LAUSR

Emerging and re-emerging viral diseases pose a serious and continuous threat to the human society and place a heavy burden on the ecological system. Because of globalization, endemic viruses could be transmitted quickly across long distances, causing pandemic outbreaks. This has happened during the outbreak of the avian influenza viruses, Ebola virus, and Zika virus in recent years (Gao, 2018). Sudden viral attacks always evoke a large number of questions from the public. People ask what the pathogen is and where it is from, by what mechanism it infects the body, how they can prevent infection, what the population’s cross-protection level may be, and whether there is any valid drug or vaccine. Virologists worldwide have made efforts to answer these critical questions. Great progress has been made in basic research of viral diseases, as well as in constructing prevention and control systems such as the World Health Organization (WHO) and national centers for disease control and prevention (CDC). However, in view of the huge complexity in the outbreak of viral diseases associated with pathogens, hosts, vectors, surroundings and other factors, timely and effective responses to emerging viral diseases remain extremely challenging. Up to now, studies and applications in viral diseases have mostly been passive, retrospective, and isolated, a far cry from the active, prospective, and systematic studies that must be performed if we are to improve disease surveillance, prevention, and control. The emergence of high-throughput omics technologies provides a good avenue for changing the collective mindset concerning the defense of viral diseases. With the development of next-generation sequencing (NGS) technologies, large quantities of omics data have been accumulated concerning pathogens, hosts, and even vectors in viral diseases. These data could be integrated with traditional surveillance and functional data for better description of viral diseases from genotype to phenotype. For example, NGS generates rich gene segments and genome sequences for pathogens, which could eventually be used for tracing the origin and source of emerging viruses (Wu et al., 2013). Therefore, the use of omics technology in the study of viral diseases may cause the birth of an interdisciplinary field, systems virology (Law et al., 2013; Rasmussen and Katze, 2016), focusing on the understanding, prevention, and control of viral diseases from the perspective of pathogens, hosts, vectors, and surroundings via systems biological methods. NGS technologies have been widely used to resolve the viral genomes and further to find the source, transmission and evolution of the (re)-emerging viruses (Shi et al., 2017). By sequencing the viral genomes from the isolated strains or clinical samples, researchers have successfully discovered the origins and mutation patterns of several emerging viral outbreaks in recent years, including influenza viruses (Gao et al., 2013; Li et al., 2004; Wu et al., 2013; Deng et al., 2017), Zika virus (Fu et al., 2017; Wang et al., 2016; Deng et al., 2016) and others. In addition to being used in viral microevolution, NGS promotes notable progress in two other levels of evolutionary analysis for viruses, including macroevolution among different viruses and the evolution of quasispecies of a specific virus within its host. One direction of the study of viral macroevolution was the beginning of the Global Virome Project in 2018 (Carroll et