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


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)


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.


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  • 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



    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


    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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