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SCIENCE CHINA Life Sciences, Volume 60, Issue 12: 1317-1330(2017) https://doi.org/10.1007/s11427-017-9211-0

Pathogen genomic surveillance elucidates the origins, transmission and evolution of emerging viral agents in China

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  • ReceivedOct 20, 2017
  • AcceptedNov 1, 2017
  • PublishedNov 28, 2017

Abstract

In the past twenty years, numerous novel zoonotic viral agents with pandemic potential have emerged in China, such as the severe acute respiratory syndrome (SARS) coronavirus and, more recently, the avian-origin influenza A/H7N9 virus, which have caused outbreaks among humans with high morbidity and mortality. In addition, several emerging and re-emerging viral pathogens have also been imported into China from travelers, e.g. the Middle East respiratory syndrome (MERS) coronavirus and Zika virus (ZIKV). Herein, we review these emerging viral pathogens in China and focus on how surveillance by pathogen genomics has been employed to discover and annotate novel pathogenic agents, identify natural reservoirs, monitor the transmission events and delineate their evolution and adaption to the human host. We also highlight the application of genomic sequencing in the recent Ebola epidemics in Western Africa. In summary, genomic sequencing has become a standard research tool in the field of emerging infectious diseases which has been proven invaluable in containing these viral infections and reducing burden of disease in humans and animals. Genomic surveillance of pathogenic agents will serve as a key epidemiological and research tool in the modern era of precision infectious diseases and in the future studies of virosphere.


Funded by

China Ministry of Science and Technology(MOST)

Taishan Scholars program of Shandong province(ts201511056 to Weifeng Shi)


Acknowledgment

We were grateful to Dr. Michael J. Carr (Hokkaido University) for review of the manuscript. This work was supported by the China Ministry of Science and Technology (MOST) Key Research and Development Program (2017ZX10104001) and the Taishan Scholars program of Shandong province (ts201511056 to Weifeng Shi).


Interest statement

The author(s) declare that they have no conflict of interest.


References

[1] Aguirre de Cárcer D., López-Bueno A., Pearce D.A., Alcamí A.. Biodiversity and distribution of polar freshwater DNA viruses. Sci Adv, 2015, 1: e1400127-e1400127 CrossRef PubMed ADS Google Scholar

[2] Amimo J.O., El Zowalaty M.E., Githae D., Wamalwa M., Djikeng A., Nasrallah G.K.. Metagenomic analysis demonstrates the diversity of the fecal virome in asymptomatic pigs in East Africa. Arch Virol, 2016, 161: 887-897 CrossRef PubMed Google Scholar

[3] Anderson N.G., Gerin J.L., Anderson N.L.. Global screening for human viral pathogens. Emerg Infect Dis, 2003, 9: 768-773 CrossRef PubMed Google Scholar

[4] Ash C., Hurtley S., Lavine M., Simpson S.. Paradigms in the virosphere. Science, 2006, 312: 869-869 CrossRef Google Scholar

[5] Baize, S., Pannetier, D., Oestereich, L., Rieger, T., Koivogui, L., Magassouba, N., Soropogui, B., Sow, M.S., Keita, S., De Clerck, H., Tiffany, A., Dominguez, G., Loua, M., Traore, A., Kolie, M., Malano, E.R., Heleze, E., Bocquin, A., Mely, S., Raoul, H., Caro, V., Cadar, D., Gabriel, M., Pahlmann, M., Tappe, D., Schmidt-Chanasit, J., Impouma, B., Diallo, A.K., Formenty, P., Van Herp, M., and Gunther, S. (2014). Emergence of Zaire Ebola virus disease in Guinea. N Engl J Med 371, 1418–1425. Google Scholar

[6] Bao C., Cui L., Zhou M., Hong L., Gao G.F., Wang H.. Live-animal markets and influenza A (H7N9) virus infection. N Engl J Med, 2013, 368: 2337-2339 CrossRef PubMed Google Scholar

[7] Bellas C.M., Anesio A.M., Barker G.. Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions. Front Microbiol, 2015, 6: 656 CrossRef Google Scholar

[8] Bi Y., Chen Q., Wang Q., Chen J., Jin T., Wong G., Quan C., Liu J., Wu J., Yin R., Zhao L., Li M., Ding Z., Zou R., Xu W., Li H., Wang H., Tian K., Fu G., Huang Y., Shestopalov A., Li S., Xu B., Yu H., Luo T., Lu L., Xu X., Luo Y., Liu Y., Shi W., Liu D., Gao G.F.. Genesis, evolution and prevalence of H5N6 avian influenza viruses in China. Cell Host Microbe, 2016a, 20: 810-821 CrossRef PubMed Google Scholar

[9] Bi Y., Liu H., Xiong C., Di Liu C., Shi W., Li M., Liu S., Chen J., Chen G., Li Y., Yang G., Lei Y., Xiong Y., Lei F., Wang H., Chen Q., Chen J., Gao G.F.. Novel avian influenza A (H5N6) viruses isolated in migratory waterfowl before the first human case reported in China, 2014. Sci Rep, 2016b, 6: 29888 CrossRef PubMed ADS Google Scholar

[10] Bi Y., Mei K., Shi W., Liu D., Yu X., Gao Z., Zhao L., Gao G.F., Chen J., Chen Q.. Two novel reassortants of avian influenza A (H5N6) virus in China. J Gen Virol, 2015, 96: 975-981 CrossRef PubMed Google Scholar

[11] Bodewes R., Ruiz-Gonzalez A., Schapendonk C.M., van den Brand J.M., Osterhaus A.D., Smits S.L.. Viral metagenomic analysis of feces of wild small carnivores. Virol J, 2014, 11: 89 CrossRef Google Scholar

[12] Bolling B.G., Weaver S.C., Tesh R.B., Vasilakis N.. Insect-specific virus discovery: significance for the Arbovirus community. Viruses, 2015, 7: 4911-4928 CrossRef PubMed Google Scholar

[13] Boonham N., Kreuze J., Winter S., van der Vlugt R., Bergervoet J., Tomlinson J., Mumford R.. Methods in virus diagnostics: from ELISA to next generation sequencing. Virus Res, 2014, 186: 20-31 CrossRef PubMed Google Scholar

[14] Boonham N., Tomlinson J., Mumford R.. Microarrays for rapid identification of plant viruses. Annu Rev Phytopathol, 2007, 45: 307-328 CrossRef Google Scholar

[15] Breiman R.F., Evans M.R., Preiser W., Maguire J., Schnur A., Li A., Bekedam H., MacKenzie J.S.. Role of China in the quest to define and control severe acute respiratory syndrome. Emerg Infect Dis, 2003, 9: 1037-1041 CrossRef PubMed Google Scholar

[16] Brum J.R., Ignacio-Espinoza J.C., Roux S., Doulcier G., Acinas S.G., Alberti A., Chaffron S., Cruaud C., de Vargas C., Gasol J.M., Gorsky G., Gregory A.C., Guidi L., Hingamp P., Iudicone D., Not F., Ogata H., Pesant S., Poulos B.T., Schwenck S.M., Speich S., Dimier C., Kandels-Lewis S., Picheral M., Searson S., Searson S., Bork P., Bowler C., Sunagawa S., Wincker P., Karsenti E., Sullivan M.B.. Patterns and ecological drivers of ocean viral communities. Science, 2015, 348: 1261498-1261498 CrossRef PubMed Google Scholar

[17] Calvet G., Aguiar R.S., Melo A.S.O., Sampaio S.A., de Filippis I., Fabri A., Araujo E.S.M., de Sequeira P.C., de Mendonça M.C.L., de Oliveira L., Tschoeke D.A., Schrago C.G., Thompson F.L., Brasil P., dos Santos F.B., Nogueira R.M.R., Tanuri A., de Filippis A.M.B.. Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. Lancet Infect Dis, 2016, 16: 653-660 CrossRef Google Scholar

[18] Chan-yeung M., Xu R.H.. SARS: epidemiology. Respirology, 2003, 8: S9-S14 CrossRef Google Scholar

[19] Check Hayden E.. Latest Ebola data rule out rapid mutation. Nature, 2015, : in press doi: 10.1038/nature.2015.17554 CrossRef Google Scholar

[20] Chen H.Y., Yuan H., Gao R., Zhang J., Wang D., Xiong Y., Fan G.Y., Yang F., Li X., Zhou J., Zou S., Yang L., Chen T., Dong L., Bo H., Zhao X., Zhang Y., Lan Y., Bai T., Dong J., Li Q., Wang S.W., Zhang Y.P., Li H., Gong T., Shi Y., Ni X., Li J., Zhou J., Fan J., Wu J., Zhou X., Hu M., Wan J., Yang W.Z., Li D.X., Wu G., Feng Z.J., Gao G.F., Wang Y., Jin Q., Liu M., Shu Y.. Clinical and epidemiological characteristics of a fatal case of avian influenza A H10N8 virus infection: a descriptive study. Lancet, 2014, 383: 714-721 CrossRef Google Scholar

[21] Chen Y., Liang W., Yang S., Wu N., Gao H., Sheng J., Yao H., Wo J., Fang Q., Cui D., Li Y., Yao X., Zhang Y., Wu H., Zheng S., Diao H., Xia S., Zhang Y., Chan K.H., Tsoi H.W., Teng J.L.L., Song W., Wang P., Lau S.Y., Zheng M., Chan J.F.W., To K.K.W., Chen H., Li L., Yuen K.Y.. Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome. Lancet, 2013, 381: 1916-1925 CrossRef Google Scholar

[22] Chowell G., Abdirizak F., Lee S., Lee J., Jung E., Nishiura H., Viboud C.. Transmission characteristics of MERS and SARS in the healthcare setting: a comparative study. BMC Med, 2015, 13: 210 CrossRef PubMed Google Scholar

[23] Cui L., Liu D., Shi W., Pan J., Qi X., Li X., Guo X., Zhou M., Li W., Li J., Haywood J., Xiao H., Yu X., Pu X., Wu Y., Yu H., Zhao K., Zhu Y., Wu B., Jin T., Shi Z., Tang F., Zhu F., Sun Q., Wu L., Yang R., Yan J., Lei F., Zhu B., Liu W., Ma J., Wang H., Gao G.F.. Dynamic reassortments and genetic heterogeneity of the human-infecting influenza A (H7N9) virus. Nat Commun, 2014, 5: 3142 CrossRef PubMed ADS Google Scholar

[24] Daubney, R.H.J., Hudson, J.R., and Garnham, P.C. (1931). Enzootic hepatitis or Rift Valley Fever. An undescribed virus disease of sheep cattle and man from East Africa. J Pathol 34, 545–579. Google Scholar

[25] del Rio C., Mehta A.K., Lyon Iii G.M., Guarner J.. Ebola hemorrhagic fever in 2014: the tale of an evolving epidemic. Ann Intern Med, 2014, 161: 746-748 CrossRef PubMed Google Scholar

[26] Deng Y.Q., Zhao H., Li X.F., Zhang N.N., Liu Z.Y., Jiang T., Gu D.Y., Shi L., He J.A., Wang H.J., Sun Z.Z., Ye Q., Xie D.Y., Cao W.C., Qin C.F.. Isolation, identification and genomic characterization of the Asian lineage Zika virus imported to China. Sci China Life Sci, 2016, 59: 428-430 CrossRef PubMed Google Scholar

[27] Dick G.W.A., Kitchen S.F., Haddow A.J.. Zika Virus (I). Isolations and serological specificity. Trans R Soc Trop Med Hyg, 1952, 46: 509-520 CrossRef Google Scholar

[28] Enserink M.. SARS in CHINA: China’s missed chance. Science, 2003, 301: 294-296 CrossRef PubMed Google Scholar

[29] Faria N.R., Azevedo R.S.S., Kraemer M.U.G., Souza R., Cunha M.S., Hill S.C., Thézé J., Bonsall M.B., Bowden T.A., Rissanen I., Rocco I.M., Nogueira J.S., Maeda A.Y., Vasami F.G.S., Macedo F.L.L., Suzuki A., Rodrigues S.G., Cruz A.C.R., Nunes B.T., Medeiros D.B.A., Rodrigues D.S.G., Queiroz A.L.N., da Silva E.V.P., Henriques D.F., da Rosa E.S.T., de Oliveira C.S., Martins L.C., Vasconcelos H.B., Casseb L.M.N., Simith D.B., Messina J.P., Abade L., Lourenço J., Alcantara L.C.J., de Lima M.M., Giovanetti M., Hay S.I., de Oliveira R.S., Lemos P.S., de Oliveira L.F., de Lima C.P.S., da Silva S.P., de Vasconcelos J.M., Franco L., Cardoso J.F., Vianez-Júnior J.L.S.G., Mir D., Bello G., Delatorre E., Khan K., Creatore M., Coelho G.E., de Oliveira W.K., Tesh R., Pybus O.G., Nunes M.R.T., Vasconcelos P.F.C.. Zika virus in the Americas: early epidemiological and genetic findings. Science, 2016, 352: 345-349 CrossRef PubMed ADS Google Scholar

[30] Gao G.F.. Influenza and the live poultry trade. Science, 2014, 344: 235-235 CrossRef PubMed ADS Google Scholar

[31] Gao, R., Cao, B., Hu, Y., Feng, Z., Wang, D., Hu, W., Chen, J., Jie, Z., Qiu, H., Xu, K., Xu, X., Lu, H., Zhu, W., Gao, Z., Xiang, N., Shen, Y., He, Z., Gu, Y., Zhang, Z., Yang, Y., Zhao, X., Zhou, L., Li, X., Zou, S., Zhang, Y., Li, X., Yang, L., Guo, J., Dong, J., Li, Q., Dong, L., Zhu, Y., Bai, T., Wang, S., Hao, P., Yang, W., Zhang, Y., Han, J., Yu, H., Li, D., Gao, G.F., Wu, G., Wang, Y., Yuan, Z., and Shu, Y. (2013). Human infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med 368, 1888–1897. Google Scholar

[32] Gire S.K., Goba A., Andersen K.G., Sealfon R.S.G., Park D.J., Kanneh L., Jalloh S., Momoh M., Fullah M., Dudas G., Wohl S., Moses L.M., Yozwiak N.L., Winnicki S., Matranga C.B., Malboeuf C.M., Qu J., Gladden A.D., Schaffner S.F., Yang X., Jiang P.P., Nekoui M., Colubri A., Coomber M.R., Fonnie M., Moigboi A., Gbakie M., Kamara F.K., Tucker V., Konuwa E., Saffa S., Sellu J., Jalloh A.A., Kovoma A., Koninga J., Mustapha I., Kargbo K., Foday M., Yillah M., Kanneh F., Robert W., Massally J.L.B., Chapman S.B., Bochicchio J., Murphy C., Nusbaum C., Young S., Birren B.W., Grant D.S., Scheiffelin J.S., Lander E.S., Happi C., Gevao S.M., Gnirke A., Rambaut A., Garry R.F., Khan S.H., Sabeti P.C.. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science, 2014, 345: 1369-1372 CrossRef PubMed ADS Google Scholar

[33] Guan W.D., Mok C.K.P., Chen Z.L., Feng L.Q., Li Z.T., Huang J.C., Ke C.W., Deng X., Ling Y., Wu S.G., Niu X.F., Perera R.A., Da Xu Y., Zhao J., Zhang L.Q., Li Y.M., Chen R.C., Peiris M., Chen L., Zhong N.S.. Characteristics of traveler with middle east respiratory syndrome, China, 2015. Emerg Infect Dis, 2015, 21: 2278-2280 CrossRef PubMed Google Scholar

[34] Guan Y., Zheng B.J., He Y.Q., Liu X.L., Zhuang Z.X., Cheung C.L., Luo S.W., Li P.H., Zhang L.J., Guan Y.J., Butt K.M., Wong K.L., Chan K.W., Lim W., Shortridge K.F., Yuen K.Y., Peiris J.S.M., Poon L.L.M.. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science, 2003, 302: 276-278 CrossRef PubMed ADS Google Scholar

[35] Haagmans B.L., Andeweg A.C., Osterhaus A.D.M.E.. The application of genomics to emerging zoonotic viral diseases. PLoS Pathog, 2009, 5: e1000557 CrossRef PubMed Google Scholar

[36] Haddow A.D., Schuh A.J., Yasuda C.Y., Kasper M.R., Heang V., Huy R., Guzman H., Tesh R.B., Weaver S.C.. Genetic characterization of Zika virus strains: geographic expansion of the Asian lineage. PLoS Negl Trop Dis, 2012, 6: e1477 CrossRef PubMed Google Scholar

[37] Hannigan G.D., Zheng Q., Meisel J.S., Minot S.S., Bushman F.D., Grice E.A.. Evolutionary and functional implications of hypervariable loci within the skin virome. PeerJ, 2017, 5: e2959 CrossRef PubMed Google Scholar

[38] Hayes E.B.. Zika virus outside Africa. Emerg Infect Dis, 2009, 15: 1347-1350 CrossRef PubMed Google Scholar

[39] He J.F., Peng G.W., Min J., Yu D.W., Liang W.J., Zhang S.Y., Xu R.H., Zheng H.Y., Wu X.W., Xu J., Wang Z.H., Fang L., Zhang X., Li H., Yan X.G., Lu J.H., Hu Z.H., Huang J.C., Wan Z.Y., Hou J.L., Lin J.Y., Song H.D., Wang S.Y., Zhou X.J., Zhang G.W., Gu B.W., Zheng H.J., Zhang X.L., He M., Zheng K., Wang B.F., Fu G., Wang X.N., Chen S.J., Chen Z., Hao P., Tang H., Ren S.X., Zhong Y., Guo Z.M., Liu Q., Miao Y.G., Kong X.Y., He W.Z., Li Y.X., Wu C.I., Zhao G.P., Chiu R.W.K., Chim S.S.C., Tong Y., Chan P.K.S., Tam J.S., Lo Y.M.D.. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science, 2004, 303: 1666-1669 CrossRef PubMed ADS Google Scholar

[40] Holmes, E.C. (2007). Viral evolution in the genomic age. PLoS Biol 5, e278. Google Scholar

[41] Holmes E.C., Dudas G., Rambaut A., Andersen K.G.. The evolution of Ebola virus: insights from the 2013–2016 epidemic. Nature, 2016, 538: 193-200 CrossRef PubMed ADS Google Scholar

[42] Hsu, B.M., Wu, S.F., Huang, S.W., Tseng, Y.J., Ji, D.D., Chen, J.S., and Shih, F.C. (2010). Differentiation and identification of Shigella spp. and enteroinvasive Escherichia coli in environmental waters by a molecular method and biochemical test. Water Res 44, 949–955. Google Scholar

[43] Jiang H., Wu P., Uyeki T.M., He J., Deng Z., Xu W., Lv Q., Zhang J., Wu Y., Tsang T.K., Kang M., Zheng J., Wang L., Yang B., Qin Y., Feng L., Fang V.J., Gao G.F., Leung G.M., Yu H., Cowling B.J.. Preliminary epidemiologic assessment of human infections with highly pathogenic avian influenza A(H5N6) virus, China. Clin Infect Dis, 2017, 65: 383-388 CrossRef PubMed Google Scholar

[44] Jiang X.Q., Zhang Z.J., Zhuang D.M., Carr M.J., Zhang R.L., Lv Q., Shi W.F.. Non-coding regions of the Ebola virus genome contain indispensable phylogenetic and evolutionary information. Sci China Life Sci, 2015, 58: 682-686 CrossRef PubMed Google Scholar

[45] Jiao P., Cao L., Yuan R., Wei L., Song Y., Shen D., Gong L., Luo K., Ren T., Liao M.. Complete genome sequence of an H10N8 avian influenza virus isolated from a live bird market in southern China. J Virol, 2012, 86: 7716-7716 CrossRef PubMed Google Scholar

[46] Ke C., Mok C.K.P., Zhu W., Zhou H., He J., Guan W., Wu J., Song W., Wang D., Liu J., Lin Q., Chu D.K.W., Yang L., Zhong N., Yang Z., Shu Y., Peiris J.S.M.. Human infection with highly pathogenic avian influenza A(H7N9) virus, China. Emerg Infect Dis, 2017, 23: 1332-1340 CrossRef PubMed Google Scholar

[47] Kim J.I., Kim Y.J., Lemey P., Lee I., Park S., Bae J.Y., Kim D., Kim H., Jang S.I., Yang J.S., Kim H., Kim D.W., Nam J.G., Kim S.S., Kim K., Myun Lee J., Song M.K., Song D., Chang J., Hong K.J., Bae Y.S., Song J.W., Lee J.S., Park M.S.. The recent ancestry of Middle East respiratory syndrome coronavirus in Korea has been shaped by recombination. Sci Rep, 2016, 6: 18825 CrossRef PubMed ADS Google Scholar

[48] Krishna N.K., Cunnion K.M.. Role of molecular diagnostics in the management of infectious disease emergencies. Med Clin North Am, 2012, 96: 1067-1078 CrossRef PubMed Google Scholar

[49] Lam T.T.Y., Zhou B., Wang J., Chai Y., Shen Y., Chen X., Ma C., Hong W., Chen Y., Zhang Y., Duan L., Chen P., Jiang J., Zhang Y., Li L., Poon L.L.M., Webby R.J., Smith D.K., Leung G.M., Peiris J.S.M., Holmes E.C., Guan Y., Zhu H.. Dissemination, divergence and establishment of H7N9 influenza viruses in China. Nature, 2015, 522: 102-105 CrossRef PubMed ADS Google Scholar

[50] Lee J., Chowell G., Jung E.. A dynamic compartmental model for the Middle East respiratory syndrome outbreak in the Republic of Korea: a retrospective analysis on control interventions and superspreading events. J Theor Biol, 2016, 408: 118-126 CrossRef PubMed Google Scholar

[51] Lee J.Y., Kim Y.J., Chung E.H., Kim D.W., Jeong I., Kim Y., Yun M.R., Kim S.S., Kim G., Joh J.S.. The clinical and virological features of the first imported case causing MERS-CoV outbreak in South Korea, 2015. BMC Infect Dis, 2017, 17: 498 CrossRef PubMed Google Scholar

[52] Li C., Xu D., Ye Q., Hong S., Jiang Y., Liu X., Zhang N., Shi L., Qin C.F., Xu Z.. Zika virus disrupts neural progenitor development and leads to microcephaly in mice. Cell Stem Cell, 2016a, 19: 672 CrossRef PubMed Google Scholar

[53] Li W., Shi Z., Yu M., Ren W., Smith C., Epstein J.H., Wang H., Crameri G., Hu Z., Zhang H., Zhang J., McEachern J., Field H., Daszak P., Eaton B.T., Zhang S., Wang L.F.. Bats are natural reservoirs of SARS-like coronaviruses. Science, 2005, 310: 676-679 CrossRef PubMed ADS Google Scholar

[54] Li X., Zhang Z., Yu A., Ho S.Y.W., Carr M.J., Zheng W., Zhang Y., Zhu C., Lei F., Shi W.. Global and local persistence of influenza A(H5N1) virus. Emerg Infect Dis, 2014, 20: 1287-1295 CrossRef PubMed Google Scholar

[55] Li X.F., Han J.F., Shi P.Y., Qin C.F.. Zika virus: a new threat from mosquitoes. Sci China Life Sci, 2016b, 59: 440-442 CrossRef PubMed Google Scholar

[56] Linsuwanon P., Poovorawan Y., Li L., Deng X., Vongpunsawad S., Delwart E.. The fecal virome of children with hand, foot, and mouth disease that tested PCR negative for pathogenic enteroviruses. PLoS ONE, 2015, 10: e0135573 CrossRef PubMed ADS Google Scholar

[57] Liu D., Shi W., Shi Y., Wang D., Xiao H., Li W., Bi Y., Wu Y., Li X., Yan J., Liu W., Zhao G., Yang W., Wang Y., Ma J., Shu Y., Lei F., Gao G.F.. Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses. Lancet, 2013, 381: 1926-1932 CrossRef Google Scholar

[58] Liu J., Sun Y., Shi W., Tan S., Pan Y., Cui S., Zhang Q., Dou X., Lv Y., Li X., Li X., Chen L., Quan C., Wang Q., Zhao Y., Lv Q., Hua W., Zeng H., Chen Z., Xiong H., Jiang C., Pang X., Zhang F., Liang M., Wu G., Gao G.F., Liu W.J., Li A., Wang Q.. The first imported case of Rift Valley fever in China reveals a genetic reassortment of different viral lineages. Emerg Microbes Infect, 2017a, 6: e4 CrossRef PubMed Google Scholar

[59] Liu L., Wu W., Zhao X., Xiong Y., Zhang S., Liu X., Qu J., Li J., Nei K., Liang M., Shu Y., Hu G., Ma X., Li D.. Complete genome sequence of Zika virus from the first imported case in mainland China. Genome Announc, 2016, 4: e00291-16 CrossRef Google Scholar

[60] Liu Y., Liu J., Du S., Shan C., Nie K., Zhang R., Li X.F., Zhang R., Wang T., Qin C.F., Wang P., Shi P.Y., Cheng G.. Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes. Nature, 2017b, 545: 482-486 CrossRef PubMed ADS Google Scholar

[61] Marra M.A., Jones S.J.M., Astell C.R., Holt R.A., Brooks-Wilson A., Butterfield Y.S.N., Khattra J., Asano J.K., Barber S.A., Chan S.Y., Cloutier A., Coughlin S.M., Freeman D., Girn N., Griffith O.L., Leach S.R., Mayo M., McDonald H., Montgomery S.B., Pandoh P.K., Petrescu A.S., Robertson A.G., Schein J.E., Siddiqui A., Smailus D.E., Stott J.M., Yang G.S., Plummer F., Andonov A., Artsob H., Bastien N., Bernard K., Booth T.F., Bowness D., Czub M., Drebot M., Fernando L., Flick R., Garbutt M., Gray M., Grolla A., Jones S., Feldmann H., Meyers A., Kabani A., Li Y., Normand S., Stroher U., Tipples G.A., Tyler S., Vogrig R., Ward D., Watson B., Brunham R.C., Krajden M., Petric M., Skowronski D.M., Upton C., Roper R.L.. The genome sequence of the SARS-associated coronavirus. Science, 2003, 300: 1399-1404 CrossRef PubMed ADS Google Scholar

[62] McHardy, A.C., and Adams, B. (2009). The role of genomics in tracking the evolution of influenza A virus. PLoS Pathog 5, e1000566. Google Scholar

[63] Mlakar J., Korva M., Tul N., Popović M., Poljšak-Prijatelj M., Mraz J., Kolenc M., Resman Rus K., Vesnaver Vipotnik T., Fabjan Vodušek V., Vizjak A., Pižem J., Petrovec M., Avšič Županc T.. Zika virus associated with microcephaly. N Engl J Med, 2016, 374: 951-958 CrossRef PubMed Google Scholar

[64] Mushegian A., Shipunov A., Elena S.F.. Changes in the composition of the RNA virome mark evolutionary transitions in green plants. BMC Biol, 2016, 14: 68 CrossRef PubMed Google Scholar

[65] Nanyingi M.O., Munyua P., Kiama S.G., Muchemi G.M., Thumbi S.M., Bitek A.O., Bett B., Muriithi R.M., Njenga M.K.. A systematic review of Rift Valley Fever epidemiology 1931–2014. Infect Ecol Epidemiol, 2015, 5: 28024 CrossRef Google Scholar

[66] Neumann G., Noda T., Kawaoka Y.. Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature, 2009, 459: 931-939 CrossRef PubMed ADS Google Scholar

[67] Ni M., Chen C., Qian J., Xiao H.X., Shi W.F., Luo Y., Wang H.Y., Li Z., Wu J., Xu P.S., Chen S.H., Wong G., Bi Y., Xia Z.P., Li W., Lu H.J., Ma J., Tong Y.G., Zeng H., Wang S.Q., Gao G.F., Bo X.C., Liu D.. Intra-host dynamics of Ebola virus during 2014. Nat Microbiol, 2016, 1: 16151 CrossRef PubMed Google Scholar

[68] Oh, M.D., Choe, P.G., Oh, H.S., Park, W.B., Lee, S.M., Park, J., Lee, S.K., Song, J.S., and Kim, N.J. (2015). Middle east respiratory syndrome coronavirus superspreading event involving 81 persons, Korea 2015. J Korean Med Sci 30, 1701–1705. Google Scholar

[69] Paez-Espino D., Eloe-Fadrosh E.A., Pavlopoulos G.A., Thomas A.D., Huntemann M., Mikhailova N., Rubin E., Ivanova N.N., Kyrpides N.C.. Uncovering Earth’s virome. Nature, 2016, 536: 425-430 CrossRef PubMed ADS Google Scholar

[70] Pan M., Gao R., Lv Q., Huang S., Zhou Z., Yang L., Li X., Zhao X., Zou X., Tong W., Mao S., Zou S., Bo H., Zhu X., Liu L., Yuan H., Zhang M., Wang D., Li Z., Zhao W., Ma M., Li Y., Li T., Yang H., Xu J., Zhou L., Zhou X., Tang W., Song Y., Chen T., Bai T., Zhou J., Wang D., Wu G., Li D., Feng Z., Gao G.F., Wang Y., He S., Shu Y.. Human infection with a novel, highly pathogenic avian influenza A (H5N6) virus: virological and clinical findings. J Infect, 2016, 72: 52-59 CrossRef PubMed Google Scholar

[71] Peiris J.S.M., Guan Y., Yuen K.Y.. Severe acute respiratory syndrome. Nat Med, 2004, 10: S88-S97 CrossRef PubMed Google Scholar

[72] Qi W., Shi W., Li W., Huang L., Li H., Wu Y., Yan J., Jiao P., Zhu B., Ma J., Gao G.F., Liao M., Liu D.. Continuous reassortments with local chicken H9N2 virus underlie the human-infecting influenza A (H7N9) virus in the new influenza season, Guangdong, China. Protein Cell, 2014a, 5: 878-882 CrossRef PubMed Google Scholar

[73] Qi W., Zhou X., Shi W., Huang L., Xia W., Liu D., Li H., Chen S., Lei F., Cao L., Wu J., He F., Song W., Li Q., Li H., Liao M., Liu M.. Genesis of the novel human-infecting influenza A(H10N8) virus and potential genetic diversity of the virus in poultry, China. Euro Surveill, 2014b, 19: 20841 CrossRef Google Scholar

[74] Qin E., He X., Tian W., Liu Y., Li W., Wen J., Wang J., Fan B., Wu Q., Chang G., Cao W., Xu Z., Yang R., Wang J., Yu M., Li Y., Xu J., Si B., Hu Y., Peng W., Tang L., Jiang T., Shi J., Ji J., Zhang Y., Ye J., Wang C.’., Han Y., Zhou J., Deng Y., Li X., Hu J., Wang C., Yan C., Zhang Q., Bao J., Li G., Chen W., Fang L., Li C., Lei M., Li D., Tong W., Tian X., Wang J., Zhang B., Zhang H., Zhang Y., Zhao H., Zhang X., Li S., Cheng X., Zhang X., Liu B., Zeng C., Li S., Tan X., Liu S., Dong W., Wang J., Wong G.K.S., Yu J., Wang J., Zhu Q., Yang H.. A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in south China. Genomics Proteomics Bioinformatics, 2003a, 1: 101-107 CrossRef Google Scholar

[75] Qin E., Zhu Q., Yu M., Fan B., Chang G., Si B., Yang B.’., Peng W., Jiang T., Liu B., Deng Y., Liu H., Zhang Y., Wang C.’., Li Y., Gan Y., Li X., Lü F., Tan G., Cao W., Yang R., Wang J., Li W., Xu Z., Li Y., Wu Q., Lin W., Chen W., Tang L., Deng Y., Han Y., Li C., Lei M., Li G., Li W., Lü H., Shi J., Tong Z., Zhang F., Li S., Liu B., Liu S., Dong W., Wang J., Wong G.K.S., Yu J., Yang H.. A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01). Chin Sci Bull, 2003b, 48: 941-948 CrossRef Google Scholar

[76] Quick J., Loman N.J., Duraffour S., Simpson J.T., Severi E., Cowley L., Bore J.A., Koundouno R., Dudas G., Mikhail A., Ouédraogo N., Afrough B., Bah A., Baum J.H.J., Becker-Ziaja B., Boettcher J.P., Cabeza-Cabrerizo M., Camino-Sánchez Á., Carter L.L., Doerrbecker J., Enkirch T., Dorival I.G., Hetzelt N., Hinzmann J., Holm T., Kafetzopoulou L.E., Koropogui M., Kosgey A., Kuisma E., Logue C.H., Mazzarelli A., Meisel S., Mertens M., Michel J., Ngabo D., Nitzsche K., Pallasch E., Patrono L.V., Portmann J., Repits J.G., Rickett N.Y., Sachse A., Singethan K., Vitoriano I., Yemanaberhan R.L., Zekeng E.G., Racine T., Bello A., Sall A.A., Faye O., Faye O., Magassouba N., Williams C.V., Amburgey V., Winona L., Davis E., Gerlach J., Washington F., Monteil V., Jourdain M., Bererd M., Camara A., Somlare H., Camara A., Gerard M., Bado G., Baillet B., Delaune D., Nebie K.Y., Diarra A., Savane Y., Pallawo R.B., Gutierrez G.J., Milhano N., Roger I., Williams C.J., Yattara F., Lewandowski K., Taylor J., Rachwal P., J. Turner D., Pollakis G., Hiscox J.A., Matthews D.A., Shea M.K.O., Johnston A.M.D., Wilson D., Hutley E., Smit E., Di Caro A., Wölfel R., Stoecker K., Fleischmann E., Gabriel M., Weller S.A., Koivogui L., Diallo B., Keïta S., Rambaut A., Formenty P., Günther S., Carroll M.W.. Real-time, portable genome sequencing for Ebola surveillance. Nature, 2016, 530: 228-232 CrossRef PubMed ADS Google Scholar

[77] Robertson B.H., Nicholson J.K.A.. New microbiology tools for public health and their implications. Annu Rev Public Health, 2005, 26: 281-302 CrossRef PubMed Google Scholar

[78] Rota P.A., Oberste M.S., Monroe S.S., Nix W.A., Campagnoli R., Icenogle J.P., Peñaranda S., Bankamp B., Maher K., Chen M.H., Tong S., Tamin A., Lowe L., Frace M., DeRisi J.L., Chen Q., Wang D., Erdman D.D., Peret T.C.T., Burns C., Ksiazek T.G., Rollin P.E., Sanchez A., Liffick S., Holloway B., Limor J., McCaustland K., Olsen-Rasmussen M., Fouchier R., Günther S., Osterhaus A.D.M.E., Drosten C., Pallansch M.A., Anderson L.J., Bellini W.J.. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science, 2003, 300: 1394-1399 CrossRef PubMed ADS Google Scholar

[79] Roux S., Brum J.R., Dutilh B.E., Sunagawa S., Duhaime M.B., Loy A., Poulos B.T., Solonenko N., Lara E., Poulain J., Pesant S., Kandels-Lewis S., Dimier C., Picheral M., Searson S., Cruaud C., Alberti A., Duarte C.M., Gasol J.M., Vaqué D., Vaqué D., Bork P., Acinas S.G., Wincker P., Sullivan M.B.. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature, 2016, 537: 689-693 CrossRef PubMed ADS Google Scholar

[80] Shi M., Lin X.D., Tian J.H., Chen L.J., Chen X., Li C.X., Qin X.C., Li J., Cao J.P., Eden J.S., Buchmann J., Wang W., Xu J., Holmes E.C., Zhang Y.Z.. Redefining the invertebrate RNA virosphere. Nature, 2016a, 540: 539-543 CrossRef PubMed ADS Google Scholar

[81] Shi W., Shi Y., Wu Y., Liu D., Gao G.F.. Origin and molecular characterization of the human-infecting H6N1 influenza virus in Taiwan. Protein Cell, 2013, 4: 846-853 CrossRef Google Scholar

[82] Shi W., Zhang Z., Ling C., Carr M.J., Tong Y., Gao G.F.. Increasing genetic diversity of Zika virus in the Latin American outbreak. Emerg Microbes Infect, 2016b, 5: e68 CrossRef PubMed Google Scholar

[83] Smith G.J.D., Fan X.H., Wang J., Li K.S., Qin K., Zhang J.X., Vijaykrishna D., Cheung C.L., Huang K., Rayner J.M., Peiris J.S.M., Chen H., Webster R.G., Guan Y.. Emergence and predominance of an H5N1 influenza variant in China. Proc Natl Acad Sci USA, 2006, 103: 16936-16941 CrossRef PubMed ADS Google Scholar

[84] Su S., Wong G., Shi W., Liu J., Lai A.C.K., Zhou J., Liu W., Bi Y., Gao G.F.. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends MicroBiol, 2016, 24: 490-502 CrossRef PubMed Google Scholar

[85] Sun H., Pu J., Wei Y., Sun Y., Hu J., Liu L., Xu G., Gao W., Li C., Zhang X., Huang Y., Chang K.C., Liu X., Liu J.. Highly pathogenic avian influenza H5N6 viruses exhibit enhanced affinity for human type sialic acid receptor and in-contact transmission in model ferrets. J Virol, 2016, 90: 6235-6243 CrossRef PubMed Google Scholar

[86] Sun, J., Wu, Zhong, H., Guan, D., Zhang, H., Tan, Q., Zhou, H., Zhang, M., Ning, D., Zhang, B., Ke, C., Song, T., Lin, J., Zhang, Y., Koopmans, M., and Gao, G.F. (2017). Returning ex-patriot Chinese to Guangdong, China, increase the risk for local transmission of Zika virus. J Infect S0163–4453, 30231. Google Scholar

[87] Tsetsarkin K.A., Vanlandingham D.L., McGee C.E., Higgs S.. A single mutation in chikungunya virus affects vector specificity and epidemic potential. PLoS Pathog, 2007, 3: e201 CrossRef PubMed Google Scholar

[88] Tong Y.G., Shi W.F., Liu D., Qian J., Liang L., Bo X.C., Liu J., Ren H.G., Fan H., Ni M., Sun Y., Jin Y., Teng Y., Li Z., Kargbo D., Dafae F., Kanu A., Chen C.C., Lan Z.H., Jiang H., Luo Y., Lu H.J., Zhang X.G., Yang F., Hu Y., Cao Y.X., Deng Y.Q., Su H.X., Sun Y., Liu W.S., Wang Z., Wang C.Y., Bu Z.Y., Guo Z.D., Zhang L.B., Nie W.M., Bai C.Q., Sun C.H., An X.P., Xu P.S., Zhang X.L.L., Huang Y., Mi Z.Q., Yu D., Yao H.W., Feng Y., Xia Z.P., Zheng X.X., Yang S.T., Lu B., Jiang J.F., Kargbo B., He F.C., Gao G.F., Cao W.C., Tong Y.G., Qian J., Sun Y., Lu H.J., Zhang X.G., Yang F., Hu Y., Cao Y.X., Deng Y.Q., Su H.X., Sun Y., Liu W.S., Wang Z., Wang C.Y., Bu Z.Y., Guo Z.D., Zhang L.B., Nie W.M., Bai C.Q., Sun C.H., Feng Y., Jiang J.F., Gao G.F.. Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone. Nature, 2015, 524: 93-96 CrossRef PubMed ADS Google Scholar

[89] Ventura C.V., Maia M., Bravo-Filho V., Góis A.L., Belfort Jr R.. Zika virus in Brazil and macular atrophy in a child with microcephaly. Lancet, 2016, 387: 228 CrossRef Google Scholar

[90] Wang D., Yang L., Zhu W., Zhang Y., Zou S., Bo H., Gao R., Dong J., Huang W., Guo J., Li Z., Zhao X., Li X., Xin L., Zhou J., Chen T., Dong L., Wei H., Li X., Liu L., Tang J., Lan Y., Yang J., Shu Y.. Two outbreak sources of influenza A (H7N9) viruses have been established in China. J Virol, 2016, 90: 5561-5573 CrossRef PubMed Google Scholar

[91] Wang J., Li C.C., Diao Y.X., Sun X.Y., Hao D.M., Liu X., Ge P.P.. Different outcomes of infection of chickens and ducks with a duck-origin H9N2 influenza A virus. Acta Virol, 2014, 58: 223-230 CrossRef Google Scholar

[92] Wang Y., Liu D., Shi W., Lu R., Wang W., Zhao Y., Deng Y., Zhou W., Ren H., Wu J., Wang Y., Wu G., Gao G.F., Tan W.. Origin and possible genetic recombination of the middle east respiratory syndrome coronavirus from the first imported case in China: phylogenetics and coalescence analysis. mBio, 2015, 6: e01280-15 CrossRef PubMed Google Scholar

[93] Wei S.H., Yang J.R., Wu H.S., Chang M.C., Lin J.S., Lin C.Y., Liu Y.L., Lo Y.C., Yang C.H., Chuang J.H., Lin M.C., Chung W.C., Liao C.H., Lee M.S., Huang W.T., Chen P.J., Liu M.T., Chang F.Y.. Human infection with avian influenza A H6N1 virus: an epidemiological analysis. Lancet Respirat Med, 2013, 1: 771-778 CrossRef Google Scholar

[94] Wong G., Liu W., Liu Y., Zhou B., Bi Y., Gao G.F.. MERS, SARS, and Ebola: the role of super-spreaders in infectious disease. Cell Host Microbe, 2015, 18: 398-401 CrossRef PubMed Google Scholar

[95] Wu B., Wang C., Dong G., Guo Y., Nolte D.L., Deliberto T.J., Xu J., Duan M., He H.. New evidence suggests southern China as a common source of multiple clusters of highly pathogenic H5N1 Avian influenza virus. J Infect Dis, 2010, 202: 452-458 CrossRef PubMed Google Scholar

[96] Wu J., Yi L., Zou L., Zhong H., Liang L., Song T., Song Y., Su J., Ke C.. Imported case of MERS-CoV infection identified in China, May 2015: detection and lesson learned. Euro Surveill, 2015, 20: 21158 CrossRef Google Scholar

[97] Xie Q., Cao Y.J., Su J., Wu X.B., Wan C.S., Ke C.W., Zhao W., Zhang B.. Genomic sequencing and analysis of the first imported Middle East Respiratory Syndrome Coronavirus (MERS CoV) in China. Sci China Life Sci, 2015, 58: 818-820 CrossRef PubMed Google Scholar

[98] Yang J.R., Liu M.T.. Human infection caused by an avian influenza A (H7N9) virus with a polybasic cleavage site in Taiwan, 2017. J Formosan Med Association, 2017, 116: 210-212 CrossRef PubMed Google Scholar

[99] Yuan J., Zhang L., Kan X., Jiang L., Yang J., Guo Z., Ren Q.. Origin and molecular characteristics of a novel 2013 Avian influenza A(H6N1) virus causing human infection in Taiwan. Clin Infect Dis, 2013, 57: 1367-1368 CrossRef PubMed Google Scholar

[100] Yuan L., Huang X.Y., Liu Z.Y., Zhang F., Zhu X.L., Yu J.Y., Ji X., Xu Y.P., Li G., Li C., Wang H.J., Deng Y.Q., Wu M., Cheng M.L., Ye Q., Xie D.Y., Li X.F., Wang X., Shi W., Hu B., Shi P.Y., Xu Z., Qin C.F.. A single mutation in the prM protein of Zika virus contributes to fetal microcephaly. Science, 2017, : in press doi: 10.1126/science.aam7120 CrossRef PubMed Google Scholar

[101] Zhang F., Bi Y., Wang J., Wong G., Shi W., Hu F., Yang Y., Yang L., Deng X., Jiang S., He X., Liu Y., Yin C., Zhong N., Gao G.F.. Human infections with recently-emerging highly pathogenic H7N9 avian influenza virus in China. J Infect, 2017, 75: 71-75 CrossRef PubMed Google Scholar

[102] Zhang H., Xu B., Chen Q., Chen J., Chen Z.. Characterization of an H10N8 influenza virus isolated from Dongting lake wetland. Virol J, 2011, 8: 42 CrossRef PubMed Google Scholar

[103] Zhang L., Zhang Z., Weng Z., Shi W.. Substitution rates of the internal genes in the novel Avian H7N9 influenza virus. Clin Infect Dis, 2013, 57: 1213-1215 CrossRef PubMed Google Scholar

[104] Zhang R., Chen T., Ou X., Liu R., Yang Y., Ye W., Chen J., Yao D., Sun B., Zhang X., Zhou J., Sun Y., Chen F., Wang S.P.. Clinical, epidemiological and virological characteristics of the first detected human case of avian influenza A(H5N6) virus. Infect Genet Evol, 2016a, 40: 236-242 CrossRef PubMed Google Scholar

[105] Zhang Y., Chen W., Wong G., Bi Y., Yan J., Sun Y., Chen E., Yan H., Lou X., Mao H., Xia S., Gao G.F., Shi W., Chen Z.. Highly diversified Zika viruses imported to China, 2016. Protein Cell, 2016b, 7: 461-464 CrossRef PubMed Google Scholar

[106] Zhu F.C., Hou L.H., Li J.X., Wu S.P., Liu P., Zhang G.R., Hu Y.M., Meng F.Y., Xu J.J., Tang R., Zhang J.L., Wang W.J., Duan L., Chu K., Liang Q., Hu J.L., Luo L., Zhu T., Wang J.Z., Chen W.. Safety and immunogenicity of a novel recombinant adenovirus type-5 vector-based Ebola vaccine in healthy adults in China: preliminary report of a randomised, double-blind, placebo-controlled, phase 1 trial. Lancet, 2015, 385: 2272-2279 CrossRef Google Scholar

[107] Zhu F.C., Wurie A.H., Hou L.H., Liang Q., Li Y.H., Russell J.B.W., Wu S.P., Li J.X., Hu Y.M., Guo Q., Xu W.B., Wurie A.R., Wang W.J., Zhang Z., Yin W.J., Ghazzawi M., Zhang X., Duan L., Wang J.Z., Chen W.. Safety and immunogenicity of a recombinant adenovirus type-5 vector-based Ebola vaccine in healthy adults in Sierra Leone: a single-centre, randomised, double-blind, placebo-controlled, phase 2 trial. Lancet, 2017a, 389: 621-628 CrossRef Google Scholar

[108] Zhu W., Zhou J., Li Z., Yang L., Li X., Huang W., Zou S., Chen W., Wei H., Tang J., Liu L., Dong J., Wang D., Shu Y.. Biological characterisation of the emerged highly pathogenic avian influenza (HPAI) A(H7N9) viruses in humans, in mainland China, 2016 to 2017. Euro Surveill, 2017b, 22: 30533 CrossRef PubMed Google Scholar

  • Figure 1

    (Color online) Emerging viral pathogens identified in China since 2013.

  • Figure 2

    (Color online) A workflow illustrating the application of next-generation sequencing to clinical samples. Panel A illustrates the strategy how to select Sanger sequencing and next-generation sequencing and panel B illustrates the basic strategy employed for next-generation sequencing. The dashed line in panel B means that this step depends on the nucleic acid type: it is necessary for RNA but not necessary for DNA.

  • Table 1   The diagnostic methods available for detecting and identifying causative microbial agents

    Diagnostic methods

    Advantages

    Disadvantages

    Culture (Krishna and Cunnion, 2012)

    1. Proliferation

    2. Presence of pathogenicity or fatal

    3. Applied to antibiotic susceptibility testing

    1. Lack of susceptible cell or tissue, or fastidious in culturing conditions

    2. Labor intensive, requiring highly skilled laboratory personnel

    3. Expensive and time-consuming process

    4. Probability of the occurrence of adaptive mutations

    5. False positive results from other pathogens or non-pathogens

    6. Operated in labs with a corresponding bio-safety level

    7. Not suitable for detection of multiple samples

    Serology (Krishna and Cunnion, 2012)

    1. One of the industry standard formats

    2. High levels of repeatability and reproducibility

    3. Easy to establish and use

    1. False-negative results from patients early in the acute phase, or patients with immune dysregulation including immune-compromise, immune-suppression, or patients who have been treated with intravenous immunoglobulin in the preceding year

    2. Not suitable for the emergency setting

    3. Requirements for acute and convalescent samples for confirmation

    Biochemical tests (Hsu et al., 2010)

    Simple and cheap

    Limited range and volume of tests

    Molecular methods

    Real-time polymerase chain reaction (Boonham et al., 2014; Robertson and Nicholson, 2005)

    1. One of the industry standard formats

    2. High levels of repeatability and reproducibility

    3. Easy to establish and use

    4. Enhance detection limits

    5. Suitable for the emergency setting

    6. Rapider than culture

    1. Prior knowledge of the causative agents is needed

    2. Not applicable to high-throughput testing

    3. Requirements for A single sample

    Loop-mediated isothermal amplification (LAMP) (Boonham et al., 2014)

    1. Suitable to perform in the field or resource poor locations

    2. More sensitivity and generic application than lateral flow devices (LFDs)

    1. Hard to establish

    2. High cost of reagents

    Hybridisation-based array platforms

    cDNA/oligonucleotide microarrays (Boonham et al., 2014; Boonham et al., 2007)

    1. Extend the limits of multiplex testing

    2. Suited to screening for both known/unknown viruses

    1. Prior knowledge of the causative agents is needed

    2. Intricate data processing

    3. Not suitable for unknown causative agent

    Sequencing

    Sanger sequencing

    1. High accuracy

    2. Simple, rapid and inexpensive

    1. Flux is <1,000 bp

    2. Not suitable for targets with genetic drift in primer sites, or large fragments missing samples, or samples with co-infections of same viral types

    Next-generation sequencing (NGS) (Boonham et al., 2014)

    1. Flux is larger and stable

    2. A large volume of data and rich information

    3. Facilitate the parallel analysis of multiple marker (genetic or protein) without the use of specific reagent

    4. Suitable for virus discovery

    1. Intricate data processing

    2. High cost of instrumentations and reagents

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