Overview
Background
Dr Andrii Slonchak is a head of Systems Virology Laboratory at QIMR Berghofer. Andrii Slonchak obtained his PhD in Molecular Biology in 2010 from the Institute of Molecular Biology and Genetics (Kyiv, Ukraine). In 2013 he joined the University of Queensland, where he completed his postdoctoral training in the RNA Virology Laboratory under the mentorship of Prof. Alexander Khromykh. In 2023 he was awarded ARC Future Fellowship, and in 2025 appointed Team Head of the Systems Virology Laboratory at QIMR Berghofer.
The Systems Virology Laboratory investigates virus-host and virus-vector interactions at molecular, cellular and organism levels using a combination of advanced multi-omics techniques, bioinformatics, molecular virology and RNA structural biology. We utilise advanced model systems such as stem cell derived organoids to study viral pathogenesis and apply single-cell and spatial transcriptomics combined with computational modelling to map cellular responses to arboviruses and uncover viral strategies for immune evasion. We aim to identify regulatory pathways driving viral replication, transmission and pathogenesis that can be targeted for development of effective defence strategies against medically significant arboviruses like Dengue, Zika, West Nile and Japanese encephalitis viruses.
Availability
- Dr Andrii Slonchak is:
- Available for supervision
- Media expert
Fields of research
Qualifications
- Doctor of Philosophy, Institution to be confirmed
Research interests
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Dissecting the mechanisms of flavivirus neuro-pathogenesis using the systems biology approach.
Flaviviruses are major human pathogens responsible for recurring outbreaks and severe neurological complications. Neurotropic flaviviruses such as West Nile virus (WNV) and Japanese Encephalitis virus (JEV) can infect the adult brain, leading to encephalitis and potentially fatal outcomes. In contrast, Zika virus (ZIKV) primarily targets the developing fetal brain, causing congenital microcephaly. Despite their public health impact, the molecular mechanisms underlying flavivirus neuropathogenesis remain poorly defined. The key challenges that limit our ability to understand the mechanisms of flavivirus encephalitis are (i) the lack of experimental models that capture the complex cellular environment of the human brain, especially in the context of an immune response, and (ii) limited technologies to interrogate these systems at high resolution. This project addresses both gaps by using human brain organoids as an ex vivo model of flavivirus neuroinfection. Organoids are differentiated from induced pluripotent stem cells and engineered to include diverse brain cell types thereby better recapitulating the neurovascular and immune microenvironment. These organoids are used as an infection model for encephalitic (WNV, JEV) and non-encephalitic (ZIKV) flaviviruses. To analyse virus-host interactions at cellular resolution, we have developed a novel flavivirus-inclusive single-cell RNA sequencing (scRNA-seq) protocol. This allows us to distinguish infected and bystander cells, map virus-induced transcriptional changes across cell types, and uncover host pathways linked to susceptibility and immune response. We will further investigate the functional significance of identified pathways through loss-of-function studies to determine their role in viral replication and pathogenesis. Additionally, the project explores the role of flaviviral noncoding RNAs known as subgenomic flavivirus RNA (sfRNA) as virulence factor in the nervous system. By leveraging cutting-edge organoid models and high-resolution omics tools, this project will significantly advance our understanding of flavivirus neurotropism and reveal new molecular targets for therapeutic intervention.
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Molecular mechanisms of superinfection exclusion
Flaviviruses are a large group of RNA viruses that include well-known human pathogens such as Zika virus (ZIKV) and West Nile virus (WNV). These viruses are transmitted between humans and animals through mosquito bites, causing outbreaks that threaten global health. Alongside these mosquito-borne viruses, there is another group of flaviviruses, called insect-specific flaviviruses (ISFs), that only infect mosquitoes and cannot be passed on to humans. Interestingly, some ISFs give mosquitoes a form of “immunity” against infection with pathogenic flaviviruses. This phenomenon, known as superinfection exclusion, prevents mosquitoes from carrying and transmitting viruses like ZIKV or WNV once they are already infected with certain ISFs. However, not all ISFs work this way. For example, viruses such as Parramatta River virus, Palm Creek virus, and Binjari virus can block infection with mosquito-borne flaviviruses, while Culex flavivirus does not. Why some ISFs protect mosquitoes from secondary infection and others do not remains a mystery. Our project aims to uncover the molecular mechanisms behind superinfection exclusion. We will investigate both the viral components and the mosquito genes that determine whether an ISF can block infection by a pathogenic flavivirus. By comparing ISFs that induce exclusion with those that do not, we hope to identify the key viral proteins, genome regions, and host pathways involved in this process. This research will provide the first detailed understanding of how insect-specific flaviviruses interfere with the ability of mosquitoes to transmit human pathogens. The findings will not only answer a long-standing question in flavivirus biology but could also inform new strategies to reduce the spread of mosquito-borne diseases. By combining advanced approaches in genomics, proteomics, and virus engineering, this project will generate fundamental new knowledge and establish innovative tools that will be valuable for the broader scientific community. Ultimately, uncovering how ISFs naturally protect mosquitoes from flavivirus infection could help guide future efforts to harness these viruses for the biological control of dangerous mosquito-borne pathogens.
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Noncoding RNAs of insect-specific flaviviruses: biogenesis and functions
The goal of this project is to obtain an understanding of how insect-specific flaviviruses (ISFs) utilise viral noncoding RNAs to enable their replication in mosquitoes. These viruses only replicate in mosquitoes, and not in humans or animals. They can be employed as the biocontrol agents for mosquito-borne diseases as they make mosquitoes incapable of disease transmission. However, it is currently unknown how exactly insect-specific flaviviruses affect mosquitoes and this information is vital for informed design of ISF-based interventions. The project will generate new knowledge on functions of noncoding RNAs in ISFs that are hypothesised to have immunomodulatory role in mosquitoes.
Research impacts
Dr Slonchak pioneered the use of human brain organoids to model viral neurovirulence and was among the first to apply single-cell and spatial transcriptomics to study virus–host interactions. His work on flaviviral noncoding RNA (sfRNA) highly advanced our understanding of flavivirus immune evasion and has been published in leading journals, including Nature Communications and Science Advances.
Dr Slonchak now leads cutting-edge research that utilises the power of innovative disease model systems, advanced transcriptomics, and systems biology to map cellular responses to arboviruses in vertebrate hosts and mosquito vectors. His team seeks to uncover viral strategies of immune evasion and translate these discoveries into novel antiviral therapeutic and disease prevention approaches.
Works
Search Professor Andrii Slonchak’s works on UQ eSpace
Featured
2024
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. (2024). Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2. Science Advances, 10 (23) eadj4735, 1-23. doi: 10.1126/sciadv.adj4735
Featured
2022
Journal Article
Zika virus noncoding RNA cooperates with the viral protein NS5 to inhibit STAT1 phosphorylation and facilitate viral pathogenesis
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
Featured
2022
Journal Article
Structural analysis of 3’UTRs in insect flaviviruses reveals novel determinants of sfRNA biogenesis and provides new insights into flavivirus evolution
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
Featured
2020
Journal Article
Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes
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
Featured
2019
Journal Article
Determinants of Zika virus host tropism uncovered by deep mutational scanning
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
2025
Journal Article
Twelfth scientific biennial meeting of the Australasian Virology Society: AVS12 2024
Monson, Ebony A., Loterio, Robson K., Roby, Justin A., Adhikari, Anurag, Bull, Rowena A., Carr, Jill M., Chatzileontiadou, Demetra S. M., Cheng, Colin X., Coulibaly, Fasséli, Davis, Samantha K., Deerain, Joshua M., Douglas, Mark W., Drummer, Heidi E., Eyre, Nicholas S., Freppel, Wesley, Gowripalan, Anjali, Grant, Emma J., Gras, Stephanie, Guthmiller, Jenna J., Herrero, Lara J., Hesping, Eva, Horsburgh, Bethany A., Hyde, Jennifer L., Koutsakos, Marios, Mackenzie, Jason M., Mahar, Jackie E., McCoullough, Laura C., McMillan, Christopher L. D., Modhiran, Naphak ... Tate, Michelle D. (2025). Twelfth scientific biennial meeting of the Australasian Virology Society: AVS12 2024. Journal of Virology, 99 (5), e0225524. doi: 10.1128/jvi.02255-24
2025
Journal Article
Evolution of Zika virus in <i>Rag1</i>-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication fitness
Nakayama, Eri, Tang, Bing, Stewart, Romal, Cox, Abigail L, Yan, Kexin, Bishop, Cameron R, Dumenil, Troy, Nguyen, Wilson, Slonchak, Andrii, Sng, Julian, Khromykh, Alexander A, Lutzky, Viviana P, Rawle, Daniel J and Suhrbier, Andreas (2025). Evolution of Zika virus in Rag1-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication fitness. Virus Evolution, 11 (1) veaf021, veaf021. doi: 10.1093/ve/veaf021
2024
Journal Article
The flavivirus Non-Structural Protein 5 (NS5): structure, functions, and targeting for development of vaccines and therapeutics
Goh, Jarvis Z. H., De Hayr, Lachlan, Khromykh, Alexander A. and Slonchak, Andrii (2024). The flavivirus Non-Structural Protein 5 (NS5): structure, functions, and targeting for development of vaccines and therapeutics. Vaccines, 12 (8) 865, 865. doi: 10.3390/vaccines12080865
2024
Journal Article
Xinyang flavivirus, from Haemaphysalis flava ticks in Henan Province, China, defines a basal, likely tick-only Orthoflavivirus clade
Wang, Lan-Lan, Cheng, Qia, Newton, Natalee D., Wolfinger, Michael T., Morgan, Mahali S., Slonchak, Andrii, Khromykh, Alexander A., Cheng, Tian-Yin and Parry, Rhys H. (2024). Xinyang flavivirus, from Haemaphysalis flava ticks in Henan Province, China, defines a basal, likely tick-only Orthoflavivirus clade. Journal of General Virology, 105 (5) 001991, 1-13. doi: 10.1099/jgv.0.001991
2023
Journal Article
A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) from the UK
Parry, Rhys H., Slonchak, Andrii, Campbell, Lewis J., Newton, Natalee D., Debat, Humberto J., Gifford, Robert J. and Khromykh, Alexander A. (2023). A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) from the UK. Journal of General Virology, 104 (12) 001927, 1-12. doi: 10.1099/jgv.0.001927
2023
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, 10 (23) eadj4735, eadj4735. doi: 10.1101/2023.06.12.544552
2023
Journal Article
Noncoding RNA of Zika virus affects interplay between Wnt-signaling and pro-apoptotic pathways in the developing brain tissue
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
2023
Journal Article
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, 1-3. doi: 10.1128/msphere.00165-23
2023
Journal Article
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, 1-3. doi: 10.1128/jvi.00451-23
2023
Journal Article
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, 1-3. doi: 10.1128/mbio.00815-23
2022
Journal Article
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
2022
Journal Article
The distinguishing NS5-M114V mutation in American Zika virus isolates has negligible impacts on virus replication and transmission potential
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
2022
Journal Article
Neural epidermal growth factor-like like protein 2 is expressed in human oligodendroglial cell types
Shaker, Mohammed R., Kahtan, Amna, Prasad, Renuka, Lee, Ju-Hyun, Pietrogrande, Giovanni, Leeson, Hannah C., Sun, Woong, Wolvetang, Ernst J. and Slonchak, Andrii (2022). Neural epidermal growth factor-like like protein 2 is expressed in human oligodendroglial cell types. Frontiers in Cell and Developmental Biology, 10 803061, 803061. doi: 10.3389/fcell.2022.803061
2021
Journal Article
Injection site vaccinology of a recombinant vaccinia-based vector reveals diverse innate immune signatures
Hazlewood, Jessamine E., Dumenil, Troy, Le, Thuy T., Slonchak, Andrii, Kazakoff, Stephen H., Patch, Ann-Marie, Gray, Lesley-Ann, Howley, Paul M., Liu, Liang, Hayball, John D., Yan, Kexin, Rawle, Daniel J., Prow, Natalie A. and Suhrbier, Andreas (2021). Injection site vaccinology of a recombinant vaccinia-based vector reveals diverse innate immune signatures. PLoS Pathogens, 17 (1) e1009215, 1-39. doi: 10.1371/journal.ppat.1009215
2020
Journal Article
Sequencing of historical isolates, k‐mer mining and high serological cross‐reactivity with Ross River virus argue against the presence of Getah virus in Australia
Rawle, Daniel J., Nguyen, Wilson, Dumenil, Troy, Parry, Rhys, Warrilow, David, Tang, Bing, Le, Thuy T., Slonchak, Andrii, Khromykh, Alexander A., Lutzky, Viviana P., Yan, Kexin and Suhrbier, Andreas (2020). Sequencing of historical isolates, k‐mer mining and high serological cross‐reactivity with Ross River virus argue against the presence of Getah virus in Australia. Pathogens, 9 (10) 848, 1-17. doi: 10.3390/pathogens9100848
Supervision
Availability
- Dr Andrii Slonchak is:
- Available for supervision
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Available projects
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Multiple projects
Systems virology laboratory offers multiple reserch projects for the students of different levels. Students must have high GPA and background in virology/immunology or bioinformatics. Please enquire by email: a.slonchak@uqedu.au
Supervision history
Current supervision
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Doctor Philosophy
Why certain viruses don't get along in mosquitoes: Dissecting the mechanism of superinfection exclusion
Principal Advisor
Other advisors: Professor Alexander Khromykh
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Doctor Philosophy
Functions of Noncoding Viral RNA in Insect-Specific Flaviviruses
Principal Advisor
Other advisors: Professor Alexander Khromykh
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Doctor Philosophy
Cooperation between sfRNA and non-structural protein NS5 for flavivirus immune evasion
Associate Advisor
Other advisors: Dr Naphak Modhiran, Professor Alexander Khromykh
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Doctor Philosophy
Engineering chimeric viruses as protective and safe vaccines against mosquito-borne viral disease
Associate Advisor
Other advisors: Professor Alexander Khromykh, Associate Professor Jody Peters
Completed supervision
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2022
Doctor Philosophy
Zika virus: Developing and exploiting mouse models for preclinical evaluation of new vaccines
Associate Advisor
Media
Enquiries
Contact Dr Andrii Slonchak directly for media enquiries about:
- Bioinformatics
- Dengue
- Noncoding RNA
- RNA biology
- Virology
- West Nile virus
- Zika
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