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Microbiology Logo Microbiology & Immunology
Te Tari Moromoroiti me te Ārai Mate

Professor Miguel Quiñones-Mateu

Research interests:

Viral evolution, HIV, SARS-CoV-2/COVID-19, Antiviral Drug and Vaccine Strategies, Novel Methodologies

Current research:

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:

  • SARS-CoV-2 / COVID-19
    • Rapid response to this emergent virus by implementing a molecular diagnostic test (in collaboration with A/Prof James Ussher) and completing the first isolation and characterization of SARS-CoV-2 in New Zealand
    • Discovery and characterization of anti-SARS-CoV-2 agents
    • Developing novel vaccine strategies as part of the Vaccine Alliance Aotearoa New Zealand (VAANZ) Program
  • HIV / AIDS
    • HIV drug resistance studies in Africa
    • HIV molecular epidemiology in Fiji
  • Metagenomics studies in New Zealand
    • Virome of Yellow-eyed penguin (Megadyptes antipodes)
    • Virome of Kākāpō (Strigops habroptilus)
    • Virome of ticks (Haemaphysalis longicornis


Screen Shot 2020 04 07 at 12.45.00 AM

Quiñones-Mateu Lab March 2020

Current Group Members


Prof. Miguel Quiñones-Mateu
Principal Investigator
Office: +64 3 479 7703



Blair Lawley2 Rhodri Harfoot Leanor Hernandez2  
Dr Blair Lawley - Scientific Officer Dr Rhodri Harfoot - Research Fellow Dr Leonor C. Hernández - Laboratory Manager  
Shubhra Sinha2 Joanna Kuang     
 Dr Shubhra Sinha - Research Fellow  Joanna Kuang, MSc - Research Assistant    


Postgraduate Students

Atlesh Cody Hird    
Atlesh Sudhakar - MSc Student

  Cody Hird - MSc Student



  • Margot Allais (MSc Student) 2022
  • Joanna Kuang (MSc Student) 2022
  • Rebecca Hall (MSc Student) 2020
  • Francesca Hills (4th Year BBiomedSci Honors Student) 2020 
  • Mathilda Saunders 4th Year BSc Honors Student) 2020
  • Florence Patlong (4th Year BSc Honors Student) 2019  


Current Sources of Funding

  • Webster Family Chair in Viral Pathogenesis, University of Otago, New Zealand
  • Ministry of Business Innovation & Employment (MBIE), New Zealand
  • Ministry of Health, New Zealand 
  • National Institutes of Health (NIH), USA
  • Otago Global Health Institute, University of Otago, New Zealand



  • HIV-1 Genotyping and Coreceptor Tropism Assay - Patent No. US 10,144,976
  • Method for Detecting HIV-1 Coreceptor Tropism - Patent No. US 11,105, 805



       PubMed Logo  View Prof Quiñones-Mateu on PubMed

         Google Scholar logo for website    View Prof Quiñones-Mateu on Google Scholar

Past 10 years


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