Professor Alexander Khromykh

Primary research interest
Molecular mechanisms of replication and virus-host interactions of positive strand RNA viruses
Additional roles
- Group Leader, RNA Virology Laboratory
- Theme Leader, Infection and Immunology
- Deputy Director (Virology), Australian Infectious Diseases Research Centre
- Director, Centre of Excellence in the Global Virus Network
About me
I have a PhD degree in Molecular Virology. I worked as a Postdoctoral Fellow at the University of Ottawa in Canada. I then joined Sir Albert Sakzewski Virus Research Centre in Brisbane and became a laboratory Head. I was awarded NHMRC Senior Research Fellowship and moved my laboratory to St Lucia campus in 2005 to take up an appointment with SCMB.
I was the founding Director of SCMB’s Centre for Infectious Disease Research and am currently the Deputy Director of the Australian Infectious Diseases Research Centre and the Director of Centre of Excellence in the Global Virus Network. I have authored 150 publications including papers in Science, Nature Microbiology, Science Translational Medicine, Nature Communications and 5 book chapters.
Research focus and collaborations
My group's main areas of research are molecular virology, viral pathogenesis, and virus-host interactions. The viruses we study are encephalitic flaviviruses such as West Nile virus and Zika virus. More recently SARS-COV-2 has become one of the main research focus. 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, deep mutational scanning, transient and stable expression of viral proteins and noncoding RNAs, viral replication and virulence assays, microarrays, mass spectrometry, next generation sequencing analysis, 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 group has also been interested in developing viruses and replicons as vectors for vaccine and cancer therapy applications.
Projects
- Molecular pathogenesis of flaviviruses and coronaviruses
- Viral evasion of host immune responses
- Viral and host small regulatory RNAs
- Flavivirus non-coding subgenomic RNA
- Replicon-based vaccine and cancer therapy vectors
- Oncolytic viral therapy
Collaborators
- Roy Hall, Jody Peters, Daniel Watterson, David Muller, Keith Chappell, Ernst Wolvetang, Vito Ferro, Kirsty Short - The University of Queensland
- Andreas Suhrbier, QIMR Berghofer Medical Research.
- Jason Mackenzie, University of Melbourne
- Sonia Best, National Institutes of Health, USA
- Jeffrey Wilusz, Colorado State University, USA
- Aaron Brault, CDC, USA
- Gorben Pijlman, Wageningen University, The Netherlands
- Andrew Tuplin, University of Leeds, UK
- Jesse Bloom, Fred Hutchinson Cancer Research Centre, USA
Funded projects
- Khromykh A., Slonchak A, Modhiran, N (2022-2024) How the synergy between flavivirus protein and noncoding RNA defeats antiviral response. NHMRC Ideas Grant. $783,516.
- Khromykh A., Amarilla Ortiz, A., Burr, L., Bloom, J. (2022-2025) Predicting and preparing for the unfolding evolution of SARS-CoV-2. NHMRC Ideas Grant. $999,836.
- Hall, R., Peters, J., Muller, D., Suhrbrier, A., Khromykh, A.,Young, P. (2020-2022) Chimeric insect-specific viruses as novel vaccines for mosquito-borne diseases. NHMRC Development Grant. $1,017,285.
- Khromykh, A., Hall, R., Peters, J., Slonchak, A., Hugo, L. (2019-2022) Noncoding RNAs of insect-specific flaviviruses: biogenesis and functions. ARC Discovery Projects. $434,000.
- Hall, R., Khromykh, A., Bielefeldt-Ohmann, H., Peters, J., Setoh, Y. (2018-2020) Chimeric insect-specific flaviviruses: a new generation of diagnostics and vaccines against mosquito-borne viral disease. NHMRC Project Grant. $549,936.
- Khromykh, A., Suhrbier, A., Devine, G., Setoh, Y., Prow, N. (2018-2021) Viral and host factors determining outcome of Zika virus infection. NHMRC Project Grant. $910,780.
- Khromykh, A. (2017-2019) The role of non-coding viral RNAs in flavivirus infection and exosomal signalling. NHMRC Project Grant. $683,447
- Asgari, S., Khromykh, A. (2014-2016) Wolbachia and West Nile virus in mosquitoes: friends or foes? NHMRC Project Grant. $542,562
- Khromykh A.A. (2014-2019). Pathogenic flaviviruses: molecular mechanisms of disease, host response and vaccines. NHMRC Senior Research Fellowship. $840,665.
- Khromykh A.A. (2013-2015).The role of noncoding subgenomic flavivirus RNA in virus-host interactions. NHMRC Project Grant. $602,877
- Khromykh, A.A., Hall, R., Bielefeldt-Ohmann, H., Lobigs, M. (2013-2015). Molecular pathogenesis of emerging West Nile viruses. NHMRC Project Grant. $573,627
- Hall, R.A., Khromykh, A.A., van den Hurk, A. (2012-2014). Do insect-specific flaviviruses regulate the transmission of mosquito-borne diseases in Australia? ARC Discovery. $405,000
- Khromykh, A.A., Asgari, S. (2012-2014). Role of flavivirus-encoded small regulatory RNAs in virus-mosquito vector interactions. NHMRC Project Grant. $528,675
- Hall, R.A., Khromykh, A.A., Van-den-Hurk, A., Bielefeldt-Ohmann, H., Kirkland, P. (2012-2014). Emergence of a virulent strain of West Nile virus causing fatal equine encephalitis in South Eastern Australia. ARC Linkage, $390,000
Teaching interests
Achievements and awards
- 2014 NHMRC Senior Research Fellowship
- 2009 NHMRC Senior Research Fellowship
- 2008 Long-term Invitation Fellowship, Japanese Society for Promotion of Science/Australian Academy of Science
- 2004 NHMRC Senior Research Fellowship
- Featured in an article in Research Media, Europe's leading portal for scientific dissemination
- Featured in several UQ News articles:
Featured publications
- 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 , Khromykh, Alexander A. (2021). A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses. Nature Communications, 12 (1) 3431, 3431. doi: 10.1038/s41467-021-23779-5
- Modhiran, Naphak, Song, Hao, Liu, Lidong, Bletchly, Cheryl, Brillault, Lou, Amarilla, Alberto A., Xu, Xiaoying, Qi, Jianxun, Chai, Yan, Cheung, Stacey T. M., Traves, Renee, Setoh, Yin Xiang, Bibby, Summa, Scott, Connor A. P., Freney, Morgan E., Newton, Natalee D., Khromykh, Alexander A., Chappell, Keith J., Muller, David A., Stacey, Katryn J., Landsberg, Michael J., Shi, Yi, Gao, George F., Young, Paul R. and Watterson, Daniel (2021). A broadly protective antibody that targets the flavivirus NS1 protein. Science, 371 (6525), 190-194. doi: 10.1126/science.abb9425
- Slonchak, Andrii, Hugo, Leon E., Freney, Morgan E., Hall-Mendelin, Sonja, Amarilla, Alberto A., Torres, Francisco J., Setoh, Yin Xiang, Peng, Nias Y. G., Sng, Julian D. J., Hall, Roy A., van den Hurk, Andrew F., Devine, Gregor J.and Khromykh, Alexander A. (2020). Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes. Nature Communications, 11(1) 2205, 2205. doi: 10.1038/s41467-020-16086-y
- Hobson-Peters, Jody, Harrison, Jessica J., Watterson, Daniel, Hazlewood, Jessamine E., Vet, Laura J., Newton, Natalee D., Warrilow, David, Colmant, Agathe M. G., Taylor, Carmel, Huang, Bixing, Piyasena, Thisun B. H., Chow, Weng Kong, Setoh, Yin Xiang, Tang, Bing, Nakayama, Eri, Yan, Kexin, Amarilla, Alberto A., Wheatley, Sarah, Moore, Peter R., Finger, Mitchell, Kurucz, Nina, Modhiran, Naphak, Young, Paul R., Khromykh, Alexander A., Bielefeldt-Ohmann, Helle, Suhrbier, Andreas and Hall, Roy A. (2019). A recombinant platform for flavivirus vaccines and diagnostics using chimeras of a new insect-specific virus. Science Translational Medicine, 11 (522) eaax7888, eaax7888. doi: 10.1126/scitranslmed.aax7888
- Setoh, Yin Xiang, Amarilla, Alberto A., Peng, Nias Y. G., Griffiths, Rebecca E., Carrera, Julio, Freney, Morgan E., Nakayama, Eri, Ogawa, Shinya, Watterson, Daniel, Modhiran, Naphak, Nanyonga, Faith Elizabeth, Torres, Francisco J., Slonchak, Andrii, Periasamy, Parthiban, Prow, Natalie A., Tang, Bing, Harrison, Jessica, Hobson-Peters, Jody, Cuddihy, Thom, Cooper-White, Justin, Hall, Roy A., Young, Paul R., Mackenzie, Jason M., Wolvetang, Ernst, Bloom, Jesse D., Suhrbier, Andreas and Khromykh, Alexander A. (2019). Determinants of Zika virus host tropism uncovered by deep mutational scanning. Nature Microbiology, 4 (5), 876-887. doi: 10.1038/s41564-019-0399-4
Researcher biography
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.