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174 results on '"Parry, Rhys"'

1. Diverse RNA viruses of parasitic nematodes can elicit antibody responses in vertebrate hosts

Author

Quek, Shannon, Hadermann, Amber, Wu, Yang, De Coninck, Lander, Hegde, Shrilakshmi, Boucher, Jordan R., Cresswell, Jessica, Foreman, Ella, Steven, Andrew, LaCourse, E. James, Ward, Stephen A., Wanji, Samuel, Hughes, Grant L., Patterson, Edward I., Wagstaff, Simon C., Turner, Joseph D., Parry, Rhys H., Kohl, Alain, Heinz, Eva, Otabil, Kenneth Bentum, Matthijnssens, Jelle, Colebunders, Robert, and Taylor, Mark J.

Published
2024
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4. Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology

Author

Aguado, Julio, Amarilla, Alberto A., Taherian Fard, Atefeh, Albornoz, Eduardo A., Tyshkovskiy, Alexander, Schwabenland, Marius, Chaggar, Harman K., Modhiran, Naphak, Gómez-Inclán, Cecilia, Javed, Ibrahim, Baradar, Alireza A., Liang, Benjamin, Peng, Lianli, Dharmaratne, Malindrie, Pietrogrande, Giovanni, Padmanabhan, Pranesh, Freney, Morgan E., Parry, Rhys, Sng, Julian D. J., Isaacs, Ariel, Khromykh, Alexander A., Valenzuela Nieto, Guillermo, Rojas-Fernandez, Alejandro, Davis, Thomas P., Prinz, Marco, Bengsch, Bertram, Gladyshev, Vadim N., Woodruff, Trent M., Mar, Jessica C., Watterson, Daniel, and Wolvetang, Ernst J.

Published
2023
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6. SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike protein

Author

Albornoz, Eduardo A., Amarilla, Alberto A., Modhiran, Naphak, Parker, Sandra, Li, Xaria X., Wijesundara, Danushka K., Aguado, Julio, Zamora, Adriana Pliego, McMillan, Christopher L. D., Liang, Benjamin, Peng, Nias Y. G., Sng, Julian D. J., Saima, Fatema Tuj, Fung, Jenny N., Lee, John D., Paramitha, Devina, Parry, Rhys, Avumegah, Michael S., Isaacs, Ariel, Lo, Martin W., Miranda-Chacon, Zaray, Bradshaw, Daniella, Salinas-Rebolledo, Constanza, Rajapakse, Niwanthi W., Wolvetang, Ernst J., Munro, Trent P., Rojas-Fernandez, Alejandro, Young, Paul R., Stacey, Katryn J., Khromykh, Alexander A., Chappell, Keith J., Watterson, Daniel, and Woodruff, Trent M.

Published
2023
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10. The RNA interference response to alphanodavirus replication in Phlebotomus papatasi sand fly cells.

Author

Alexander, Akira J. T., Parry, Rhys H., Ratinier, Maxime, Arnaud, Frédérick, and Kohl, Alain

Subjects
*SMALL interfering RNA, *NON-coding RNA, *RNA interference, *PHLEBOTOMUS, *PSYCHODIDAE
Abstract

In this study, we identified and assembled a strain of American nodavirus (ANV) in the Phlebotomus papatasi‐derived PP9ad cell line. This strain most closely resembles Flock House virus and ANV identified in the Drosophila melanogaster S2/S2R cell line. Through small RNA sequencing and analysis, we demonstrate that ANV replication in PP9ad cells is primarily targeted by the exogenous small interfering RNA (exo‐siRNA) pathway, with minimal engagement from the PIWI‐interacting RNA (piRNA) pathway. In mosquitoes such as Aedes and Culex, the PIWI pathway is expanded and specialised, which actively limits virus replication. This is unlike in Drosophila spp., where the piRNA pathway does not restrict viral replication. In Lutzomyia sandflies (family Psychodidae), close relatives of Phlebotomus species and Drosophila, there appears to be an absence of virus‐derived piRNAs. To investigate whether this absence is due to a lack of PIWI pathway proteins, we analysed the piRNA and siRNA diversity and repertoire in PP9ad cells. Previous assemblies of P. papatasi genome (Ppap_1.0) have revealed a patchy repertoire of the siRNA and piRNA pathways. Our analysis of the updated P. papatasi genome (Ppap_2.1) has shown no PIWI protein expansion in sandflies. We found that both siRNA and piRNA pathways are transcriptionally active in PP9ad cells, with genomic mapping of small RNAs generating typical piRNA signatures. Our results suggest that the piRNA pathway may not respond to virus replication in these cells, but an antiviral response is mounted via the exo‐siRNA pathway. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Multiple novel Caliciviruses identified from stoats (Mustela erminea) in the United Kingdom

Author

Hinds, Joseph, Apaa, Ternenge, Parry, Rhys H., Withers, Amy J., MacKenzie, Laura, Staley, Ceri, Morrison, Joshua, Bennett, Malcolm, Bremner-Harrison, Samantha, Chadwick, Elizabeth A., Hailer, Frank, Harrison, Stephen, Lambin, Xavier, Loose, Matthew, Mathews, Fiona, Tarlinton, Rachael, Blanchard, Adam, Hinds, Joseph, Apaa, Ternenge, Parry, Rhys H., Withers, Amy J., MacKenzie, Laura, Staley, Ceri, Morrison, Joshua, Bennett, Malcolm, Bremner-Harrison, Samantha, Chadwick, Elizabeth A., Hailer, Frank, Harrison, Stephen, Lambin, Xavier, Loose, Matthew, Mathews, Fiona, Tarlinton, Rachael, and Blanchard, Adam

Abstract

The Caliciviridae family, comprising positive-sense RNA viruses, is characterised by its non-enveloped, small virions, broad host range, and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease, though they can lead to haemorrhagic or respiratory infections. Our study employed a metagenomics analysis of faecal samples from Stoats (Mustela erminea), identifying two novel Calicivirus species, tentatively named Stoat vesivirus and Stoat valovirus. Stoat vesivirus was identified in three samples (ST008, ST006, ST004), exhibiting a genome wide nucleotide identity of approximately 92%. The complete coding sequences of these samples were 8471 (ST004) and 8322 (ST006) nucleotides in length, respectively. Each comprised three open reading frames (ORF), closely resembling the Vesivirus mink calicivirus (China/2/2016), with 70-72% similarity in ORF1, 61-62% in ORF2 and 71% in ORF3. Phylogenetic analysis robustly supported Stoat vesivirus as belonging within the Vesivirus genus. The second Calivicirus (Stoat valovirus), detected solely in sample ST008, was 6527 nucleotides in length and with complete coding sequences present. It shared highest similarity with St-Valerien swine virus and Marmot norovirus HT16, showing 39.5% and 38.8% protein identity with ORF1 and 43.3% and 42.9% for VP1. Phylogenetic analysis suggested that while Stoat valovirus is borderline for new genus demarcation criteria, with greater than 60% divergence at ORF1, it clusters basally within the Valovirus genus, supporting its inclusion in this genus.

Published
2024

13. Detection of Dengue Virus 1 and Mammalian Orthoreovirus 3, with Novel Reassortments, in a South African Family Returning from Thailand, 2017.

Author

Jansen van Vuren, Petrus, Parry, Rhys H., and Pawęska, Janusz T.

Subjects
*GENOMICS, *MOSQUITO-borne diseases, *DENGUE viruses, *ARBOVIRUSES, *VIRUS identification, *FEVER
Abstract

In July 2017, a family of three members, a 46-year-old male, a 45-year-old female and their 8-year-old daughter, returned to South Africa from Thailand. They presented symptoms consistent with mosquito-borne diseases, including fever, headache, severe body aches and nausea. Mosquito bites in all family members suggested recent exposure to arthropod-borne viruses. Dengue virus 1 (Genus Orthoflavivirus) was isolated (isolate no. SA397) from the serum of the 45-year-old female via intracerebral injection in neonatal mice and subsequent passage in VeroE6 cells. Phylogenetic analysis of this strain indicated close genetic identity with cosmopolitan genotype 1 DENV1 strains from Southeast Asia, assigned to major lineage K, minor lineage 1 (DENV1I_K.1), such as GZ8H (99.92%) collected in November 2018 from China, and DV1I-TM19-74 isolate (99.72%) identified in Bangkok, Thailand, in 2019. Serum samples from the 46-year-old male yielded a virus isolate that could not be confirmed as DENV1, prompting unbiased metagenomic sequencing for virus identification and characterization. Illumina sequencing identified multiple segments of a mammalian orthoreovirus (MRV), designated as Human/SA395/SA/2017. Genomic and phylogenetic analyses classified Human/SA395/SA/2017 as MRV-3 and assigned a tentative genotype, MRV-3d, based on the S1 segment. Genomic analyses suggested that Human/SA395/SA/2017 may have originated from reassortments of segments among swine, bat, and human MRVs. The closest identity of the viral attachment protein σ1 (S1) was related to a human isolate identified from Tahiti, French Polynesia, in 1960. This indicates ongoing circulation and co-circulation of Southeast Asian and Polynesian strains, but detailed knowledge is hampered by the limited availability of genomic surveillance. This case represents the rare concurrent detection of two distinct viruses with different transmission routes in the same family with similar clinical presentations. It highlights the complexity of diagnosing diseases with similar sequelae in travelers returning from tropical areas. [ABSTRACT FROM AUTHOR]

Published
2024
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14. A ~40-kb flavi-like virus does not encode a known error-correcting mechanism.

Author

Petrone, Mary E., Grove, Joe, Mélade, Julien, Mifsud, Jonathon C. O., Parry, Rhys H., Marzinelli, Ezequiel M., and Holmes, Edward C.

Subjects
GENOME size, VIRAL genomes, RNA viruses, NIDOVIRUSES, NUCLEIC acids
Abstract

It is commonly held that there is a fundamental relationship between genome size and error rate, manifest as a notional "error threshold" that sets an upper limit on genome sizes. The genome sizes of RNA viruses, which have intrinsically high mutation rates due to a lack of mechanisms for error correction, must therefore be small to avoid accumulating an excessive number of deleterious mutations that will ultimately lead to population extinction. The proposed exceptions to this evolutionary rule are RNA viruses from the order Nidovirales (such as coronaviruses) that encode error-correcting exonucleases, enabling them to reach genome lengths greater than 40 kb. The recent discovery of large-genome flavi-like viruses (Flaviviridae), which comprise genomes up to 27 kb in length yet seemingly do not encode exonuclease domains, has led to the proposal that a proofreading mechanism is required to facilitate the expansion of nonsegmented RNA virus genomes above 30 kb. Herein, we describe a ~40 kb flavi-like virus identified in a Haliclona sponge metatranscriptome that does not encode a known exonuclease. Structural analysis revealed that this virus may have instead captured cellular domains associated with nucleic acid metabolism that have not been previously found in RNA viruses. Phylogenetic inference placed this virus as a divergent pesti-like lineage, such that we have provisionally termed it "Maximus pesti-like virus." This virus represents an instance of a flavi-like virus achieving a genome size comparable to that of the Nidovirales and demonstrates that RNA viruses have evolved multiple solutions to overcome the error threshold. [ABSTRACT FROM AUTHOR]

Published
2024
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16. A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses

Author

Amarilla, Alberto A., Sng, Julian D. J., Parry, Rhys, Deerain, Joshua M., Potter, James R., Setoh, Yin Xiang, Rawle, Daniel J., Le, Thuy T., Modhiran, Naphak, Wang, Xiaohui, Peng, Nias Y. G., Torres, Francisco J., Pyke, Alyssa, Harrison, Jessica J., Freney, Morgan E., Liang, Benjamin, McMillan, Christopher L. D., Cheung, Stacey T. M., Guevara, Darwin J. Da Costa, Hardy, Joshua M., Bettington, Mark, Muller, David A., Coulibaly, Fasséli, Moore, Frederick, Hall, Roy A., Young, Paul R., Mackenzie, Jason M., Hobson-Peters, Jody, Suhrbier, Andreas, Watterson, Daniel, and Khromykh, Alexander A.

Published
2021
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21. SARS-CoV-2 omicron BA.5 and XBB variants have increased neurotropic potential over BA.1 in K18-hACE2 mice and human brain organoids

Author

Stewart, Romal, primary, Yan, Kexin, additional, Ellis, Sevannah A., additional, Bishop, Cameron R., additional, Dumenil, Troy, additional, Tang, Bing, additional, Nguyen, Wilson, additional, Larcher, Thibaut, additional, Parry, Rhys, additional, Sng, Julian De Jun, additional, Khromykh, Alexander A., additional, Sullivan, Robert K. P., additional, Lor, Mary, additional, Meunier, Frédéric A., additional, Rawle, Daniel J., additional, and Suhrbier, Andreas, additional

Published
2023
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25. TMPRSS2 activation of Omicron lineage Spike glycoproteins is regulated by TMPRSS2 cleavage of ACE2

Author

Aggarwal, Anupriya, primary, Fichter, Christina, additional, Milogiannakis, Vanessa, additional, Akerman, Anouschka, additional, Ison, Timothy, additional, Ruiz Silva, Mariana, additional, Esneau, Camille, additional, Bartlett, Nathan, additional, Burrell, Louise, additional, Patel, Sheila, additional, Churchill, Melissa, additional, Angelovich, Thomas, additional, Parry, Rhys, additional, Sng, Julian D, additional, Neely, Greg G, additional, Moreno, Cesar L, additional, Loo, Lipin, additional, Kelleher, Anthony D, additional, Brilot, Fabienne, additional, Khromykh, Alexander, additional, and Turville, Stuart Grant, additional

Published
2023
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27. The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 gamma variant.

Author

Pegg, Cassandra L, Modhiran, Naphak, Parry, Rhys H, Liang, Benjamin, Amarilla, Alberto A, Khromykh, Alexander A, Burr, Lucy, Young, Paul R, Chappell, Keith, Schulz, Benjamin L, and Watterson, Daniel

Subjects
SARS-CoV-2, VIRAL proteins, CONVALESCENT plasma, GLYCANS, AMINO acids, ASPARAGINE
Abstract

The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity towards the viral spike protein, whether acquired from infection or vaccination. Mutations that impact N -glycosylation of spike may be particularly important in influencing antigenicity, but their consequences are difficult to predict. Here, we compare the glycosylation profiles and antigenicity of recombinant viral spike of ancestral Wu-1 and the Gamma strain, which has two additional N -glycosylation sites due to amino acid substitutions in the N-terminal domain (NTD). We found that a mutation at residue 20 from threonine to asparagine within the NTD caused the loss of NTD-specific antibody COVA2-17 binding. Glycan site-occupancy analyses revealed that the mutation resulted in N -glycosylation switching to the new sequon at N20 from the native N17 site. Site-specific glycosylation profiles demonstrated distinct glycoform differences between Wu-1, Gamma, and selected NTD variant spike proteins, but these did not affect antibody binding. Finally, we evaluated the specificity of spike proteins against convalescent COVID-19 sera and found reduced cross-reactivity against some mutants, but not Gamma spike compared to Wuhan spike. Our results illustrate the impact of viral divergence on spike glycosylation and SARS-CoV-2 antibody binding profiles. [ABSTRACT FROM AUTHOR]

Published
2024
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28. Statement in Support of: “Virology under the Microscope—a Call for Rational Discourse”

Author

Speck, Peter, primary, Mackenzie, Jason, additional, Bull, Rowena A., additional, Slobedman, Barry, additional, Drummer, Heidi, additional, Fraser, Johanna, additional, Herrero, Lara, additional, Helbig, Karla, additional, Londrigan, Sarah, additional, Moseley, Gregory, additional, Prow, Natalie, additional, Hansman, Grant, additional, Edwards, Robert, additional, Ahlenstiel, Chantelle, additional, Abendroth, Allison, additional, Tscharke, David, additional, Hobson-Peters, Jody, additional, Kriiger-Loterio, Robson, additional, Parry, Rhys, additional, Marsh, Glenn, additional, Harding, Emma, additional, Jacques, David A., additional, Gartner, Matthew J., additional, Lee, Wen Shi, additional, McAuley, Julie, additional, Vaz, Paola, additional, Sainsbury, Frank, additional, Tate, Michelle D., additional, Sinclair, Jane, additional, Imrie, Allison, additional, Rawlinson, Stephen, additional, Harman, Andrew, additional, Carr, Jillian M., additional, Monson, Ebony A., additional, Hibma, Merilyn, additional, Mahony, Timothy J., additional, Tu, Thomas, additional, Center, Robert J., additional, Shrestha, Lok Bahadur, additional, Hall, Robyn, additional, Warner, Morgyn, additional, Ward, Vernon, additional, Anderson, Danielle E., additional, Eyre, Nicholas S., additional, Netzler, Natalie E., additional, Peel, Alison J., additional, Revill, Peter, additional, Beard, Michael, additional, Legione, Alistair R., additional, Spencer, Alexandra J., additional, Idris, Adi, additional, Forwood, Jade, additional, Sarker, Subir, additional, Purcell, Damian F. J., additional, Bartlett, Nathan, additional, Deerain, Joshua M., additional, Brew, Bruce J., additional, Asgari, Sassan, additional, Farrell, Helen, additional, Khromykh, Alexander, additional, Enosi Tuipulotu, Daniel, additional, Anderson, David, additional, Mese, Sevim, additional, Tayyar, Yaman, additional, Edenborough, Kathryn, additional, Uddin, Jasim Muhammad, additional, Hussain, Abrar, additional, Daymond, Connor J. I., additional, Agius, Jacinta, additional, Johnson, Karyn N., additional, Shirmast, Paniz, additional, Abedinzadeshahri, Mahdi, additional, MacDiarmid, Robin, additional, Ashley, Caroline L., additional, Laws, Jay, additional, Furfaro, Lucy L., additional, Burton, Thomas D., additional, Johnson, Stephen M. R., additional, Telikani, Zahra, additional, Petrone, Mary, additional, Roby, Justin A., additional, Samer, Carolyn, additional, Suhrbier, Andreas, additional, Van Der Kamp, April, additional, Cunningham, Anthony, additional, Donato, Celeste, additional, Mahar, Jackie, additional, Black, Wesley D., additional, Vasudevan, Subhash, additional, Lenchine, Roman, additional, Spann, Kirsten, additional, Rawle, Daniel J., additional, Rudd, Penny, additional, Neil, Jessica, additional, Kingston, Richard, additional, Newsome, Timothy P., additional, Kim, Ki Wook, additional, Mak, Johnson, additional, Lowry, Kym, additional, Bryant, Nathan, additional, Meers, Joanne, additional, Roberts, Jason A., additional, McMillan, Nigel, additional, Labzin, Larisa I., additional, Slonchak, Andrii, additional, Hugo, Leon E., additional, Henzeler, Bennett, additional, Newton, Natalee D., additional, David, Cassandra T., additional, Reading, Patrick C., additional, Esneau, Camille, additional, Briody, Tatiana, additional, Nasr, Najla, additional, McNeale, Donna, additional, McSharry, Brian, additional, Fakhri, Omid, additional, Horsburgh, Bethany A., additional, Logan, Grant, additional, Howley, Paul, additional, and Young, Paul, additional

Published
2023
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31. Senolytic therapy alleviates physiological human brain aging and COVID-19 neuropathology

Author

Aguado, Julio, primary, Amarilla, Alberto A., additional, Taherian Fard, Atefeh, additional, Albornoz, Eduardo A., additional, Tyshkovskiy, Alexander, additional, Schwabenland, Marius, additional, Chaggar, Harman K., additional, Modhiran, Naphak, additional, Gómez-Inclán, Cecilia, additional, Javed, Ibrahim, additional, Baradar, Alireza A., additional, Liang, Benjamin, additional, Dharmaratne, Malindrie, additional, Pietrogrande, Giovanni, additional, Padmanabhan, Pranesh, additional, Freney, Morgan E., additional, Parry, Rhys, additional, Sng, Julian D.J., additional, Isaacs, Ariel, additional, Khromykh, Alexander A., additional, Rojas-Fernandez, Alejandro, additional, Davis, Thomas P., additional, Prinz, Marco, additional, Bengsch, Bertram, additional, Gladyshev, Vadim N., additional, Woodruff, Trent M., additional, Mar, Jessica C., additional, Watterson, Daniel, additional, and Wolvetang, Ernst J., additional

Published
2023
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33. Increased neurovirulence of omicron BA.5 and XBB variants over BA.1 in K18-hACE2 mice and human brain organoids

Author

Stewart, Romal, primary, Yan, Kexin, additional, Ellis, Sevannah A., additional, Bishop, Cameron, additional, Dumenil, Troy, additional, Tang, Bing, additional, Nguyen, Wilson, additional, Larcher, Thibaut, additional, Parry, Rhys, additional, Jun Sng, Julian De, additional, Khromykh, Alexander A., additional, Sullivan, Robert K. P., additional, Lor, Mary, additional, Meunier, Frédéric A., additional, Rawle, Daniel J., additional, and Suhrbier, Andreas, additional

Published
2022
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34. GPR183 antagonism reduces macrophage infiltration in influenza and SARS-CoV-2 infection

Author

Foo, Cheng Xiang, primary, Bartlett, Stacey, additional, Chew, Keng Yih, additional, Ngo, Minh Dao, additional, Bielefeldt-Ohmann, Helle, additional, Arachchige, Buddhika Jayakody, additional, Matthews, Benjamin, additional, Reed, Sarah, additional, Wang, Ran, additional, Smith, Christian, additional, Sweet, Matthew J., additional, Burr, Lucy, additional, Bisht, Kavita, additional, Shatunova, Svetlana, additional, Sinclair, Jane E., additional, Parry, Rhys, additional, Yang, Yuanhao, additional, Lévesque, Jean-Pierre, additional, Khromykh, Alexander, additional, Rosenkilde, Mette Marie, additional, Short, Kirsty R., additional, and Ronacher, Katharina, additional

Published
2022
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35. The Troublesome Ticks Research Protocol: Developing a Comprehensive, Multidiscipline Research Plan for Investigating Human Tick-Associated Disease in Australia

Author

Barbosa, Amanda D., primary, Long, Michelle, additional, Lee, Wenna, additional, Austen, Jill M., additional, Cunneen, Mike, additional, Ratchford, Andrew, additional, Burns, Brian, additional, Kumarasinghe, Prasad, additional, Ben-Othman, Rym, additional, Kollmann, Tobias R., additional, Stewart, Cameron R., additional, Beaman, Miles, additional, Parry, Rhys, additional, Hall, Roy, additional, Tabor, Ala, additional, O’Donovan, Justine, additional, Faddy, Helen M., additional, Collins, Marjorie, additional, Cheng, Allen C., additional, Stenos, John, additional, Graves, Stephen, additional, Oskam, Charlotte L., additional, Ryan, Una M., additional, and Irwin, Peter J., additional

Published
2022
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36. SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike protein

Author

Albornoz, Eduardo A., primary, Amarilla, Alberto A., additional, Modhiran, Naphak, additional, Parker, Sandra, additional, Li, Xaria X., additional, Wijesundara, Danushka K., additional, Aguado, Julio, additional, Zamora, Adriana Pliego, additional, McMillan, Christopher L. D., additional, Liang, Benjamin, additional, Peng, Nias Y. G., additional, Sng, Julian D. J., additional, Saima, Fatema Tuj, additional, Fung, Jenny N., additional, Lee, John D., additional, Paramitha, Devina, additional, Parry, Rhys, additional, Avumegah, Michael S., additional, Isaacs, Ariel, additional, Lo, Martin W., additional, Miranda-Chacon, Zaray, additional, Bradshaw, Daniella, additional, Salinas-Rebolledo, Constanza, additional, Rajapakse, Niwanthi W., additional, Wolvetang, Ernst J., additional, Munro, Trent P., additional, Rojas-Fernandez, Alejandro, additional, Young, Paul R., additional, Stacey, Katryn J., additional, Khromykh, Alexander A., additional, Chappell, Keith J., additional, Watterson, Daniel, additional, and Woodruff, Trent M., additional

Published
2022
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37. Reporter Flaviviruses as Tools to Demonstrate Homologous and Heterologous Superinfection Exclusion

Author

Torres, Francisco J., primary, Parry, Rhys, additional, Hugo, Leon E., additional, Slonchak, Andrii, additional, Newton, Natalee D., additional, Vet, Laura J., additional, Modhiran, Naphak, additional, Pullinger, Brody, additional, Wang, Xiaohui, additional, Potter, James, additional, Winterford, Clay, additional, Hobson-Peters, Jody, additional, Hall, Roy A., additional, and Khromykh, Alexander A., additional

Published
2022
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39. Oxysterols drive inflammation via GPR183 during influenza virus and SARS-CoV-2 infection

Author

Foo, Cheng Xiang, primary, Bartlett, Stacey, additional, Chew, Keng Yih, additional, Ngo, Minh Dao, additional, Bielefeldt-Ohmann, Helle, additional, Arachchige, Buddhika Jayakody, additional, Matthews, Benjamin, additional, Reed, Sarah, additional, Wang, Ran, additional, Sweet, Matthew J., additional, Burr, Lucy, additional, Sinclair, Jane E., additional, Parry, Rhys, additional, Khromykh, Alexander, additional, Short, Kirsty R., additional, Rosenkilde, Mette Marie, additional, and Ronacher, Katharina, additional

Published
2022
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40. Smokefree Streets : A Pilot Study of Methods to Inform Policy

Author

Parry, Rhys, Prior, Bridget, Sykes, Adrian J., Tay, Jo-Lyn, Walsh, Beth, Wright, Nicholas, Pearce, Karina, Richmond, Georgia, Robertson, Andrew, Roselan, Jalilah, Shum, Puai Yee, Taylor, Greg, Thachanamurthy, Praveene, Zheng, Tony Tianwei, Wilson, Nick, and Thomson, George

Published
2011

41. SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike-ACE2 receptor interaction

Author

Albornoz, Eduardo A, primary, Amarilla, Alberto A, additional, Modhiran, Naphak, additional, Parker, Sandra, additional, Li, Xaria X, additional, Wijesundara, Danushka K, additional, Pliego Zamora, Adriana, additional, McMillan, Christopher LD, additional, Liang, Benjamin, additional, Peng, Nias Y.G, additional, Sng, Julian D.J, additional, Tuj Saima, Fatema, additional, Paramitha, Devina, additional, Parry, Rhys, additional, Avumegah, Michael S, additional, Isaacs, Ariel, additional, Lo, Martin, additional, Miranda-Chacon, Zaray, additional, Bradshaw, Daniella, additional, Salinas-Rebolledo, Constanza, additional, Rajapakse, Niwanthi W, additional, Munro, Trent, additional, Rojas-Fernandez, Alejandro, additional, Young, Paul R, additional, Stacey, Katryn J, additional, Khromykh, Alexander A, additional, Chappell, Keith J, additional, Watterson, Daniel, additional, and Woodruff, Trent M, additional

Published
2022
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42. Mutational analysis of Aedes aegypti Dicer 2 provides insights into the biogenesis of antiviral exogenous small interfering RNAs

Author

Gestuveo, Rommel J., primary, Parry, Rhys, additional, Dickson, Laura B., additional, Lequime, Sebastian, additional, Sreenu, Vattipally B., additional, Arnold, Matthew J., additional, Khromykh, Alexander A., additional, Schnettler, Esther, additional, Lambrechts, Louis, additional, Varjak, Margus, additional, and Kohl, Alain, additional

Published
2022
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48. Structural analysis of 3’UTRs in insect flaviviruses reveals novel determinant of sfRNA biogenesis and provides new insights into flavivirus evolution

Author

Slonchak, Andrii, primary, Parry, Rhys, additional, Pullinger, Brody, additional, Sng, Julian D.J., additional, Wang, Xiaohui, additional, Buck, Teresa F, additional, Torres, Francisco J, additional, Harrison, Jessica J, additional, Colmant, Agathe M G, additional, Hobson-Peters, Jody, additional, Hall, Roy A, additional, Tuplin, Andrew, additional, and Khromykh, Alexander A, additional

Published
2021
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49. Identification and RNAi Profile of a Novel Iflavirus Infecting Senegalese Aedes vexans arabiensis Mosquitoes

Author

Parry, Rhys, Naccache, Fanny, Ndiaye, El Hadji, Fall, Gamou, Castelli, Ilaria, Lühken, Renke, Medlock, Jolyon, Cull, Benjamin, Hesson, Jenny C., Montarsi, Fabrizio, Failloux, Anna-Bella, Kohl, Alain, Schnettler, Esther, Diallo, Mawlouth, Asgari, Sassan, Dietrich, Isabelle, Becker, Stefanie C., University of Queensland [Brisbane], University of Veterinary Medicine [Hannover], Pôle Zoologie médicale [Dakar], Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Arbovirus et Virus de Fièvres Hémorragiques [Dakar, Sénégal], Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), Universität Hamburg (UHH), Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), Public Health England [Salisbury] (PHE), Uppsala University, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), MRC - University of Glasgow Centre for Virus Research, German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems (DZIF), The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Sassan Asgari is supported by the Australian Research Council, grant number DP190102048. Alain Kohl is supported by the UK Medical Research Council (MC_UU_12014/8). Rhys Parry is supported by a University of Queensland scholarship. Isabelle Dietrich is supported by the Biotechnology and Biological Sciences Research Council (grant numbers BBS/E/I/00007033 and BBS/E/I/00007035). Jenny C. Hesson is supported by the Swedish Society for Medical Research., Institut Pasteur [Paris], and Institute for Animal Health, the Pirbright Institute

Subjects
virus discovery, [SDV]Life Sciences [q-bio], MESH: RNA Interference, lcsh:QR1-502, MESH: Picornaviridae, MESH: Aedes, MESH: Molecular Sequence Annotation, Microbiology, lcsh:Microbiology, Mikrobiologi, Aedes vexans, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: RNA, Viral, RNAi, MESH: RNA, Small Interfering, iflavirus, MESH: Sequence Analysis, RNA, MESH: Animals, MESH: Mosquito Vectors, MESH: Genome, Viral, MESH: Computational Biology
Abstract

The inland floodwater mosquito Aedes vexans (Meigen, 1830) is a competent vector of numerous arthropod-borne viruses such as Rift Valley fever virus (Phenuiviridae) and Zika virus (Flaviviridae). Aedes vexans spp. have widespread Afrotropical distribution and are common European cosmopolitan mosquitoes. We examined the virome of Ae. vexans arabiensis samples from Bark&eacute, dji village, Senegal, with small RNA sequencing, bioinformatic analysis, and RT-PCR screening. We identified a novel 9494 nt iflavirus (Picornaviridae) designated here as Aedes vexans iflavirus (AvIFV). Annotation of the AvIFV genome reveals a 2782 amino acid polyprotein with iflavirus protein domain architecture and typical iflavirus 5&rsquo, internal ribosomal entry site and 3&rsquo, poly-A tail. Aedes vexans iflavirus is most closely related to a partial virus sequence from Venturia canescens (a parasitoid wasp) with 56.77% pairwise amino acid identity. Analysis of AvIFV-derived small RNAs suggests that AvIFV is targeted by the exogenous RNA interference pathway but not the PIWI-interacting RNA response, as ~60% of AvIFV reads corresponded to 21 nt Dicer&minus, 2 virus-derived small RNAs and the 24&ndash, 29 nt AvIFV read population did not exhibit a &ldquo, ping-pong&rdquo, signature. The RT-PCR screens of archival and current (circa 2011&ndash, 2020) Ae. vexans arabiensis laboratory samples and wild-caught mosquitoes from Bark&eacute, dji suggest that AvIFV is ubiquitous in these mosquitoes. Further, we screened wild-caught European Ae. vexans samples from Germany, the United Kingdom, Italy, and Sweden, all of which tested negative for AvIFV RNA. This report provides insight into the diversity of commensal Aedes viruses and the host RNAi response towards iflaviruses.

Published
2020
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50. Wolbachia Endosymbiont of the Horn Fly (Haematobia irritans irritans): a Supergroup A Strain with Multiple Horizontally Acquired Cytoplasmic Incompatibility Genes

Author

Madhav, Mukund, Parry, Rhys, Morgan, Jess A. T., James, Peter, Asgari, Sassan, Madhav, Mukund, Parry, Rhys, Morgan, Jess A. T., James, Peter, and Asgari, Sassan

Abstract

The horn fly, Haematobia irritans irritans, is a hematophagous parasite of livestock distributed throughout Europe, Africa, Asia, and the Americas. Welfare losses on livestock due to horn fly infestation are estimated to cost between $1 billion and $2.5 billion (U.S. dollars) annually in North America and Brazil. The endosymbiotic bacterium Wolbachia pipientis is a maternally inherited manipulator of reproductive biology in arthropods and naturally infects laboratory colonies of horn flies from Kerrville, TX, and Alberta, Canada, but it has also been identified in wild-caught samples from Canada, the United States, Mexico, and Hungary. Reassembly of PacBio long-read and Illumina genomic DNA libraries from the Kerrville H. i. irritans genome project allowed for a complete and circularized 1.3-Mb Wolbachia genome (wIrr). Annotation of wIrr yielded 1,249 coding genes, 34 tRNAs, 3 rRNAs, and 5 prophage regions. Comparative genomics and whole-genome Bayesian evolutionary analysis of wIrr compared to published Wolbachia genomes suggested that wIrr is most closely related to and diverged from Wolbachia supergroup A strains known to infect Drosophila spp. Whole-genome synteny analyses between wIrr and closely related genomes indicated that wIrr has undergone significant genome rearrangements while maintaining high nucleotide identity. Comparative analysis of the cytoplasmic incompatibility (CI) genes of wIrr suggested two phylogenetically distinct CI loci and acquisition of another cifB homolog from phylogenetically distant supergroup A Wolbachia strains, suggesting horizontal acquisition of these loci. The wIrr genome provides a resource for future examination of the impact Wolbachia may have in both biocontrol and potential insecticide resistance of horn flies.IMPORTANCE Horn flies, Haematobia irritans irritans, are obligate hematophagous parasites of cattle having significant effects on production and animal welfare. Control of horn flies mainly relies on the use of inse

Published
2020

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