
Overview
Background
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.
Availability
- Professor Alexander Khromykh is:
- Available for supervision
- Media expert
Fields of research
Qualifications
- Bachelor of Science, Tomsk State University
- Doctor of Philosophy, The Institute for Molecular Virology
Research interests
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Molecular pathogenesis of RNA viruses
Viruses of main interest include West Nile virus, Zika virus and SARS-CoV-2 virus. A particular strength is in the developing infectious clones and replicons and utilising them to study virus replication, to identify viral determinants of pathogenicity and to develop vaccines and antivirals.
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Evasion of host antiviral response by pathogenic RNA viruses
We apply advanced molecular methodologies including screening with viral RNAi libraries to identify new host antiviral genes and to dissect mechanisms employed by pathogenic RNA viruses to evade antiviral responses.
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The role of viral and host noncoding RNAs in virus-host interaction
We study biogenesis of novel viral noncoding RNAs and elucidate mechanisms by which both, viral and host noncoding RNAs shape the outcomes of infection with pathogenic RNA viruses.
Research impacts
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.
Works
Search Professor Alexander Khromykh’s works on UQ eSpace
2017
Journal Article
Characterization of recombinant Flaviviridae viruses possessing a small reporter-tag
Tamura, Tomokazu, Fukuhara, Takasuke, Uchida, Takuro, Ono, Chikako, Mori, Hiroyuki, Sato, Asuka, Fauzyah, Yuzy, Okamoto, Toru, Kurosu, Takeshi, Setoh, Yin Xiang, Imamura, Michio, Tautz, Norbert, Sakoda, Yoshihiro, Khromykh, Alexander A., Chayama, Kazuaki and Matsuura, Yoshiharu (2017). Characterization of recombinant Flaviviridae viruses possessing a small reporter-tag. Journal of Virology, 92 (2) e01582-17, 1-19. doi: 10.1128/JVI.01582-17
2017
Journal Article
Differential Diagnosis of Flavivirus Infections in Horses Using Viral Envelope Protein Domain III Antigens in Enzyme-Linked Immunosorbent Assay
Piyasena, Thisun B. H., Setoh, Yin X., Hobson-Peters, Jody, Prow, Natalie A., Bielefeldt-Ohmann, Helle, Khromykh, Alexander A., Perera, David, Cardosa, Mary J., Kirkland, Peter D. and Hall, Roy A. (2017). Differential Diagnosis of Flavivirus Infections in Horses Using Viral Envelope Protein Domain III Antigens in Enzyme-Linked Immunosorbent Assay. Vector Borne and Zoonotic Diseases, 17 (12), 825-835. doi: 10.1089/vbz.2017.2172
2017
Journal Article
Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence
Setoh, Yin Xiang, Amarilla, Alberto A., Peng, Nias Y., Slonchak, Andrii, Periasamy, Parthiban, Figueiredo, Luiz T. M., Aquino, Victor H. and Khromykh, Alexander A. (2017). Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence. Archives of Virology, 163 (1), 255-258. doi: 10.1007/s00705-017-3561-4
2017
Journal Article
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
2017
Journal Article
Infectious DNAs derived from insect-specific flavivirus genomes enable identification of pre- and post-entry host restrictions in vertebrate cells
Piyasena, Thisun B. H. , Setoh, Yin X., Hobson-Peters, Jody, Newton, Natalee D. , Bielefeldt-Ohmann, Helle, McLean, Breeanna J. , Vet, Laura J. , Khromykh, Alexander A. and Hall, Roy A. (2017). Infectious DNAs derived from insect-specific flavivirus genomes enable identification of pre- and post-entry host restrictions in vertebrate cells. Scientific Reports, 7 (1) 2940, 2940.1-2940.11. doi: 10.1038/s41598-017-03120-1
2017
Journal Article
De novo generation and characterization of new Zika virus isolate using sequence data from a microcephaly case
Setoh, Yin Xiang, Prow, Natalie A., Peng, Nias, Hugo, Leon E., Devine, Gregor, Hazlewood, Jessamine E., Suhrbier, Andreas and Khromykh, Alexander A. (2017). De novo generation and characterization of new Zika virus isolate using sequence data from a microcephaly case. mSphere, 2 (3) e00190-17, 1-11. doi: 10.1128/mSphereDirect.00190-17
2017
Journal Article
Chimeric viruses between Rocio and West Nile: the role for Rocio prM-E proteins in virulence and inhibition of interferon-α/β signaling
Amarilla, Alberto A., Setoh, Yin X., Periasamy, Parthiban, Peng, Nias Y., Pali, Gabor , Figueiredo, Luiz T., Khromykh, Alexander and Aquino, Victor H. (2017). Chimeric viruses between Rocio and West Nile: the role for Rocio prM-E proteins in virulence and inhibition of interferon-α/β signaling. Scientific Reports, 7 (1) 44642, 44642.1-44642.8. doi: 10.1038/srep44642
2017
Journal Article
Genetic characterization of Cacipacoré virus from ticks collected in São Paulo State, Brazil
de Figueiredo, Glauciane Garcia, Amarilla, Alberto Anastacio, de Souza, William Marciel, Fumagalli, Marcılio Jorge, de Figueiredo, Mario Luis, Szabó, Matias Pablo Juan, Badra, Soraya Jabur, Setoh, Yin Xiang, Khromykh, Alexander A., Aquino, Victor Hugo and Figueiredo, Luiz Tadeu Moraes (2017). Genetic characterization of Cacipacoré virus from ticks collected in São Paulo State, Brazil. Archives of Virology, 162 (6), 1-4. doi: 10.1007/s00705-017-3279-3
2017
Journal Article
Successful post-exposure prophylaxis of Ebola infected non-human primates using Ebola glycoprotein-specific equine IgG
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
2016
Journal Article
The in vitro and in vivo antiviral properties of combined monoterpene alcohols against West Nile virus infection
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
2016
Journal Article
Virulence and evolution of West Nile Virus, Australia, 1960-2012
Prow, Natalie A., Edmonds, Judith H., Williams, David T., Setoh, Yin X., Bielefeldt-Ohmann, Helle, Suen, Willy W., Hobson-Peters, Jody, van den Hurk, Andrew F., Pyke, Alyssa T., Hall-Mendelin, Sonja, Northill, Judith A., Johansen, Cheryl A., Warrilow, David, Wang, Jianning, Kirkland, Peter D., Doggett, Stephen, Andrade, Christy C., Brault, Aaron C., Khromykh, Alexander A. and Hall, Roy A. (2016). Virulence and evolution of West Nile Virus, Australia, 1960-2012. Emerging Infectious Diseases, 22 (8), 1353-1362. doi: 10.3201/eid2208.151719
2016
Journal Article
Human miRNA miR-532-5p exhibits antiviral activity against West Nile virus via suppression of host genes SESTD1 and TAB3 required for virus replication
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
2015
Journal Article
Functional non-coding RNAs derived from the flavivirus 3' untranslated region
Clarke, B. D., Roby, J. A., Slonchak, A. and Khromykh, A. A. (2015). Functional non-coding RNAs derived from the flavivirus 3' untranslated region. Virus Research, 206, 53-61. doi: 10.1016/j.virusres.2015.01.026
2015
Journal Article
The I22V and L72S substitutions in West Nile virus prM protein promote enhanced prM/E heterodimerisation and nucleocapsid incorporation
Setoh, Yin Xiang, Tan, Cindy Si En, Prow, Natalie A., Hobson-Peters, Jody, Young, Paul R., Khromykh, Alexander A. and Hall, Roy A. (2015). The I22V and L72S substitutions in West Nile virus prM protein promote enhanced prM/E heterodimerisation and nucleocapsid incorporation. Virology Journal, 12 (1) 72, 72.1-72.5. doi: 10.1186/s12985-015-0303-7
2015
Journal Article
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.
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
2015
Journal Article
Viral RNA intermediates as targets for detection and discovery of novel and emerging mosquito-borne viruses
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
2015
Journal Article
A Kunjin replicon virus-like particle vaccine provides protection against ebola virus infection in nonhuman primates
Pyankov, Oleg V., Bodnev, Sergey A., Pyankova, Olga G., Solodkyi, Vladislav V., Pyankov, Stepan A., Setoh, Yin Xiang, Volchkova, Valentina A., Suhrbier, Andreas, Volchkov, Viktor V., Agafonov, Alexander A. and Khromykh, Alexander A. (2015). A Kunjin replicon virus-like particle vaccine provides protection against ebola virus infection in nonhuman primates. Journal of Infectious Diseases, 212 (Supp.), S1-S4. doi: 10.1093/infdis/jiv019
2015
Journal Article
Comparison of attenuated and virulent West Nile virus strains in human monocyte-derived dendritic cells as a model of initial human infection
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
2015
Journal Article
Systematic analysis of viral genes responsible for differential virulence between American and Australian West Nile virus strains
Setoh, Yin Xiang, Prow, Natalie A., Rawle, Daniel J., Tan, Cindy Si En, Edmonds, Judith H., Hall, Roy A. and Khromykh, Alexander A. (2015). Systematic analysis of viral genes responsible for differential virulence between American and Australian West Nile virus strains. Journal of General Virology, 96 (Pt 6), 1297-1308. doi: 10.1099/vir.0.000069
2015
Journal Article
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
Funding
Current funding
Past funding
Supervision
Availability
- Professor Alexander Khromykh is:
- Available for supervision
Before you email them, read our advice on how to contact a supervisor.
Available projects
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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.
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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.
Supervision history
Current supervision
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Doctor Philosophy
Predicting and preparing for the unfolding evolution of SARS-CoV-2
Principal Advisor
Other advisors: Dr Rhys Parry
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Doctor Philosophy
Predicting and preparing for the unfolding evolution of SARS-CoV-2
Principal Advisor
Other advisors: Dr Rhys Parry
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Doctor Philosophy
Cooperation between sfRNA and non-structural protein NS5 for flavivirus immune evasion
Principal Advisor
Other advisors: Dr Naphak Modhiran, Dr Andrii Slonchak
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Doctor Philosophy
Engineering chimeric viruses as protective and safe vaccines against mosquito-borne viral disease
Associate Advisor
Other advisors: Dr Andrii Slonchak, Associate Professor Jody Peters
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Doctor Philosophy
Mechanisms of host restriction underpinning the safety and efficacy of novel chimeric flaviviral vaccines
Associate Advisor
Other advisors: Associate Professor Jody Peters, Dr Natalee Newton
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Doctor Philosophy
Functions of Noncoding Viral RNA in Insect-Specific Flaviviruses
Associate Advisor
Other advisors: Dr Andrii Slonchak
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Doctor Philosophy
Why certain viruses don't get along in mosquitoes: Dissecting the mechanism of superinfection exclusion
Associate Advisor
Other advisors: Dr Andrii Slonchak
Completed supervision
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2023
Doctor Philosophy
Uncovering host determinants of Zika virus replication using an in vivo and in vitro RNAi screening approach
Principal Advisor
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2022
Doctor Philosophy
Uncovering molecular determinants in ZIKV-NS5 related to replication, virulence, and transmissibility
Principal Advisor
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2015
Doctor Philosophy
Characterisation of the Flaviviral Non-Structural Protein NS1'
Principal Advisor
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2014
Doctor Philosophy
Second Generation Single-Round Infectious Particle (SRIP)-Producing Flavivirus Vaccine
Principal Advisor
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2010
Doctor Philosophy
Role of nonstructural protein NS2A in Flavivirus assembly and secretion
Principal Advisor
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2005
Master Philosophy
INFECTION OF HUMAN MONOCYTE-DERIVED DENDRITIC CELLS WITH KUNJIN VIRUS IN VITRO
Principal Advisor
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2013
Doctor Philosophy
Defining regions of interaction between the MTase and POL domains of West Nile virus NS5 as potential targets for antiviral drug design
Joint Principal Advisor
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2018
Doctor Philosophy
Molecular Mechanisms of Evolutionary Adaption in Insect-specific Flaviviruses
Associate Advisor
Other advisors: Associate Professor Jody Peters
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2015
Doctor Philosophy
The role of the type I interferon in the immunobiology of chikungunya virus.
Associate Advisor
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2014
Doctor Philosophy
Understanding immunobiology of chikungunya virus disease using mouse models
Associate Advisor
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2013
Doctor Philosophy
Stalking the West Nile Virus NS2B/NS3 protease as a target for infection control and as a key player in virus factories
Associate Advisor
Other advisors: Professor David Fairlie
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2011
Doctor Philosophy
Characterisation Of Intracellular Replication and Pathogenesis of Murine Norovirus 1
Associate Advisor
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2009
Doctor Philosophy
The interferon-induced antiviral protein MxA: functional and therapeutic aspects relating to virus infection
Associate Advisor
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2005
Doctor Philosophy
INDUCTION OF LONG LASTING PROTECTIVE CD8+ T LYMPHOCYTE RESPONSES BY KUNJIN REPLICON-BASED VACCINE VECTORS
Associate Advisor
Media
Enquiries
Contact Professor Alexander Khromykh directly for media enquiries about:
- COVID-19
- Ebola virus
- Flaviviruses
- Gene delivery systems
- Gene expression
- Immunisation
- Molecular virology
- Noncoding RNAs
- SARS-CoV-2
- Vaccines
- Virus-host interactions
- Viruses
- West Nile Virus
- Zika virus
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