, 9 (4) e96107, e96107. doi: 10.1371/journal.pone.0096107
Loop de loop: viral RNA evades IFIT1 targeting
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NS1' colocalizes with NS1 and can substitute for NS1 in West Nile virus replication
Young, Lucy B., Melian, Ezequiel Balmori and Khromykh, Alexander A. (2013). NS1' colocalizes with NS1 and can substitute for NS1 in West Nile virus replication. Journal of Virology, 87 (16), 9384-9390. doi: 10.1128/JVI.01101-13
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Effect of Wolbachia on replication of West Nile Virus in mosquito cell line and adult mosquitoes
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Noncoding flavivirus RNA displays RNA interference suppressoractivity in insect and mammalian cells
Schnettler, Esther, Sterken, Mark G., Leung, Jason Y., Metz, Stefan W., Geertsema, Corinne, Goldbach, Rob W., Vlak, Just M., Kohl, Alain, Khromykh, Alexander A. and Pijlman, Gorben P. (2012). Noncoding flavivirus RNA displays RNA interference suppressoractivity in insect and mammalian cells. Journal of Virology, 86 (24), 13486-13500. doi: 10.1128/JVI.01104-12
Moon, Stephanie L., Anderson, John R., Kumagai, Yutaro, Wilusz, Carol J., Akira, Shizuo, Khromykh, Alexander A. and Wilusz, Jeffrey (2012). A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability. RNA, 18 (11), 2029-2040. doi: 10.1261/rna.034330.112
Setoh, Y. X., Prow, N. A., Hobson-Peters, J., Lobigs, M., Young, P. R., Khromykh, A. A. and Hall, R. A. (2012). Identification of residues in West Nile virus premembrane protein that influence viral particle secretion and virulence. Journal of General Virology, 93 (Part 9), 1965-1975. doi: 10.1099/vir.0.044453-0
Interferon response factors 3 and 7 protect against Chikungunya virus hemorrhagic fever and shock
Rudd, Penny A., Wilson, Jane, Gardner, Joy, Larcher, Thibaut, Babarit, Candice, Le, Thuy T., Anraku, Itaru, Kumagai, Yutaro, Loo, Yueh-Ming, Gale Jr, Michael, Akira, Shizuo, Khromykh, Alexander A. and Suhrbier, Andreas (2012). Interferon response factors 3 and 7 protect against Chikungunya virus hemorrhagic fever and shock. Journal of Virology, 86 (18), 9888-9898. doi: 10.1128/JVI.00956-12
Characterization of virulent West Nile virus Kunjin Strain, Australia, 2011
Frost, Melinda J., Zhang, Jing, Edmonds, Judith H., Prow, Natalie A., Gu, Xingnian, Davis, Rodney, Hornitzky, Christine, Arzey, Kathleen E., Finlaison, Deborah, Hick, Paul, Read, Andrew, Hobson-Peters, Jody, May, Fiona J., Doggett, Stephen L., Haniotis, John, Russell, Richard C., Hall, Roy A., Khromykh, Alexander A. and Kirkland, Peter D. (2012). Characterization of virulent West Nile virus Kunjin Strain, Australia, 2011. Emerging Infectious Diseases, 18 (5), 792-800. doi: 10.3201/eid1805.111720
Schuessler, Andrea, Funk, Anneke, Lazear, Helen M., Cooper, Daphne A., Torres, Shessy, Daffis, Stephane, Jha, Babal Kant, Kumagai, Yutaro, Takeuchi, Osamu, Hertzog, Paul, Silverman, Robert, Akira, Shizuo, Barton, David J., Diamond, Michael S. and Khromykh, Alexander A. (2012). West Nile virus noncoding subgenomic RNA contributes to viral evasion of the type I interferon-mediated antiviral response. Journal of Virology, 86 (10), 5708-5718. doi: 10.1128/JVI.00207-12
Hussain, Mazhar, Torres, Shessy, Schnettler, Esther, Funk, Anneke, Grundhoff, Adam, Pijlman, Gorben P., Khromykh, Alexander A. and Asgari, Sassan (2012). West Nile virus encodes a microRNA-like small RNA in the 3' untranslated region which up-regulates GATA4 mRNA and facilitates virus replication in mosquito cells. Nucleic Acids Research, 40 (5), 2210-2223. doi: 10.1093/nar/gkr848
Reynard, O., Mokhonov, V., Mokhonova, E., Leung, J., Page, A., Mateo, M., Pyankova, O., Georges-Courbot, M. C., Raoul, H., Khromykh, A. A. and Volchkov, V. E. (2011). Kunjin virus replicon-based vaccines expressing Ebola virus glycoprotein GP protect the guinea pig against lethal Ebola virus infection. Journal of Infectious Diseases, 204 (3), S1060-S1065. doi: 10.1093/infdis/jir347
Determinants of attenuation in the envelope protein of the flavivirus Alfuy
Prow, Natalie A., May, Fiona J., Westlake, Daniel J., Hurrelbrink, Robert J., Biron, Rebecca M., Leung, Jason Y., McMinn, Peter C., Clark, David C., Mackenzie, John S., Lobigs, Mario, Khromykh, Alexander A. and Hall, Roy A. (2011). Determinants of attenuation in the envelope protein of the flavivirus Alfuy. Journal of General Virology, 92 (10), 2286-2296. doi: 10.1099/vir.0.034793-0
Faham, Abdus, Herringson, Thomas, Parish, Chris, Suhrbier, AandreaS, Khromykh, Alexander A. and Altin, Joseph G. (2011). pDNA-lipoplexes engrafted with flagellin-related peptide induce potent immunity and anti-tumour effects. Vaccine, 29 (40), 6911-6919. doi: 10.1016/j.vaccine.2011.07.045
Daffis, Stephane, Lazear, Helen M., Liu, Wen Jun, Audsley, Michelle, Engle, Michael, Khromykh, Alexander A. and Diamond, Michael S. (2011). The naturally attenuated Kunjin strain of West Nile virus shows enhanced sensitivity to the host type I interferon response. Journal of Virology, 85 (11), 5664-5668. doi: 10.1128/JVI.00232-11
Virulence determinants between New York 99 and Kunjin strains of West Nile virus
Audsley, Michelle, Edmonds, Judith, Liu, Wenjun, Mokhonov, Vlad, Mokhonova, Ekaterina, Melian, Ezequeil Balmori, Prow, Natalie, Hall, Roy A. and Khromykh, Alexander A. (2011). Virulence determinants between New York 99 and Kunjin strains of West Nile virus. Virology, 414 (1), 63-73. doi: 10.1016/j.virol.2011.03.008
Rattanasena, Paweena, Anraku, Itaru, Gardner, Joy, Le, Thuy T., Wang, Xiang Ju, Khromykh, Alexander A. and Suhrbier, Andreas (2011). Prime-boost vaccinations using recombinant flavivirus replicon and vaccinia virus vaccines: An ELISPOT analysis. Immunology and Cell Biology, 89 (3), 426-436. doi: 10.1038/icb.2010.99
RNA structures required for production of subgenomic flavivirus RNA
Funk, Anneke, Truong, Katherine, Nagasaki, Tomoko, Torres, Shessy, Floden, Nadia, Balmori Melian, Ezequiel, Edmonds, Judy, Dong, Hongping, Shi, Pei-Yong and Khromykh, Alexander A. (2010). RNA structures required for production of subgenomic flavivirus RNA. Journal of Virology, 84 (21), 11407-11417. doi: 10.1128/JVI.01159-10
Fros, Jelke J., Liu, Wen Jun, Prow, Natalie A., Geertsema, Corinne, Ligtenberg, Maarten, Vanlandingham, Dana L., Schnettler, Esther, Vlak, Just M., Suhrbier, Andreas, Khromykh, Alexander A. and Pijlman, Gorben P. (2010). Chikungunya virus nonstructural protein 2 inhibits type I/II interferon-stimulated JAK-STAT signaling. Journal of Virology, 84 (20), 10877-10887. doi: 10.1128/JVI.00949-10
Nanopatch-targeted skin vaccination against West Nile virus and chikungunya virus in mice
Prow, Tarl W., Chen, Xianfeng, Prow, Natalie A., Fernando, Germain J. P., Tan, Cindy S. E., Raphael, Anthony P., Chang, David, Ruutu, Merja P., Jenkins, Derek W. K., Pyke, Alyssa, Crichton, Michael L., Raphaelli, Kristin, Goh, Lucas Y. H., Frazer, Ian H., Roberts, Michael S., Gardner, Joy, Khromykh, Alexander A., Suhrbier, Andreas, Hall, Roy A. and Kendall, Mark A. F. (2010). Nanopatch-targeted skin vaccination against West Nile virus and chikungunya virus in mice. Small, 6 (16), 1776-1784. doi: 10.1002/smll.201000331
Laurent-Rolle, Maudry, Boer, Elena F., Lubick, Kirk J., Wolfinbarger, James B., Carmody, Aaron B., Rockx, Barry, Liu, Wenjun, Ashour, Joseph, Shupert, W. Lesley, Holbrook, Michael R., Barrett, Alan D., Mason, Peter W., Bloom, Marshall E., Garcia-Sastre, Adolfo, Khromykh, Alexander A. and Best, Sonja M. (2010). The NS5 protein of the virulent West Nile virus NY99 strain is a potent antagonist of type I interferon-mediated JAK-STAT signaling. Journal of Virology, 84 (7), 3503-3515. doi: 10.1128/JVI.01161-09
Mertens, E, Kajaste-Rudnitski, A, Torres, S, Funk, A, Frenkiel, MP, Iteman, I, Khromykh, AA and Despres, P (2010). Viral determinants in the NS3 helicase and 2K peptide that promote West Nile virus resistance to antiviral action of 2′,5′-oligoadenylate synthetase 1b. Virology, 399 (1), 176-185. doi: 10.1016/j.virol.2009.12.036
Balmori Melian, Ezequiel, Hinzman, Edward, Nagasaki, Tomoko, Firth, Andrew E., Wills, Norma M., Nouwens, Amanda S., Blitvich, Bradley J., Leung, Jason, Funk, Anneke, Atkins, John F., Hall, Roy and Khromykh, Alexander A. (2010). NS1 ' of flaviviruses in the Japanese encephalitis virus serogroup is a product of ribosomal frameshifting and plays a role in viral neuroinvasiveness. Journal of Virology, 84 (3), 1641-1647. doi: 10.1128/JVI.01979-09
Hall, Roy A., Tan, Si En, Selisko, Barbara, Slade, Rachael, Hobson-Peters, Jody, Canard, Bruno, Hughes, Megan, Leung, Jason Y., Balmori-Melian, Ezequiel, Hall-Mendelin, Sonja, Pham, Kim B., Clark, David C., Prow, Natalie A. and Khromykh, Alexander A. (2009). Monoclonal antibodies to the West Nile virus NS5 protein map to linear and conformational epitopes in the methyltransferase and polymerase domains. Journal of General Virology, 90 (12), 2912-2922. doi: 10.1099/vir.0.013805-0
Generating flavivirus vaccine candidates by modulating interferon sensitivity
Funk, Anneke and Khromykh, Alexander (2009). Generating flavivirus vaccine candidates by modulating interferon sensitivity. Expert Review of Vaccines, 8 (9), 1157-1160. doi: 10.1586/ERV.09.73
West Nile virus: The current climate
Prow, Natalie A., Khromykh, Alexander A. and Hall, Roy A. (2009). West Nile virus: The current climate. Medical Laboratory Observer, 41 (4), 10-15.
Hoang-Le, D., Smeenk, L., Anraku, I., Pijlman, G. P., Wang, X. J., De Vrij, J., Liu, W. J., Le, T. T., Schroder, W. A., Khromykh, Alexander A. and Suhrbier, A. (2009). A Kunjin replicon vector encoding granulocyte macrophage colony-stimulating factor for intra-tumoral gene therapy. Gene Therapy, 16 (2), 190-199. doi: 10.1038/gt.2008.169
Pijlman, Gorben P., Funk, Anneke, Kondratieva, Natasha, Leung, Jason, Torres, Shessy, Van der Aa, Lieke, Liu, Wen Jun, Palmenberg, Ann C., Shi, Pei-Yong, Hall, Roy A. and Khromykh, Alexander A. (2008). A highly structured,nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity. Cell Host and Microbe, 4 (6), 579-591. doi: 10.1016/j.chom.2008.10.007
Kunjin replicon-based simian immunodeficiency virus gag vaccines
Anraku, Itaru, Mokhonov, Vladislav V., Rattanasena, Paweena, Mokhonova, Ekaterina I., Leung, Jason, Pijlman, Gorben, Cara, Andrea, Schroder, Wayne A., Khromykh, Alexander A. and Suhrbier, Andreas (2008). Kunjin replicon-based simian immunodeficiency virus gag vaccines. Vaccine, 26 (26), 3268-3276. doi: 10.1016/j.vaccine.2008.04.001
Role of Nonstructural Protein NS2A in Flavivirus Assembly
Leung, Jason Y., Pijlman, Gorben P., Kondratieva, Natasha, Hyde, Jennifer, Mackenzie, Jason M. and Khromykh, Alexander A. (2008). Role of Nonstructural Protein NS2A in Flavivirus Assembly. Journal of Virology, 82 (10), 4731-4741. doi: 10.1128/JVI.00002-08
Evaluation of recombinant Kunjin replicon SIV vaccines for protective efficacy in macaques
Kent, Stephen J., De Rose, Robert, Mokhonov, Vlad V., Mokhonova, Ekaterina I., Fernandez, Caroline S., Alcantara, Sheilajen, Rollman, Erik, Mason, Rosemarie D., Loh, Liyen, Peut, Viv, Reece, Jeanette C., Wang, Xiang Ju, Wilson, Kim M., Suhrbier, Andreas and Khromykh, Alexander (2008). Evaluation of recombinant Kunjin replicon SIV vaccines for protective efficacy in macaques. Virology, 374 (2), 528-534. doi: 10.1016/j.virol.2008.01.006
Single-round infectious particles enhance immunogenicity of a DNA vaccine against West Nile virus
Chang, David C., Liu, Wen J., Anraku, Itaru, Clark, David C., Pollitt, Christopher C., Suhrbier, Andreas, Hall, Roy A. and Khromykh, Alexander A. (2008). Single-round infectious particles enhance immunogenicity of a DNA vaccine against West Nile virus. Nature Biotechnology, 26 (5), 571-577. doi: 10.1038/nbt1400
Drug evaluation: ChimeriVax-West Nile vaccine
Hall, RA and Khromykh, AA (2007). Drug evaluation: ChimeriVax-West Nile vaccine. Current Opinion In Molecular Therapeutics, 9 (5), 498-504.
Cholesterol Manipulation by West Nile Virus Perturbs the Cellular Immune Response
Mackenzie, Jason M., Khromykh, Alexander and Parton, Robert G. (2007). Cholesterol Manipulation by West Nile Virus Perturbs the Cellular Immune Response. Cell Host and Microbe, 2 (4), 229-239. doi: 10.1016/j.chom.2007.09.003
Pugachev, KV, Schwaiger, J, Brown, N, Zhang, ZX, Catalan, J, Mitchell, FS, Ocran, SW, Rumyantsev, AA, Khromykh, AA, Monath, TP and Guirakhoo, F (2007). Construction and biological characterization of artificial recombinants between a wild type flavivirus (Kunjin) and a live chimeric flavivirus vaccine (ChimeriVax-JE). Vaccine, 25 (37-38), 6661-6671. doi: 10.1016/j.vaccine.2007.07.016
Hoenen, A., Liu, W., Kochs, G., Khromykh, A. and Mackenzie, J. (2007). West Nile virus-induced cytoplasmic membrane structures provide partial protection against the interferon-induced antiviral MxA protein. Journal of General Virology, 88 (11), 3013-3017. doi: 10.1099/vir.0.83125-0
Mastrangelo, E, Milani, M, Bollati, M, Selisko, B, Peyrane, F, Pandini, V, Sorrentino, G, Canard, B, Konarev, PV, Svergun, DI, de Lamballerie, X, Coutard, B, Khromykh, AA and Bolognesi, M (2007). Crystal structure and activity of Kunjin virus NS3 helicase; Protease and helicase domain assembly in the full length NS3 protein. Journal of Molecular Biology, 372 (2), 444-455. doi: 10.1016/j.jmb.2007.06.055
Crystal structure of the RNA polymerase domain of the West Nile Virus non-structural protein 5
Malet, H., Egloff, M., Selisko, B., Butcher, R., Wright, P., Roberts, M., Gruez, A., Sulzenbacher, G., Vonrhein, C., Bricogne, G., Mackenzie, J., Khromykh, A., Davidson, A. and Canard, B. (2007). Crystal structure of the RNA polymerase domain of the West Nile Virus non-structural protein 5. The Journal of Biological Chemistry, 282 (14), 10678-10689. doi: 10.1074/jbc.M607273200
Pyankov, O. V., Agranovski, I. E., Pyankova, O., Mokhonova, E., Mokhonov, V., Safatov, A. S. and Khromykh, A. A. (2007). Using a bioaerosol personal sampler in combination with real-time PCR analysis for rapid detection of airborne viruses. Environmental Microbiology, 9 (4), 992-1000. doi: 10.1111/j.1462-2920.2006.01226.x
Pijlman, Gorben P., Kondratieva, Natasha and Khromykh, Alexander A. (2006). Translation of the flavivirus Kunjin NS3 gene in cis but not its RNA sequence or secondary structure is essential for efficient RNA packaging. Journal of Virology, 80 (22), 11255-11264. doi: 10.1128/JVI.01559-06
Ebola virus glycoprotein GP is not cytotoxic when expressed constitutively at a moderate level
Alazard-Dany, N., Volchkova, V., Reynard, O., Carbonnelle, C., Dolnik, O., Ottmann, M., Khromykh, A. and Volchkov, V. E. (2006). Ebola virus glycoprotein GP is not cytotoxic when expressed constitutively at a moderate level. Journal of General Virology, 87 (5), 1247-1257. doi: 10.1099/vir.0.81361-0
Roosendaal, Jojanneke, Westaway, Edwin G., Khromykh, Alexander and Mackenzie, Jason M. (2006). Regulated Cleavages at the West Nile Virus NS4A-2K-NS4B Junctions Play a Major Role in Rearranging Cytoplasmic Membranes and Golgi Trafficking of the NS4A Protein. Journal of Virology, 80 (9), 4623-4632. doi: 10.1128/JVI.80.9.4623-4632.2006
Liu, Wen Jun, Wang, Xiang Ju, Clark, David C., Lobigs, Mario, Hall, Roy A. and Khromykh, Alexander A. (2006). A single amino acid substitution in the west nile virus nonstructural protein NS2A disables its ability to inhibit alpha/beta interferon induction and attenuates virus virulence in mice. Journal of Virology, 80 (5), 2396-2404. doi: 10.1128/JVI.80.5.2396-2404.2006
Pijlman, Gorben P., Suhrbier, Andreas and Khromykh, Alexander A. (2006). Kunjin virus replicons: an RNA-based, non-cytopathic viral vector system for protein production, vaccine and gene therapy applications. Expert Opinion On Biological Therapy, 6 (2), 135-145. doi: 10.1517/14712598.6.2.135
Comparative mechanistic studies of de novo RNA synthesis by flavivirus RNA-dependent RNA polymerases
Selisko, B., Dutartre, H., Guillemot, J. C., Debarnot, C., Benarroch, D., Khromykh, A., Despres, P., Egloff, M. P. and Canard, B. (2006). Comparative mechanistic studies of de novo RNA synthesis by flavivirus RNA-dependent RNA polymerases. Virology, 351 (1), 145-158. doi: 10.1016/j.virol.2006.03.026
Preliminary crystallographic characterization of an RNA helicase from Kunjin virus
Mastrangelo, Eloise, Bollati, Michela, Milani, Mario, Brisbarre, Nadege, de Lamballerie, Xavier, Coutard, Bruno, Canard, Bruno, Khromykh, Alexander and Bolognesi, Martino (2006). Preliminary crystallographic characterization of an RNA helicase from Kunjin virus. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 62 (9), 876-879. doi: 10.1107/S1744309106028776
Liu, Wen Jun, Wang, Xiang Ju, Mokhonov, Vladislav V., Shi, Pei-Yong, Randall, Richard and Khromykh, Alexander A. (2005). Inhibition of interferon signaling by the New York 99 strain and Kunjin subtype of West Nile virus involves blockage of STAT1 and STAT2 activation by nonstructural proteins. Journal of Virology, 79 (3), 1934-1942. doi: 10.1128/JVI.79.3.1934-1942.2005
Tannis, Laura Lee, Gauthier, Andree, Evelegh, Carole, Parsons, Robin, Nyholt, Dana, Khromykh, Alexander and Brarnson, Jonathan L. (2005). Semliki Forest virus and Kunjin virus RNA replicons elicit comparable cellular immunity but distinct humoral immunity. Vaccine, 23 (33), 4189-4194. doi: 10.1016/j.vaccine.2005.04.005
Liu, Wen Jun, Chen, Hua Bo, Xiang, Ju Wang, Huang, Hester and Khromykh, Alexander A. (2004). Analysis of adaptive mutations in Kunjin virus replicon RNA reveals a novel role for the flavivirus nonstructural protein NS2A in inhibition of beta interferon promoter-driven transcription. Journal of Virology, 78 (22), 12225-12235. doi: 10.1128/JVI.78.22.12225-12235.2004
Hall, Roy A. and Khromykh, Alexander A. (2004). West Nile virus vaccines. Expert Opinion On Biological Therapy, 4 (8), 1295-1305. doi: 10.1517/14712598.4.8.1295
Herd, Karen A., Harvey, Tracey, Khromykh, Alexander A. and Tindle, Robert W. (2004). Recombinant Kunjin virus replicon vaccines induce protective T-cell immunity against human papillomavirus 16 E7-expressing tumour. Virology, 319 (2), 237-248. doi: 10.1016/j.virol.2003.10.032
Tetracycline-Inducible packaging cell line for production of Flavivirus replicon particles.
Harvey, Tracey, Liu, Wen Jun, Wang, Xiang Ju, Linedale,Richard, Jacobs,Michael, Davidson, Andrew, Le,Thuy T. T., Anraku,Itaru, Suhrbier,Andreas, Pei-Yong, Shi and Khromykh, Alexander A. (2004). Tetracycline-Inducible packaging cell line for production of Flavivirus replicon particles.. Journal of Virology, 78 (1), 531-538. doi: 10.1128/JVI.78.1.531-538.2004
West nile virus core protein: Tetramer structure and ribbon formation
Dokland, T., Walsh, M., Mackenzie, J. M., Khromykh, A. A., Ee, K. H. and Wang, S. F. (2004). West nile virus core protein: Tetramer structure and ribbon formation. Structure, 12 (7), 1157-1163. doi: 10.1016/j.str.2004.04.024
Significance in replication of the terminal nucleotides of the Flavivirus genome
Khromykh, Alexander A., Kondratieva, Natasha, Sgro, Jean-Yves, Palmenberg, Ann and Westaway, Edwin G. (2003). Significance in replication of the terminal nucleotides of the Flavivirus genome. Journal of Virology, 77 (19), 10623-10629. doi: 10.1128/JVI.77.19.10623-10629.2003
Kunjin virus replicon vectors for human immunodeficiency virus vaccine development
Tracey Harvey, Anraku, Itaru, Linedale, Richard, Harrich, David, Mackenzie, Jason, Suhrbier, Andreas and Khromykh, Alexander A. (2003). Kunjin virus replicon vectors for human immunodeficiency virus vaccine development. Journal of Virology, 77 (14), 7796-7803. doi: 10.1128/JVI.77.14.7796-7803.2003
Liu, Wen Jun, Chen, Hua Bo and Khromykh, Alexander A. (2003). Molecular and functional analyses of Kunjin virus infectious cDNA clones demonstrate the essential roles for NS2A in virus assembly and for a nonconservative residue in NS3 in RNA replication. Journal of Virology, 77 (14), 7804-7813. doi: 10.1128/JVI.77.14.7804-7813.2003
Generation of CTL responses using Kunjin replicon RNA
Ward, Scott M., Tindle, Robert W., Khromykh, Alexander A. and Gowans, Eric J. (2003). Generation of CTL responses using Kunjin replicon RNA. Immunology And Cell Biology, 81 (1), 73-78. doi: 10.1046/j.0818-9641.2002.01137.x
Hall, R. A., Nisbet, D. J., Pham, K.B., Pyke, A. T., Smith, G. A. and Khromykh, A. (2003). DNA vaccine coding for the full-length infectious Kunjin virus RNA protects mice against the New York strain of West Nile virus. Proceedings of The National Academy of Sciences of The United States of America, 100 (18), 10460-10464. doi: 10.1073/pnas.1834270100
Liu, Wen Jun, Sedlak, Petra L., Kondratieva, Natasha and Khromykh, Alexander A. (2002). Complementation analysis of the flavivirus Kunjin NS3 and NS5 proteins defines the minimal regions essential for formation of a replication complex and shows a requirement of NS3 in cis for virus assembly. Journal of Virology, 76 (21), 10766-10775. doi: 10.1128/JVI.76.21.10766-10775.2002
Kunjin virus replicon vaccine vectors induce protective CD8(+) T-cell immunity
Anraku, Itaru, Harvey, Tracey J., Linedale, Richard, Gardner, Joy, Harrich, David, Suhrbier, Andreas and Khromykh, Alexander A. (2002). Kunjin virus replicon vaccine vectors induce protective CD8(+) T-cell immunity. Journal of Virology, 76 (8), 3791-3799. doi: 10.1128/JVI.76.8.3791-3799.2002
Biological significance of glycosylation of the envelope protein of Kunjin virus
Scherret, J., Mackenzie, J. S., Khromykh, A. and Hall, R. A. (2001). Biological significance of glycosylation of the envelope protein of Kunjin virus. Annals of the New York Academy of Sciences, 951 (West Nile Virus: Detection, Surveillance, And Control), 361-363. doi: 10.1111/j.1749-6632.2001.tb02719.x
Essential role of cyclization sequences in Flavivirus RNA replication
Khromykh, Alexander A., Meka, Hedije, Guyatt, Kimberley J. and Westaway, Edwin G. (2001). Essential role of cyclization sequences in Flavivirus RNA replication. Journal of Virology, 75 (14), 6719-6728. doi: 10.1128/JVI.75.14.6719-6728.2001
Khromykh, Alexander A., Varnavski, Andrei N., Sedlak, Petra L. and Westaway, Edwin G. (2001). Coupling between replication and packaging of flavivirus RNA: Evidence derived from the use of DNA-based full-length cDNA clones of kunjin virus. Journal of Virology, 75 (10), 4633-4640. doi: 10.1128/JVI.75.10.4633-4640.2001
Guyatt, K. J., Westaway, E. G. and Khromykh, A. A. (2001). Expression and purification of enzymatically active recombinant RNA-dependent RNA polymerase (NS5) of the flavivirus Kunjin. Journal of Virological Methods, 92 (1), 37-44. doi: 10.1016/S0166-0934(00)00270-6
Mackenzie, Jason M., Khromykh, Alexander A. and Westaway, Edwin G. (2001). Stable expression of noncytopathic Kunjin replicons simulates both ultrastructural and biochemical characteristics observed during replication of Kunjin virus. Virology, 279 (1), 161-172. doi: 10.1006/viro.2000.0691
Replicon-based vectors of positive strand RNA viruses.
Khromykh, A. A. (2000). Replicon-based vectors of positive strand RNA viruses.. Current Opinion in Molecular Therapeutics, 2 (5), 555-569.
Varnavski, Andrei N., Young, Paul R. and Khromykh, Alexander A. (2000). Stable High-Level Expression of Heterologous Genes In Vitro and In Vivo by Noncytopathic DNA-Based Kunjin Virus Repicon Vectors. Journal of Virology, 74 (9), 4394-4403. doi: 10.1128/JVI.74.9.4394-4403.2000
cis- and trans- Acting Elements in Flavivirus RNA Replication
Khromykh, Alexander A., Sedlak, Petra L. and Westaway, Edwin G. (2000). cis- and trans- Acting Elements in Flavivirus RNA Replication. Journal of Virology, 74 (7), 3253-3263. doi: 10.1128/JVI.74.7.3253-3263.2000
Khromykh, Alexander A., Sedlak, Petra L., Guyatt, Kimberley J., Hall, Roy A. and Westaway, Edwin G. (1999). Efficient trans-complementation of the flavivirus kunjin NS5 protein but not of the NS1 protein requires its coexpression with other components of the viral replicase. Journal of Virology, 73 (12), 10272-10280. doi: 10.1128/jvi.73.12.10272-10280.1999
Khromykh, Alexander A., Sedlak, Petra L. and Westaway, Edwin G. (1999). trans-complementation analysis of the flavivirus Kunjin ns5 gene reveals an essential role for translation of its N-terminal half in RNA replication. Journal of Virology, 73 (11), 9247-9255.
Nascent flavivirus RNA colocalized in situ with double-stranded RNA in stable replication complexes
Westaway, EG, Khromykh, AA and Mackenzie, JM (1999). Nascent flavivirus RNA colocalized in situ with double-stranded RNA in stable replication complexes. Virology, 258 (1), 108-117. doi: 10.1006/viro.1999.9683
Noncytopathic flavivirus replicon RNA-based system for expression and delivery of heterologous genes
Varnavski, AN and Khromykh, AA (1999). Noncytopathic flavivirus replicon RNA-based system for expression and delivery of heterologous genes. Virology, 255 (2), 366-375. doi: 10.1006/viro.1998.9564
Hall, R. A., Khromykh, A. A., Mackenzie, J. M., Scherret, J., Khromykh, T. and Mackenzie, J. S. (1999). Loss of dimerisation of the nonstructural protein NS1 of Kunjin virus delays viral replication and reduces virulence in mice, but still allows secretion of NS1. Virology, 264 (1), 66-75. doi: 10.1006/viro.1999.9956
Khromykh, Alexander A., Kenney, Mark T. and Westaway, Edwin G. (1998). trans-complementation of flavivirus RNA polymerase gene NS5 by using kunjin virus replicon-expressing BHK cells. Journal of Virology, 72 (9), 7270-7279.
Khromykh, Alexander A., Varnavski, Andrei N. and Westaway, Edwin G. (1998). Encapsidation of the flavivirus kunjin replicon RNA by using a complementation system providing kunjin virus structural proteins in trans. Journal of Virology, 72 (7), 5967-5977.
Mackenzie, JM, Khromykh, AA, Jones, MK and Westaway, EG (1998). Subcellular localization and some biochemical properties of the flavivirus Kunjin nonstructural proteins NS2A and NS4A. Virology, 245 (2), 203-215. doi: 10.1006/viro.1998.9156
Cloning and expression of the ataxia-telangiectasia gene in baculovirus
Scott, SP, Zhang, N, Khanna, KK, Khromykh, A, Hobson, K, Watters, D and Lavin, MF (1998). Cloning and expression of the ataxia-telangiectasia gene in baculovirus. Biochemical and Biophysical Research Communications, 245 (1), 144-148. doi: 10.1006/bbrc.1998.8137
Westaway, Edwin G., MacKenzie, Jason M., Kenney, Mark T., Jones, Malcolm K. and Khromykh, Alexander A. (1997). Ultrastructure of Kunjin virus-infected cells: Colocalization of NS1 and NS3 with double-stranded RNA, and of NS2B with NS3, in virus-induced membrane structures. Journal of Virology, 71 (9), 6650-6661. doi: 10.1128/jvi.71.9.6650-6661.1997
Proteins C and NS4B of the flavivirus Kunjin translocate independently into the nucleus
Westaway, EG, Khromykh, AA, Kenney, MT, Mackenzie, JM and Jones, MK (1997). Proteins C and NS4B of the flavivirus Kunjin translocate independently into the nucleus. Virology, 234 (1), 31-41. doi: 10.1006/viro.1997.8629
Subgenomic replicons of the flavivirus Kunjin: construction and applications
Khromykh, A. A. and Westaway, E. G. (1997). Subgenomic replicons of the flavivirus Kunjin: construction and applications. Journal of Virology, 71 (2), 1497-1505.
Khromykh, A. A., Harvey, T. J., Abedinia, M. and Westaway, E. G. (1996). Expression and purification of all seven nonstructural proteins of the flavivirus Kunjin in the E.coli and the baculovirus systems. Journal of Virological Methods, 61 (1-2), 47-58. doi: 10.1016/0166-0934(96)02068-X
RNA binding properties of core protein of the flavivirus Kunjin
Khromykh, AA and Westaway, EG (1996). RNA binding properties of core protein of the flavivirus Kunjin. Archives of Virology, 141 (3-4), 685-699. doi: 10.1007/BF01718326
Khromykh, A. A., Meka, H. and Westaway, E. G. (1995). Preparation of recombinant baculovirus by transfection of a ligated cDNA fragment without prior plasmid amplification in E. coli. BioTechniques, 19 (3), 356-358+360.
Khromykh, A. A. and Westaway, E. G. (1994). Completion of Kunjin virus RNA sequence and recovery of an infectious RNA transcribed from stably cloned full-length cDNA. Journal of Virology, 68 (7), 4580-4588. doi: 10.1128/jvi.68.7.4580-4588.1994
Khromykh, A. A., Beliaev, A. S., Rukavishnikov, M. I., Daniliuk, N. K. and Sandakhchiev, L. S. (1990). Expression of antigens of the tick-borne encephalitis virus by various recombinant variants of the vaccinia virus Ekspressiia antigenov virusa kleshchevogo éntsefalita razlichnymi rekombinantnymi variantami virusa ospovaktsiny. Doklady Akademii nauk SSSR, 310 (4), 996-999.
Expression of tick encephalitis virus antigens cloned in vaccinia virus
Khromykh, A. A., Belyaev, A. S., Rukhavishnikov Yu, M., Danilyuk, N. K. and Sandakhchiev, L. S. (1990). Expression of tick encephalitis virus antigens cloned in vaccinia virus. Doklady Biological Sciences, 310 (1-6), 41-43.
Zika Virus sfRNA plays an essential role in the infection of insects and mammals
Slonchak, Andrii, Hugo, Leon E., Freney, Morgan, Amarilla, Alberto A., Hall-Mendelin, Sonja, Yan, Kexin, Torres, Francisco, Setoh, Yin Xiang, Peng, Nias, Chaggar, Harman K., Hurk, Andrew Van Den, Wolvetang, Ernst, Suhrbier, Andreas, Devine, Gregor J. and Khromykh, Alexander A. (2020). Zika Virus sfRNA plays an essential role in the infection of insects and mammals. Viruses 2020—Novel Concepts in Virology, Barcelona, Spain, 5–7 February 2020. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2020050112
Liebscher, Susan, Chappell, K. J., Stoermer, Martin J., Watterson, Daniel, Webb, Richard I., Khromykh, Alexander A., Fairlie, David P. and Young, Paul R. (2010). Sneaking up on West Nile Virus NS2B/NS3 protease subcellular activity utilising dye-quenched substrates. PlusStrand 2010: The Ninth International Symposium on Positive-Strand RNA Viruses, Atlanta, GA, U.S.A., 17-21 May 2010.
Evasion of host innate immune response by West Nile virus.
Khromykh, A. (2009). Evasion of host innate immune response by West Nile virus.. TLROZ 2009: Patterns Recognition Receptors in Health and Disease, Surfers Paradise, Australia, 28-30 October 2009.
Flavivirus subgenomic non-coding RNA is required to overcome the host innate immune response
Funk, A., Torres, S., Edmonds, J., Pijlman, G., Hall, R., Lobigs, M., Kumagai, Y., Takeuchi, O., Akira, S. and Khromykh, A. (2009). Flavivirus subgenomic non-coding RNA is required to overcome the host innate immune response. 5th Australian Virology Group Meeting, Lorne, Australia, 13-17 December 2009. Australia: Australian Virology Group.
Molecular basis for the resistance of West Nile virus to antiviral activity of Oas1b
Martens, E., Iteman, I., Frenkiel, M.-P., Simon-Chazottes, D., Funk, A., Khromykh, A. and Kajaste-Rudnitski, P. (2009). Molecular basis for the resistance of West Nile virus to antiviral activity of Oas1b. 28th Annual Meeting of American Society for Virology, Vancouver, Canada, 11-15 July 2009.
The role of flavivirus subgenomic non-coding RNA in overcoming host innate immune response
Funk, A., Torres, S., Truong, K., Edmonds, J., Pijlman, G., Hall, R., Lobigs, M., Kumagai, Y., Takeuchi, O., Akira, S. and Khromykh, A. (2009). The role of flavivirus subgenomic non-coding RNA in overcoming host innate immune response. TLROZ 2009: Patterns Recognition Receptors in Health and Disease, Gold Coast , Australia, 28-30 October 2009.
Truong, K., Funk, A., Torres, S. and Khromykh, A. (2009). The role of pseudoknot interactions in stabilizing flavivirus RNA structure and generation of nuclease resistant flavivirus RNA.. 5th Australian Virology Group Meeting, Lorne, Australia, 13-17 December 2009.
The role of small subgenomic RNA in flavivirus replication and pathogenicity.
Khromykh, A. (2009). The role of small subgenomic RNA in flavivirus replication and pathogenicity.. NITD Conference on Dengue, Manila, Philippines, 31 Aug - 4 Sept 2009.
The role of subgenomic non-coding RNA in flavivirus-host interactions and viral pathogenicity
Khromykh, A., Funk, A., Torres, S., Edmonds, J., Pijlman, G., Hall, R., Lobigs, M., Kumagai, Y., Takeuchi, O. and Akira, S. (2009). The role of subgenomic non-coding RNA in flavivirus-host interactions and viral pathogenicity. 28th Annual Meeting of American Society for Virology, Vancouver, Canada, 11-15 July 2009.
Flavivirus replication and cellular RNA decay machinery
Khromykh, A.A. (2008). Flavivirus replication and cellular RNA decay machinery. 3rd AREVA-Pasteur Forum "Mosquito- and tick-borne viruses and their environment, Shanghai, China, 12-14 June, 2008.
Flavivirus subgenomic RNA generated by the mRNA decay machinery supports efficient virus replication
Pijlman, G.P., Funk, A., Kondratieva, N., Leung, J., Van der Aa, L., Liu, W., Palmenberg, , A.C., Hall, R.A. and Khromykh, A. (2008). Flavivirus subgenomic RNA generated by the mRNA decay machinery supports efficient virus replication. American Society for Virology Annual Meeting, Ithaca, USA, 12-16 July, 2008.
Pijlman, G.P., Funk, A., Kondratieva, N., Leung, J., Van der Aa, L., Liu, W., Palmenberg, A.C., Hall, R.A. and Khromykh, A.A. (2008). Flaviviruses employ cellular mRNA decay machinery to generate subgenomic non-coding RNA required for pathogenicity. International Congress of Virology, Istanbul, Turkey, 10-15 Aug, 2008.
Funk, A., Pijlman, G.P., Kondratieva, N., Leung, J., Van der Aa, L., Liu, W., Palmenberg, A.C., Shi, P.-Y., Hall, R.A. and Khromykh, A. (2008). Flaviviruses employ cellular mRNA decay machinery to generate subgenomic non-coding RNA required for pathogenicity. Arbovirus Research in Australia Meeting, Coffs Harbour, Australia, 15-19 Sept, 2008.
The role of small non-coding RNAs in flavivirus replication and pathogenicity
Pijlman, G.P., Funk, A., Kondratieva, N., Leung, J., Van der Aa, L., Liu, W., Palmenberg, A.C., Hall, R.A. and Khromykh, A.A. (2008). The role of small non-coding RNAs in flavivirus replication and pathogenicity. Society for General Microbiology Meeting, Edinburgh, Scotland, 31 Mar - 3 Apr, 2008.
Cholesterol is good, just ask the flaviviruses
Mackenzie, J M, Khromykh, A and Parton, R G (2006). Cholesterol is good, just ask the flaviviruses. Annual Scientific Meeting & Exhibition - Aust Society for Micry, Gold Coast, 2-6 July, 2006.
Flavivirus replication and virus-host interactions
Khromykh, A (2006). Flavivirus replication and virus-host interactions. Annual Scientific Meeting & Exhibition - Aust Society for Micr, Gold Coast, 2-6 July, 2006.
Mackenzie, J M, Liu, W, Parton, R G and Khromykh, A (2006). Inhibition of interferon signaling in flavivirus-infected cells is associated with virus-induced cholesterol re-distribution. 13th International Mtg on Hepatitis C Virus & Related Viruses, Cairns, 27-31 Aug, 2006.
Kunjin replicon vectors for HIV/SIV vaccine development
Anraku, I., Mokhonova, V., Rattanasena, P., Pijlman, G P, Suhrbier, A and Khromykh, A (2006). Kunjin replicon vectors for HIV/SIV vaccine development. Aust Centre for HIV & Hepatitis Virology Research, Lorne, 8-11 Oct, 2006.
Modulation of interferon response by West Nile
Khromykh, A, Liu, W, Wang,, Clark, D. C. J. and Hall, R A (2006). Modulation of interferon response by West Nile. Keystone Symposia, Keystone, Colorado, 6-11 Jan, 2006.
A bigmac a day keeps the flavivirus away
Mackenzie, J. M., Khromykh, A. and Parton, R. G. (2005). A bigmac a day keeps the flavivirus away. 3rd Australian Virology Group Meeting, Phillip Is, 9-12 Dec, 2005.
Liu, W., Wang, D.Z., Clark, M., Lobigs, M. and Khromykh, A. (2005). A single amino acid in the West Nile virus nonstructural protein NS2A disables its ability to inhibit interferon alpha/beta induction and attenuates virus virulence in mice. 3rd Australian Virology Group Meeting, Phillip Is, 9-12 Dec, 2005.
Kunjin (West Nile) virus-based vaccines
Khromykh, A. (2005). Kunjin (West Nile) virus-based vaccines. Novel Vaccines Against Infectious Diseases, Semmering, Austria, 14-17 April, 2005.
Requirement of flavivirus Kunjin NS3 translation in cis for packaging of viral RNA
Pijlman, G. P. and Khromykh, A. (2005). Requirement of flavivirus Kunjin NS3 translation in cis for packaging of viral RNA. 24th Annual Meeting of American Society for Virology, Pennsylvania, 18-22 June, 2005.
The role of the nonstructural protein NS2A in flavivirus assembly
Leung, J, Mackenzie, J. M., Khromykh, A. and Pijlman, G. P. (2005). The role of the nonstructural protein NS2A in flavivirus assembly. 3rd Australian Virology Group Meeting, Phillip Is, 9-12 Dec, 2005.
West Nile manipulates cholesterol balance affecting the lipid raft formation and function
Mackenzie, J. M., Khromykh, A. and Parton, R. G. (2005). West Nile manipulates cholesterol balance affecting the lipid raft formation and function. 24th Annual Meeting of American Society for Virology, Pennsylvania, 18-22 June, 2005.
Identification of a region of the flavivirus nonstructural protein 1 (NS1) involved in dimerization
Clark, D. C., Khromykh, A. A., Mackenzie, J. S. and Hall, R. A. (2001). Identification of a region of the flavivirus nonstructural protein 1 (NS1) involved in dimerization. 1st Australian Virology Group Meeting, Fraser Island, December, 2001.
Cartwright, L., Hall, R. A., Khromykh, A., Poidinger, M. and Mackenzie, J. S. (2001). The role of conserved RNA structures in the untranslated regions of the flavivirus genome in viral replication. 8th Arbovirus Research Symposium, Couran Cove, Qld, 3-7 July, 2000. Brisbane: QUT.
Investigation of the structure and function of the flavivirus non-coding regions
Cartwright, L., Hall, R. A., Khromykh, A. A., Mackenzie, J. S. and Poidinger, M. (1999). Investigation of the structure and function of the flavivirus non-coding regions. 11th International Congress of Virology, Sydney, 9-13 August 1999. Aust.: Int. Union of Microbiological Societies.
Hall, R. A., Khromykh, A. A., Poidinger, M., Scherret, J., Mackenzie, J. M., MacKenzie, J. S. and Khromykh, T. (1999). Loss of dimerisation of the NS1 protein of Kunjin virus slows replication in cell culture and reduces virulence in mice. 11th International Congress of Virology, Sydney, 9-13 August 1999. Aust.: Int. Union of Microbiological Societies.
The effect of glycoslation of the envelope protein in Kujin replication and pathogenesis
Scherret, J., Khromykh, A. A., Calvert, A. E., Mackenzie, J. S. and Hall, R. A. (1999). The effect of glycoslation of the envelope protein in Kujin replication and pathogenesis. 11th International Congress of Virology, Sydney, 9-13 August 1999. Aust.: Int. Union of Microbiological Societies.
Dmitriev, IP, Khromykh, AA, Ignatyev, GM, Gainullina, MN, Ageenko, VA, Dryga, SA, Vorobyeva, MS and Sandakhchiev, LS (1996). Immunization with recombinant vaccinia viruses expressing structural and part of the nonstructural region of tick-borne encephalitis virus cDNA protect mice against lethal encephalitis. Symposium on New Approaches to Vaccine Development (NAVD 95), Vienna Austria, Apr 11-14, 1995. AMSTERDAM: ELSEVIER SCIENCE BV. doi: 10.1016/0168-1656(95)00141-7
Predicting and preparing for the unfolding evolution of SARS-CoV-2
(2022–2025) NHMRC IDEAS Grants
How the synergy between flavivirus protein and noncoding RNA defeats antiviral response
(2022–2024) NHMRC IDEAS Grants
Chimeric insect-specific viruses as novel vaccines for mosquito-borne diseases
(2020–2023) NHMRC Development Grant
Noncoding RNAs of insect-specific flaviviruses: biogenesis and functions
(2019–2023) ARC Discovery Projects
Viral and host factors determining outcome of Zika virus infection
(2018–2021) NHMRC Project Grant
(2018–2020) NHMRC Project Grant
(2018) UQ Major Equipment and Infrastructure
The role of non-coding viral RNAs in flavivirus infection and exosomal signalling
(2017–2019) NHMRC Project Grant
(2016–2018) NHMRC Project Grant
Instrumentation for the analysis of cellular and metabolic phenotypes
(2016) UQ Major Equipment and Infrastructure
(2015) UQ Major Equipment and Infrastructure
(2014–2019) NHMRC Research Fellowship
Wolbachia and West Nile virus in mosquitoes: friends or foes?
(2014–2016) NHMRC Project Grant
(2014) UQ Major Equipment and Infrastructure
Molecular pathogenesis of emerging West Nile viruses
(2013–2015) NHMRC Project Grant
The role of noncoding subgenomic flavivirus RNA in virus-host interactions
(2013–2015) NHMRC Project Grant
Kunjin virus replicon vector plasmid evaluation
(2013–2014) UniQuest Pty Ltd
(2012–2015) ARC Linkage Projects
Do insect-specific flaviviruses regulate the transmission of mosquito-borne diseases in Australia?
(2012–2014) ARC Discovery Projects
Role of flavivirus-encoded small regulatory RNAs in virus-mosquito vector interactions
(2012–2014) NHMRC Project Grant
Regulatory cellular microRNAs and their role in insect anti-viral responses
(2011–2013) ARC Discovery Projects
Viral factors contributing to flavivirus-induced cell death and pathogenicity
(2011–2013) NHMRC Project Grant
Cell culture facilities for studying host-pathogen interactions and immune function
(2011) UQ Major Equipment and Infrastructure
Mass spectrometer for biomolecule discovery, structural analysis and quantification.
(2011) UQ Major Equipment and Infrastructure
(2010–2013) Queensland Institute of Medical Research
The role of subgenomic non-coding viral RNA in flavivirus pathogenicity
(2010–2013) NHMRC Project Grant
(2010–2012) NHMRC Project Grant
An integrated high -throughput fluorescence imaging facility
(2010) UQ Major Equipment and Infrastructure
NHMRC Research Fellowship (SRFA): Flavivirus replication
(2009–2013) NHMRC Research Fellowship
Detection of imported exotic strains of West Nile virus for national biosecurity surveillance.
(2009–2012) ARC Discovery Projects
(2009–2011) Griffith University
Infrastructure for biochemistry and infectious disease resarch in molecualr biosciences
(2009) UQ School/Centre Co-Funding
Role of cellular lipids in flavivirus replication
(2008–2010) NHMRC Project Grant
West Nile virus replication and host response
(2008–2010) NHMRC Project Grant
Molecular Epidemiology and pathogenesis of mosquito-borne viruses
(2008) NHMRC Equipment Grant
Viral factors involved in flavivirus replication and virus-host interactions
(2007–2010) NHMRC Project Grant
Virulence determinants of encephalitic flaviviruses
(2007–2010) NHMRC Project Grant
(2007–2009) Griffith University
Inhibitors Of West Nile Virus Protease As Antiviral Drugs
(2007–2009) NHMRC Project Grant
Development of technique for rapid detection of pathogenic ariborne particles (PR06-0054)
(2007–2008) Griffith University
Attenuated West Nile virus vaccine
(2005–2010) United States National Institutes of Health
Cellular microenvironments facilitating the replication and propagation of flaviviruses
(2005–2008) NHMRC Project Grant
How do flaviviruses modulate interferon response
(2005–2008) NHMRC Project Grant
NHMRC_Equipment Grant = Three Class II Biohazard cabinets and one -86OC Freezer
(2005) NHMRC Equipment Grant
The West Nile viral protease NS3: a target for antiviral drug and vaccine design
(2005) NHMRC Project Grant
NHMRC Senior Research Fellowship
(2004–2008) NHMRC Research Fellowship
Flavivirus RNA replication and virus assembly
(2004–2007) NHMRC Project Grant
A Hybrid Fowlpox-Kunjin virus vector for the delivery of HIV/AIDS vaccines
(2004–2005) CSIRO
Induction of protective immune responses to SIV Gag by Kunjin replicon vaccine in non-human primates
(2004–2005) University of Melbourne
Development of Kunjin replicon-based Ebola vaccine
(2003–2007) United States National Institutes of Health
Development of a personal sampler for viable airborne bacteria, fungi and virus
(2003–2006) Griffith University
New system for gene therapy and protein production
(2003–2005) Queensland Institute of Medical Research
Novel polytope VLP vaccines for respiratory syncytial virus (RSV) infection in children
(2003–2004) Royal Children's Hospital Foundation
Molecular analyses of Favivirus RNA Replication, Packaging and Complementation
(2001–2003) NHMRC Project Grant
Kunjin virus replicon as a vector for HIV vaccine
(2000–2003) United States National Institutes of Health
Flavivirus replication - Biogenesis, ultrastructure and functions of induced membranes.
(2000–2002) NHMRC Project Grant
Cooperation between sfRNA and non-structural protein NS5 for flavivirus immune evasion
Doctor Philosophy — Principal Advisor
Other advisors:
Predicting and preparing for the unfolding evolution of SARS-CoV-2
Doctor Philosophy — Principal Advisor
Other advisors:
Mechanisms of host restriction underpinning the safety and efficacy of novel chimeric flaviviral vaccines
Doctor Philosophy — Associate Advisor
Other advisors:
Uncovering host determinants of Zika virus replication using an in vivo and in vitro RNAi screening approach
(2023) Doctor Philosophy — Principal Advisor
Uncovering molecular determinants in ZIKV-NS5 related to replication, virulence, and transmissibility
(2022) Doctor Philosophy — Principal Advisor
Characterisation of the Flaviviral Non-Structural Protein NS1'
(2015) Doctor Philosophy — Principal Advisor
Second Generation Single-Round Infectious Particle (SRIP)-Producing Flavivirus Vaccine
(2014) Doctor Philosophy — Principal Advisor
West Nile Virus Vaccine Development
(2011) Doctor Philosophy — Principal Advisor
Role of nonstructural protein NS2A in Flavivirus assembly and secretion
(2010) Doctor Philosophy — Principal Advisor
INFECTION OF HUMAN MONOCYTE-DERIVED DENDRITIC CELLS WITH KUNJIN VIRUS IN VITRO
(2005) Master Philosophy — Principal Advisor
(2013) Doctor Philosophy — Joint Principal Advisor
Molecular Mechanisms of Evolutionary Adaption in Insect-specific Flaviviruses
(2018) Doctor Philosophy — Associate Advisor
Other advisors:
The role of the type I interferon in the immunobiology of chikungunya virus.
(2015) Doctor Philosophy — Associate Advisor
Understanding immunobiology of chikungunya virus disease using mouse models
(2014) Doctor Philosophy — Associate Advisor
Stalking the West Nile Virus NS2B/NS3 protease as a target for infection control and as a key player in virus factories
(2013) Doctor Philosophy — Associate Advisor
Other advisors:
Characterisation Of Intracellular Replication and Pathogenesis of Murine Norovirus 1
(2011) Doctor Philosophy — Associate Advisor
(2009) Doctor Philosophy — Associate Advisor
Characterisation of Kunjin Replicon Vaccines
(2008) Doctor Philosophy — Associate Advisor
INDUCTION OF LONG LASTING PROTECTIVE CD8+ T LYMPHOCYTE RESPONSES BY KUNJIN REPLICON-BASED VACCINE VECTORS
(2005) Doctor Philosophy — Associate Advisor
Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.
Cooperation between sfRNA and non-structural protein NS5 for flavivirus immune evasion
This Earmarked Scholarship project is aligned with a recently awarded Category 1 research grant. It offers you the opportunity to work with leading researchers and contribute to large projects of national significance.
Flaviviruses are important human pathogens that include West Nile, Dengue, Zika, Yellow fever virus and other viruses. They have a unique ability to produce viral noncoding RNA from their 3' untranslated region by hijacking host exoribonuclease. This RNA, termed subgenomic flaviviral RNA (sfRNA), accumulates in infected cells in high abundance and facilitates viral pathogenesis by supressing antiviral response. However, the molecular mechanism that determines this activity is not fully elucidated. Recently we have discovered that sfRNA of Zika virus executes this function in cooperation with the viral protein NS5. We found that sfRNA binds to and stabilises NS5, allowing this protein to inhibit phosphorylation of transcriptional factor STAT1, a key mediator of antiviral signalling.
This project is aimed to uncover how sfRNA binding effects NS5 conformation and its ability to inhibit STAT1 phosphorylation by identifying interacting sites in both molecules, characterising structural changes in NS5 caused by sfRNA binding and creating mutant viruses incapable of sfRNA-NS5 interactions. It will also investigate whether this mechanism is conserved between all flaviviruses.
The successful candidate will have an opportunity to join one of the leading flavivirus laboratories and work in the dynamic team of internationally recognised experts at the forefront of flavivirus research. He/she will obtain experience in the wide range of classical and modern research techniques such as cryo-electron microscopy, next generation sequencing, generation of mutant viruses, immunofluorescent virus detection, quantitative PCR, Northern blotting, electrophoretic mobility shift assay, etc. He/she will have an opportunity to communicate their research at the national and international conferences and publish in the leading academic journals.
Predicting and preparing for the unfolding evolution of SARS-CoV-2
This Earmarked Scholarship project is aligned with a recently awarded Category 1 research grant. It offers you the opportunity to work with leading researchers and contribute to large projects of national significance.
SARS-CoV-2 is the cause of current COVID-19 pandemic which has already infected >270 million people and killed >5 million of them. Currently deployed and future vaccines are likely to significantly decrease the burden of pandemic, however, new viral variants are emerging that are less susceptible to vaccine-induced immunity. Hence, deeper understanding of what drives viral evolution under the pressure of vaccine-induced immune responses is needed to predict and prepare for the emergence of future variants and inform development of more effective vaccines. The project will employ deep mutational scanning methodology to identify changes in the viral spike protein responsible for altered susceptibility to vaccine-induced antibodies. The implications of identified changes on the properties of spike protein and susceptibility to vaccine-induced antibodies will be investigated using structural analysis and various functional assays. The findings will be critical for predicting viral changes that are likely to emerge in the landscape of vaccinations and provide invaluable information for pre-emptive development of vaccines that will be able to minimise future emergence of vaccine-resistant variants.