Dr Tommy Lam Tsan-yuk — Tracking the Animal Origins of Emerging Viruses | 林讚育博士 — 追蹤新發病毒的動物源頭

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The past two decades have seen outbreaks of emerging viruses that jumped from animals to infect humans, such as the H7N9 bird flu, SARS, swine flu (H1N1) and the Middle East Respiratory Syndrome (MERS). Work by Dr Tommy Lam Tsan-yuk, Assistant Professor of the School of Public Health, has enriched our understanding of these viruses.

Dr Lam focuses on the animal-human interface of emerging infectious diseases and uses a bioinformatics approach to trace the ecology, evolution and epidemiology of these new pathogens. He did his undergraduate and postgraduate studies at HKU, then went overseas for post-doctoral training before returning to HKU in 2013 — just in time for the H7N9 influenza outbreak, which had a high mortality rate.

Dr Lam worked with Professor Yi Guan’s research team to conduct a large-scale genetic analysis of the virus. His work showed that the virus jumped from aquatic birds to domestic ducks, and from there to chickens where they reassorted into viruses that could infect humans. Chickens in live poultry markets were shown to be the main source of human infections of H7N9.

“We elucidated the ecological pathway and also found the evolutionary pathway of how the virus changed in the process from infecting animals to infecting humans,” he said.

He made similar contributions in the case of the MERS virus, which was first reported in Saudi Arabia in 2012 and saw a large outbreak in Korea in 2015. Through intensive investigations in the Middle East, Dr Lam and his colleagues found that the virus had been circulating among dromedary camels in Saudi Arabia. Using genetic analysis, he also showed that the virus had evolved into five distinct lineages, one of which was the source of outbreaks in humans in Saudi Arabia and Korea.

Recently, Dr Lam was awarded a grant from the National Natural Science Foundation of China Excellent Young Scientists Fund (Hong Kong and Macau) for a project to build a database of the genome, phenotype and epidemiology of major emerging zoonotic viruses, including H7N9 and MERS viruses. This will be the first time that all the information of these viruses will be unified — currently it is published in different places — and it will enable scientists and public health officials to identify and respond quickly to new outbreaks and improve prevention and control.

“By integrating this data, we can study the genetic determinants for each genotype and track emerging pathways and transmission routes. When there is a new outbreak, for example of MERS, we will be able to compare new and published sequences to understand and predict its infectiveness and transmissibility,” he said. The results and methods will be widely available for the biggest impact. “Other laboratories that may not have much bioinformatics capacity will be able to make use of this toolbox without necessarily having to go through our labs,” he added.

Biography

Dr Tommy Lam Tsan-yuk received his BSc (Bioinformatics) and PhD (Molecular Virology) at HKU, and had postdoctoral training in Pennsylvania State University and University of Oxford. His main research interest is the evolution, epidemiology and ecology of infectious diseases. He uses integrative genomic approach to determine the patterns, drivers and mechanisms of the emergence of pathogens, especially those at human-animal interface including influenza viruses and coronaviruses, as well as some bacterial pathogens and their antibiotic resistance emergence. He is also leading the development of several computational methods and tools for the genomic analysis in the research community. Dr Lam is currently Assistant Professor of the School of Public Health.

(This article was originally published in Medical Faculty News)

過去20年出現了從動物感染人類的新發病毒大爆發，例如H7N9禽流感、沙士，豬流感（H1N1）和中東呼吸綜合症（MERS）。公共衞生學院助理教授林讚育博士的研究工作， 豐富了我們對這些病毒的理解。

林博士專注於研究人畜傳染介面的新發傳染病，並使用生物訊息學的方法追蹤這些新病原體的生態、演變和流行病學。他在香港大學完成學士及研究生學位課程後，便出國深造進行博士後研究，至2013年返回港大時，剛好碰上死亡率很高的H7N9禽流感爆發。

林博士與管軼教授的團隊於是展開研究工作，對該病毒進行大規模的基因分析，發現這種病毒從水禽傳播到家鴨身上，再轉移到雞隻，經過基因重組後，成為可以感染人類的病毒。活禽市場中的雞隻被視為是人類感染H7N9的主要源頭。

林博士說：「我們闡明了H7N9的生態途徑，也發現了病毒的相關進化途徑，即如何從感染動物到感染人類的過程。」

在中東呼吸綜合症病毒的研究，林博士也作出了相同的貢獻。2012年，沙特阿拉伯錄得首宗中東呼吸綜合症感染個案，其後於2015年在韓國出現大規模爆發。林博士與團隊在中東進行深入調查，發現該病毒是在沙特阿拉伯的單峰駱駝之間傳播；他們使用遺傳學的方法，發現該病毒已演變成五個不同譜系，其中一個就是在沙特阿拉伯和韓國爆發的人類感染源頭。

林博士去年獲得國家自然科學基金「優秀青年科學家基金」（港澳）的資助，以建立包括H7N9和中東呼吸綜合症等人畜共患的主要新發病毒的基因組、表型和流行病學的數據庫。有關這些病毒的資料現時在不同地方發佈，而該數據庫將會是首次將這些資料進行統合，這將有助科學家和公共衞生官員識別和快速應對新發病毒的爆發，並加強防疫和控制。

林博士說：「通過整合數據，我們可以研究每種基因型的關鍵遺傳因素，並追蹤新發傳染途徑和傳播路徑。每當出現新發傳染病例如中東呼吸綜合症的爆發時，我們可以比較新的研究結果與已發表的基因序列，從而了解和預測其傳染性和傳播性。」相關結果和方法將帶來廣泛的影響。他補充說：「其他沒有足夠生物訊息學能力的實驗室，日後便毋須經過我們的實驗室，也可以善用這個資料庫。」

簡歷

林讚育博士在香港大學獲取生物訊息學理學士學位和分子病毒學博士學位後，遠赴美國賓夕法尼亞州立大學和英國牛津大學接受博士後培訓。他的主要研究範疇是傳染病的演化、流行病學和生態學。林博士利用綜合基因組學方法了解尤其是人畜傳染介面的新發病原體（如流感病毒和冠狀病毒）的演化模式和傳播機制，以及一些細菌性病原體及其對抗生素所出現的耐藥性。他亦領導研究團隊研發能用於基因組分析的計算方法和工具。林博士現時是公共衞生學院助理教授。

(原文刊登於港大醫學院 Medical Faculty News)