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Our people-our expertise: Dr Alyssa Pyke

Our people-our expertise

Dr Alyssa Pyke

Qualifications | Research interests | Publications | Presentations | Awards | Grants and funding

Alyssa Pyke has comprehensive experience as a public health virologist. Her work has supported Queensland Health responses to numerous outbreaks caused by pathogenic arthropod-borne viruses such as Japanese encephalitis virus and dengue virus. She obtained her PhD in molecular virology after developing an infectious Ross River virus clone. She has worked extensively in high level containment facilities and managed a Physical Containment Level 4 (PC4) laboratory.

In her current role as a supervising senior research scientist, she is primarily involved in the surveillance, isolation and characterisation of viruses of public health significance. She has designed and introduced numerous molecular assays essential for human diagnostics and mosquito vector competence studies. She has also developed synthetic recombinant proteins for Hendra virus and Zika virus which have provided enhanced capabilities for serological diagnostics.

Alyssa is particularly interested in the emergence and evolution of arthropod-borne viruses and their phylogenetic relationships. She utilises whole genome sequencing for advancing surveillance platforms and providing insights into molecular epidemiology. Her research and investigation of exotic and endemic pathogens, such as Zika, dengue, chikungunya and Ross River viruses, includes the discovery and characterisation of two rare and highly divergent dengue viruses.

Qualifications

  • PhD in Microbiology. Thesis: Trans-complemented Ross River Virus. University of Queensland, St. Lucia, Queensland.
  • Bachelor of Applied Science, Medical Laboratory Science, Queensland University of Technology, Brisbane, Queensland.
  • Diploma of Management, TAFE Queensland, Southbank, Queensland.

Research interests and expertise

  • Detection, surveillance and characterisation of arthropod-borne viruses including dengue, chikungunya, Zika and Ross River virus
  • Emerging viruses of public health significance
  • Whole genome sequencing
  • Molecular epidemiology and virus evolution
  • Development of diagnostics and viral surveillance strategies

Publications

Pyke AT, Shivas MA, Darbro JM, Onn MB, Johnson PH, Crunkhorn A, Montgomery I, Burtonclay P, Jansen CC, van den hurk AF, (2021). Uncovering the Genetic Diversity Within the Aedes Notoscriptus Virome and Isolation of New Viruses from this Highly Urbanized and Invasive Mosquito. Virus Evolution. DOI: 10.1093/ve/veab082

Pyke A, (2021). Lymphocytic choriomeningitis virus - Australia. ProMED mail. 09-09-2021

Walker J, Pyke A, Florian p, Rodney Harris RM, Khandaker G, (2021). Re-defining the dengue-receptive area of Queensland after the 2019 dengue outbreak in Rockhampton. Medical Journal of Australia. DOI: 10.5694/mja2.51151

Walker J, Pyke A, Florian P, Moore F, Smoll N, Adegbija O, Khan A, Hasan R, Carroll H, Rodney Harris R, Khandaker G, (2021). Re-emergence of dengue virus in regional Queensland: 2019 dengue virus outbreak in Rockhampton, Central Queensland, Australia. Communicable Diseases Intelligence, 45. DOI: 10.33321/cdi.2021.45.31

Amarillo AA, Sng JDJ, Parry R, Deerain JM, Potter JR, Setoh YX, Rawle DJ, Le TT, Modhiran N, Wang X, Peng NYG, Torres FJ, Pyke A, Harrison JJ, Freney ME, Liang B, McMillan CLD, Cheung STM, Da Costa Guevara DJ, Hard JM, Bettington M, Muller DA, Coulibaly F, Moore F, Hall RA, Young PR, Mackenzie JM, Hobson-Peters J, Suhrbier A, Watterson D, Kromykh AA, (2021). A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses. Nature Communications. DOI: 10.1038/s41467-021-23779-5

Pyke AT, Nair N, van den Hurk A, Burtonclay P, Nguyen S, Barcelon J, Kistler C, Schlebusch S, McMahon J, Moore F, (2021). Replication Kinetics of B.1.351 and B.1.1.7 SARS-CoV-2 Variants of Concern Including Assessment of a B.1.1.7 Mutant Carrying a Defective ORF7a Gene. Viruses, 13. DOI: 10.3390/v13061087

Wimalasiri-Yapa BMCR, Barrero RA, Stassen L, Hafner LM, McGraw EA, Pyke AT, Jansen CC, Suhrbier A, Yakob L, Hu W, Devine GJ, Frentiu FD, (2021). Temperature modulates immune gene expression in mosquitoes during arbovirus infection. Open Biology, 11. DOI: doi.org/10.1098/rsob.20.0246

Hall-Mendelin S, Pyke AT, Ramirez AL, Staunton KM, Burtonclay P, McMahon J, Barcelon J, van den Hurk AF, (2020). Infection, Dissemination, and Replication of Urban and Sylvatic Strains of Dengue Virus Type 2 (Flaviviridae: Flavivirus) in Australian Aedes aegypti (Diptera: Culcidae). DOI: 10.1093/jme/tjaa292

Hasan J, Pyke A, Nair Neelima, Yarlagadda T, Will G, Spann K, Yarlagadda PKDV, (2020) Antiviral Nanostructured Surfaces Reduce the Viability of SARS-CoV-2. ACS Biomaterials Science & Engineering. DOI: 10.1021/acsbiomaterials.0c01091

Ramirez AL, Colmant AMG, Warrilow D, Huang B, Pyke AT, McMahon JL, Meyer DB, Graham RMA, Jennison AV, Ritchie SA, van den Hurk AF. (2020) Metagenomic analysis of the virome of mosquito excreta. mSphere. DOI: 10.1128/mSphere.00587-20

Pyke AT, Choong K, Moore F, Schlebusch S, Taylor C, Hewitson G, McMahon J, Neelima Nair, Moore P, Finger M, Burtonclay P, Wheatley S, (2020). A Case of Japanese Encephalitis with a Fatal Outcome in an Australian Who Traveled from Bali in 2019. Tropical Medicine and Infectious Disease, 5(3) 133. DOI: 10.3390/tropicalmed5030133

Pyke AT, McMahon J, Burtonclay P, Nair N, De Jong A. (2020) Genome sequences of Chikungunya virus strains from Bangladesh and Thailand. Microbiology Resource Announcements. DOI: 10.1128/MRA.01452-19

Pyke AT (2020) Japanese Encephalitis - Australia ex Indonesia (Bali). ProMED mail. Archive Number: 20200121.6904174. https://promedmail.org/promed-post/?id=6904174

Jansen CC, Shivas MA, May FJ, Pyke AT, Onn MB, Lodo K, Hall-Mendelin S, McMahon JL, Montgomery BL, Darbro JM, Doggett SL, van den Hurk AF. (2019) Epidemiologic, entomologic and virologic factors of the 2014-15 Ross River virus outbreak, Queensland, Australia. Emerging Infectious Diseases, 25(12). p. 2243-2252. DOI: 10.3201/eid2512.181810

Wimalasiri-Yapa BMCR, Stassen L, Hu W, Yakob L, McGraw EA,  Pyke AT, Jansen CC, Devine GJ, Frentiu FD, (2019) Chikungunya Virus Transmission at Low Temperature by Aedes albopictus Mosquitoes. Pathogens, 8 (3). p. 149. DOI: 10.3390/pathogens8030149

van den Hurk AF, Pyke AT, Mackenzie JS, Hall-Mendelin S, Ritchie SA (2019) Japanese Encephalitis Virus in Australia: from known known to known unknown. Tropical Medicine and Infectious Disease, 4 (1). p. 38. DOI: 10.3390/tropicalmed4010038

Pyke AT, Cameron JN, McMahon J, De Jong AJ, Burtonclay P (2019) First complete genome sequences of dengue virus serotype 2 strains from the Solomon Islands and Vanuatu. Microbiology Resource Announcements, 8 (2). e01360-18. DOI: 10.1128/MRA.01360-18

Hall-Mendelin S, Pyke AT, Moore PR, Ritchie SA, Moore F, van den Hurk AF (2018) Characterization of a Western Pacific Zika Virus strain in Australian Aedes aegypti. Vector-Borne and Zoonotic Diseases, 18(6). p. 317-322. DOI: 10.1089/vbz.2017.2232

Pyke AT (2018) The origins of dengue outbreaks in northern Queensland, Australia, 1990-2017. Microbiology Australia, 39. DOI: 10.1071/MA18027

Pyke, AT, Moore, PR, Hewitson, GR, Buttonclay, P. (2018) First reported complete genome sequence of a dengue virus serotype 4 strain from Papua New Guinea. Microbiology Resource Announcements, 7 . e01082-18. DOI: 10.1128/MRA.01082-18

Pyke AT, Moore PR, McMahon J (2018) Correspondence: New insights into chikungunya virus emergence and spread from Southeast Asia. Emerging Microbiology & Infection. 7. p. 26. DOI: 10.1038/s41426-018-0024-2

Pyke AT, Gunn W, Taylor CT, Mackay IM, McMahon J, Jelley L, Waite B, May F. (2018) On the home front: specialised reference testing for dengue in the Australasian region. Tropical Medicine and Infectious Disease, 3(3). p. 75. DOI:10.3390/tropicalmed3030075 

Moore PR, van den Hurk AF, Mackenzie JS, Pyke AT (2017) Dengue viruses in Papua New Guinea: evidence of endemicity and phylogenetic variation, including the evolution of new genetic lineages. Emerging Microbes and Infection, 6(1): e114. DOI: 10.1038/emi.2017.103

Pyke AT, Huang B, Warrilow D, Moore PR, McMahon J,  Harrower B (2017) Complete genome sequence of a highly divergent dengue virus type 2 strain, imported into Australia from Sabah, Malaysia. Genome Announcements, 5(29) pii: e00546-17. DOI: 10.1128/genomeA.00546-17

Hall-Mendelin S, Hewitson GR, Genge D, Burtonclay PJ, De Jong AJ, Pyke AT, van den Hurk AF (2017) FTA cards facilitate storage, shipment, and detection of arboviruses in infected Aedes aegypti collected in adult mosquito traps. American Journal of Tropical Medicine and Hygiene, 96(5): 1241-1243. DOI: 10.4269/ajtmh.16-0981

Huang B, Pyke AT, McMahon J, Warrilow D. (2017) Complete coding sequence of a case of Chikungunya virus imported into Australia. Genome Announcements, 5(19) pii: e00310-17. DOI: 10.1128/genomeA.00310-17

Huang B, West NP, Vider J, Cox AJ, Constantino T, Harrower B, Pyke AT, McMahon J, Northill J A, Riordan T, Warrilow D (2017) Diagnosis and typing of influenza using fluorescent barcoded probes. Scientific Reports, 7: 18092. doi:10.1038/s41598-017-18333-7

Pyke AT, Warrilow D (2016) Archival collections are important in the study of the biology, diversity, and evolution of arboviruses. Evolutionary Bioinformatics Online. 12(Suppl 2): 27-30. DOI: 10.4137/EBO.S40569

Prow N, Edmonds J, Williams DT, Setoh YX, Bielefeldt-Ohmann H, Suen WW, Hobso-Peters J, van den Hurk AF, Pyke AT, Hall-Mendelin S, Northill JA, Johansen CA, Warrilow D, Wang J, Kirland PD, Doggestt SL, Andrade CC, Brault AC, Khromykh AA, Hall RA (2016) Virulence and evolution of West Nile Virus, Australia, 1960–2012. Emerging Infectious Diseases, 22(8): 1353-62. DOI: 10.3201/eid2208.151719

Pyke AT (2016) Second dengue infection with a highly divergent sylvatic dengue virus strain – Brisbane, Queensland, Australia. ProMED mail. 07-05-2016

Pyke AT (2016) Zika virus (28) : Americas, Asia, Pacific, Atlantic, Europe, Australia. ProMED mail. Archive number: 20160524.4240474, Published 24-05-2016

Pyke AT, Moore PR, Hall-Mendelin S, McMahon JL, Harrower BJ, Constantino TR, van den Hurk AF (2016) Isolation of Zika Virus Imported from Tonga into Australia. PLoS Currents, Sep 7; 8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5028185/

Pyke AT, Moore PR, Taylor CT, Hall-Mendelin S, Cameron JN, Hewitson GR, Pukallus D, Huang B, Warrilow D, van den Hurk AF (2016) Highly divergent dengue virus type 1 genotype sets a new distance record. Scientific Reports, 6: 22356. DOI: 10.1038/srep22356

Hall-Mendelin S, Pyke AT, Moore PR, Mackay IM, McMahon J, Ritchie SA, Taylor CT, Moore F, van den Hurk AF (2016) Assessment of local mosquito species incriminates Aedes aegypti as the potential vector of Zika Virus in Australia. PLoS Neglected Tropical Diseases 10(9): e0004959. DOI: 10.1371/journal.pntd.0004959

Williams DT, Diviney SM, Niazi AU, Durr PA, Chua BH, Herring B, Pyke AT, Doggett SL, Johansen C, Mackenzie JS (2015) The molecular epidemiology and evolution of Murray Valley Encephalitis Virus: recent emergence of distinct sub-lineages of the dominant genotype 1. PLoS Neglected Tropical Diseases, 9(11): e0004240. DOI: 10.1371/journal.pntd.0004240

Pyke AT (2014) Zika virus - Pacific (10): Australia ex Cook Islands. ProMED mail. Archive number: 20140403.2378034, Published 03-04-2014

Dupont-Rouzeyrol M, Aubry M, O'Connor O, Roche C, Gourinat A-C, Guigon A, Pyke AT, Grangeon J-P, Nilles E, Chanteau S,  Aaskov J,  Cao-Lormeau VM (2014) Epidemiological and molecular features of dengue virus type-1 in New Caledonia, South Pacific, 2001–2013. Virolology Journal, 11: 61. DOI: 10.1186/1743-422X-11-61

Pyke AT, Daly MT, Cameron JN, Moore P, Taylor CT, Hewitson GR, Humphreys J, Gair R  (2014) Imported Zika virus infection from the Cook Islands into Australia. PLoS Currents Outbreaks, 6. DOI: 10.1371/currents.outbreaks.4635a54dbffba2156fb2fd76dc49f65e

Frentiu FD, Zakir T, Walker T, Popovici J, Pyke AT, van den Hurk AF, McGraw EA, O'Neill S (2014) Limited dengue virus replication in field-collected Aedes aegypti mosquitoes infected with Wolbachia. PLoS Neglected Tropical Diseases, 8(2): e2688. DOI: 10.1371/journal.pntd.0002688

Pyke AT (2014) Dengue infection with a potentially atypical dengue virus strain - Brisbane, Queensland, Australia, August 2014. ProMED mail. 10-09-2014

Pyke AT (2013) Chikungunya (08) : Papua New Guinea, Australia ex Indonesia (Bali). ProMED mail. Archive number: 20130320.1594512, Published 20-03-2013

Ritchie SA, Pyke A, Hall-Mendelin S, Day A, Mores CN, Christofferson R, Gubler Dj, Bennett SN, van den Hurk A (2013) An explosive epidemic of DENV-3 in Cairns, Australia. PLoS ONE 8(7). p1-12. DOI: 10.1371/journal.pone.0068137

Goh L, and Hobson-Peters J, Prow N, ,Gardner J, Bielefeldt-Ohmann H, Pyke AT, Suhrbier A, and Hall RA (2013) Neutralizing monoclonal antibodies to the E2 protein of chikungunya virus protect against disease in a mouse model. Clinical Immunology, 149 (3 Part B). pp. 487-497. DOI: 10.1016/j.clim.2013.10.004

van den Hurk AF, Higgs S, Hall-Mendelin S, Pyke AT, Frentiu FD, McElroy K, Day A, O'Neill SL (2012) Impact of Wolbachia on infection with chikungunya and Yellow Fever viruses in the mosquito vector Aedes aegypti. PLoS Neglected Tropical Diseases, 6(11). DOI: 10.1371/journal.pntd.0001892

Whelan P, Nguyen H, Kajkowicz K, Davis J, Smith D, Pyke A, Krause V, Markey P (2012) Evidence in Australia for a case of airport dengue. PLoS Neglected Tropical Diseases. 6(9). p1-4. DOI: 10.1371/journal.pntd.0001619

Warrilow D, Northill JA, Pyke AT (2012) Sources of dengue virus imported into Queensland, Australia, 2002-2010. Emerging Infectious Diseases, 18(11): 1850-7. DOI: 10.3201/eid1811.120014

Presentations

Aug 2021: Hidden genetic diversity of  the Aedes notoscriptus virome uncovered in Brisbane, with Pyke A, Shivas M, Darbro J, Onn, M, Johnson P, Crunkhorn A, Montgomery I, Jansen C, van den Hurk A. In: 14th MCAA and the 13th ARA Online Symposium, online.

Oct 2019: Invited speaker, 'The biting edge' - reference-based approaches for emerging arbovirus detection and surveillance. In: 36th Annual NRL Symposium on infectious diseases testing, 14 Oct 2019, QT Hotel, Gold Coast, Qld.

Sep 2018: From the front page to yesterday's news: the status of Australian mosquitoes as Zika virus vectors. With van den Hurk A, Ritchie SA, Hall-Mendelin S. In: Mosquito Control Association Australia (MCAA), September 2018.

Feb 2017: Invited speaker, The biting edge - Zika virus and other Arboviral threats. In: Eye Bank Association of Australia and New Zealand Meeting, 2 February 2016, Princess Alexandra Hospital, Qld

Nov 2017: Next generation sequencing for virus diagnostics, surveillance and discovery. With Huang B, van den Hurk AF, Lopez AR, Harrower BJ, Constantino T, McMahon J, Hewitson G, Warrilow D. In: Communicable Disease Branch Presentation (Queensland Health), November 2017, Brisbane, Qld.

Sep 2016: From the forests of Uganda to our sunburnt country: incrimination of Australian mosquitoes as Zika virus vectors. with Hall-Mendelin S, Moore PR, Mackay IM, McMahon J, Ritchie SA, Taylor CT, Moore F, van den Hurk AF, in: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4-9 September, 2016, Surfers Paradise, Qld.

Sep 2016: Epidemiological, entomological and virological investigations of the Ross River virus outbreak in Queensland, 2015. with Jansen CC, Lodo K, Hall-Mendelin S, Montgomery BL, Darbro JM, Shivas MA, van den Hurk AF, in: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4-9 September, 2016, Surfers Paradise, Qld.

Sep 2016: Invited speaker, Hitchhikers from the jungle: assessment of evolution, emergence potential and public health implications of rare and divergent dengue viruses. with Moore PR, Hall-Mendelin S, Cameron JN, Hewitson GR, Pukallus D, Huang B, Warrilow D, van den Hurk AF, in: 12th Symposium of the Mosquito Control Association of Australia and Arbovirus Research in Australia, 4-9 September, 2016, Surfers Paradise, Qld.

Sep 2016: Evoluntionary response of chikungunya virus to wolbachia. With Frentiu FD, Phillips DA, Young PR, McGraw EA, O'Neill SL. In: International congress for Tropical Medicine and Malaria, 18-22 September 2016, Brisbane, Qld.

Protocols

Awards

  • 2016 – Queensland Health Award for Excellence, Pursuing Innovation, Zika virus testing
  • 1995 – Certificate of Achievement in recognition of the quality and quantity of work during the Japanese encephalitis Queensland outbreak, Queensland Health.
  • 1992 – James Vincent Duhig Prize, Queensland University of Technology

Grants and funding

  • Queensland Health Forensic and Scientific Services Cabinet R&D Fund (2019-2021) $149,000. Pyke A, Lua L, Taylor C, Somasundaram B, Adeniyi T, Chan E, Munro C, Salla-Martret M, Tropée R, Wheatley S, Moore P, Finger M. Empowered by proteins – sustainable Flavivirus NS1 protein supplements for healthier diagnostics.
  • Queensland Health Forensic and Scientific Services Team Level Fund (2018-2019) $24,156. Pyke A, van den Hurk A, Herrero L, Madzokere E, Doggett S, Haniotis J, Hall R, Druce J, Caly L, Smith D, Imrie A, Lynch S, Melville L, Weir R, Robson J, Gibb R. Australia’s most wanted: assessment and characterisation of Australia’s leading arthritogenic arboviruses, Ross River virus and Barmah Forest virus.
  • Hot North Pilot Projects (2018-2019). $35,000. van den Hurk A, Ritchie S, Ramirez A, Meyer Steiger M, Warrilow D, Pyke A, Huang B. Application of Next Generation Sequencing of mosquito excreta to identify arboviruses, microorganisms and mosquito species.
  • Queensland Health Forensic and Scientific Services Team Level Fund (2017-2019) $10,000. Expression and purification of Zika virus NS1 protein for diagnostic and research applications. Pyke A, Lua L.
  • Queensland Health Forensic and Scientific Services Cabinet R&D Fund (2017-2018) $10,000. van den Hurk A, Hall-Mendelin S, Pyke AT, McMahon J, Ritchie S, Ramirez A. Can mosquito excreta be used to enhance surveillance of Ross River and West Nile viruses?
  • Queensland Health Forensic and Scientific Services Team Level Fund (2017) $10,000. Pyke A, Warrilow D, Huang B, Hall-Mendelin S, van den Hurk A. Assessment and expansion of arbovirus surveillance and monitoring using next generation sequencing.
  • Queensland Health Forensic and Scientific Services Cabinet R&D Fund (2016) $131,323. Pyke A, van den Hurk A, Hall R, Khromykh A, Bielefeldt-Ohmann H, Young P, Hall-Mendelin S, Hobson-Peters J, Setoh Y, Muller D. Hitchhikers from the jungle: assessment of evolution, emergence potential and public health implications of rare and divergent dengue viruses.
  • Queensland Health Forensic and Scientific Services Cabinet R&D Fund (2016-2017) $71,534. van den Hurk A, Hall-Mendelin S, Pyke AT, Moore P, Bielefeldt-Ohmann H. Virus infection and replication dynamics influence Zika virus transmission by Australian mosquitoes.
  • Queensland Health Forensic and Scientific Services Team Level Fund (2016-2017) $10,000. Pyke A, Lua L. Purification of baculovirus expressed Hendra virus nucleocapsid protein for luminex microsphere serological applications.
  • NHMRC (2016-2020) $522,580. Frentiu F, Hu W, Devine G, Yakob L, McGraw E, Suhrbier A, Pyke A, Faddy H, Jansen C. New vectors, new diseases: Understanding the risk of chikungunya transmission in Australia.
  • Queensland Health Forensic and Scientific Services Team Level Fund (2015) $9,990. van den Hurk A, Pyke A. Molecular characterisation of the Ross River virus responsible for the 2015 epidemic in south east Queensland.
  • NHMRC (2014-2016) $585,497. Harrich D, Spann K, Pyke AT, Wei T. The human eukaryotic translation elongation factor 1A is a Paramyxovirus virus dependency factor.
  • Queensland Health Forensic and Scientific Services Cabinet R&D Fund (2015) $9,990. van den Hurk A, Pyke A. Molecular characterisation of the Ross River virus responsible for the 2015 epidemic in south east Queensland.
  • Queensland Health Forensic and Scientific Services Cabinet R&D Fund (2014-2015) $28,000. van den Hurk, Pyke AT, Hall-Mendelin S, McMahon J, Taylor C. Zika virus as an emerging pathogen – the Australian context.
  • Queensland Health Forensic and Scientific Services Cabinet R&D Fund (2014-2015) $50,000. Pyke AT, van den Hurk A, Taylor C, Moore P, Hall-Mendelin S. Characterisation and correlative molecular and phenotypic analysis of an ancestral sylvatic dengue virus strain.
  • Queensland Health Forensic and Scientific Services Cabinet R&D Fund (2012) $16,133. Pyke A, Northill J. Utilisation of Baculovirus Recombinant Systems to Express Hendra and Nipah virus Proteins for Research and Applied Diagnostics.

Reviewer

Lecturer

  • University of Queensland


Dr Alyssa Pyke
Senior Research Scientist, Virology
Public and Environmental Health
Contact: alyssa.pyke@health.qld.gov.au