Directory

Duke-NUS Medical School
Directory

Su Chuan Fang Yvonne

Associate Professor

Emerging Infectious Diseases Programme, Duke-NUS Medical School

Bio Research Publications

Dr Yvonne Su is an Associate Professor in the Emerging Infectious Diseases Programme at Duke-NUS Medical School. She received her PhD and post-doctoral training in the School of Biological Sciences at the University of Hong Kong.

Assoc Prof Su’s research focuses on the evolution, emergence and transmission of respiratory viruses, primarily seasonal influenza. Her lab generates virus genome sequences from clinical samples using next-generation sequencing methods. Her studies broadly integrate phylodynamics and experimental approaches to identify key factors that drive inter-host and intra-host viral dynamics through time and space, leading to recurrent seasonal outbreaks. Her work on the pandemic H1N1 virus received the SingHealth/Duke-NUS Research Team Award in 2018 for outstanding contributions to the research and development landscape in Singapore.

She also investigates the adaptive mechanisms of interspecies transmission of influenza in avian and mammalian hosts. Her work contributes to the understanding of the origin, introduction and evolutionary relationships of emerging influenza virus subtypes and lineages. As an evolutionary biologist, she has conducted bioinformatics and phylogenetics training workshops for ASEAN countries, organized by Food and Agriculture Organization of the United Nations (FAO) and World Health Organization (WHO).

Assoc Prof Su is currently leading research on analysing the genomic data of SARS-COV-2 virus through next-generation sequencing and conducting phylogenetic analyses to track virus evolution and to monitor genetic changes in the SARS-COV-2 virus and their implications for the course of the COVID-19 pandemic.

The field of virus phylodynamics has significantly advanced our understanding of infectious disease dynamics. Robust surveillance combined with genomic sequencing provide insights into the mechanisms underlying disease outbreaks and susceptibility in humans and wildlife populations. My research uses an interdisciplinary approach by integrating molecular sequence data with phylodynamic methods to dissect the complex interplay between genetics, population dynamics, ecology, epidemiology and transmission of rapidly evolving viruses. This consists of three major components: 1) executing infectious disease surveillance in humans and animals for sample collection and applying metagenomic technologies for virus detection and prevalence; 2) utilizing robust phylodynamic approaches to identify key evolutionary mechanisms that underpin viral emergence and outbreaks; 3) integrating experimental approaches (such as reverse genetics) to test evolutionary hypotheses. Multiple projects involving influenza (human, swine and avian), parainfluenza virus, SARS-CoV-2 and other coronaviruses are ongoing through local and overseas collaborations. Part of my projects on influenza are support by the US NIAID Centers of Excellence for Influenza Research and Response (CEIRR).

Li YT, Su YCF, Smith GJD (2021) H5Nx viruses emerged during the suppression of H5N1 virus populations in poultry. Microbiology Spectrum 31:9:e0130921.

Su W, Harfoot R, Su YCF, DeBeauchamp J, Joseph U, Jayakumar J, Crumpton JC, Jeevan T, Rubrum A, Franks J, Pascua PNQ, Kackos C, Zhang Y, Zhang M, Ji Y, Bui HT, Jones JC, Kercher L, Krauss S, Pleschka S, Chan MCW, Webster RG, Wu CY, Van Reeth K, Peiris M, Webby RJ, Smith GJD, Yen HL (2021) Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Nature Microbiology 6:1455-1465.

Ali M, Yaqub T, Shahid MF, Wong FY, Mukhtar N, Naeem M, Lam P, Jayakumar J, Smith GJD, Su YCF (2021) Genetic characterization of highly pathogenic avian influenza A(H5N8) virus in Pakistani live bird markets reveals rapid diversification of clade 2.3.4.4b viruses. Viruses 13.

Su YCF, Anderson DE, Young BE, Linster M, Zhu F, Jayakumar J, Zhuang Y, Kalimuddin S, Low JGH, Tan CW, Chia WN, Mak TM, Octavia S, Chavatte JM, Lee RTC, Pada S, Tan SY, Sun L, Yan GZ, Maurer-Stroh S, Mendenhall IH, Leo YS, Lye DC, Wang LF, Smith GJD. 2020. Discovery and genomic characterization of a 382-nucleotide deletion in ORF7b and ORF8 during the early evolution of SARS-CoV-2. mBio 11:e01610-20.

Virk RK, Jayakumar J, Mendenhall IH, Moorthy M, Lam P, Linster M, Lim J, Lin C, Oon LLE, Lee HK, Koay ESC, Vijaykrishna D, Smith GJD, Su YCF (2020) Divergent evolutionary trajectories of influenza B viruses underlie their contemporaneous epidemic activity. Proceedings of the National Academy of Sciences 117:619-628.

Young BE, Fong SW, Chan YH, Mak TM, Ang LW, Anderson DE, Lee CY, Amrun SN, Lee B, Goh YS, Su YCF, Wei WE, Kalimuddin S, Chai LYA, Pada S, Tan SY, Sun L, Parthasarathy P, Chen YYC, Barkham T, Lin RTP, Maurer-Stroh S, Leo YS, Wang LF, Renia L, Lee VJ, Smith GJD, Lye DC, Ng LFP (2020) Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. Lancet 396:603-611.

Ali M, Yaqub T, Mukhtar N, Imran M, Ghafoor A, Shahid MF, Naeem M, Iqbal M, Smith GJD, Su YCF (2019) Avian influenza A(H9N2) virus in poultry worker, Pakistan, 2015. Emerging infectious diseases 25:136-139.

Mendenhall IH, Kerimbayev AA, Strochkov VM, Sultankulova KT, Kopeyev SK, Su YCF, Smith GJD, Orynbayev MB (2019) Discovery and characterization of novel bat coronavirus lineages from Kazakhstan. Viruses 11:356.

Mendenhall IH, Wen DLH, Jayakumar J, Gunalan V, Wang L, Mauer-Stroh S, Su YCF, Smith GJD (2019) Diversity and evolution of viral pathogen community in cave nectar bats (Eonycteris spelaea). Viruses 11:250.

Joseph U, Vijaykrishna D, Smith GJD, Su YCF (2017) Adaptive evolution during the establishment of European avian-like H1N1 influenza A virus in swine. Evolutionary applications 11:534-546.

Joseph U, Su YCF, Vijaykrishna D, Smith GJ (2017) The ecology and adaptive evolution of influenza A interspecies transmission. Influenza and other respiratory viruses 11:74-84.

Hurt AC, Su YCF, Aban M, Peck H, Lau H, Baas C, Deng YM, Spirason N, Ellstrom P, Hernandez J, Olsen B, Barr IG, Vijaykrishna D, Gonzalez-Acuna D (2016) Evidence for the introduction, reassortment, and persistence of diverse influenza A viruses in Antarctica. Journal of Virology 90:9674-9682.

Su YCF, Bahl J, Joseph U, Butt KM, Peck HA, Koay ESC, Oon LLE, Barr IG, Vijaykrishna D, Smith GJD (2015) Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection. Nature Communications 6:7952.