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Dr Mary Petrone

Postdoctoral Research Associate
School of Medical Sciences
Faculty of Medicine and Health

Email

mary.petrone@sydney.edu.au

Dr. Petrone completed her PhD at Yale University where she studied the genomic epidemiology of RNA viruses. As a consequence of the COVID-19 pandemic, her work focused on developing surveillance strategies for SARS-CoV-2 in the United States. Prior to starting her PhD, Dr. Petrone worked at the National Institute of Allergy and Infectious Diseases in Dr. Anthony Fauci’s laboratory where she assisted with clinical trials aimed at finding a functional cure for HIV. At the University of Sydney, Dr. Petrone is working in the laboratory of Dr. Edward Holmes to discover and characterise novel marine viruses. She is particularly interested in studying the viromes of members of ancient marine ecosystems, including cyanobacteria, corals, and tunicates.

Research interests

RNA viruses, RNA virus evolution, phylogenetics, marine ecosystems

Current research students

Project title	Research student
Clinical metagenomics for rapid pathogen diagnosis characterisation and molecular epidemiology in hospitalised adults with severe infection	Krispin HAJKOWICZ

Publications

By Type

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Journals

Vogels, C., Hill, V., Breban, M., Chaguza, C., Paul, L., Sodeinde, A., Taylor-Salmon, E., Ott, I., Petrone, M., Dijk, D., et al (2024). DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics, 25(1). [More Information]
Chaguza, C., Hahn, A., Petrone, M., Zhou, S., Ferguson, D., Breban, M., Pham, K., Peña-Hernández, M., Castaldi, C., Hill, V., et al (2023). Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Reports Medicine, 4(2). [More Information]
Du, H., Dong, E., Badr, H., Petrone, M., Grubaugh, N., Gardner, L. (2023). Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approach. EBioMedicine, 89. [More Information]
Allicock, O., Yolda-Carr, D., Earnest, R., Breban, M., Vega, N., Ott, I., Kalinich, C., Alpert, T., Petrone, M., Wyllie, A. (2023). Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples. Progress in Biophysics and Molecular Biology, 182, 103-108. [More Information]
Petrone, M., Lucas, C., Menasche, B., Breban, M., Yildirim, I., Campbell, M., Omer, S., Holmes, E., Ko, A., Grubaugh, N., et al (2023). Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants. Genome Biology and Evolution, 15(4). [More Information]
Speck, P., Mackenzie, J., Bull, R., Slobedman, B., Abendroth, A., Harman, A., Tu, T., Ashley, C., Petrone, M., Samer, C., Cunningham, A., Mahar, J., Newsome, T., Nasr, N., et al (2023). Statement in Support of: "Virology under the Microscope - a Call for Rational Discourse". mSphere, 8(3). [More Information]
Speck, P., Mackenzie, J., Bull, R., Slobedman, B., Abendroth, A., Harman, A., Tu, T., Ashley, C., Petrone, M., Samer, C., Cunningham, A., Mahar, J., Newsome, T., Nasr, N., et al (2023). Statement in Support of: “Virology under the Microscope-a Call for Rational Discourse”. Journal of Virology, 97(5). [More Information]
Speck, P., Mackenzie, J., Bull, R., Slobedman, B., Abendroth, A., Harman, A., Tu, T., Ashley, C., Petrone, M., Samer, C., Cunningham, A., Mahar, J., Newsome, T., Nasr, N., et al (2023). Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”. mBio, 14(3). [More Information]
Petrone, M., Holmes, E., Harvey, E. (2023). Through an ecological lens : An ecosystem-based approach to zoonotic risk assessment. EMBO Reports, 24(2). [More Information]
Mifsud, J., Costa, V., Petrone, M., Marzinelli, E., Holmes, E., Harvey, E. (2023). Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus Evolution, 9(1). [More Information]
Petrone, M., Rothman, J., Breban, M., Ott, I., Russell, A., Lasek-Nesselquist, E., Badr, H., Kelly, K., Omerza, G., Renzette, N., et al (2022). Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota. Communications Biology. [More Information]
Allicock, O., Petrone, M., Yolda-Carr, D., Breban, M., Walsh, H., Watkins, A., Rothman, J., Farhadian, S., Grubaugh, N., Wyllie, A. (2022). Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics. BMC Infectious Diseases, 22(1), 284. [More Information]
Baaijens, J., Zulli, A., Ott, I., Nika, I., van der Lugt, M., Petrone, M., Alpert, T., Fauver, J., Kalinich, C., Vogels, C., et al (2022). Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biology, 23(1). [More Information]
Klein, J., Brito, A., Trubin, P., Lu, P., Wong, P., Alpert, T., Peña-Hernández, M., Haynes, W., Kamath, K., Liu, F., et al (2022). Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant Recipient. The Journal of Infectious Diseases, 225(3), 374-384. [More Information]
Alpert, T., Vogels, C., Breban, M., Petrone, M., Yale IMPACT Research Team, N., Wyllie, A., Grubaugh, N., Fauver, J. (2022). Sequencing SARS-CoV-2 genomes from saliva. Virus Evolution, 8(1), 1-7. [More Information]
Petrone, M., Earnest, R., Lourenço, J., Kraemer, M., Paulino-Ramirez, R., Grubaugh, N., Tapia, L. (2021). Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic. Nature Communications, 12(1), 151. [More Information]
Wang, E., Mao, T., Klein, J., Dai, Y., Huck, J., Jaycox, J., Liu, F., Zhou, T., Israelow, B., Wong, P., et al (2021). Diverse functional autoantibodies in patients with COVID-19. Nature, 595(7866), 283-288. [More Information]
Alpert, T., Brito, A., Lasek-Nesselquist, E., Rothman, J., Valesano, A., MacKay, M., Petrone, M., Breban, M., Watkins, A., Vogels, C., et al (2021). Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States. Cell, 184(10), 2595-2604.e13. [More Information]
Lucas, C., Vogels, C., Yildirim, I., Rothman, J., Lu, P., Monteiro, V., Gehlhausen, J., Campbell, M., Silva, J., Tabachnikova, A., et al (2021). Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity. Nature, 600(7889), 523-529. [More Information]
Brito, A., Machado, L., Oidtman, R., Siconelli, M., Tran, Q., Fauver, J., Carvalho, R., Dezordi, F., Pereira, M., de Castro-Jorge, L., et al (2021). Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil. Nature Communications, 12(1), 2619. [More Information]
Vogels, C., Brito, A., Wyllie, A., Fauver, J., Ott, I., Kalinich, C., Petrone, M., Casanovas-Massana, A., Catherine Muenker, M., Moore, A., et al (2020). Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets. Nature Microbiology, 5(10), 1299-1305. [More Information]
Fauver, J., Petrone, M., Hodcroft, E., Shioda, K., Ehrlich, H., Watts, A., Vogels, C., Brito, A., Alpert, T., Muyombwe, A., et al (2020). Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell, 181(5), 990-996.e5. [More Information]
Kudo, E., Israelow, B., Vogels, C., Lu, P., Wyllie, A., Tokuyama, M., Venkataraman, A., Brackney, D., Ott, I., Petrone, M., et al (2020). Detection of SARS-CoV-2 RNA by multiplex RTqPCR. PLoS Biology, 18(10), e3000867. [More Information]
Kalinich, C., Jensen, C., Neugebauer, P., Petrone, M., Peña-Hernández, M., Ott, I., Wyllie, A., Alpert, T., Vogels, C., Fauver, J., et al (2020). Real-time public health communication of local SARS-CoV-2 genomic epidemiology. PLoS Biology, 18(8), e3000869. [More Information]
Grubaugh, N., Petrone, M., Holmes, E. (2020). We shouldn’t worry when a virus mutates during disease outbreaks. Nature Microbiology, 5, 529-530. [More Information]
Clarridge, K., Blazkova, J., Einkauf, K., Petrone, M., Refsland, E., Justement, J., Shi, V., Huiting, E., Seamon, C., Lee, G., et al (2018). Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals. PLoS Pathogens, 14(1), e1006792. [More Information]
Sneller, M., Justement, J., Gittens, K., Petrone, M., Clarridge, K., Proschan, M., Kwan, R., Shi, V., Blazkova, J., Refsland, E., et al (2017). A randomized controlled safety/efficacy trial of therapeutic vaccination in HIV-infected individuals who initiated antiretroviral therapy early in infection. Science Translational Medicine, 9(419), eaan8848. [More Information]
Bar, K., Sneller, M., Harrison, L., Justement, J., Overton, E., Petrone, M., Salantes, D., Seamon, C., Scheinfeld, B., Kwan, R., et al (2016). Effect of HIV antibody VRC01 on viral rebound after treatment interruption. New England Journal of Medicine, 375(21), 2037-2050. [More Information]

show 25 more

By Year

Expand all

2024

Vogels, C., Hill, V., Breban, M., Chaguza, C., Paul, L., Sodeinde, A., Taylor-Salmon, E., Ott, I., Petrone, M., Dijk, D., et al (2024). DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics, 25(1). [More Information]

2023

Chaguza, C., Hahn, A., Petrone, M., Zhou, S., Ferguson, D., Breban, M., Pham, K., Peña-Hernández, M., Castaldi, C., Hill, V., et al (2023). Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Reports Medicine, 4(2). [More Information]
Du, H., Dong, E., Badr, H., Petrone, M., Grubaugh, N., Gardner, L. (2023). Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approach. EBioMedicine, 89. [More Information]
Allicock, O., Yolda-Carr, D., Earnest, R., Breban, M., Vega, N., Ott, I., Kalinich, C., Alpert, T., Petrone, M., Wyllie, A. (2023). Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples. Progress in Biophysics and Molecular Biology, 182, 103-108. [More Information]
Petrone, M., Lucas, C., Menasche, B., Breban, M., Yildirim, I., Campbell, M., Omer, S., Holmes, E., Ko, A., Grubaugh, N., et al (2023). Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants. Genome Biology and Evolution, 15(4). [More Information]
Speck, P., Mackenzie, J., Bull, R., Slobedman, B., Abendroth, A., Harman, A., Tu, T., Ashley, C., Petrone, M., Samer, C., Cunningham, A., Mahar, J., Newsome, T., Nasr, N., et al (2023). Statement in Support of: "Virology under the Microscope - a Call for Rational Discourse". mSphere, 8(3). [More Information]
Speck, P., Mackenzie, J., Bull, R., Slobedman, B., Abendroth, A., Harman, A., Tu, T., Ashley, C., Petrone, M., Samer, C., Cunningham, A., Mahar, J., Newsome, T., Nasr, N., et al (2023). Statement in Support of: “Virology under the Microscope-a Call for Rational Discourse”. Journal of Virology, 97(5). [More Information]
Speck, P., Mackenzie, J., Bull, R., Slobedman, B., Abendroth, A., Harman, A., Tu, T., Ashley, C., Petrone, M., Samer, C., Cunningham, A., Mahar, J., Newsome, T., Nasr, N., et al (2023). Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”. mBio, 14(3). [More Information]
Petrone, M., Holmes, E., Harvey, E. (2023). Through an ecological lens : An ecosystem-based approach to zoonotic risk assessment. EMBO Reports, 24(2). [More Information]
Mifsud, J., Costa, V., Petrone, M., Marzinelli, E., Holmes, E., Harvey, E. (2023). Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus Evolution, 9(1). [More Information]

show 6 more

2022

Petrone, M., Rothman, J., Breban, M., Ott, I., Russell, A., Lasek-Nesselquist, E., Badr, H., Kelly, K., Omerza, G., Renzette, N., et al (2022). Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota. Communications Biology. [More Information]
Allicock, O., Petrone, M., Yolda-Carr, D., Breban, M., Walsh, H., Watkins, A., Rothman, J., Farhadian, S., Grubaugh, N., Wyllie, A. (2022). Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics. BMC Infectious Diseases, 22(1), 284. [More Information]
Baaijens, J., Zulli, A., Ott, I., Nika, I., van der Lugt, M., Petrone, M., Alpert, T., Fauver, J., Kalinich, C., Vogels, C., et al (2022). Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biology, 23(1). [More Information]
Klein, J., Brito, A., Trubin, P., Lu, P., Wong, P., Alpert, T., Peña-Hernández, M., Haynes, W., Kamath, K., Liu, F., et al (2022). Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant Recipient. The Journal of Infectious Diseases, 225(3), 374-384. [More Information]
Alpert, T., Vogels, C., Breban, M., Petrone, M., Yale IMPACT Research Team, N., Wyllie, A., Grubaugh, N., Fauver, J. (2022). Sequencing SARS-CoV-2 genomes from saliva. Virus Evolution, 8(1), 1-7. [More Information]

show 2 more

2021

Petrone, M., Earnest, R., Lourenço, J., Kraemer, M., Paulino-Ramirez, R., Grubaugh, N., Tapia, L. (2021). Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic. Nature Communications, 12(1), 151. [More Information]
Wang, E., Mao, T., Klein, J., Dai, Y., Huck, J., Jaycox, J., Liu, F., Zhou, T., Israelow, B., Wong, P., et al (2021). Diverse functional autoantibodies in patients with COVID-19. Nature, 595(7866), 283-288. [More Information]
Alpert, T., Brito, A., Lasek-Nesselquist, E., Rothman, J., Valesano, A., MacKay, M., Petrone, M., Breban, M., Watkins, A., Vogels, C., et al (2021). Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States. Cell, 184(10), 2595-2604.e13. [More Information]
Lucas, C., Vogels, C., Yildirim, I., Rothman, J., Lu, P., Monteiro, V., Gehlhausen, J., Campbell, M., Silva, J., Tabachnikova, A., et al (2021). Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity. Nature, 600(7889), 523-529. [More Information]
Brito, A., Machado, L., Oidtman, R., Siconelli, M., Tran, Q., Fauver, J., Carvalho, R., Dezordi, F., Pereira, M., de Castro-Jorge, L., et al (2021). Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil. Nature Communications, 12(1), 2619. [More Information]

show 2 more

2020

Vogels, C., Brito, A., Wyllie, A., Fauver, J., Ott, I., Kalinich, C., Petrone, M., Casanovas-Massana, A., Catherine Muenker, M., Moore, A., et al (2020). Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets. Nature Microbiology, 5(10), 1299-1305. [More Information]
Fauver, J., Petrone, M., Hodcroft, E., Shioda, K., Ehrlich, H., Watts, A., Vogels, C., Brito, A., Alpert, T., Muyombwe, A., et al (2020). Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell, 181(5), 990-996.e5. [More Information]
Kudo, E., Israelow, B., Vogels, C., Lu, P., Wyllie, A., Tokuyama, M., Venkataraman, A., Brackney, D., Ott, I., Petrone, M., et al (2020). Detection of SARS-CoV-2 RNA by multiplex RTqPCR. PLoS Biology, 18(10), e3000867. [More Information]
Kalinich, C., Jensen, C., Neugebauer, P., Petrone, M., Peña-Hernández, M., Ott, I., Wyllie, A., Alpert, T., Vogels, C., Fauver, J., et al (2020). Real-time public health communication of local SARS-CoV-2 genomic epidemiology. PLoS Biology, 18(8), e3000869. [More Information]
Grubaugh, N., Petrone, M., Holmes, E. (2020). We shouldn’t worry when a virus mutates during disease outbreaks. Nature Microbiology, 5, 529-530. [More Information]

show 2 more

2018

Clarridge, K., Blazkova, J., Einkauf, K., Petrone, M., Refsland, E., Justement, J., Shi, V., Huiting, E., Seamon, C., Lee, G., et al (2018). Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals. PLoS Pathogens, 14(1), e1006792. [More Information]

2017

Sneller, M., Justement, J., Gittens, K., Petrone, M., Clarridge, K., Proschan, M., Kwan, R., Shi, V., Blazkova, J., Refsland, E., et al (2017). A randomized controlled safety/efficacy trial of therapeutic vaccination in HIV-infected individuals who initiated antiretroviral therapy early in infection. Science Translational Medicine, 9(419), eaan8848. [More Information]

2016

Bar, K., Sneller, M., Harrison, L., Justement, J., Overton, E., Petrone, M., Salantes, D., Seamon, C., Scheinfeld, B., Kwan, R., et al (2016). Effect of HIV antibody VRC01 on viral rebound after treatment interruption. New England Journal of Medicine, 375(21), 2037-2050. [More Information]

Selected Grants

2024

Explaining virus diversity, Holmes E, Harvey E, Petrone M, Australian Research Council (ARC)/Discovery Projects (DP)

2023

Characterising viruses that infect disease-causing Apicomplexa, Petrone M, Sydney Institute for Infectious Diseases (Sydney ID)/Sydney ID Seed Grants

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Dr Mary Petrone

Publications

By Type

By Year

Selected Grants

2024

2023