Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling von Rockett, Rebecca J., Arnott, Alicia, Lam, Connie, Sadsad, Rosemarie, Timms, Verlaine, Gray, Karen-Ann, Eden, John-Sebastian, Chang, Sheryl, Gall, Mailie, Draper, Jenny, Sim, Eby M., Bachmann, Nathan L., Carter, Ian, Basile, Kerri, Byun, Roy, O’Sullivan, Matthew V., Chen, Sharon C-A, Maddocks, Susan, Sorrell, Tania C., Dwyer, Dominic E., Holmes, Edward C., Kok, Jen, Prokopenko, Mikhail, Sintchenko, Vitali

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Off-season RSV epidemics in Australia after easing of COVID-19 restrictions von Eden, John-Sebastian, Sikazwe, Chisha, Xie, Ruopeng, Deng, Yi-Mo, Sullivan, Sheena G., Michie, Alice, Levy, Avram, Cutmore, Elena, Blyth, Christopher C., Britton, Philip N., Crawford, Nigel, Dong, Xiaomin, Dwyer, Dominic E., Edwards, Kimberly M., Horsburgh, Bethany A., Foley, David, Kennedy, Karina, Minney-Smith, Cara, Speers, David, Tulloch, Rachel L., Holmes, Edward C., Dhanasekaran, Vijaykrishna, Smith, David W., Kok, Jen, Barr, Ian G.

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Where has all the influenza gone? The impact of COVID-19 on the circulation of influenza and other respiratory viruses, Australia, March to September 2020 von Sullivan, Sheena G, Carlson, Sandra, Cheng, Allen C, Chilver, Monique Bn, Dwyer, Dominic E, Irwin, Melissa, Kok, Jen, Macartney, Kristine, MacLachlan, Jennifer, Minney-Smith, Cara, Smith, David, Stocks, Nigel, Taylor, Janette, Barr, Ian G

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Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance von Rockett, Rebecca J., Draper, Jenny, Gall, Mailie, Sim, Eby M., Arnott, Alicia, Agius, Jessica E., Johnson-Mackinnon, Jessica, Fong, Winkie, Martinez, Elena, Drew, Alexander P., Lee, Clement, Ngo, Christine, Ramsperger, Marc, Ginn, Andrew N., Wang, Qinning, Fennell, Michael, Ko, Danny, Hueston, Linda, Kairaitis, Lukas, Holmes, Edward C., O’Sullivan, Matthew N., Chen, Sharon C.-A., Kok, Jen, Dwyer, Dominic E., Sintchenko, Vitali

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The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses Among Paediatric Cases in Sydney, Australia von Adam, Dillon Charles, Chen, Xin, Scotch, Matthew, MacIntyre, Chandini Raina, Dwyer, Dominic, Kok, Jen

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Is it or is it not? Lessons learned from a case of suspected vaccine strain measles von Lord, Heidi, Kok, Jen, Fletcher, Stephanie, Alexander, Kate

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Identification of bacteria in blood culture broths using matrix-assisted laser desorption-ionization Sepsityper™ and time of flight mass spectrometry von Kok, Jen, Thomas, Lee C, Olma, Thomas, Chen, Sharon C A, Iredell, Jonathan R

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Fatal Human Neurologic Infection Caused by Pigeon Avian Paramyxovirus-1, Australia von Hurley, Siobhan, Eden, John Sebastian, Bingham, John, Rodriguez, Michael, Neave, Matthew J, Johnson, Alexandra, Howard-Jones, Annaleise R, Kok, Jen, Anazodo, Antoinette, McMullan, Brendan, Williams, David T, Watson, James, Solinas, Annalisa, Kim, Ki Wook, Rawlinson, William

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Emergence of Japanese encephalitis in Australia: a diagnostic perspective von Pham, David, Howard-Jones, Annaleise R, Hueston, Linda, Jeoffreys, Neisha, Doggett, Stephen, Rockett, Rebecca J, Eden, John-Sebastian, Sintchenko, Vitali, C-A Chen, Sharon, O'Sullivan, Matthew V, Maddocks, Susan, Dwyer, Dominic E, Kok, Jen

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Facemask against viral respiratory infections among Hajj pilgrims: A challenging cluster-randomized trial von Alfelali, Mohammad, Haworth, Elizabeth A, Barasheed, Osamah, Badahdah, Al-Mamoon, Bokhary, Hamid, Tashani, Mohamed, Azeem, Mohammad I, Kok, Jen, Taylor, Janette, Barnes, Elizabeth H, El Bashir, Haitham, Khandaker, Gulam, Holmes, Edward C, Dwyer, Dominic E, Heron, Leon G, Wilson, Godwin J, Booy, Robert, Rashid, Harunor

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Deisolation in the Healthcare Setting Following Recent COVID-19 Infection von Baumgart, Samuel W L, McLachlan, Aidan, Kenny, Hayden, McKew, Genevieve, Maddocks, Susan, Chen, Sharon C-A, Kok, Jen

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Seroepidemiology of Parechovirus A3 Neutralizing Antibodies, Australia, the Netherlands, and United States von Karelehto, Eveliina, Brouwer, Lieke, Benschop, Kimberley, Kok, Jen, Basile, Kerri, McMullan, Brendan, Rawlinson, William, Druce, Julian, Nicholson, Suellen, Selvarangan, Rangaraj, Harrison, Christopher, Lankachandra, Kamani, van Eijk, Hetty, Koen, Gerrit, de Jong, Menno, Pajkrt, Dasja, Wolthers, Katja C

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Fungal Infections Other Than Invasive Aspergillosis in COVID-19 Patients von Basile, Kerri, Halliday, Catriona, Kok, Jen, Chen, Sharon C-A

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Emergent Omicron BR.2.1 sublineage of SARS-CoV-2 in New South Wales, Australia: a subvariant with high fitness but without increased disease severity von Howard-Jones, Annaleise R, Arnott, Alicia, Draper, Jenny, Gall, Mailie, Ellis, Sally, Marris, Kelsi, Selvey, Christine, Basile, Kerri, Dwyer, Dominic E, Sintchenko, Vitali, Kok, Jen

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SARS-CoV-2 Within-Host and in vitro Genomic Variability and Sub-Genomic RNA Levels Indicate Differences in Viral Expression Between Clinical Cohorts and in vitro Culture von Agius, Jessica E, Johnson-Mackinnon, Jessica C, Fong, Winkie, Gall, Mailie, Lam, Connie, Basile, Kerri, Kok, Jen, Arnott, Alicia, Sintchenko, Vitali, Rockett, Rebecca J

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SABRes: in silico detection of drug resistance conferring mutations in subpopulations of SARS-CoV-2 genomes von Fong, Winkie, Rockett, Rebecca J, Agius, Jessica E, Chandra, Shona, Johnson-Mckinnon, Jessica, Sim, Eby, Lam, Connie, Arnott, Alicia, Gall, Mailie, Draper, Jenny, Maddocks, Susan, Chen, Sharon, Kok, Jen, Dwyer, Dominic, O'Sullivan, Matthew, Sintchenko, Vitali

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An Amplicon-Based Approach for the Whole-Genome Sequencing of Human Metapneumovirus von Tulloch, Rachel L, Kok, Jen, Carter, Ian, Dwyer, Dominic E, Eden, John-Sebastian

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Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2 von Pham, David, Maddocks, Susan, Dwyer, Dominic E, Sintchenko, Vitali, Kok, Jen, Rockett, Rebecca J

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Emerging Genotype IV Japanese Encephalitis Virus Outbreak in New South Wales, Australia von Howard-Jones, Annaleise R, Pham, David, Jeoffreys, Neisha, Eden, John-Sebastian, Hueston, Linda, Kesson, Alison M, Nagendra, Vanathi, Samarasekara, Harsha, Newton, Peter, Chen, Sharon C-A, O'Sullivan, Matthew V, Maddocks, Susan, Dwyer, Dominic E, Kok, Jen

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RAPIDprep: A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples von Tulloch, Rachel L., Kim, Karan, Sikazwe, Chisha, Michie, Alice, Burrell, Rebecca, Holmes, Edward C., Dwyer, Dominic E., Britton, Philip N., Kok, Jen, Eden, John-Sebastian

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