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
2020
Conference Publication
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
2019
Journal Article
West Nile virus infection and interferon alpha treatment alter the spectrum and the levels of coding and noncoding host RNAs secreted in extracellular vesicles
Slonchak, Andrii, Clarke, Brian, Mackenzie, Jason, Amarilla, Alberto Anastacio, Setoh, Yin Xiang and Khromykh, Alexander A. (2019). West Nile virus infection and interferon alpha treatment alter the spectrum and the levels of coding and noncoding host RNAs secreted in extracellular vesicles. BMC Genomics, 20 (1) 474, 474. doi: 10.1186/s12864-019-5835-6
2018
Journal Article
Subgenomic flaviviral RNAs: what do we know after the first decade of research
Slonchak, Andrii and Khromykh, Alexander A. (2018). Subgenomic flaviviral RNAs: what do we know after the first decade of research. Antiviral Research, 159, 13-25. doi: 10.1016/j.antiviral.2018.09.006
2017
Journal Article
Lower temperatures reduce type I interferon activity and promote alphaviral arthritis
Prow, Natalie A., Tang, Bing, Gardner, Joy, Le, Thuy T., Taylor, Adam, Poo, Yee S., Nakayama, Eri, Hirata, Thiago D. C., Nakaya, Helder I., Slonchak, Andrii, Mukhopadhyay, Pamela, Mahalingam, Suresh, Schroder, Wayne A., Klimstra, William and Suhrbier, Andreas (2017). Lower temperatures reduce type I interferon activity and promote alphaviral arthritis. PL o S Pathogens, 13 (12) e1006788, e1006788. doi: 10.1371/journal.ppat.1006788
2017
Journal Article
Helicase Domain of West Nile Virus NS3 Protein Plays a Role in Inhibition of Type I Interferon Signalling
Setoh, Yin Xiang, Periasamy, Parthiban, Peng, Nias Yong Gao, Amarilla, Alberto A, Slonchak, Andrii and Khromykh, Alexander A (2017). Helicase Domain of West Nile Virus NS3 Protein Plays a Role in Inhibition of Type I Interferon Signalling. Viruses, 9 (11) 326, 1-13. doi: 10.3390/v9110326
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
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
2014
Journal Article
Expression of mosquito microRNA aae-miR-2940-5p is down-regulated in response to West Nile Virus infection to restrict viral replication
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
2011
Book Chapter
Regulation of the Glutathione S-Transferase P1 Expression in Melanoma Cells
Slonchak, Andrii, Chwieduk, Agata, Rzeszowska-Wolny, Joanna and Obolenskay, Maria (2011). Regulation of the Glutathione S-Transferase P1 Expression in Melanoma Cells. Breakthroughs in Melanoma Research. (pp. 57-76) Zagreb, Croatia: InTech. doi: 10.5772/18747
2009
Journal Article
Structure and functions of glutathione S-transferase Pl-1
Slonchak, A. M. and Obolenska, M. Yu (2009). Structure and functions of glutathione S-transferase Pl-1. Ukrain'skyi Biokhimichnyi Zhurnal, 81 (1), 5-13.
2009
Journal Article
Crosstalk between transcription factors in regulation of the human glutathione S-transferase P1 gene expression in Me45 melanoma cells
Slonchak, A. M., Chwieduk, A., Rzeszowska-Wolny, J. and Obolenskaya, M. Yu. (2009). Crosstalk between transcription factors in regulation of the human glutathione S-transferase P1 gene expression in Me45 melanoma cells. Biopolymers and Cell, 25 (3), 210-217. doi: 10.7124/bc.0007DE
2009
Journal Article
Transcription regulation in differential expression of the human GSTP1 gene in breast and choriocarcinoma cells
Slonchak, A. M., Chwieduk, A., Rzeszowska-Wolny, J. and Yu Obolenska, M. (2009). Transcription regulation in differential expression of the human GSTP1 gene in breast and choriocarcinoma cells. Ukrainskiǐ biokhimicheskiǐ zhurnal, 81 (4), 48-58.
2007
Journal Article
Some aspects of glutathione S-transferase P1-1 gene transcription regulation in human placenta
Slonchak, A. M., Martsenyuk, O. P., Rzeszowska-Wolny, J., Widlak, P. and Obolenska, M. Yu (2007). Some aspects of glutathione S-transferase P1-1 gene transcription regulation in human placenta. Ukrain'skyi Biokhimichnyi Zhurnal, 79 (4), 67-75.
Supervision
Availability
- Dr Andrii Slonchak is:
- Available for supervision
Looking for a supervisor? Read our advice on how to choose a supervisor.
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: Dr Leon Hugo, 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: Dr Leon Hugo, 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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