现任中山大学医学院教授，博士生导师。国家海外高层次人才（青年项目）、广东省珠江学者、深圳市国家级领军人才、中山大学“百人计划”中青年杰出人才。

•    Professor and doctoral supervisor at the Sun Yat-sen University 
•    Overseas High-level Talents 
•    Pearl River Scholars of Guangdong Province 
•    National Leading Talents of Shenzhen City 
•    Outstanding Young and Middle-aged Talents of Sun Yat-sen University
 

 

学术经历（Biographic details）：

•    2019年至今，中山大学医学院教授
•    From 2019 to present, Professor, School of Medicine, Sun Yat-sen University

•    2024年至今，中国微生物学会智能计算微生物学专委会 副主任委员兼执行秘书
•    From 2024 to present, Vice Chair and Executive Secretary, Special Committee on Intelligent Computational Microbiology, Chinese Society for Microbiology

•    2024年至今，中华医学会微生物与免疫学分会 委员
•    From 2024 to present, Committee Member, Microbiology and Immunology Branch, Chinese Medical Association

•    2024年至今，广东省疾病控制中心客座研究员
•    From 2024 to present, Guest Researcher, Guangdong Provincial CDC

•    2018至2019年，悉尼大学讲师
•    From 2018 to 2019, Lecturer, University of Sydney

•    2017至2019年，上海临床公共卫生中心任兼职教授
•    From 2017 to 2019, Adjunct professor at Shanghai Clinical Public Health Center

•    2015至2017年，悉尼大学博士后、副讲师
•    From 2015 to 2017, Postdoctoral fellow and associate lecturer at the University of Sydeny

•    2012至2015年，悉尼大学病毒学博士
•    From 2012 to 2015, PhD in Virology, University of Sydney

•    2009至2010、2011年，美国国家疾病控制中心访问学者
•    From 2011 to 2011, Guest researcher, US CDC, Pathogen discovery group
•    From 2009 to 2010, Guest researcher, US CDC, Rabies group

•    2009至2011年，香港大学病毒学硕士
•    From 2009 to 2011, Master of Virology, University of Hong Kong

•    2005至2008年，香港大学生物学学士
•    From 2005 to 2008, Bachelor of Biology, University of Hong Kong
 


研究方向（Fields of Research）：
病原基因组学；AI与病毒学；X病原体的发现；全感染组学；单细胞病原组学；病原体的进化和生态。
Pathogen genomics; AI for virology; Pathogen discovery; Infectome; Single-cell metagenomics; Evolution and ecology of pathogens
 

学术成果（Research Interests）：

施莽教授专注于病原基因组学、新病原发现以及病原体和宿主之间的相互作用研究，并致力于将最前沿的高通量测序技术、机器学习和生物信息学方法应用于病原体研究。在组学病原学和信息病原学等前沿学科领域做出了许多开创性的工作，包括：
Our research team uses cutting-edge high-throughput sequencing technology, bioinformatics pipelines, and machine learning algorithm to discover pathogens and characterize their interaction with the hosts. Our group lead many pioneering works in the field of infectious disease, virology and microbiology, including:

•    建立了独有的样品处理体系与高通量测序为基础的病毒筛查新体系，开发了针对病原体发现的高效快速的生物信息分析流程和AI模型 (Established a pathogen discovery system based on a unique sample processing and library preparation system, efficient bioinformatics pipeline and avant-guard AI tools)
•    发现了超过160,000种新病毒，重新定义了RNA病毒圈，改变了人们对RNA病毒的普遍性和多样性的认知 (Discovered more than 160,000 new virus species, redefined the RNA virosphere and changed people’s understanding of the ubiquity and diversity of RNA viruses)
•    建立覆盖多种类型病原体的“一样全检”的检测技术，涵盖包括病毒、细菌、真菌和宿主在内的完整全感染组信息 (Establish a “one-size-fits-all” detection technology that covers multiple types of pathogens, covering complete “infectome” information that includes viruses, bacteria, fungi and hosts)
•    阐释了病毒、宿主以及其他微生物之间的相互作用，开发了以组学为基础的系统病原学方法 (Elucidated the interactions between viruses, hosts and other microorganisms, developed an omics-based systematic pathogenomics approach.)。

作为项目负责人，施莽教授主持国家自然科学基金专项等项目，累计经费超过1000万人民币。学术成果（第一或通讯作者）发表在多家国际权威期刊上，包括《Nature》（2篇）、《Cell》（2篇）、《Nature Microbiology》、《Nature Communications》、《Nature Ecology & Evolution》、《Microbiome》和《PNAS》等，共计155篇SCI论文，总引用率超过18000次，h-index 为 59。
As the project leader, Professor Mang Shi presides over more than 10 research grants such as the National Natural Science Foundation of China. His academic achievements include a total of 155 published papers, with more than 18,000 citations and an h-index of 59.
 

 

招生学科专业（Admissions subject majors:）：
071000 生物学-05 微生物学 (Biology-05 Microbiology)，
086000 生物与医药 (Biology and Medicine)。
 

联系邮箱 (Email)：
shim23@mail.sysu.edu.cn

 

著作 (Publications)

Representative works (# joint first authorship, * joint senior authorship):

Year 2024

 

  1. Hou X, He Y, Fang P, Mei SQ, Xu Z, Wu WC, Tian JH, Zhang S, Zeng Z, Gou QY, Xin GY, Le SJ, Xia YY, Zhou Y, Hui FM, Pan YF, Eden J, Yang Z, Han C, Shu Y, Guo D, Li J, Holmes EC, Li ZR, Shi M* (2024) Using artificial intelligence to document the hidden RNA virosphere. Cell. 187:1-14. (封面文章)
  2. Pan YF, Zhao H, Gou QY, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, Xin GY, Wang J, Hou X, Peng MW, Kong JB, Chen XX, Yang CH, Mei SQ, Liao YQ, Cheng JX, Wang J, Chaolemen, Wu YH, Wang JB, An T, Huang X, Eden JS, Li J, Guo D, Liang G, Jin X, Holmes EC, Li B, Wang D, Li J, Wu WC, Shi M* (2024). Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity. Nat. Ecol. Evol. 8(5):947-959.
  3. Feng Y, Kuang GP, Pan YF, Wang J, Yang WH, Wu WC, Pan H, Wang J, Han X, Yang LF, Xin GY, Shan YT, Gou QY, Liu X, Guo DY, Liang GD, Holmes EC, Gao ZH, Shi M* (2024). Small mammals in a biodiversity hotspot harbor viruses of emergence risk. Natl. Sci. Rev. nwae463.
  4. Yang Z, Shan Y, Liu X, Chen G, Pan Y, Gou Q, Zou J, Chang Z, Zeng Q, Yang C, Kong J, Sun Y, Li S, Zhang X, Wu WC, Li C, Peng H, Holmes EC, Guo D, Shi M* (2024). VirID: Beyond Virus Discovery - An Integrated Platform for Comprehensive RNA Virus Characterization. Mol. Biol. Evol. msae202.
  5. Xie L, Luo G, Yang Z, Wu WC, Chen J, Ren Y, Zeng Z, Ye G, Pan Y, Zhao WJ, Chen YQ, Hou W, Sun Y, Guo D, Yang Z, Li J, Holmes EC, Li Y, Chen L, Shi M* (2024). The clinical outcome of COVID-19 is strongly associated with microbiome dynamics in the upper respiratory tract. J. Infect. 88(3):106118.
  6. Wu WC, Pan YF, Zhou WD, Liao YQ, Peng MW, Luo GY, Xin GY, Peng YN, An TQ, Li B, Luo H, Barrs VR, Beatty JA, Holmes EC, Zhao W, Shi M*, Shu Y (2024). Meta-transcriptomic analysis of companion animal infectomes reveals their diversity and potential roles in animal and human disease. mSphere. 9:e0043924.
  7. Kuang G, Wang J, Feng Y, Wu W, Han X, Xin G, Yang W, Pan H, Yang L, Wang J, Shi M*, Gao Z (2024). The discovery of novel variants reveals the genetic diversity and potential origin of Seoul orthohantavirus. PLoS Negl. Trop. Dis. 18:e0012478.
  8. Yang LF, Wu WC, Cai S, Wang J, Kuang GP, Yang WH, Wang J, Han X, Pan H, Shi M*, Yun Feng (2024). Transcriptomic Investigation of the Virus Spectrum Carried by Midges in Border Areas of Yunnan Province. Viruses. 16 (5), 674.
  9. Yang Z, Cai K, Liao Y, Wu W-C, Xing L, Hu M, Ren J, Zhang J, Zhu X, Yuan K, Huang H, Yang C, Zhang M, Shi M*, Lu H (2024). Total Infectome Characterization of Respiratory Infections during the 2022–23 COVID-19 Outbreak in China Revealed Extensive Coinfections with Links to SARS-CoV-2 Status, Age, and Disease Severity. Pathogens. 13(3):216.
  10. Tang X, Shang J, Chen G, Chan KHK, Shi M, Sun Y (2024). SegVir: Reconstruction of complete segmented RNA viral genomes from metatranscriptomes. Mol. Biol. Evol. 41 (8), msae171.
  11. Wu L, Liu Y, Shi W, Chang T, Liu P, Liu K, He Y, Li Z, Shi M, Jiao N, Lang AS, Dong X, Zheng Q (2024). Uncovering the hidden RNA virus diversity in Lake Nam Co: Evolutionary insights from an extreme high-altitude environment. Proc Natl Acad Sci U S A. 122(6):e2420162122.
  12. Chang WS, Harvey E, Mahar JE, Firth C, Shi M, Simon-Loriere E, Geoghegan JL, Wille M (2024). Improving the reporting of metagenomic virome-scale data. Commun. Biol. 7(1):1687.
  13. Sun Y, Xing J, Hong SL, Bollen N, Xu S, Li Y, Zhong J, Gao X, Zhu D, Liu J, Gong L, Zhou L, An T, Shi M, Wang H, Baele G, Zhang G (2024). Untangling lineage introductions, persistence and transmission drivers of HP-PRRSV sublineage 8.7. Nat. Commun. 15(1):8842.
  14. Kuhn JH, Brown K, Adkins S, de la Torre JC, Digiaro M, Ergünay K, Firth AE, Hughes HR, Junglen S, Lambert AJ, Maes P, Marklewitz M, Palacios G, Sasaya T, Shi M, Zhang Y-Z, Wolf YI, Turina M (2024). Promotion of order Bunyavirales to class Bunyaviricetes to accommodate a rapidly increasing number of related polyploviricotine viruses. J Virol. 98(10):e0106924.

 

Year 2023

 

  1. Wang J, Pan YF, Yang LF, Yang WH, Lv K, Luo CM, Wang J, Kuang GP, Wu WC, Gou QY, Xin GY, Li B, Luo HL, Chen S, Shu YL, Guo D, Gao ZH, Liang G, Li J, Chen YQ, Holmes EC, Feng Y, Shi M* (2023). Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nat. Commun. 14(1):4079.
  2. Lu M, He WT, Pettersson JH, Baele G, Shi M, Holmes EC, He N, Su S (2023). Zoonotic risk assessment among farmed mammals. Cell. 186(9).
  3. Luo XL#, Lu S#, Qin C#, Shi M#, Lu XB, Wang L, Ga S, Jin D, Ma XL, Yang J, Dai Y, Bao LL, Cheng YP, Ge YJ, Bai YB, Zhu WT, Pu J, Sun H, Huang YY, Xu MC, Lei WJ, Dong K, Yang CX, Jiao YF, Lv Q, Li FD, Xu J (2023). Emergence of an ancient and pathogenic mammarenavirus. Emerg. Microbes & Infect. 12(1).
  4. Le SJ, Xin GY, Wu WC, Shi M* (2023). Genetic Diversity and Evolution of Viruses Infecting Felis catus: A Global Perspective. Viruses. 15(6).
  5. Gou Q, Shi M* (2023). Detection of mosquito-borne viruses based on high-throughput sequencing. Chin. J. Lab. Med. 46 (9), 958-963
  6. Kuang G, Xu Z, Wang J, Gao Z, Yang W, Wu W, Liang G, Shi M*, Feng Y (2023). Nelson Bay Reovirus Isolated from Bats and Blood-Sucking Arthropods Collected in Yunnan Province, China. Microbiol. Spectr. 11(4).
  7. Xin G, Kuang Q, Le S, Wu W, Gao Q, Gao H, Xu Z, Zheng Z, Lu G, Gong L, Wang H, Zhang G, Shi M*, Sun Y (2023). Origin, genomic diversity and evolution of African swine fever virus in East Asia. Virus Evol. 9(2):vead060.
  8. Wang J, Wang J, Kuang G, Wu W, Yang L, Yang W, Pan H, Han X, Yang T, Shi M*, Feng Y. (2023). Meta-transcriptomics for the diversity of tick-borne virus in Nujiang, Yunnan Province. Front. Cell Infect. Microbiol. 13:1283019.
  9. Chen G, Tang X, Shi M, Sun Y (2023). VirBot: an RNA viral contig detector for metagenomic data. Bioinformatics. 39(3).
  10. Yang L, Wang Z, Wang L, Vrancken B, Wang R, Wei Y, Rader B, Wu CH, Chen Y, Wu P, Li B, Lin Q, Dong L, Cui Y, Shi M, Brownstein JS, Stenseth NC, Yang R, Tian H (2023). Association of vaccination, international travel, public health and social measures with lineage dynamics of SARS-CoV-2. Proc Natl Acad Sci U S A. 120(33):e2305403120.
  11. Ma Y, Li P, Hu Y, Qiu T, Wang L, Lu H, Lv K, Xu M, Zhuang J, Liu X, He S, He B, Liu S, Liu L, Wang Y, Yue X, Zhai Y, Luo W, Mai H, Kuang Y, Chen S, Ye F, Zhou N, Zhao W, Chen J, Chen S, Xiong X, Shi M, Pan JA, Chen YQ (2023). Spike substitution T813S increases Sarbecovirus fusogenicity by enhancing the usage of TMPRSS2. PLoS Pathog. 19(5).
  12. Le Lay C, Hamm JN, Williams TJ, Shi M, Cavicchioli R, Holmes EC (2023). Viral community composition of hypersaline lakes. Virus Evolution. 9 (2), vead057
  13. Le Lay C, Stott MB, Shi M, Sadiq S, Holmes EC (2023). A metatranscriptomic analysis of geothermal hot springs reveals diverse RNA viruses including the phylum lenarviricota. Virology. 109873
  14. Pan Y, Liu M, Sosa A, Li B, Shi M, Pan X (2023). Hierarchical metacommunity structure of fungal endophytes. New Phytologist. 239(4):1464-1474.
  15. Jiang JZ, Fang YF, Wei HY, Zhu P, Liu M, Yuan WG, Yang LL, Guo YX, Jin T, Shi M, Yao T, Lu J, Ye LT, Shi SK, Wang M, Duan M, Zhang DC (2023). A remarkably diverse and well-organized virus community in a filter-feeding oyster. Microbiome. 11(1):2.
  16. Wu J, Liu W, Zhu L, Li N, Luo G, Gu M, Peng M, Zeng S, Wu S, Zhang S, Chen Q, Cai M, Cao W, Jiang Y, Luo C, Tian D, Shi M, Shu Y, Chang G, Luo H (2023). Dysbiosis of oropharyngeal microbiome and antibiotic resistance in hospitalized COVID‐19 patients. J. Med. Virol. 95(4):e28727.
  17. Yim-Im W, Anderson TK, Paploski IAD, VanderWaal K, Gauger P, Krueger K, Shi M, Main R, Zhang J (2023). Refining PRRSV-2 genetic classification based on global ORF5 sequences and investigation of their geographic distributions and temporal changes. Microbiol Spectr. 11(6):e0291623.

 

Year 2022

 

  1. He WT, Hou X, Zhao J, Sun J, He H, Si W, Wang J, Jiang Z, Yan Z, Xing G, Lu M, Suchard MA, Ji X, Gong W, He B, Li J, Lemey P, Guo D, Tu C, Holmes EC, Shi M*, Su S (2022). Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell. 185(7):1117-1129.
  2. Wang J, Gou QY, Luo GY, Hou X, Liang G, Shi M* (2022). Total RNA sequencing of Phlebotomus chinensis sandflies in China revealed viral, bacterial, and eukaryotic microbes potentially pathogenic to humans. Emerg. Microbes & Infect. 11(1):2080-2092.
  3. Shi W, Shi M#, Que TC, Cui XM, Ye RZ, Xia LY, Hou X, Zheng JJ, Jia N, Xie X, Wu WC, He MH, Wang HF, Wei YJ, Wu AQ, Zhang SF, Pan YS, Chen PY, Wang Q, Li SS, Zhong YL, Li YJ, Tan LH, Zhao L, Jiang JF, Hu YL, Cao WC (2022). Trafficked Malayan pangolins contain viral pathogens of humans. Nat. Microbiol. 7(8):1259-1269.
  4. Huang X, Wu W, Tian X, Hou X, Cui X, Xiao Y, Jiao Q, Zhou P, Liu L, Shi W, Chen L, Sun Y, Yang Y, Chen J, Zhang G, Liu J, Holmes EC, Cai X, An T, Shi M* (2022).  A total infectome approach to understand the etiology of infectious disease in pigs. Microbiome. 10(1):73.
  5. Shi M, Zhao S, Yu B, Wu WC, Hu Y, Tian JH, Yin W, Ni F, Hu HL, Geng S, Tan L, Peng Y, Song ZG, Wang W, Chen YM, Holmes EC, Zhang YZ. Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China. PLoS Pathog. 18(2):e1010259.
  6. Feng Y, Gou QY, Yang WH, Wu WC, Wang J, Holmes EC, Liang G, Shi M* (2022). A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes. Virus Evol. 8(1):veac006.
  7. Tian J, Hou X, Ge M, Xu H, Yu B, Liu J, Shao R, Holmes EC, Lei C, Shi M* (2022). The diversity and evolutionary relationships of ticks and tick-borne bacteria collected in China. Parasit. & Vectors. 15(1).
  8. Chen L, Shen L, Wu W, Guan W, Zhou J, Luo G, Chen Q, Zhou H, Deng Z, Chen Y, Zhao W, Jin W, Qiu M, Zheng Q, Wang Y, Liu C, Bai X, Guo D, Holmes EC, Zhong N, Shi M*, Yang Z (2022). Co-infecting pathogens can contribute to inflammatory responses and severe symptoms in COVID-19. J. Thorac. Dis. 14(2):355-370.
  9. Zhu W, Yang J, Lu S, Huang Y, Jin D, Pu J, Liu L, Li Z, Shi M*, Xu J (2022). Novel pegiviruses infecting wild birds and rodents. Virol. Sin. 37(2):208-214.
  10. Zhu P, Liu GF, Liu C, Yang LL, Liu M, Xie KM, Shi SK, Shi M *, Jiang JZ (2022). Novel RNA viruses in oysters revealed by virome. iMeta. 1(4).
  11. Tian FJ, Li J, Liu WL, Liu YJ, Hu YJ, Tu QH, Li Y, Bai Y, Shi M*, Que TC, Hu YL, Tong YG (2022). Virome in healthy pangolins reveals compatibility with multiple potentially zoonotic viruses. Zool Res. 43(6):977-988.
  12. Liao M, Xie Y, Shi M, Cui J (2022). Over two decades of research on the marine RNA virosphere. iMeta. 1(4):e59.
  13. Tian FJ, Li J, Liu WL, Liu YJ, Hu YJ, Tu QH, Li Y, Bai Y, Shi M*, Que TC, Hu YL, Tong YG (2022). Virome in healthy pangolins reveals compatibility with multiple potentially zoonotic viruses. Zool. Res. 43(6):977-988.
  14. Xu X, Wang J, Liu H, Wang Q, Fu S, Zhang J, Wang B, He Y, Li F, Nie K, Xu S, Wang H, Lu X, Shi M*, Liang G (2022). Two Rhabdoviruses, One Novel, Isolated from Armigeres subalbatus in China. Pathogens. 11(6):624.
  15. Jia T, Chang WS, Marcelino VR, Zhao S, Liu X, You Y, Holmes EC, Shi M*, Zhang C (2022). Characterization of the Gut Microbiome and Resistomes of Wild and Zoo-Captive Macaques. Front. Vet. Sci. 8:778556.
  16. Xu ZY, Gao H, Kuang QY, Xing JB, Wang ZY, Cao XY, Xu SJ, Liu J, Huang Z, Zheng ZZ, Gong L, Wang H, Shi M*, Zhang GH, Sun YK (2022). Clinical sequencing uncovers the genomic characteristics and mutation spectrum of the 2018 African swine fever virus in Guangdong, China. Front. Vet. Sci. 9.
  17. Cui X, Xia D, Huang X, Sun Y, Shi M, Zhang J, Li G, Yang Y, Wang H, Cai X, An T (2022). Analysis of Recombinant Characteristics Based on 949 PRRSV-2 Genomic Sequences Obtained from 1991 to 2021 Shows That Viral Multiplication Ability Contributes to Dominant Recombination. Microbiol. Spectr. 10(5).
  18. Van Brussel K, Wang X, Shi M, Carrai M, Feng S, Li J, Holmes EC, Beatty JA, Barrs VR (2022). The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats. Transbound. Emerg. Dis. 69(5), e2952-e2966.
  19. Wang X, Carrai M, Van Brussel K, Feng S, Beatty JA, Shi M, Holmes EC, Li J, Barrs VR (2022). Low Intrahost and Interhost Genetic Diversity of Carnivore Protoparvovirus 1 in Domestic Cats during a Feline Panleukopenia Outbreak. Viruses. 14(7):1412.
  20. Walker PJ, Freitas-Astúa J, Bejerman N, Blasdell KR, Breyta R, Dietzgen RG, Fooks AR, Kondo H, Kurath G, Kuzmin IV, Ramos-González PL, Shi M, Stone DM, Tesh RB, Tordo N, Vasilakis N, Whitfield AE (2022). ICTV Virus Taxonomy Profile: Rhabdoviridae 2022. J. Gen. Virol. 103(6).
  21. Cao L, Li Y, Yang S, Li G, Zhou Q, Sun J, …, Deng X, Zhang W, Lin C, Shi M, Li CM, Zhang Y, Zhang L, Dai J, Lu H, Zhao J, Zhang X, Guo D (2022). The adenosine analog prodrug ATV006 is orally bioavailable and has preclinical efficacy against parental SARS-CoV-2 and variants. Sci. Transl. Med. 14(661).
  22. Di Paola N, Dheilly NM, Junglen S, Paraskevopoulou S, Postler TS, Shi M, Kuhn JH (2022). Jingchuvirales: a New Taxonomical Framework for a Rapidly Expanding Order of Unusual Monjiviricete Viruses Broadly Distributed among Arthropod Subphyla. Appl. Environ. Microbiol. 88(6).
  23. Xu Z, Feng Y, Chen X, Shi M, Fu S, Yang W, Liu WJ, Gao GF, Liang G (2022). Virome of bat-infesting arthropods: highly divergent viruses in different vectors. J. Virol. 96(4):e0146421.
  24. He B, Liu S, Xu M, Hu Y, Lv K, Wang Y, Ma Y, Zhai Y, Yue X, Liu L, Lu H, Zhou S, Li P, Mai G, Huang X, Li C, Chen S, Ye S, Zhao P, Yang Y, Li X, Jie Y, Shi M, Yang J, Shu Y, Chen YQ (2022). Comparative global B cell receptor repertoire difference induced by SARS-CoV-2 infection or vaccination via single-cell V (D) J sequencing. Emerg. Microbes Infect. 11(1):2007-2020.

 

Year 2021

 

  1. Chen XX, Wu WC, Shi M* (2021). Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing. Viruses. 13:1042.
  2. Xu Z, Fan N, Hou X, Wang J, Fu S, Song J, Shi M*, Liang G* (2021). Isolation and identification of a novel phlebovirus, Hedi virus, from sandflies collected in China. Viruses. 13:772.
  3. Liu X, Guo L, Xu T, Lu X, Ma M, Sheng W, Wu Y, Peng H, Cao L, Zheng F, Huang S, Yang Z, Du J, Shi M*, Guo D* (2021). A comprehensive evolutionary and epidemiological characterization of insertion and deletion mutations in SARS-CoV-2 genomes. Virus Evol. 7(2):veab104.
  4. Bordicchia M, Fumian TM, Van Brussel K, Russo AG, Carrai M, Le SJ, Pesavento PA, Holmes EC, Martella V, White P, Beatty JA, Shi M*, Barrs VR* (2021). Feline Calicivirus Virulent Systemic Disease: Clinical Epidemiology, Analysis of Viral Isolates and In Vitro Efficacy of Novel Antivirals in Australian Outbreaks. Viruses. 13(10):2040.
  5. He B, Liu S, Wang Y, Xu M, Cai W, Liu J, Bai W, Ye S, Ma Y, Hu H, Meng H, Sun T, Li Y, Luo H, Shi M, Du X, Zhao W, Chen S, Yang J, Zhu H, Jie Y, Yang Y, Guo D, Wang Q, Liu Y, Yan H, Wang M, Chen YQ (2021). Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq. Signal Transduct. Target Ther. 6(1):195.
  6. Wille M, Shi M, Hurt AC, Klaassen M, Holmes EC (2021). RNA virome abundance and diversity is associated with host age in a bird species. Virology. 561:98-106.
  7. Binkley L, Deressa A, Shi M, Jara M, Escobar LE, Mauldin MR, Matheny A, O'Quin J, Pieracci EG, Kling C, Hartloge C, Yimer G, Abate E, Gebreyes W, Reynolds M, Belay E, Shiferaw M, Nakazawa Y, Velasco-Villa A (2021). Use of partial N-gene sequences as a tool to monitor progress on rabies control and elimination efforts in Ethiopia. Acta Trop. 221:106022.
  8. Dong X, Wang G, Hu T, Li J, Li C, Cao Z, Shi M, Wang Y, Zou P, Song J, Gao W, Meng F, Yang G, Tang KFJ, Li C, Shi W, Huang J (2021). A Novel Virus of Flaviviridae Associated with Sexual Precocity in Macrobrachium rosenbergii. mSystems. 6:e0000321.
  9. Jin YY, Lin H, Cao L, Wu WC, Ji Y, Du L, Jiang Y, Xie Y, Tong K, Xing F, Zheng F, Shi M, Pan JA, Peng X, Guo D (2021). A Convenient and Biosafe Replicon with Accessory Genes of SARS-CoV-2 and Its Potential Application in Antiviral Drug Discovery. Virol. Sin. 17:1-11.
  10. Cheng S, Wu D, Li J, Zou Y, Wan Y, Shen L, Zhu L, Shi M, Hou L, Xu T, Jiao N, Li Y, Huang Y, Tang Z, Xu M, Jiang S, Li M, Yan G, Lan P, Zhu R (2021). Risk factors for the critical illness in SARS-CoV-2 infection: a multicenter retrospective cohort study. Respir. Res. 21:277.
  11. Guo L, Lu X, Liu X, Li P, Wu J, Xing F, Peng H, Xiao X, Shi M, Liu Z, Li XD, Guo D (2021). Metatranscriptomic analysis reveals the virome and viral genomic evolution of medically important mites. J. Virol. 95:e01686-20.

 

Year 2020

 

  1. Chen L, Liu W, Zhang Q, Xu K, Ye G, Wu W, Sun Z, Liu F, Wu K, Zhong B, Mei Y, Zhang W, Chen Y, Li Y*, Shi M*, Lan K*, Liu Y* (2020). RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerg. Microbes & Infect. 9(1):313-319.
  2. Song R, Han B, Song M, Wang L, Conlon CP, Dong T, Tian D, Zhang W, Chen Z, Zhang F, Shi M*, Li X* (2020). Clinical and epidemiological features of COVID-19 family clusters in Beijing, China. J. Infect. 81(2):e26-e30.
  3. Sun YK, Chen YJ, Cai Y, Li Q, Xie JX, Liang G, Gao Q, Yu ZQ, Lu G, Huang LZ, Ma CQ, Gong L, Wang H, Shi M*, Zhang GH* (2020). Insights into the evolutionary history and epidemiological characteristics of the emerging lineage 1 porcine reproductive and respiratory syndrome viruses in China. Transbound. Emerg. Dis. 67(6):2630-2641.
  4. Li CX, Li W, Zhou J, Zhang B, Feng Y, Xu CP, Lu YY, Holmes EC, Shi M*. High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection (2020). Sci. Rep. 10(1):3963.
  5. Wan Y, Li J, Shen L, Zou Y, Hou L, Zhu L, Faden HS, Tang Z, Shi M, Jiao N, Li Y, Cheng S, Huang Y, Wu D, Xu Z, Pan L, Zhu J, Yan G, Zhu R, Lan P (2020). Enteric involvement in hospitalised patients with COVID-19 outside Wuhan. Lancet Gastroenterol Hepatol. Lancet Gastroenterol. Hepatol. 5 (6):534-535.
  6. Wu H, Pang R, Cheng T, Xue L, Zeng H, Lei T, Chen M, Wu S, Ding Y, Zhang J, Shi M, Wu Q (2020). Abundant and Diverse RNA Viruses in Insects Revealed by RNA-Seq Analysis: Ecological and Evolutionary Implications. mSystems. 5(4):e00039-20.
  7. Mahar JE, Shi M, Hall RN, Strive T, Holmes EC (2020). Comparative Analysis of RNA Virome Composition in Rabbits and Associated Ectoparasites. J. Virol. 94(11):e02119-19.
  8. Brussel KV, Wang X, Shi M, Carrai M, Li J, Martella V, Beatty JA, Holmes EC, Barrs VR (2020).  Identification of Novel Astroviruses in the Gastrointestinal Tract of Domestic Cats. Viruses. 12:1301.
  9. Turnbull OMH, Ortiz-Baez AS, Eden JS, Shi M, Williamson JE, Gaston TF, Zhang YZ, Holmes EC, Geoghegan JL (2020). Meta-transcriptomic identification of divergent Amnoonviridae in fish. Viruses. 12:1254.
  10. Wang J, Fu S, Xu Z, Cheng J, Shi M, Fan N, Song J, Tian X, Cheng J, Ni S, He Y, Lei W, Li F, Peng H, Wang B, Wang H, Lu X, Ma Y, Liang G (2020). Emerging Sand Fly–Borne Phlebovirus in China. Emerg. Infect. Dis. 26:2435-2438.
  11. Lay CL, Shi M, Buček A, Bourguignon T, Lo N, Holmes EC (2020). Unmapped RNA virus diversity in termites and their symbionts. Viruses. 12:1145.
  12. Porter AF, Pettersson JH, Chang WS, Harvey E, Rose K, Shi M, Eden JS, Buchmann J, Moritz C, Holmes EC (2020). Novel hepaci-and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evol. 6:veaa064.
  13. Obbard DJ, Shi M, Roberts KE, Longdon B, Dennis AB (2020). A new lineage of segmented RNA viruses infecting animals. Virus Evol. 6 (1), vez061.
  14. Chang WS, Eden JS, Hall J, Shi M, Rose K, Holmes EC (2020). Metatranscriptomic analysis of virus diversity in urban wild birds with paretic disease. J. Virol. 94:e00606-20.
  15. Mahar JE, Shi M, Hall RN, Strive T, Holmes EC (2020). Comparative Analysis of RNA Virome Composition in Rabbits and Associated Ectoparasites. J. Virol. 94(11):e02119-19.
  16. Chen LJ, Guo JJ, Guo WW, Shen EX, Wang X, Li KJ, Yan J, Shi M, Li YR, Hou W (2020). Molecular Epidemiology and Vaccine Compatibility Analysis of Seasonal Influenza Viruses in Wuhan, 2016-2019. Virol. Sin. 96(10):e29858.
  17. Wille M, Harvey E, Shi M, Gonzalez-Acuña D, Holmes EC, Hurt AC (2020). Sustained RNA virome diversity in Antarctic penguins and their ticks. ISME J. 14(7):1768-1782.
  18. Xiong Y, Liu Y, Cao L, Wang D, Guo M, Jiang A, Guo D, Hu W, Yang J, Tang Z, Wu H, Lin Y, Zhang M, Zhang Q, Shi M, Liu Y, Zhou Y, Lan K, Chen Y (2020). Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Emerg. Microbes & Infect. 9(1):761-770.
  19. Yu F, Yan Y, Shi M, Liu HZ, Zhang HL, Yang YB, Huang XY, Gauger PC, Zhang J, Zhang YH, Tong GZ, Tian ZJ, Chen JJ, Cai XH, Liu D, Li G, An TQ (2020). Phylogenetics, genomic recombination, and NSP2 polymorphic patterns of porcine reproductive and respiratory syndrome virus in China and the United States in 2014–2018. J. Virol. 01813-19.
  20. Tsoleridis T, Chappell JG, Monchatre-Leroy E, Umhang G, Shi M, Bennett M, Tarlinton RE, McClure CP, Holmes EC, Ball JK (2020). Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits. Viruses 12 (1), 47.
  21. Carrai M, Van Brussel K, Shi M, Li CX, Chang WS, Munday JS, Voss K, McLuckie A, Taylor D, Laws A, Holmes EC, Barrs VR, Beatty JA (2020). Identification of A Novel Papillomavirus Associated with Squamous Cell Carcinoma in A Domestic Cat. Viruses. 12 (1), 124.

 

Year 2015-2019

 

  1. Shi M, Lin XD, Chen X, Tian JH, Chen LJ, Li K, Wang W, Eden JS, Shen JJ, Liu L, Holmes EC, Zhang YZ (2018). The evolutionary history of vertebrate RNA viruses. Nature. 556(7700):197-202.
  2. Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, Qin XC, Li J, Cao JP, Eden JS, Buchmann J, Wang W, Xu J, Holmes EC, Zhang YZ (2016). Redefining the invertebrate RNA virosphere. Nature. 540:539-543.
  3. Shi M, White VL, Schlub T, Eden JS, Hoffmann AA, Holmes EC (2018). No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster. Proc. Biol. Sci. 285(1883):20181165.
  4. Shi M, Neville P, Nicholson J, Eden J-S, Imrie A, Holmes EC (2017). High pesolution meta-transcriptomics reveals the ecological dynamics of mosquito-associated RNA viruses in Western Australia. J. Virol. 91:e00680-17.
  5. Shi M, Lin XD, Vasilakis N, Tian JH, Li CX, Chen LJ, Eastwood G, Diao XN, Chen MH, Chen X, Qin XC, Widen SG, Wood TG, Tesh RB, Xu J, Holmes EC, Zhang YZ (2015). Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. J. Virol. 90:659-669.
  6. Shi M, Holmes EC, Zhang YZ. Meta-transcriptomics and the evolutionary biology of RNA viruses (2018). Virus Res. 243:83-90.
  7. Li CX#, Shi M#, Tian JH, Lin XD, Kang YJ, Chen LJ, Qin XC, Xu J, Holmes EC, Zhang YZ (2015). Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative sense RNA viruses. eLife. 4:e05378.
  8. Tao Y#, Shi M#, Chommanard C, Queen K, Zhang J, Markotter W, Kuzmin IV, Holmes EC, Tong S (2017). Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. J. Virol. 91:e01953-16.
  9. Aghazadeh M#, Shi M#, Barrs VR, McLuckie AJ, Lindsay SA, Jameson B, Hampson B, Holmes EC, Beatty JA (2018). A Novel Hepadnavirus Identified in an Immunocompromised Domestic Cat in Australia. Viruses. 10:2
  10. Zhao K, Ye C, Chang XB, Jiang CG, Wang SJ, Cai XH, Tong GZ, Tian ZJ, Shi M*, An TQ (2015). Importation and recombination are responsible for the latest emergence of highly pathogenic Porcine Reproductive and Respiratory Syndrome virus in China. J. Virol. 89:10712-10716.
  11. Zhang YZ, Shi M, Holmes EC (2018). Using metagenomics to characterize an expanding virosphere. Cell. 172:1168-1172.
  12. Ye C, Zhang QZ, Tian ZJ, Zheng H, Zhao K, Liu F, Guo JC, Tong W, Jiang CG, Wang SJ, Shi M, Chang XB, Jiang YF, Peng JM, Zhou YJ, Tang YD, Sun MX, Cai XH, An TQ, Tong GZ (2015). Genomic characterization of emergent pseudorabies virus in China reveals marked sequence divergence: Evidence for the existence of two major genotypes. Virology. 483:32-43.
  13. Wille M, Shi M, Klaassen M, Hurt AC, Holmes EC (2019). Virome heterogeneity and connectivity in waterfowl and shorebird communities. ISME J. 13(10):2603-26
  14. Porter AF, Shi M, Eden JS, Zhang YZ, Holmes EC (2019). Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics. Viruses 11 (12), 1092
  15. Chang WS, Eden JS, Hartley WJ, Shi M, Rose K, Holmes EC (2019). Metagenomic discovery and co-infection of diverse wobbly possum disease viruses and a novel hepacivirus in Australian brushtail possums. One Health Outlook. 1 (1), 5.
  16. Chang WS, Pettersson JH, Le Lay C, Shi M, Lo N, Wille M, Eden JS, Holmes EC (2019). Novel hepatitis D-like agents in vertebrates and invertebrates. Virus Evol. 5 (2), vez021
  17. Zhou H, Ma Z, Hu T, Bi Y, Mamuti A, Yu R, Carr MJ, Shi M, Li J, Sharshov K, Gao GF, Shi W (2019). Tamdy Virus in Ixodid Ticks Infesting Bactrian Camels, Xinjiang, China, 2018. Emerg. Infect. Dis. 25(11):2136-2138.
  18. Bucek A, Šobotník J, He S, Shi M, McMahon DP, Holmes EC, Roisin Y, Lo N, Bourguignon T (2019). Evolution of termite symbiosis informed by transcriptome-based phylogenies. Curr. Biol. 29 (21), 3728-3734. e4
  19. Pettersson JH, Shi M, Eden JS, Holmes EC, Hesson JC (2019). Meta-transcriptomic comparison of the RNA viromes of the mosquito vectors Culex pipiens and Culex torrentium in northern Europe. Viruses. 11 (11), 1033d
  20. Marcelino VR, Wille M, Hurt AC, González-Acuña D, Klaassen M, Schlub TE, Eden JS, Shi M, Iredell JR, Sorrell TC, Holmes EC (2019). Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes. BMC biology. 17 (1), 31.
  21. Mahar JE, Hall RN, Shi M, Mourant R, Huang N, Strive T, Holmes EC (2019). The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus. Virus Evol. 5 (1), vez005.
  22. Chong R, Shi M, Grueber CE, Holmes EC, Hogg CJ, Belov K, Barrs VR. Fecal viral diversity of captive and wild Tasmanian devils characterized using virion-enriched metagenomics and meta-transcriptomics (2019). J. Virol. 00205-19.
  23. Harvey E, Rose K, Eden JS, Lo N, Abeyasuriya T, Shi M, Doggett SL, Holmes EC. Extensive Diversity of RNA Viruses in Australian Ticks (2019). J Virol. 93 (3), e01358-18.
  24. Wille M, Netter HJ, Littlejohn M, Yuen L, Shi M, Eden JS, Klaassen M, Holmes EC, Hurt AC. A Divergent Hepatitis D-Like Agent in Birds (2019). Viruses. 10(12), E720.
  25. Wille M, Eden JS, Shi M, Klaassen M, Hurt AC, Holmes EC. Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds (2018). Mol. Ecol. 27:5263-5278.
  26. Geoghegan JL, Di Giallonardo F, Cousins K, Shi M, Williamson JE, Holmes EC (2018). Hidden diversity and evolution of viruses in market fish. Virus Evol. 4:031.
  27. Zhang YZ, Wu WC, Shi M, Holmes EC (2018). The diversity, evolution and origins of vertebrate RNA viruses. Curr. Opin. Virol. 31:9-16.
  28. Aghazadeh M, Shi M, Pesavento PA, Durham AC, Polley T, Donahoe SL, Troyer RM, Barrs VR, Holmes EC, Beatty JA (2018). Transcriptome Analysis and In Situ Hybridization for FcaGHV1 in Feline Lymphoma. Viruses. 30.
  29. Russo AG, Eden JS, Enosi Tuipulotu D, Shi M, Selechnik D, Shine R, Rollins LA, Holmes EC, White PA (2018). Viral discovery in the invasive Australian cane toad (Rhinella marina) using metatranscriptomic and genomic approaches. J. Virol. 00768-18.
  30. Di Giallonardo F, Schlub TE, Shi M, Holmes EC (2017). Dinucleotide composition in animal RNA viruses is shaped more by virus family than by host species. J. Virol. 91:e02381-16.
  31. Paden CR, Yusof MFBM, Al Hammadi ZM, Queen K, Tao Y, …, Sasse J, Weber S, Shi M, Zhang J, Li Y, Pham H, Kim L, Hall AJ, Gerber SI, Al Hosani FI, Tong S, Al Muhairi SSM (2017). Zoonotic origin and transmission of Middle East respiratory syndrome coronavirus in the UAE. Zoonoses Public Health. 65(3):322-333.
  32. Yusof MF, Queen K, Eltahir YM, Paden CR, Al Hammadi ZMAH, Tao Y, Li Y, Khalafalla AI, Shi M, Zhang J, Mohamed MSAE, Ahmed MHAE, Azeez IA, Bensalah OK, Eldahab ZS, Al Hosani FI, Gerber SI, Hall AJ, Tong S, Al Muhairi SS (2017). Diversity of Middle East respiratory syndrome coronaviruses in 109 dromedary camels based on full genome sequencing, Abu Dhabi, United Arab Emirates. Emerg. Microbes & Infect. 6:e101.
  33. Pettersson JH, Shi M, Bohlin J, Eldholm V, Brynildsrud OB, Paulsen KM, Andreassen A, Holmes EC (2017). Characterizing the virome of Ixodes ricinus ticks from northern Europe. Sci. Rep. 7:10870.
  34. Eden J-S, Rose K, Ng J, Shi M, Wang Q, Sintchenko V, Holmes EC (2017). Francisella tularensis ssp holarctica in Ringtail Possums, Australia. Emerg. Infect. Diseases. 23:1198–1201.
  35. Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A (2017). A diverse range of novel RNA viruses in geographically distinct honeybee populations. J. Virol. 91:e00158-17.
  36. Velasco-Villa A, Mauldin MR, Shi M, Escobar LE, Gallardo-Romero NF, Damon I, Olson VA, Streicker DG, Emerson G (2017). The history of rabies in the Western Hemisphere. Antiviral Res. 146:221-232.
  37. Velasco-Villa A, Escobar LE, Sanchez A, Shi M, Streicker DG, Gallardo-Romero NF, Vargas-Pino F, Gutierrez-Cedillo V, Damon I, Emerson G (2017). Successful strategies implemented towards the elimination of canine rabies in the Western Hemisphere. Antiviral Res. 143:1-12.
  38. Chen LJ, Lin XD, Tian JH, Liao Y, Ying XH, Shao JW, Yu B, Guo JJ, Wang MR, Peng Y, Shi M, Holmes EC, Yang ZQ, Zhang YZ (2017). Diversity, evolution and population dynamics of avian influenza viruses circulating in the live poultry markets in China. Virology. 505:33-41.
  39. Li K, Lin XD, Huang KY, Zhang B, Shi M, Guo WP, Wang MR, Wang W, Xing JG, Li MH, Hong WS, Holmes EC, Zhang YZ (2016). Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans. Virology. 494:168-77.
  40. Afonso CL, Amarasinghe GK, Bányai K, Bào Y, Basler CF, …, Shi M, Smither SJ, Stenglein MD, Stone DM, …, Xiè JT, Yuen KY, Zhang YZ, Kuhn JH. Taxonomy of the order Mononegavirales: update 2016 (2016). Arch. Virol. 161:2351-60.
  41. Chen LJ, Lin XD, Guo WP, Tian JH, Wang W, Ying XH, Wang MR, Yu B, Yang ZQ, Shi M, Holmes EC, Zhang YZ (2016). Diversity and evolution of avian influenza viruses in live poultry markets, free range poultry and wild wetland birds in China. J. Gen. Virol. 97:844-54.
  42. Guo WP, Lin XD, Chen YP, Liu Q, Wang W, Wang CQ, Li MH, Sun XY, Shi M, Holmes EC, Zhang YZ (2015). Fourteen types of co-circulating recombinant enterovirus were associated with hand, foot, and mouth disease in children from Wenzhou, China. J. Clin. Virol. 70:29-38.
  43. Li K, Lin XD, Wang W, Shi M, Guo WP, Zhang XH, Xing JG, He JR, Wang K, Li MH, Cao JH, Jiang ML, Holmes EC, Zhang YZ (2015). Isolation and characterization of a novel arenavirus harbored by Rodents and Shrews in Zhejiang province, China. Virology. 476:37-42.
  44. Brar MS, Shi M, Murtaugh MP, Leung FC (2015). Evolutionary diversification of type 2 porcine reproductive and respiratory syndrome virus. J. Gen. Virol. 96:1570-1580.
  45. Wang W, Lin XD, Guo WP, Zhou RH, Wang MR, Wang CQ, Ge S, Mei SH, Li MH, Shi M, Holmes EC, Zhang YZ (2015). Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China. Virology. 474:19-27.

 

Before year 2015

 

  1. Qin XC#, Shi M#, Tian JH, Lin XD, Gao DY, He JR, Wang JB, Li CX, Kang YJ, Yu B, Zhou DJ, Xu J, Plyusnin A, Holmes EC, Zhang YZ (2014). A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proc Natl Acad Sci U S A. 111(18):6744-9.
  2. Shi M, Jagger BW, Wise HM, Digard P, Holmes EC, Taubenberger JK (2012). Evolutionary conservation of the PA-X open reading frame in segment 3 of influenza A virus. J. Virol. 86:12411-12413.
  3. Shi M, Holmes EC, Brar MS, Leung FC (2013). Recombination is associated with an outbreak of novel highly pathogenic porcine reproductive and respiratory syndrome viruses in China. J. Virol. 87:10904-10907.
  4. Shi M, Lemey P, Singh Brar M, Suchard MA, Murtaugh MP, Carman S, D'Allaire S, Delisle B, Lambert MÈ, Gagnon CA, Ge L, Qu Y, Yoo D, Holmes EC, Leung FC (2013). The spread of type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: a phylogeographic approach. Virology. 447:146-154.
  5. Shi M, Lam TT, Hon CC, Hui RK, Faaberg KS, Wennblom T, Murtaugh MP, Stadejek T, Leung FC (2010). Molecular epidemiology of PRRSV: a phylogenetic perspective. Virus Res. 154:7-17.
  6. Shi M, Lam TT, Hon CC, Murtaugh MP, Davies PR, Hui RK, Li J, Wong LT, Yip CW, Jiang JW, Leung FC (2010). Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses. J. Virol. 84:8700-11.
  7. Tao Y#, Shi M#, Conrardy C, Kuzmin IV, Recuenco S, Agwanda B, Alvarez DA, Ellison JA, Gilbert AT, Moran D, Niezgoda M, Lindblade KA, Holmes EC, Breiman RF, Rupprecht CE, Tong S (2013). Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. J. Gen. Virol. 94:738-748.
  8. Kang YJ, Diao XN, Zhao GY, Chen MH, Xiong Y, Shi M, Fu WM, Guo YJ, Pan B, Chen XP, Holmes EC, Gillespie JJ, Dumler SJ, Zhang YZ (2014). Extensive diversity of Rickettsiales bacteria in two species of ticks from China and the evolution of the Rickettsiales. BMC Evol. Biol. 14:167.
  9. Brar MS, Shi M, Hui RK, Leung FC (2014). Genomic evolution of porcine reproductive and respiratory syndrome virus (PRRSV) isolates revealed by deep sequencing. PLoS One. 9:e88807.
  10. Tong S, Zhu X, Li Y, Shi M, Zhang J, Bourgeois M, Yang H, Chen X, Recuenco S, Gomez J, Chen LM, Johnson A, Tao Y, Dreyfus C, Yu W, McBride R, Carney PJ, Gilbert AT, Chang J, Guo Z, Davis CT, Paulson JC, Stevens J, Rupprecht CE, Holmes EC, Wilson IA, Donis RO (2013). New world bats harbor diverse influenza A viruses. PLoS Pathog. 9:e1003657.
  11. Lam TT, Chong YL, Shi M, Hon CC, Li J, Martin DP, Tang JW, Mok CK, Shih SR, Yip CW, Jiang J, Hui RK, Pybus OG, Holmes EC, Leung FC (2013). Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infect. Genet. Evol. 18:367-378.
  12. Seetahal JF, Velasco-Villa A, Allicock OM, Adesiyun AA, Bissessar J, Amour K, Phillip-Hosein A, Marston DA, McElhinney LM, Shi M, Wharwood CA, Fooks AR, Carrington CV (2013). Evolutionary history and phylogeography of rabies viruses associated with outbreaks in Trinidad. PLoS Negl. Trop. Dis. 7:e2365.
  13. Kuzmin IV, Shi M, Orciari LA, Yager PA, Velasco-Villa A, Kuzmina NA, Streicker DG, Bergman DL, Rupprecht CE (2012). Molecular inferences suggest multiple host shifts of rabies viruses from bats to mesocarnivores in Arizona during 2001-2009. PLoS Pathog. 8:e1002786.
  14. Tao Y, Tang K, Shi M, Conrardy C, Li KS, Lau SK, Anderson LJ, Tong S (2012). Genomic characterization of seven distinct bat coronaviruses in Kenya. Virus Res.167:67-73.
  15. Lam TT, Hon CC, Lemey P, Pybus OG, Shi M, Tun HM, Li J, Jiang J, Holmes EC, Leung FC (2012). Phylodynamics of H5N1 avian influenza virus in Indonesia. Mol. Ecol. 2:3062-3077.
  16. Tong S, Li Y, Rivailler P, Conrardy C, Castillo DA, Chen LM, Recuenco S, Ellison JA, Davis CT, York IA, Turmelle AS, Moran D, Rogers S, Shi M, Tao Y, Weil MR, Tang K, Rowe LA, Sammons S, Xu X, Frace M, Lindblade KA, Cox NJ, Anderson LJ, Rupprecht CE, Donis RO (2012). A distinct lineage of influenza A virus from bats. Proc. Natl. Acad. Sci. USA 109:4269-4274.
  17. Van Doorsselaere J, Brar MS, Shi M, Karniychuk U, Leung FC, Nauwynck HJ (2012). Complete genome characterization of a East European Type 1 subtype 3 porcine reproductive and respiratory syndrome virus. Virus Genes. 44:51-54.
  18. Cai S, Li J, Wong MT, Jiao P, Fan H, Liu D, Liao M, Jiang J, Shi M, Lam TT, Ren T, Leung FC (2011). Genetic characterization and evolutionary analysis of 4 Newcastle disease virus isolate full genomes from waterbirds in South China during 2003-2007. Vet. Microbiol. 152:46-54.
  19. Brar MS, Shi M, Ge L, Carman S, Murtaugh MP, Leung FC (2011). Porcine reproductive and respiratory syndrome virus in Ontario, Canada 1999 to 2010: genetic diversity and restriction fragment length polymorphisms. J. Gen. Virol. 92:1391-1397.
  20. Tun HM, Shi M, Wong CL, Ayudhya SN, Amonsin A, Thanawonguwech R, Leung FC (2011). Genetic diversity and multiple introductions of porcine reproductive and respiratory syndrome viruses in Thailand. Virol. J. 8:164.
  21. Aréchiga-Ceballos N, Velasco-Villa A, Shi M, Flores-Chávez S, Barrón B, Cuevas-Domínguez E, González-Origel A, Aguilar-Setién A (2010). New rabies virus variant found during an epizootic in white-nosed coatis from the Yucatan Peninsula. Epidemiol. Infect.15:1-4.
  22. Yip CW, Hon CC, Shi M, Lam TT, Chow KY, Zeng F, Leung FC (2009). Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses. Infect. Genet. Evol. 9:1185-1196.
  23. Hon CC, Lam TT, Yip CW, Wong RT, Shi M, Jiang J, Zeng F, Leung FC (2008). Phylogenetic evidence for homologous recombination within the family Birnaviridae. J. Gen. Virol. 89:3156-64.