Association between Gut Microbiota Composition and Long-Term Vaccine Immunogenicity following Three Doses of CoronaVac
Vaccines
Li-Na Zhang, Jing-Tong Tan, Ho-Yu Ng, Yun-Shi Liao, Rui-Qi Zhang, Kwok-Hung Chan, Ivan Fan-Ngai Hung, Tommy Tsan-Yuk Lam, Ka-Shing Cheung
2024/ 3
microbiome, coronavirus, vaccine immunogenicity
The Predictive Value of Gut Microbiota Composition for Sustained Immunogenicity following Two Doses of CoronaVac
International Journal of Molecular Sciences
Ho-Yu Ng, Yunshi Liao, Ruiqi Zhang, Kwok-Hung Chan, Wai-Pan To, Chun-Him Hui, Wai-Kay Seto, Wai K Leung, Ivan FN Hung, Tommy TY Lam, Ka-Shing Cheung
2024/ 2
microbiome, coronavirus, vaccine immunogenicity
Probable airborne transmission of Burkholderia pseudomallei causing an urban outbreak of melioidosis during typhoon season in Hong Kong, China
Emerging Microbes & Infections
Wing-Gi Wu, Marcus Ho-Hin Shum, Ivan Tak-Fai Wong, Kelvin Keru Lu, Lam-Kwong Lee, Jake Siu-Lun Leung, Hiu-Yin Lao, Annie Wing-Tung Lee, Pak-Ting Hau, Chloe Toi-Mei Chan, Harmen Fung-Tin Wong, Sharon Ka-Yee Fung, Sally Choi-Ying Wong, Iain Chi-Fung Ng, Timothy Ting-Leung Ng, Ning Chow, Alex Yat-Man Ho, Mei Fan Hung, Franklin Wang-Ngai Chow, Maureen Mo-Lin Wong, Wing-Kin To, Tommy Tsan-Yuk Lam, Kristine Shik Luk, Gilman Kit-Hang Siu
2023/12
melioidosis
Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes
Nature Microbiology
Xue-Bing Ni, Xiao-Ming Cui, Jin-Yue Liu, Run-Ze Ye, Yu-Qian Wu, Jia-Fu Jiang, Yi Sun, Qian Wang, Marcus Ho-Hin Shum, Qiao-Cheng Chang, Lin Zhao, Xiao-Hu Han, Ke Ma, Shi-Jing Shen, Ming-Zhu Zhang, Wen-Bin Guo, Jin-Guo Zhu, Lin Zhan, Liang-Jing Li, Shu-Jun Ding, Dai-Yun Zhu, Jie Zhang, Luo-Yuan Xia, Xiang-Yong Oong, Xiang-Dong Ruan, Hong-Ze Shao, Teng-Cheng Que, Guang-Yuan Liu, Chun-Hong Du, En-Jiong Huang, Xin Wang, Li-Feng Du, Chong-Cai Wang, Wen-Qiang Shi, Yu-Sheng Pan, Yu-Hao Zhou, Jiang-Li Qu, Jiang Ma, Cai-Wei Gong, Qi-Qing Chen, Qian Qin, Tick Genome and Microbiome Consortium (TIGMIC), Tommy Tsan-Yuk Lam, Na Jia, Wu-Chun Cao
2023/1
ticks, virome
High Diversity of Tick-associated Microbiota from Five Tick Species in Yunnan, China
Zoonoses
Jie Zhang, Xue-Bing Ni, Zi-Yun Chen, Yun Zhang, Ran Wei, Zheng-Da Gong, Dai-Yun Zhu, Xiao-Ming Cui, Zong-Ti Shao, Hong-Bo Liu, Yu-Qiong Li, Jian Wang, Zi-Hou Gao, Xing-De Duan, Hang Jiang, Jia-Fu Jiang, Tommy Tsan-Yuk Lam, En-Jiong Huang, Na Jia, Chun-Hong Du
2023/ 8
ticks
Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples
Environmental Science & Technology
Xiaole Yin, Xi Chen, Xiao-Tao Jiang, Ying Yang, Bing Li, Marcus Ho-Hin Shum, Tommy TY Lam, Gabriel M Leung, Joan Rose, Concepcion Sanchez-Cid, Timothy M Vogel, Fiona Walsh, Thomas U Berendonk, Janet Midega, Chibuzor Uchea, Dominic Frigon, Gerard D Wright, Carlos Bezuidenhout, Renata C Picão, Shaikh Z Ahammad, Per Halkjær Nielsen, Philip Hugenholtz, Nicholas J Ashbolt, Gianluca Corno, Despo Fatta-Kassinos, Helmut Bürgmann, Heike Schmitt, Chang-Jun Cha, Amy Pruden, Kornelia Smalla, Eddie Cytryn, Yu Zhang, Min Yang, Yong-Guan Zhu, Arnaud Dechesne, Barth F Smets, David W Graham, Michael R Gillings, William H Gaze, Célia M Manaia, Mark CM van Loosdrecht, Pedro JJ Alvarez, Martin J Blaser, James M Tiedje, Edward Topp, Tong Zhang
2023/ 6
AMR
Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health
Journal of Virology
Peiwen Chen, Ziying Jin, Liuxia Peng, Zuoyi Zheng, Yiu-Man Cheung, Jing Guan, Liming Chen, Yiteng Huang, Xiaohui Fan, Zengfeng Zhang, Dongmei Shi, Jin Xie, Rirong Chen, Boheng Xiao, Chun Hung Yip, David K Smith, Wenshan Hong, Yongmei Liu, Lifeng Li, Jia Wang, Edward C Holmes, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan
2023/ 6
influenza
Probable airborne transmission of Burkholderia pseudomallei causing an urban outbreak of melioidosis during typhoon season in Hong Kong, China
Emerging Microbes & Infections
Wing-Gi Wu, Marcus Ho-Hin Shum, Ivan Tak-Fai Wong, Kelvin Keru Lu, Lam-Kwong Lee, Jake Siu-Lun Leung, Hiu-Yin Lao, Annie Wing-Tung Lee, Pak-Ting Hau, Chloe Toi-Mei Chan, Harmen Fung-Tin Wong, Sharon Ka-Yee Fung, Sally Choi-Ying Wong, Iain Chi-Fung Ng, Timothy Ting-Leung Ng, Ning Chow, Alex Yat-Man Ho, Mei Fan Hung, Franklin Wang-Ngai Chow, Maureen Mo-Lin Wong, Wing-Kin To, Tommy Tsan-Yuk Lam, Kristine Shik Luk, Gilman Kit-Hang Siu
2023/ 5
melioidosis
Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals
Nature Communications
Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Daisy YM Ng, Lydia DJ Chang, Gigi YZ Liu, Samuel MS Cheng, Tommy TY Lam, Malik Peiris, Matthew R McKay, Leo LM Poon
2023/ 3
coronavirus
Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling
Scientific Reports
Junhao Su, Wui Wang Lui, YanLam Lee, Zhenxian Zheng, Gilman Kit-Hang Siu, Timothy Ting-Leung Ng, Tong Zhang, Tommy Tsan-Yuk Lam, Hiu-Yin Lao, Wing-Cheong Yam, Kingsley King-Gee Tam, Kenneth Siu-Sing Leung, Tak-Wah Lam, Amy Wing-Sze Leung, Ruibang Luo
2023/ 3
microbiome, bioinformatics tools
New insights into the impact of microbiome on horizontal and vertical transmission of a tick-borne pathogen
Authors
Microbiome
Li-Feng Du, Ming-Zhu Zhang, Ting-Ting Yuan, Xue-Bing Ni, Wei Wei, Xiao-Ming Cui, Ning Wang, Tao Xiong, Jie Zhang, Yu-Sheng Pan, Dai-Yun Zhu, Liang-Jing Li, Luo-Yuan Xia, Tian-Hong Wang, Ran Wei, Hong-Bo Liu, Yi Sun, Lin Zhao, Tommy Tsan-Yuk Lam, Wu-Chun Cao, Na Jia
2023/ 3
ticks, microbiome
Skin infectome of patients with a tick bite history
Frontiers in Cellular and Infection Microbiology
Jie Zhang, Yuan-Chun Zheng, Yan-Li Chu, Xiao-Ming Cui, Ran Wei, Cai Bian, Hong-Bo Liu, Nan-Nan Yao, Rui-Ruo Jiang, Qiu-Bo Huo, Ting-Ting Yuan, Jie Li, Lin Zhao, Lian-Feng Li, Qian Wang, Wei Wei, Jin-Guo Zhu, Mei-Chao Chen, Yan Gao, Fei Wang, Jin-Ling Ye, Ju-Liang Song, Jia-Fu Jiang, Tommy Tsan-Yuk Lam, Xue-Bing Ni, Na Jia
2023/ 2
ticks
One Health Surveillance of Antimicrobial Use and Resistance: Challenges and Successes of Implementing Surveillance Programs in Sri Lanka
Antibiotics
Sujeewa Ariyawansa, Kuruwitage N Gunawardana, Muditha M Hapudeniya, Nimal J Manelgamage, Chinthana R Karunarathne, Roshan P Madalagama, Kamalika H Ubeyratne, Darshana Wickramasinghe, Hein M Tun, Peng Wu, Tommy TY Lam, Olivia SK Chan
2023/ 2
AMR
Highly pathogenic avian influenza A (H5N1) virus clade 2.3. 4.4 b in wild birds and live bird markets, Egypt
Pathogens
Rabeh El-Shesheny, Yassmin Moatasim, Sara H Mahmoud, Yi Song, Ahmed El Taweel, Mokhtar Gomaa, Mina Nabil Kamel, Mohamed El Sayes, Ahmed Kandeil, Tommy TY Lam, Pamela P McKenzie, Richard J Webby, Ghazi Kayali, Mohamed Ahmed Ali
2022/12
influenza
Nematode and Acanthocephalan Parasites of Confiscated Sunda pangolins, Manis javanica Desmarest, 1822 (Mammalia: Pholidota: Manidae), with an Updated List of the Parasites of Pangolins
Diversity
Diane P Barton, Paolo Martelli, Brian M Worthington, Tommy T-Y Lam, Xiaocheng Zhu, Shokoofeh Shamsi
2022/11
pangolins
Leo Poon, Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Lydia Chang, Gigi Liu, Daisy Ng, Samuel Cheng, Tommy Tsan-Yuk Lam, Malik Peiris, Matthew McKay
Research Square
Leo Poon, Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Lydia Chang, Gigi Liu, Daisy Ng, Samuel Cheng, Tommy Tsan-Yuk Lam, Malik Peiris, Matthew McKay
2022/ 8
coronavirus
Australia as a global sink for the genetic diversity of avian influenza A virus
PLoS Pathogens
Michelle Wille, Victoria Grillo, Silvia Ban de Gouvea Pedroso, Graham W Burgess, Allison Crawley, Celia Dickason, Philip M Hansbro, Md Ahasanul Hoque, Paul F Horwood, Peter D Kirkland, Nina Yu-Hsin Kung, Stacey E Lynch, Sue Martin, Michaela McArthur, Kim O’Riley, Andrew J Read, Simone Warner, Bethany J Hoye, Simeon Lisovski, Trent Leen, Aeron C Hurt, Jeff Butler, Ivano Broz, Kelly R Davies, Patrick Mileto, Matthew J Neave, Vicky Stevens, Andrew C Breed, Tommy TY Lam, Edward C Holmes, Marcel Klaassen, Frank YK Wong
2022/ 5
influenza
Unlocking capacities of genomics for the COVID-19 response and future pandemics
Nature Methods
Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Pelin Icer Baykal, Zoia Comarova, Angela Lu, Yuri Porozov, Tetyana I Vasylyeva, Joel O Wertheim, Braden T Tierney, Charles Y Chiu, Ren Sun, Aiping Wu, Malak S Abedalthagafi, Victoria M Pak, Shivashankar H Nagaraj, Adam L Smith, Pavel Skums, Bogdan Pasaniuc, Andrey Komissarov, Christopher E Mason, Eric Bortz, Philippe Lemey, Fyodor Kondrashov, Niko Beerenwinkel, Tommy Tsan-Yuk Lam, Nicholas C Wu, Alex Zelikovsky, Rob Knight, Keith A Crandall, Serghei Mangul
2022/ 4
coronavirus, genomics, bio/epi-informatics
Association between inflammatory cytokines and anti-SARS-CoV-2 antibodies in hospitalized patients with COVID-19
Immunity & Ageing
Xixi Jing, Min Xu, Deye Song, Tingting Yue, Yali Wang, Pan Zhang, Yanjun Zhong, Min Zhang, Tommy Tsan-Yuk Lam, Nuno Rodrigues Faria, Erik De Clercq, Guangdi Li
2022/ 3
coronavirus
Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong
Nature communications
Haogao Gu, Ruopeng Xie, Dillon C Adam, Joseph L-H Tsui, Daniel K Chu, Lydia DJ Chang, Sammi SY Cheuk, Shreya Gurung, Pavithra Krishnan, Daisy YM Ng, Gigi YZ Liu, Carrie KC Wan, Samuel SM Cheng, Kimberly M Edwards, Kathy SM Leung, Joseph T Wu, Dominic NC Tsang, Gabriel M Leung, Benjamin J Cowling, Malik Peiris, Tommy TY Lam, Vijaykrishna Dhanasekaran, Leo LM Poon
2022/ 2
coronavirus
Surveillance of Rodent Pests for SARS-CoV-2 and Other Coronaviruses, Hong Kong
Emerging infectious diseases
Elliott F Miot, Brian M Worthington, Kar Hon Ng, Lucy de Guilhem de Lataillade, Mac P Pierce, Yunshi Liao, Ronald Ko, Marcus H Shum, William Y Cheung, Edward C Holmes, Kathy S Leung, Huachen Zhu, Leo L Poon, Malik J Peiris, Yi Guan, Gabriel M Leung, Joseph T Wu, Tommy T Lam
2022/ 2
coronavirus
Genomic characterization of a new CRF01_AE/CRF07_BC case from a MSM patient in Guangdong, China
Journal of Medical Virology
Xu‐He Huang, Guolong Yu, Chenli Zheng, Ping‐Ping Zhou, Claire Anderson, Jin Zhao, Tommy Tsan‐Yuk Lam, Yan Li, Lin Chen, Peng Lin, Ming Zhang, Jin Yan, Xiang He
2021/11
other viruses
Highly Pathogenic Avian Influenza A (H5N6) Virus Clade 2.3. 4.4 h in Wild Birds and Live Poultry Markets, Bangladesh
Emerging Infectious Diseases
Jasmine CM Turner, Subrata Barman, Mohammed M Feeroz, M Kamrul Hasan, Sharmin Akhtar, Trushar Jeevan, David Walker, John Franks, Patrick Seiler, Nabanita Mukherjee, Lisa Kercher, Pamela McKenzie, Tommy Lam, Rabeh El-Shesheny, Richard J Webby
2021/ 9
influenza
Unlocking capacities of viral genomics for the COVID-19 pandemic response
ArXiv
Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Zoia Comarova, Angela Lu, Yuri Porozov, Aiping Wu, Malak S Abedalthagafi, Shivashankar H Nagaraj, Adam L Smith, Pavel Skums, Jason Ladner, Tommy Tsan-Yuk Lam, Nicholas C Wu, Alex Zelikovsky, Rob Knight, Keith A Crandall, Serghei Mangul
2021/ 4
coronavirus, bio/epi-informatics
Genetic variation of multiple serotypes of enteroviruses associated with hand, foot and mouth disease in Southern China
Virologica Sinica
Yonghong Zhou, Le Van Tan, Kaiwei Luo, Qiaohong Liao, Lili Wang, Qi Qiu, Gang Zou, Ping Liu, Nguyen To Anh, Nguyen Thi Thu Hong, Min He, Xiaoman Wei, Shuanbao Yu, Tommy Tsan-Yuk Lam, Jie Cui, H Rogier van Doorn, Hongjie Yu
2021/ 2
other viruses
Australia as a global sink for the genetic diversity of avian influenza A virus
bioRxiv
Michelle Wille, Victoria Tiggy Grillo, Silvia Ban de Gouvea Pedroso, Graham W Burgess, Allison Crawley, Celia Dickason, Philip M Hansbro, Md Ahasanul Hoque, Paul F Horwood, Peter D Kirkland, Nina Yu-Hsin Kung, Stacey E Lynch, Sue Martin, Michaela McArthur, Kim O’Riley, Andrew J Read, Simone Warner, Bethany J Hoye, Simeon Lisovski, Trent Leen, Aeron C Hurt, Jeff Butler, Ivano Broz, Kelly R Davies, Patrick Mileto, Matthew Neave, Vicky Stevens, Andrew Breed, Tommy TY Lam, Edward C Holmes, Marcel Klaassen, Frank YK Wong
2021/ 1
influenza
Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance
Journal of genetics
Hung Hui Chung, Cynthia Keranti Anak Kamar, Leonard Whye Kit Lim, Jill Sela Roja, Yunshi Liao, Tommy Tsan-Yuk Lam, Yee Ling Chong
2020/12
genomics
Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration
Computational Biology and Chemistry
Leonard Whye Kit Lim, Cynthia Keranti Anak Kamar, Jill Sela Roja, Hung Hui Chung, Yunshi Liao, Tommy Tsan-Yuk Lam, Yee Ling Chong
2020/12
genomics
Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities
Cell
Na Jia, Jinfeng Wang, Wenqiang Shi, Lifeng Du, Yi Sun, Wei Zhan, Jia-Fu Jiang, Qian Wang, Bing Zhang, Peifeng Ji, Lesley Bell-Sakyi, Xiao-Ming Cui, Ting-Ting Yuan, Bao-Gui Jiang, Wei-Fei Yang, Tommy Tsan-Yuk Lam, Qiao-Cheng Chang, Shu-Jun Ding, Xian-Jun Wang, Jin-Guo Zhu, Xiang-Dong Ruan, Lin Zhao, Jia-Te Wei, Run-Ze Ye, Teng Cheng Que, Chun-Hong Du, Yu-Hao Zhou, Jing Xia Cheng, Pei-Fang Dai, Wen-Bin Guo, Xiao-Hu Han, En-Jiong Huang, Lian-Feng Li, Wei Wei, Yu-Chi Gao, Jing-Ze Liu, Hong-Ze Shao, Xin Wang, Chong-Cai Wang, Tian-Ci Yang, Qiu-Bo Huo, Wei Li, Hai-Ying Chen, Shen-En Chen, Ling-Guo Zhou, Xue-Bing Ni, Jun-Hua Tian, Yue Sheng, Tao Liu, Yu-Sheng Pan, Luo-Yuan Xia, Jie Li, Fangqing Zhao, Wu-Chun Cao, Microbiome Consortium
2020/ 9
ticks, genomics
Comparative seasonalities of influenza A, B and ‘common cold’coronaviruses–setting the scene for SARS-CoV-2 infections and possible unexpected host immune interactions
The Journal of infection
Yang Liu, Tommy TY Lam, Florence YL Lai, Mel Krajden, Steven J Drews, Todd F Hatchette, Pieter LA Fraaij, Jeroen JA van Kampen, Darmaa Badarch, Pagbajabyn Nymadawa, Kok Keng Tee, Hong Kai Lee, Evelyn SC Koay, Lance Jennings, Marion Koopmans, Julian W Tang
2020/ 8
influenza, coronavirus
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
Nature
Tommy Tsan-Yuk Lam, Na Jia, Ya-Wei Zhang, Marcus Ho-Hin Shum, Jia-Fu Jiang, Hua-Chen Zhu, Yi-Gang Tong, Yong-Xia Shi, Xue-Bing Ni, Yun-Shi Liao, Wen-Juan Li, Bao-Gui Jiang, Wei Wei, Ting-Ting Yuan, Kui Zheng, Xiao-Ming Cui, Jie Li, Guang-Qian Pei, Xin Qiang, William Yiu-Man Cheung, Lian-Feng Li, Fang-Fang Sun, Si Qin, Ji-Cheng Huang, Gabriel M Leung, Edward C Holmes, Yan-Ling Hu, Yi Guan, Wu-Chun Cao
2020/ 7
coronavirus
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
Proceedings of the National Academy of Sciences
Carla Mavian, Sergei Kosakovsky Pond, Simone Marini, Brittany Rife Magalis, Anne-Mieke Vandamme, Simon Dellicour, Samuel V Scarpino, Charlotte Houldcroft, Julian Villabona-Arenas, Taylor K Paisie, Nídia S Trovão, Christina Boucher, Yun Zhang, Richard H Scheuermann, Olivier Gascuel, Tommy Tsan-Yuk Lam, Marc A Suchard, Ana Abecasis, Eduan Wilkinson, Tulio de Oliveira, Ana I Bento, Heiko A Schmidt, Darren Martin, James Hadfield, Nuno Faria, Nathan D Grubaugh, Richard A Neher, Guy Baele, Philippe Lemey, Tanja Stadler, Jan Albert, Keith A Crandall, Thomas Leitner, Alexandros Stamatakis, Mattia Prosperi, Marco Salemi
2020/ 6
coronavirus
Sequencing and characterisation of complete mitochondrial DNA genome for Trigonopoma pauciperforatum (Cypriniformes: Cyprinidae: Danioninae) with phylogenetic consideration
Tropical life sciences research
Hung Hui Chung, Leonard Whye Kit Lim, Yunshi Liao, Tommy Tsan-Yuk Lam, Yee Ling Chong
2020/ 4
genomics
Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference—application to H5N1 spread in the Mekong region
Bioinformatics
Simon Dellicour, Philippe Lemey, Jean Artois, Tommy T Lam, Alice Fusaro, Isabella Monne, Giovanni Cattoli, Dmitry Kuznetsov, Ioannis Xenarios, Gwenaelle Dauphin, Wantanee Kalpravidh, Sophie Von Dobschuetz, Filip Claes, Scott H Newman, Marc A Suchard, Guy Baele, Marius Gilbert
2020/ 4
influenza, bio/epi-informatics
Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data
Molecular biology and evolution
Li-Gen Wang, Tommy Tsan-Yuk Lam, Shuangbin Xu, Zehan Dai, Lang Zhou, Tingze Feng, Pingfan Guo, Casey W Dunn, Bradley R Jones, Tyler Bradley, Huachen Zhu, Yi Guan, Yong Jiang, Guangchuang Yu
2020/ 2
bio/epi-informatics
Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia
New England journal of medicine
Qun Li, Xuhua Guan, Peng Wu, Xiaoye Wang, Lei Zhou, Yeqing Tong, Ruiqi Ren, Kathy SM Leung, Eric HY Lau, Jessica Y Wong, Xuesen Xing, Nijuan Xiang, Yang Wu, Chao Li, Qi Chen, Dan Li, Tian Liu, Jing Zhao, Man Liu, Wenxiao Tu, Chuding Chen, Lianmei Jin, Rui Yang, Qi Wang, Suhua Zhou, Rui Wang, Hui Liu, Yinbo Luo, Yuan Liu, Ge Shao, Huan Li, Zhongfa Tao, Yang Yang, Zhiqiang Deng, Boxi Liu, Zhitao Ma, Yanping Zhang, Guoqing Shi, Tommy TY Lam, Joseph T Wu, George F Gao, Benjamin J Cowling, Bo Yang, Gabriel M Leung, Zijian Feng
2020/ 1
coronavirus
Sequencing and characterization of complete mitogenome DNA for Rasbora myersi (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance
Gene Reports
Leonard Whye Kit Lim, Jill Sela Roja, Cynthia Keranti Anak Kamar, Hung Hui Chung, Yunshi Liao, Tommy Tsan-Yuk Lam, Yee Ling Chong
2019/12
genomics
Comparative global epidemiology of influenza, respiratory syncytial and parainfluenza viruses, 2010–2015
Journal of Infection
Tommy T Lam, Julian W Tang, Florence Y Lai, Hassan Zaraket, Ghassan Dbaibo, Seweryn Bialasiewicz, Sarah Tozer, Jean-Michel Heraud, Steven J Drews, Todd Hachette, Paul KS Chan, Evelyn SC Koay, Hong Kai Lee, Kok Keng Tee, Yang Liu, Pieter LA Fraaij, Lance Jennings, Matti Waris, Mel Krajden, André Corriveau, Hamid Jalal, Hidekazu Nishimura, Pagbajabyn Nymadawa, Darmaa Badarch, Aripuana Watanabe, Alice Kabanda, Theo Sloots, Jen Kok, Dominic E Dwyer, Marion Koopmans
2019/10
influenza, other respiratory viruses, other viruses
Emergence of human infection with Jingmen tick virus in China: A retrospective study
EBioMedicine
Na Jia, Hong-Bo Liu, Xue-Bing Ni, Lesley Bell-Sakyi, Yuan-Chun Zheng, Ju-Liang Song, Jie Li, Bao-Gui Jiang, Qian Wang, Yi Sun, Ran Wei, Ting-Ting Yuan, Luo-Yuan Xia, Yan-Li Chu, Wei Wei, Lian-Feng Li, Jin-Ling Ye, Qing-Yu Lv, Xiao-Ming Cui, Yi Guan, Yi-Gang Tong, Jia-Fu Jiang, Tommy Tsan-Yuk Lam, Wu-Chun Cao
2019/ 5
arbovirus, ticks
Neuraminidase inhibitor susceptibility and evolutionary analysis of human influenza B isolates from three Asian countries during 2012–2015
Infection, Genetics and Evolution
Akinobu Hibino, Elie Massaad, Hiroki Kondo, Reiko Saito, Takashi Odagiri, Nobuhiro Takemae, Ryota Tsunekuni, Takehiko Saito, Yadanar Kyaw, Nay Lin, Yi Yi Myint, Htay Htay Tin, Nguyen Le Khanh Hang, Ren Yagami, Yugo Shobugawa, Tommy Lam, Hassan Zaraket, Japanese Influenza Collaborative Study Group
2018/ 8
influenza
Large-scale complete-genome sequencing and phylodynamic analysis of eastern equine encephalitis virus reveals source-sink transmission dynamics in the United States
Journal of virology
Yi Tan, Tommy Tsan-Yuk Lam, Lea A Heberlein-Larson, Sandra C Smole, Albert J Auguste, Scott Hennigan, Rebecca A Halpin, Nadia Fedorova, Vinita Puri, Timothy B Stockwell, Meghan H Shilts, Theodore Andreadis, Philip M Armstrong, Robert B Tesh, Scott C Weaver, Thomas R Unnasch, Alexander T Ciota, Laura D Kramer, Suman R Das
2018/ 6
arbovirus, mosquitoes
Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance
The Lancet Infectious Diseases
Julian W Tang, Tommy T Lam, Hassan Zaraket, W Ian Lipkin, Steven J Drews, Todd F Hatchette, Jean-Michel Heraud, Marion P Koopmans, Ashta Mary Abraham, Amal Baraket, Seweryn Bialasiewicz, Miguela A Caniza, Paul KS Chan, Cheryl Cohen, André Corriveau, Benjamin J Cowling, Marcela Echavarria, Ron Fouchier, Pieter LA Fraaij, Todd F Hachette, Hamid Jalal, Lance Jennings, Alice Kabanda, Herve A Kadjo, Mohammed Rafiq Khanani, Evelyn SC Koay, Mel Krajden, Hong Kai Lee, W Ian Lipkin, Julius Lutwama, David Marchant, Hidekazu Nishimura, Pagbajabyn Nymadawa, Benjamin A Pinsky, Sanjiv Rughooputh, Joseph Rukelibuga, Taslimarif Saiyed, Anita Shet, Theo Sloots, JJ Muyembe Tamfum, Stefano Tempia, Sarah Tozer, Florette Treurnicht, Matti Waris, Aripuana Watanabe, Emile Okitolonda Wemakoy
2017/10
other respiratory viruses
Molecular evolution and intraclade recombination of enterovirus D68 during the 2014 outbreak in the United States
Journal of virology
Yi Tan, Ferdaus Hassan, Jennifer E Schuster, Ari Simenauer, Rangaraj Selvarangan, Rebecca A Halpin, Xudong Lin, Nadia Fedorova, Timothy B Stockwell, Tommy Tsan-Yuk Lam, James D Chappell, Tina V Hartert, Edward C Holmes, Suman R Das
2016/ 2
other viruses
Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia
Science
Jamal SM Sabir, Tommy T-Y Lam, Mohamed MM Ahmed, Lifeng Li, Yongyi Shen, Salah EM Abo-Aba, Muhammd I Qureshi, Mohamed Abu-Zeid, Yu Zhang, Mohammad A Khiyami, Njud S Alharbi, Nahid H Hajrah, Meshaal J Sabir, Mohammed HZ Mutwakil, Saleh A Kabli, Faten AS Alsulaimany, Abdullah Y Obaid, Boping Zhou, David K Smith, Edward C Holmes, Huachen Zhu, Yi Guan
2016/ 1
coronavirus
Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013
Journal of virology
Simon J Watson, Pinky Langat, Scott M Reid, Tommy Tsan-Yuk Lam, Matthew Cotten, Michael Kelly, Kristien Van Reeth, Yu Qiu, Gaëlle Simon, Emilie Bonin, Emanuela Foni, Chiara Chiapponi, Lars Larsen, Charlotte Hjulsager, Iwona Markowska-Daniel, Kinga Urbaniak, Ralf Dürrwald, Michael Schlegel, Anita Huovilainen, Irit Davidson, Ádám Dán, Willie Loeffen, Stephanie Edwards, Michel Bublot, Thais Vila, Jaime Maldonado, Laura Valls, ESNIP3 Consortium, Ian H Brown, Oliver G Pybus, Paul Kellam
2015/ 7
influenza
Dissemination, divergence and establishment of H7N9 influenza viruses in China
Nature
Tommy Tsan-Yuk Lam, Boping Zhou, Jia Wang, Yujuan Chai, Yongyi Shen, Xinchun Chen, Chi Ma, Wenshan Hong, Yin Chen, Yanjun Zhang, Lian Duan, Peiwen Chen, Junfei Jiang, Yu Zhang, Lifeng Li, Leo Lit Man Poon, Richard J Webby, David K Smith, Gabriel M Leung, Joseph SM Peiris, Edward C Holmes, Yi Guan, Huachen Zhu
2015/ 6
influenza
Occurrence and reassortment of avian influenza A (H7N9) viruses derived from coinfected birds in China
Journal of virology
Wei Liu, Hang Fan, Jayna Raghwani, Tommy Tsan-Yuk Lam, Jing Li, Oliver G Pybus, Hong-Wu Yao, Ying Wo, Kun Liu, Xiao-Ping An, Guang-Qian Pei, Hao Li, Hong-Yu Wang, Jian-Jun Zhao, Tao Jiang, Mai-Juan Ma, Xian Xia, Yan-De Dong, Tong-Yan Zhao, Jia-Fu Jiang, Yin-Hui Yang, Yi Guan, Yigang Tong, Wu-Chun Cao
2014/11
influenza
Expansion of genotypic diversity and establishment of 2009 H1N1 pandemic-origin internal genes in pigs in China
Journal of virology
Huyi Liang, Tommy Tsan-Yuk Lam, Xiaohui Fan, Xinchun Chen, Yu Zeng, Ji Zhou, Lian Duan, Maying Tse, Chung-Hei Chan, Lifeng Li, Tak-Ying Leung, Chun-Hung Yip, Chung-Lam Cheung, Boping Zhou, David K Smith, Leo Lit-Man Poon, Malik Peiris, Yi Guan, Huachen Zhu
2014/ 9
influenza
Emergence and evolution of avian H5N2 influenza viruses in chickens in Taiwan
Journal of virology
Chang-Chun David Lee, Huachen Zhu, Pei-Yu Huang, Liuxia Peng, Yun-Cheng Chang, Chun-Hung Yip, Yao-Tsun Li, Chung-Lam Cheung, Richard Compans, Chinglai Yang, David K Smith, Tommy Tsan-Yuk Lam, Chwan-Chuen King, Yi Guan
2014/ 5
influenza
Comparison of mutation patterns in full-genome A/H3N2 influenza sequences obtained directly from clinical samples and the same samples after a single MDCK passage
PLoS One
Hong Kai Lee, Julian Wei-Tze Tang, Debra Han-Lin Kong, Tze Ping Loh, Donald Kok-Leong Chiang, Tommy Tsan-Yuk Lam, Evelyn Siew-Chuan Koay
2013/11
influenza
The genesis and source of the H7N9 influenza viruses causing human infections in China
Nature
Tommy Tsan-Yuk Lam, Jia Wang, Yongyi Shen, Boping Zhou, Lian Duan, Chung-Lam Cheung, Chi Ma, Samantha J Lycett, Connie Yin-Hung Leung, Xinchun Chen, Lifeng Li, Wenshan Hong, Yujuan Chai, Linlin Zhou, Huyi Liang, Zhihua Ou, Yongmei Liu, Amber Farooqui, David J Kelvin, Leo LM Poon, David K Smith, Oliver G Pybus, Gabriel M Leung, Yuelong Shu, Robert G Webster, Richard J Webby, Joseph SM Peiris, Andrew Rambaut, Huachen Zhu, Yi Guan
2013/10
influenza
Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments
Infection, Genetics and Evolution
Tommy Tsan-Yuk Lam, Yee Ling Chong, Mang Shi, Chung-Chau Hon, Jun Li, Darren P Martin, Julian Wei-Tze Tang, Chee-Keng Mok, Shin-Ru Shih, Chi-Wai Yip, Jingwei Jiang, Raymond Kin-Hei Hui, Oliver G Pybus, Edward C Holmes, Frederick Chi-Ching Leung
2013/ 8
influenza
The rapidly expanding CRF01_AE epidemic in China is driven by multiple lineages of HIV-1 viruses introduced in the 1990s
AIDS (London, England)
Yi Feng, Xiang He, Jenny H Hsi, Fan Li, Xingguang Li, Quan Wang, Yuhua Ruan, Hui Xing, Tommy Tsan-Yuk Lam, Oliver G Pybus, Yutaka Takebe, Yiming Shao
2013/ 7
other viruses
Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus
Emerging infectious diseases
Matthew Cotten, Tommy T Lam, Simon J Watson, Anne L Palser, Velislava Petrova, Paul Grant, Oliver G Pybus, Andrew Rambaut, Yi Guan, Deenan Pillay, Paul Kellam, Eleni Nastouli
2013/ 5
coronavirus
Molecular characterization of the fecal microbiota in patients with nonalcoholic steatohepatitis–a longitudinal study
PloS one
Vincent Wai-Sun Wong, Chi-Hang Tse, Tommy Tsan-Yuk Lam, Grace Lai-Hung Wong, Angel Mei-Ling Chim, Winnie Chiu-Wing Chu, David Ka-Wai Yeung, Patrick Tik-Wan Law, Hoi-Shan Kwan, Jun Yu, Joseph Jao-Yiu Sung, Henry Lik-Yuen Chan
2013/ 4
microbiome
The evolutionary dynamics of influenza A virus adaptation to mammalian hosts
Philosophical Transactions of the Royal Society B: Biological Sciences
S Bhatt, TT Lam, SJ Lycett, AJ Leigh Brown, TA Bowden, EC Holmes, Y Guan, JLN Wood, IH Brown, P Kellam, Combating Swine Influenza Consortium, OG Pybus, Ian Brown, Sharon Brookes, Anna Germundsson, Alex Cook, Susanna Williamson, Stephen Essen, Fanny Garcon, George Gunn, Manuel Sanchez, Diogo Marques, James Wood, Dan Tucker, Ian McCrone, Julia Gog, Roberto Saenz, Meg Staff, Pablo Murcia, Wendy Barclay, Christl Donnelly, Ruth A Elderfield, Paul Kellam, Greg Baillie, Eve Coulter, Barbara Wieland, Alex Mastin, John McCauley, Andy Leigh Brown, Sam Lycett, Mark Woolhouse, Oliver Pybus, Samir Bhatt, Andrew Hayward, David Ishola, Alan Archibald, Tom Freeman, Bryan Charleston, Eric LeFevre, Mick Bailey, Charlotte Inman, Chris Stokes, Kin Chow Chang, Stephen Dunham, Gavin White, Jonathan Nguyen-Van-Tam, Joanne Enstone
2013/ 3
influenza
Epidemiological dynamics and phylogeography of influenza virus in southern China
The Journal of infectious diseases
Xiaowen Cheng, Yi Tan, Mingliang He, Tommy Tsan-Yuk Lam, Xing Lu, Cécile Viboud, Jianfan He, Shunxiang Zhang, Jianhua Lu, Chunli Wu, Shishong Fang, Xin Wang, Xu Xie, Hanwu Ma, Martha I Nelson, Hsiang-fu Kung, Edward C Holmes, Jinquan Cheng
2013/ 1
influenza
Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds
Ecology letters
Tommy Tsan‐Yuk Lam, Hon S Ip, Elodie Ghedin, David E Wentworth, Rebecca A Halpin, Timothy B Stockwell, David J Spiro, Robert J Dusek, James B Bortner, Jenny Hoskins, Bradley D Bales, Dan R Yparraguirre, Edward C Holmes
2012/ 1
influenza
Novel reassortment of Eurasian avian-like and pandemic/2009 influenza viruses in swine: infectious potential for humans
Journal of virology
Huachen Zhu, Boping Zhou, Xiaohui Fan, Tommy TY Lam, Jia Wang, Antony Chen, Xinchun Chen, Honglin Chen, Robert G Webster, Richard Webby, Joseph SM Peiris, David K Smith, Yi Guan
2011/10
influenza
Genetic characterization and evolutionary analysis of 4 Newcastle disease virus isolate full genomes from waterbirds in South China during 2003–2007
Veterinary microbiology
Shaoxin Cai, Jun Li, Mabel Ting Wong, Peirong Jiao, Huiying Fan, Dawei Liu, Ming Liao, Jingwei Jiang, Mang Shi, Tommy Tsan-Yuk Lam, Tao Ren, Frederick Chi-Ching Leung
2011/ 8
other viruses
Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States
Journal of virology
Martha I Nelson, Yi Tan, Elodie Ghedin, David E Wentworth, Kirsten St. George, Laurel Edelman, Eric T Beck, Jiang Fan, Tommy Tsan-Yuk Lam, Swati Kumar, David J Spiro, Lone Simonsen, Cecile Viboud, Edward C Holmes, Kelly J Henrickson, James M Musser
2011/ 1
influenza
Pandemic H1N1/2009 virus in swine: prevalence and genesis of reassortants with the potential to infect humans
ESWI Influenza Conference
H Zhu, L Li, Y Zeng, J Zhou, Z Zheng, R Chen, R Zheng, L Duan, CH Yip, K Huang, TY Lam, J Wang, H Chen, RG Webster, R Webby, JSM Peiris, DK Smith, Y Guan
2011
influenza
Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses
Journal of virology
Mang Shi, Tommy Tsan-Yuk Lam, Chung-Chau Hon, Michael P Murtaugh, Peter R Davies, Raymond Kin-Hei Hui, Jun Li, Lina Tik-Wim Wong, Chi-Wai Yip, Jin-Wai Jiang, Frederick Chi-Ching Leung
2010/ 9
other viruses
Evolutionary genetics of human enterovirus 71: origin, population dynamics, natural selection, and seasonal periodicity of the VP1 gene
Journal of virology
Kok Keng Tee, Tommy Tsan-Yuk Lam, Yoke Fun Chan, Jon M Bible, Adeeba Kamarulzaman, CY William Tong, Yutaka Takebe, Oliver G Pybus
2010/ 4
other viruses
Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans
Journal of general virology
Junfa Yuan, Chung-Chau Hon, Yan Li, Dingming Wang, Gelin Xu, Huajun Zhang, Peng Zhou, Leo LM Poon, Tommy Tsan-Yuk Lam, Frederick Chi-Ching Leung, Zhengli Shi
2010/ 4
coronavirus
The sequence and de novo assembly of the giant panda genome
Nature
Ruiqiang Li, Wei Fan, Geng Tian, Hongmei Zhu, Lin He, Jing Cai, Quanfei Huang, Qingle Cai, Bo Li, Yinqi Bai, Zhihe Zhang, Yaping Zhang, Wen Wang, Jun Li, Fuwen Wei, Heng Li, Min Jian, Jianwen Li, Zhaolei Zhang, Rasmus Nielsen, Dawei Li, Wanjun Gu, Zhentao Yang, Zhaoling Xuan, Oliver A Ryder, Frederick Chi-Ching Leung, Yan Zhou, Jianjun Cao, Xiao Sun, Yonggui Fu, Xiaodong Fang, Xiaosen Guo, Bo Wang, Rong Hou, Fujun Shen, Bo Mu, Peixiang Ni, Runmao Lin, Wubin Qian, Guodong Wang, Chang Yu, Wenhui Nie, Jinhuan Wang, Zhigang Wu, Huiqing Liang, Jiumeng Min, Qi Wu, Shifeng Cheng, Jue Ruan, Mingwei Wang, Zhongbin Shi, Ming Wen, Binghang Liu, Xiaoli Ren, Huisong Zheng, Dong Dong, Kathleen Cook, Gao Shan, Hao Zhang, Carolin Kosiol, Xueying Xie, Zuhong Lu, Hancheng Zheng, Yingrui Li, Cynthia C Steiner, Tommy Tsan-Yuk Lam, Siyuan Lin, Qinghui Zhang, Guoqing Li, Jing Tian, Timing Gong, Hongde Liu, Dejin Zhang, Lin Fang, Chen Ye, Juanbin Zhang, Wenbo Hu, Anlong Xu, Yuanyuan Ren, Guojie Zhang, Michael W Bruford, Qibin Li, Lijia Ma, Yiran Guo, Na An, Yujie Hu, Yang Zheng, Yongyong Shi, Zhiqiang Li, Qing Liu, Yanling Chen, Jing Zhao, Ning Qu, Shancen Zhao, Feng Tian, Xiaoling Wang, Haiyin Wang, Lizhi Xu, Xiao Liu, Tomas Vinar, Yajun Wang, Tak-Wah Lam, Siu-Ming Yiu, Shiping Liu, Hemin Zhang, Desheng Li, Yan Huang, Xia Wang, Guohua Yang, Zhi Jiang, Junyi Wang, Nan Qin, Li Li, Jingxiang Li, Lars Bolund, Karsten Kristiansen, Gane Ka-Shu Wong, Maynard Olson, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang, Jun Wang
2010/ 1
genomics
A phylogeny-based evolutionary, demographic and geographic dissection of north American type porcine reproductive and respiratory syndrome virus (NA-PRRSV)
International PRRS Symposium
M Shi, TY Lam, CC Hon, MP Murtaugh, P Davies, RKH Hui, J Li, TWL Wong, J Jiang, CW Yip, FCC Leung
2009
other respiratory viruses
Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus
Journal of virology
Chung-Chau Hon, Tsan-Yuk Lam, Zheng-Li Shi, Alexei J Drummond, Chi-Wai Yip, Fanya Zeng, Pui-Yi Lam, Frederick Chi-Ching Leung
2008/ 2
coronavirus
Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B
Journal of virology
Chung-Chau Hon, Tsan-Yuk Lam, Alexei Drummond, Andrew Rambaut, Yiu-Fai Lee, Chi-Wai Yip, Fanya Zeng, Pui-Yi Lam, Patrick TW Ng, Frederick CC Leung
2006/ 9
other viruses