Dr Mang Shi

Postdoctoral Research Associate
School of Life and Environmental Sciences

Member of the Charles Perkins Centre

D17 - Charles Perkins Centre
The University of Sydney


Website Level 5 West Room 57, D17 - Charles Perkins Centre

Research interests

  • Macroevolution of RNA viruses
  • Pathogen discovery for clinical and environmental samples
  • Metatranscriptomics and its application in virome studies

Selected grants

2017

  • Centre for Pathogen Discovery; Holmes E, Sintchenko V, Lo N, Shi M, Eden J, Hudson B; DVC Research/Sydney Research Excellence Initiative 2020 (SREI).

Selected publications

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Journals

  • Shi, M., Zhang, Y., Holmes, E. (2018). Meta-transcriptomics and the evolutionary biology of RNA viruses. Virus Research, 243, 83-90. [More Information]
  • Remnant, E., Shi, M., Buchmann, G., Blacquiere, T., Holmes, E., Beekman, M., Ashe, A. (2017). A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. Journal of Virology, 91(16), e00158-17. [More Information]
  • Pettersson, J., Shi, M., Bohlin, J., Eldholm, V., Brynildsrud, O., Paulsen, K., Andreassen, A., Holmes, E. (2017). Characterizing the virome of Ixodes ricinus ticks from northern Europe. Scientific Reports, 7(1), 1-6. [More Information]
  • Di Giallonardo, F., Schlub, T., Shi, M., Holmes, E. (2017). Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species. Journal of Virology, 91(8), 1-15. [More Information]
  • Chen, L., Lin, X., Tian, J., Liao, Y., Ying, X., Shao, J., Yu, B., Guo, J., Wang, M., Peng, Y., Shi, M., Holmes, E., et al (2017). Diversity, evolution and population dynamics of avian influenza viruses in the live poultry markets in China. Virology, 505, 33-41. [More Information]
  • Eden, J., Rose, K., Ng, J., Shi, M., Wang, Q., Sintchenko, V., Holmes, E. (2017). Francisella tularensis subsp. holarctica in Ringtail Possums, Australia. Emerging Infectious Diseases, 23(7), 1198-1201. [More Information]
  • Shi, M., Neville, P., Nicholson, J., Eden, J., Imrie, A., Holmes, E. (2017). High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia. Journal of Virology, 91(17), e00680-17. [More Information]
  • Velasco-Villa, A., Escobar, L., Sanchez, A., Shi, M., Streicker, D., Gallardo-Romero, N., 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 Research, 143, 1-12. [More Information]
  • Tao, Y., Shi, M., Chommanard, C., Queen, K., Markotter, W., Kuzmin, I., Holmes, E., Tong, S. (2017). Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. Journal of Virology, 91(5), e01953-16. [More Information]
  • Velasco-Villa, A., Mauldin, M., Shi, M., Escobar, L., Gallardo-Romero, N., Damon, I., Olson, V., Streicker, D., Emerson, G. (2017). The history of rabies in the Western Hemisphere. Antiviral Research, 146, 221-232. [More Information]
  • Shi, M., Lin, X., Vasilakis, N., Tian, J., Li, C., Chen, L., Eastwood, G., Diao, X., Chen, M., Chen, X., Holmes, E., et al (2016). Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. Journal of Virology, 90(2), 659-669. [More Information]
  • Chen, L., Lin, X., Guo, W., Tian, J., Wang, W., Ying, X., Wang, M., Yu, B., Yang, Z., Shi, M., Holmes, E., et al (2016). Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China. Journal of General Virology, 97(4), 844-854. [More Information]
  • Li, K., Lin, X., Huang, K., Zhang, B., Shi, M., Guo, W., Wang, M., Wang, W., Xing, J., Li, M., Holmes, E., et al (2016). Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans. Virology, 494, 168-177. [More Information]
  • Shi, M., Lin, X., Tian, J., Chen, L., Chen, X., Li, C., Qin, X., Li, J., Cao, J., Eden, J., Buchmann, J., Holmes, E., et al (2016). Redefining the invertebrate RNA virosphere. Nature, 540(7634), 539-543. [More Information]
  • Wang, W., Lin, X., Guo, W., Zhou, R., Wang, M., Wang, C., Ge, S., Mei, S., Li, M., Shi, M., Holmes, E., et al (2015). Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China. Virology, 474, 19-27. [More Information]
  • Brar, M., Shi, M., Murtaugh, M., Leung, F. (2015). Evolutionary diversification of type 2 porcine reproductive and respiratory syndrome virus. Journal of General Virology, 96(7), 1570-1580. [More Information]
  • Guo, W., Lin, X., Chen, Y., Liu, Q., Wang, W., Wang, C., Li, M., Sun, X., Shi, M., Holmes, E., et al (2015). Fourteen types of co-circulating recombinant enterovirus wereassociated with hand, foot, and mouth disease in children fromWenzhou, China. Journal Of Clinical Virology, 70(1), 29-38. [More Information]
  • Ye, C., Zhang, Q., Tian, Z., Zheng, H., Zhao, K., Liu, F., Guo, J., Tong, W., Jiang, C., Wang, S., Shi, M., et al (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. [More Information]
  • Zhao, K., Ye, C., Chang, X., Jiang, C., Wang, S., Cai, X., Tong, G., Tian, Z., Shi, M., An, T. (2015). Importation and recombination are responsible for the latest emergence of highly pathogenic porcine reproductive and respiratory syndrome virus in China. Journal of Virology, 89(20), 10712-10716. [More Information]
  • Li, C., Shi, M., Tian, J., Lin, X., Kang, Y., Chen, L., Qin, X., Xu, J., Holmes, E., Zhang, Y. (2015). Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLife, 2015 (4), 1-34. [More Information]
  • Qin, X., Shi, M., Tian, J., Lin, X., Gao, D., He, J., Wang, J., Li, C., Kang, Y., Yu, B., Holmes, E., et al (2014). A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 111(18), 6744-6749. [More Information]
  • Brar, M., Shi, M., Hui, R., Leung, F. (2014). Genomic evolution of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) isolates revealed by deep sequencing. PloS One, 9(4), 1-12. [More Information]
  • Devault, A., Golding, G., Waglechner, N., Enk, J., Kuch, M., Tien, J., Shi, M., Fisman, D., Dhody, A., Forrest, S., Holmes, E., et al (2014). Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849. The New England Journal of Medicine, 370(4), 334-340. [More Information]
  • Tao, Y., Shi, M., Conrardy, C., Kuzmin, I., Recuenco, S., Agwanda, B., Alvarez, D., Ellison, J., Gilbert, A., Moran, D., Holmes, E., et al (2013). Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. Journal of General Virology, 94(Part 4), 738-748. [More Information]
  • Tong, S., Zhu, X., Li, Y., Shi, M., Zhang, J., Bourgeois, M., Yang, H., Chen, X., Recuenco, S., Gomez, J., Holmes, E., et al (2013). New World Bats Harbor Diverse Influenza A Viruses. PLoS Pathogens, 9(10), 1-12. [More Information]
  • Shi, M., Holmes, E., Brar, M., Leung, F. (2013). Recombination Is Associated with an Outbreak of Novel Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Viruses in China. Journal of Virology, 87(19), 10904-10907. [More Information]
  • Lam, T., Chong, Y., Shi, M., Hon, C., Li, J., Martin, D., Tang, J., Mok, C., Shih, S., Yip, C., Holmes, E., et al (2013). Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infection, Genetics and Evolution, 18, 367-378. [More Information]
  • Shi, M., Lemey, P., Brar, M., Suchard, M., Murtaugh, M., Carman, S., D'Allaire, S., Delisle, B., Lambert, M., Gagnon, C., Qu, Y., Holmes, E., et al (2013). The spread of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: A phylogeographic approach. Virology, 447(1-2), 146-154. [More Information]

2018

  • Shi, M., Zhang, Y., Holmes, E. (2018). Meta-transcriptomics and the evolutionary biology of RNA viruses. Virus Research, 243, 83-90. [More Information]

2017

  • Remnant, E., Shi, M., Buchmann, G., Blacquiere, T., Holmes, E., Beekman, M., Ashe, A. (2017). A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. Journal of Virology, 91(16), e00158-17. [More Information]
  • Pettersson, J., Shi, M., Bohlin, J., Eldholm, V., Brynildsrud, O., Paulsen, K., Andreassen, A., Holmes, E. (2017). Characterizing the virome of Ixodes ricinus ticks from northern Europe. Scientific Reports, 7(1), 1-6. [More Information]
  • Di Giallonardo, F., Schlub, T., Shi, M., Holmes, E. (2017). Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species. Journal of Virology, 91(8), 1-15. [More Information]
  • Chen, L., Lin, X., Tian, J., Liao, Y., Ying, X., Shao, J., Yu, B., Guo, J., Wang, M., Peng, Y., Shi, M., Holmes, E., et al (2017). Diversity, evolution and population dynamics of avian influenza viruses in the live poultry markets in China. Virology, 505, 33-41. [More Information]
  • Eden, J., Rose, K., Ng, J., Shi, M., Wang, Q., Sintchenko, V., Holmes, E. (2017). Francisella tularensis subsp. holarctica in Ringtail Possums, Australia. Emerging Infectious Diseases, 23(7), 1198-1201. [More Information]
  • Shi, M., Neville, P., Nicholson, J., Eden, J., Imrie, A., Holmes, E. (2017). High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia. Journal of Virology, 91(17), e00680-17. [More Information]
  • Velasco-Villa, A., Escobar, L., Sanchez, A., Shi, M., Streicker, D., Gallardo-Romero, N., 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 Research, 143, 1-12. [More Information]
  • Tao, Y., Shi, M., Chommanard, C., Queen, K., Markotter, W., Kuzmin, I., Holmes, E., Tong, S. (2017). Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. Journal of Virology, 91(5), e01953-16. [More Information]
  • Velasco-Villa, A., Mauldin, M., Shi, M., Escobar, L., Gallardo-Romero, N., Damon, I., Olson, V., Streicker, D., Emerson, G. (2017). The history of rabies in the Western Hemisphere. Antiviral Research, 146, 221-232. [More Information]

2016

  • Shi, M., Lin, X., Vasilakis, N., Tian, J., Li, C., Chen, L., Eastwood, G., Diao, X., Chen, M., Chen, X., Holmes, E., et al (2016). Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. Journal of Virology, 90(2), 659-669. [More Information]
  • Chen, L., Lin, X., Guo, W., Tian, J., Wang, W., Ying, X., Wang, M., Yu, B., Yang, Z., Shi, M., Holmes, E., et al (2016). Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China. Journal of General Virology, 97(4), 844-854. [More Information]
  • Li, K., Lin, X., Huang, K., Zhang, B., Shi, M., Guo, W., Wang, M., Wang, W., Xing, J., Li, M., Holmes, E., et al (2016). Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans. Virology, 494, 168-177. [More Information]
  • Shi, M., Lin, X., Tian, J., Chen, L., Chen, X., Li, C., Qin, X., Li, J., Cao, J., Eden, J., Buchmann, J., Holmes, E., et al (2016). Redefining the invertebrate RNA virosphere. Nature, 540(7634), 539-543. [More Information]

2015

  • Wang, W., Lin, X., Guo, W., Zhou, R., Wang, M., Wang, C., Ge, S., Mei, S., Li, M., Shi, M., Holmes, E., et al (2015). Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China. Virology, 474, 19-27. [More Information]
  • Brar, M., Shi, M., Murtaugh, M., Leung, F. (2015). Evolutionary diversification of type 2 porcine reproductive and respiratory syndrome virus. Journal of General Virology, 96(7), 1570-1580. [More Information]
  • Guo, W., Lin, X., Chen, Y., Liu, Q., Wang, W., Wang, C., Li, M., Sun, X., Shi, M., Holmes, E., et al (2015). Fourteen types of co-circulating recombinant enterovirus wereassociated with hand, foot, and mouth disease in children fromWenzhou, China. Journal Of Clinical Virology, 70(1), 29-38. [More Information]
  • Ye, C., Zhang, Q., Tian, Z., Zheng, H., Zhao, K., Liu, F., Guo, J., Tong, W., Jiang, C., Wang, S., Shi, M., et al (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. [More Information]
  • Zhao, K., Ye, C., Chang, X., Jiang, C., Wang, S., Cai, X., Tong, G., Tian, Z., Shi, M., An, T. (2015). Importation and recombination are responsible for the latest emergence of highly pathogenic porcine reproductive and respiratory syndrome virus in China. Journal of Virology, 89(20), 10712-10716. [More Information]
  • Li, C., Shi, M., Tian, J., Lin, X., Kang, Y., Chen, L., Qin, X., Xu, J., Holmes, E., Zhang, Y. (2015). Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLife, 2015 (4), 1-34. [More Information]

2014

  • Qin, X., Shi, M., Tian, J., Lin, X., Gao, D., He, J., Wang, J., Li, C., Kang, Y., Yu, B., Holmes, E., et al (2014). A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 111(18), 6744-6749. [More Information]
  • Brar, M., Shi, M., Hui, R., Leung, F. (2014). Genomic evolution of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) isolates revealed by deep sequencing. PloS One, 9(4), 1-12. [More Information]
  • Devault, A., Golding, G., Waglechner, N., Enk, J., Kuch, M., Tien, J., Shi, M., Fisman, D., Dhody, A., Forrest, S., Holmes, E., et al (2014). Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849. The New England Journal of Medicine, 370(4), 334-340. [More Information]

2013

  • Tao, Y., Shi, M., Conrardy, C., Kuzmin, I., Recuenco, S., Agwanda, B., Alvarez, D., Ellison, J., Gilbert, A., Moran, D., Holmes, E., et al (2013). Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. Journal of General Virology, 94(Part 4), 738-748. [More Information]
  • Tong, S., Zhu, X., Li, Y., Shi, M., Zhang, J., Bourgeois, M., Yang, H., Chen, X., Recuenco, S., Gomez, J., Holmes, E., et al (2013). New World Bats Harbor Diverse Influenza A Viruses. PLoS Pathogens, 9(10), 1-12. [More Information]
  • Shi, M., Holmes, E., Brar, M., Leung, F. (2013). Recombination Is Associated with an Outbreak of Novel Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Viruses in China. Journal of Virology, 87(19), 10904-10907. [More Information]
  • Lam, T., Chong, Y., Shi, M., Hon, C., Li, J., Martin, D., Tang, J., Mok, C., Shih, S., Yip, C., Holmes, E., et al (2013). Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infection, Genetics and Evolution, 18, 367-378. [More Information]
  • Shi, M., Lemey, P., Brar, M., Suchard, M., Murtaugh, M., Carman, S., D'Allaire, S., Delisle, B., Lambert, M., Gagnon, C., Qu, Y., Holmes, E., et al (2013). The spread of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: A phylogeographic approach. Virology, 447(1-2), 146-154. [More Information]

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