Viral evolution, HIV, SARS-CoV-2/COVID-19, Antiviral Drug and Vaccine Strategies, Novel Methodologies
We are interested in viral evolution and diversity, while developing innovative methodologies and approaches to study novel antiviral and vaccine strategies.
Lately, we have been working on three main research areas:
Quiñones-Mateu Lab March 2020
Prof. Miguel Quiñones-Mateu
Principal Investigator
miguel.quinones-mateu@otago.ac.nz
Office: +64 3 479 7703
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| Dr Blair Lawley - Scientific Officer | Dr Rhodri Harfoot - Research Fellow | Dr Leonor C. Hernández - Laboratory Manager | |
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| Dr Shubhra Sinha - Research Fellow | Joanna Kuang, MSc - Research Assistant | ||
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| Atlesh Sudhakar - MSc Student |
Cody Hird - MSc Student |
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View Prof Quiñones-Mateu on PubMed
View Prof Quiñones-Mateu on Google Scholar
Harfoot, R., Lawley, B., Hernandez, L.C., Kuang, J., Grant, J., Treece, J.M., Lequeux, S., Day, R., Jack, S., Stanton, J-A.L., Bostina, M., Ussher, J.E., and Quiñones-Mateu, M.E.* (2022). Characterization of the first SARS-CoV-2 isolates from Aotearoa New Zealand as part of a rapid response to the COVID-19 pandemic. Viruses, 14:366
De Caluwe, L., Heyndrickx, L., Coppens, S., Vereecken, K., Quiñones-Mateu, M.E., Merits, A., Arien, K.K., and Bartholomeeusen, K. (2022). Chikungunya virus’ high genomic plasticity enables rapid adaptation to restrictive A549 cells. Viruses, 14:282
Joussef-Piña, S., Nankya, I., Nalukwago, S., Baseke, J., Rwambuya, S., Winner, D., Kyeyune, F., Chervenak, K., Thiel, B., Assad, R., Dobrowolski, C., Luttge, B., Lawley, B., Kityo, C.M., Boom, W.H., Karn, J., and Quiñones-Mateu, M.E.* (2022). Reduced and highly diverse peripheral HIV-1 reservoir in virally suppressed patients infected with non-B HIV-1 strains in Uganda. Retrovirology, 19:1
Harfoot, R., Yung, D.B.Y., Anderson, W.A., Wild, C.E.K., Coetzee, N., Hernández, L.C., Lawley, B., Pletzer, D., Derraik, J.G.B., Anderson, Y.C., and Quiñones-Mateu, M.E.* (2022). Ultraviolet-C irradiation, heat and storage as potential methods of inactivating SARS-CoV-2 and bacterial pathogens on filtering facepiece respirators. Pathogens, 11:83
Stanton, J-A.L., O’Brien, R., Hall, R.J., Chernyavtseva, A., Ha, H.J., Jelly, L., Mace, P.D., Klenov, A., Treece, J.M., Fraser, J., Clow, F., Clarke, L., Su, Y., Kurup, H.M., Filichev, V.V., Rolleston, W., Law, L., Rendle, P.M., Harris, L.D., Wood, J.M., Scully, T.W., Ussher, J.E., Grant, J., Hore, T.A., Moser, T.V., Harfoot, R., Lawley, B., Quiñones-Mateu, M.E., Collins, P., and Blaikie, R. (2022). Uncoupling molecular testing for SARS-CoV-2 from international supply chains. Frontiers in Public Health, 9:808751
Lawley, B., Grant, J., , Harfoot, R., Treece, J., Day, R., Hernandez, L.C., Stanton, J-A.L., Ussher, J.E., and Quiñones-Mateu, M.E.* (2021). Rapid response to SARS-CoV-2 in Aotearoa New Zealand: implementation of a diagnostic test and characterization of the first COVID-19 cases in the South Island. Viruses, 13:2222
Writing Committee for the REMAP-CAP Investigators (2021). Effect of convalescent plasma on organ support-free days in critically ill patients with COVID-19 - A randomized clinical trial. JAMA, 326:1690-1702
Ndashimye, E., Li, Y, Reyes, P.S., Avino, M., Olabode, A.S., Kityo, C.M., Kyeyune, F., Nankya, I., Quiñones-Mateu, M.E., Barr, S., & Arts, E.J. (2021). High level resistance to bictegravir and cabotegravir in subtype A and D HIV-1 infected patients failing raltegravir with multiple primary resistance mutations. Journal of Antimicrobial Chemotherapy, doi:10.1093/jac/dkab276
Cruz-Lebron, A., Johnson, R., Mazahery, C., Troyer, Z., Joussef-Piña, S., Quiñones-Mateu, M.E., Hazen, S.L., and Levine, A. (2021). Chronic opioid use modulates human enteric microbiota and intestinal barrier integrity. Gut Microbes, 13:1946368
Ameratunga, R., Woon, S-T., Steele, R., Snell, R., Medlicott, N., Mears, E., Leung, E.Y., Lehnert, K., Jordan, A., Das, S., Abbott, W., Longhurst, H., and Quiñones-Mateu, M.E. (2021). Perspective: The nose and the stomach play a critical role in the NZACE2-Pātari* (modified ACE2) drug treatment project of SARS-CoV-2 infection. Expert Review of Clinical Immunology, 17:553-560
Cruz-Lebron, A., D’argenio Garcia, L., Talla, A., Joussef-Piña, S., Quiñones-Mateu M.E., Sekaly, R-F., Ladislau de Carvalho, K.I., and Levine, A.D. (2020). Decreased enteric bacterial compostion and diversity in South American Crohn’s disease vary with the choice of treatment strategy and time since diagnosis. Journal of Crohn’s and Colitis, 14:791-800
Taiwo, B., Quiñones-Mateu, M.E., Smith, K., Zheng, L., Gulick, T., Nyaku-Rutgers, A.N., Sax, P., Ha, B., Kumwenda, J., Olefsky, M., Godfrey, C., and Wallis, C. (2020). Prior case of resistance to dolutegravir plus lamivudine dual therapy. AIDS Research and Human Retroviruses, 36:254
Lee, E.R., Parkin, N., Jennings, C., Brumme, C.J., Enns, E., Casadella, M., Howison, M., Avila-Rios, S., Capina, R., Marinier, E., Van Domselaar, G., Noguera-Julian, M., Harrigan, R., Quiñones-Mateu M.E., Paredes, R., Kantor, R., Sandstrom, P. and Ji, H. (2020). Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance typing. Scientific Reports, 10:1634
Ussher, J.E., Le Gros, G., Quiñones-Mateu M.E., Gulab, S., and Yiannoutsos, M. (2020). The case for New Zealand to have its own COVID-19 vaccine programme. New Zealand Medical Journal, 133:112
Ndembi, N., Murtala-Ibrahim, F, Tola, M., Jumare, J., Aliyu, A., Alabi, P., Mensah, C., Abimiku, A., Quiñones-Mateu, M.E., Crowell, T.A., Rhee, S.Y., Shafer, R.W., Gupta, R., Blattner, W., Charurat, M., and Dakum, P. (2020). Predictors of first-line antiretroviral therapy failure among adults and adolescents living with HIV/AIDS in a large prevention and treatment program in Nigeria. AIDS Research and Therapy, 17:64
Helbig, K.J., Bull, R.A., Ambrose, R., Beard, M., Blanchard, H., Boecking, T., Chau, B., Colmant, A., Crosse, K., Purcell, D.F.J., Fraser, J., Hayward, J., Hamilton, S., Husain, M., MacDiarmid, R., Mackenzie, J., Moseley, G., Nguyen, T.H.O., Quiñones-Mateu, M.E., Robinson, K., Rodrigo, C., Rodriguez, J., Rudd, P., Werno, A., White, P., Young, P., Hibma, M., Drummer, H., and Tachedjian, G. (2020). Tenth Scientific Biennial Meeting of the Australasian Virology Society – AVS10 2019. Viruses, 12:621
Ameratunga, R., Lehnert, K., Leung, E., Comoletti, D., Snell, R., Woon, S-T., Abbott, W., Mears, E., Steele, R., McKee, J., Muscroft-Taylor, A., Ameratunga, S., Medlicott, N., Das, S., Rolleston, W., Quiñones-Mateu, M.E., Petousis-Harris, H., and Jordan, A. (2020). Inhaled modified angiotensin enzyme 2 (ACE2) as a decoy to mitigate SARS-CoV-2 infection. New Zealand Medical Journal, 133:112
Ndashimye, E., Avino, M., Li, Y., Kyeyune, F., Tan, C., Meadows, A., Solis, P., Gibson, R., Olabode, A.S., Poon, A.F.Y, Nankya, I., Kityo, C.,Quiñones-Mateu M.E., and Arts, E.J. (2020). Accumulation of integrase strand transfer inhibitor resistance mutations confers high-level resistance to dolutegravir in non-B subtype HIV-1 strains from patients failing raltegravir in Uganda. Journal of Antimicrobial Chemotherapy, 75:3525-3533
Grant, C., Griffin, I., McConnell, M., Quiñones-Mateu, M.E., Schumayer, D., and Hutchinson, D. (2020). Re-opening after COVID-19 in New Zealand. Journal of Conservation and Museum Studies, 18:4
Bonar, M.M., Tabler C.O., Haqqani, A.A., Lapointe, L.E., Galiatsos, J.A., Joussef-Piña, S., Quiñones-Mateu M.E., and Tilton, J.C. (2020). Nanoscale flow cytometry reveals interpatient variability in HIV protease activity that correlates with viral infectivity and identifies drug-resistant viruses. Scientific Reports, 10:18101
Datir, R., Kemp, S., El Bouzidi, K., Mlchocova, P., Goldstein, R., Breuer, J., Towers, G.J., Jolly, G., Quiñones-Mateu, M.E., Dakum, P.S., Ndembi, N., and Gupta, R.K. (2020). In vivo emergence of a novel protease inhibitor resistance signature in HIV-1 matrix. mBio, 11:e02036-20
Poon, A.F.Y., Ndashimye, E., Avino, M., Gibson, R.M., Kityo, C., Kyeyune, F., Nankya, I., Quiñones-Mateu M.E., and Arts, E.J. (2019). First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda. AIDS Research and Therapy, 16:3
Silver, N., Paynter, M., McAllister, G., Atchley, M., Sayir, C., Short, J., Winner, D., Alouani, D.J., Sharkey, F.H., Bergefall, K., Templeton, K., Carrington, D., and Quiñones-Mateu, M.E.* (2018). Characterization of minority drug resistant HIV-1 variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay. AIDS Research and Therapy, 15:18
Yendewa, G.A., Poveda, E., Yendewa, S.A., Sahr, F., Quiñones-Mateu, M.E, and Salata, R.A. (2018). HIV/AIDS in Sierra Leone: characterizing the hidden epidemic. AIDS Reviews, 20:104-113
Ndashimye, E., Avino, M., Kyeyune, F., Nankya, I., Gibson, R.M., Nabulime, E., Poon, A.F.Y., Kityo, C., Mugyenyi, P., Quiñones-Mateu M.E., and Arts, E.J. (2018). Absence of HIV-1 drug resistance mutations supports the use of dolutegravir in Uganda. AIDS Research and Human Retroviruses, 34:404-414
Tomas, M.E., Mana, T.S.C., Wilson, B.M., Nerandzic, M.M., Joussef-Piña, S., Quiñones-Mateu, M.E., and Donskey, C.J. (2018). Tapering courses of oral vancomycin induce persistent disruption of the microbiota that provide colonization resistance to Clostridium difficile and vancomycin-resistant enterococci in mice. Antimicrobial Agents and Chemotherapy, 62:e02237-17
Kanwar, A., Marshall, S.H., Perez, F., Tomas, M., Jacobs, M.R., Hujer, A.M., Domitrovic, T.N., Rudin, S.D., Rojas, L.J., Kreiswirth, B.N., Chen, L., Quiñones-Mateu, M.E., van Duin, D., Bonomo, R.A., for the Antibacterial Resistance Leadership Group. (2018). Emergence of resistance to colistin during the treatment of bloodstream infection caused by Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae. Open Forum Infectious Diseases, 5:ofy054
Gibson, R.M., Nickel, G., Crawford, M., Kyeyune, F., Venner, C., Nankya, I., Nabulime, E., Ndashimye, E., Poon, A.J.F., Salata, R.A., Kityo, C., Mugyenyi, P., Quiñones-Mateu M.E., and Arts, E.J. (2017). Sensitive detection of HIV-1 resistance to zidovudine and impact on treatment outcomes in low- to middle-income countries. Infectious Diseases of Poverty, 6:163
Orrú, C.D., Yuan, J., Appleby, B.S., Li, B., Li, Y., Winner, D., Wang, Z., Zhan, Y., Rodgers, M., Rarick, J., Wyza, R.E., Joshi, T., Wang, G., Cohen, M.L., Zhang, S., Groveman, B.R., Petersen R.B., Ironside J.W., Quiñones-Mateu M.E., Safar, J.G., Kong, Q., Caughey, B., and Zou, W-E. (2017). Prion seeding activity and infectivity in skin samples from patients with sporadic Creutzfeldt-Jacob disease. Science Translational Medicine, 9, eaam7785
Brenner, B.G., Ibanescu, R-I., Oliveira, M., Roger, M., Hardy, I., Routy, J-P, Kyeyune, F., Quiñones-Mateu M.E., and Wainberg, M.A and Montreal PHI Cohort Study Group. (2017). Human immunodeficiency virus type 1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture than viral isolates from singleton/small clusters. Journal of Antimicrobial Chemotherapy, 72:2171-2183
Weber, J. Gibson, R.M., Sácká, L., Strunin, D., Hodek, J., Weberová, J., Pávová, M., Alouani, D.J., Asaad, R., Rodriguez, B., Lederman, M.M., and Quiñones-Mateu, M.E.* (2017). Impaired human immunodeficiency virus type 1 replicative fitness in atypical viremic non-progressor individuals. AIDS Research and Therapy, 14:15
Aralaguppe, S.G., Winner, D., Singh, K., Sarafianos, S.G., Quiñones-Mateu M.E., Sonnerborg, A., and Neogi, U. (2017). Increased replication capacity following evolution of PYxE insertion in Gag-p6 associated is associated with enhanced virulence in HIV-1 subtype C from east Africa. Journal of Medical Virology, 89:106-111
Li, Q., Karim, A.F., Ding, X., Das, B., Dobrowolski, C., Gibson, R.M., Quiñones-Mateu M.E., Karn, J., and Rojas, R.E. (2016). Novel high throughput pooled shRNA screening identifies NQO1 as a potential drug target for host directed therapy for tuberculosis. Scientific Reports, 6:27566
Kyeyune, F., Gibson, R.M., Nankya, I., Venner, C., Metha, S., Akao, J., Ndashimye, E., Kityo, C.M., Salata, R.A., Mugyenyi, P., Arts, E.J., and Quiñones-Mateu M.E.* (2016). Low-frequency drug resistance in HIV-infected Ugandans on antiretroviral treatment is associated with regimen failure. Antimicrobial Agents and Chemotherapy, 60:3380-3397
Virk, S.M., Gibson, R.M., Quiñones-Mateu M.E.*, and Barnholtz-Sloan, J.S., (2015). Identification of variants in primary and recurrent glioblastoma using a cancer-specific gene panel and whole exome sequencing. PLoS ONE, 10:e0124178
Gibson, R.M., Weber, J., Winner, D., Miller, M.D., and Quiñones-Mateu M.E.* (2014). Contribution of human immunodeficiency virus type 1 minority variants to reduced drug susceptibility in patients on an integrase strand transfer inhibitor-based therapy. PLoS ONE, 9:e104512
Quiñones-Mateu M.E.*, Avila, S., Reyes-Teran, G., and Martinez, M.A. (2014). Next-generation sequencing: becoming a critical tool in clinical virology? Journal of Clinical Virology, 61:9-19
Rodriguez, A.K., Garzaro, D.J., Loureiro, C.L., Gutierrez, C.R., Ameli, G., Jaspe, R.C., Porto, L., Monsalve, F., Pozada, A., Vasquez, L., Quiñones-Mateu M.E., Pujol, F.H., and Rangel, H.R. (2014). HIV-1 and GBV-C co-infection in Venezuela. Journal of Infection in Developing Countries, 8:863-868
Gibson, R.M., Meyer, A.M., Winner, D., Archer, J., Feyertag, F., Ruiz-Mateos, E., Leal, M., Robertson, D.L., Schmotzer, C.L., and Quiñones-Mateu M.E.* (2014). Sensitive Deep Sequencing-based HIV-1 Genotyping Assay to Simultaneously Determine Susceptibility to Protease, Reverse Transcriptase, Integrase, and Maturation Inhibitors, as well as HIV-1 Coreceptor Tropism. Antimicrobial Agents and Chemotherapy, 58:2167-2185
Gibson, R.M., Schmotzer, C.L., and Quiñones-Mateu M.E.* (2014). Next-generation sequencing to help monitor patients infected with HIV: ready for clinical use? Current Infectious Disease Reports, 16:401-410
Quiñones-Mateu M.E.* & Endris V. (2014). The sequencing continuum for clinical research: from Sanger to Next Gen [Science Webinar Series]. Science, 343:1159
Weber, J., Rose, J.D., Vazquez, A.C., Winner, D., Margot, N.A., McColl, D.J., Miller, M.D., and Quiñones-Mateu M.E.* (2013). Resistance mutations outside the integrase coding region have an effect on human immunodeficiency virus replicative fitness but do not affect its susceptibility to integrase strand transfer inhibitors. PLoS ONE, 8:e65631
Weber, J., Vazquez, A.C., Winner, D., Gibson, R., Rhea, A.M., Rose, J.D., Wylie, D., Henry, K., Wright, A., King, K., Archer, J., Poveda, E., Soriano, V., Robertson, D.L., Olivo, P.D., Arts, E.J., and Quiñones-Mateu M.E.* (2013). Sensitive cell-based assay to determine human immunodeficiency virus type 1 coreceptor tropism Journal of Clinical Microbiology, 51:1517-1527
Archer, J., Weber, J., Henry, K., Winner, D., Gibson, R., Lee, L., Paxinos, E., Arts, E.J., Robertson, D.L., Mimms, L., and Quiñones-Mateu M.E.* (2012). Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS ONE, 7:e49602
Tebit, D.M., Ndembi, N., Weinberg, A., and Quiñones-Mateu M.E.* (2012). Mucosal transmission of human immunodeficiency virus. Current HIV Research, 10:3-8
Quiñones-Mateu M.E.*, and Vanham, G. (2012). HIV microbicides: where are we now? (Editorial). Current HIV Research, 10:1-2
Weber, J., Vazquez, A.C, Winner, D. Rose, J.D., Wylie, D., Rhea, A., Henry, K., Pappas, J., Wright, A., Mohamed, N., Gibson, R., Rodriguez, B., Soriano, V., King, K., Arts, E.J., Olivo, P.D., and Quiñones-Mateu M.E.* (2011). Novel method for simultaneous quantification of phenotypic resistance to maturation, protease, reverse transcriptase, and integrase inhibitors based on 3’Gag(p2/p7/p1/p6)/PR/RT/INT-recombinant viruses: a useful tool in the multi-target era of antiretroviral therapy. Antimicrobial Agents and Chemotherapy, 55:3729-3742 (PMCID: PMC3147656)
Selhorst P., Vazquez A.C., Terrazas-Aranda, K., Michiels, J., Vereecken, K., Heyndrickx, L., Weber, J., Quiñones-Mateu M.E., Arien, K.K., and Vanham, G. (2011). Human immunodeficiency virus type 1 (cross-) resistance to non-nucleoside reverse transcriptase inhibitors currently under development as microbicides. Antimicrobial Agents and Chemotherapy, 55:1403-1413 (PMCID: PMC3067143)
Jegede O., Khodyakova A., Chernov M., Weber, J., Menendez-Arias, L., Gudkov A., and Quiñones-Mateu M.E.* (2011). Identification of low-molecular weight inhibitors of HIV-1 reverse transcriptase using a cell-based high-throughput screening system. Antiviral Research, 91:94-98 (PMCID: PMC3144253)
Quiñones-Mateu M.E.* and Schols, D. (2011). Virus-inhibitory peptide: a natural HIV entry inhibitor in search for a formal target in the viral genome (Editorial comment) AIDS, 25:1663-1664
