Genomic Epidemiology Data Infrastructure Needs for SARS-CoV-2 Modernizing Pandemic Response Strategies (2020) / Chapter Skim
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2 Application of Genomic Epidemiology in Previous Infectious Disease Outbreaks
2 Application of Genomic Epidemiology in Previous Infectious Disease Outbreaks
Pages 19-32
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From page 19... ...
Previous efforts to combine and analyze viral genome sequence data with clinical and epidemiological data have demonstrated the value of this approach and have indicated its potential to transform the response to infectious disease outbreaks in the future. PREVIOUS EFFORTS TO INTEGRATE ANALYSES OF GENOMIC, CLINICAL, AND EPIDEMIOLOGICAL DATA SARS-CoV The severe acute respiratory syndrome coronavirus (SARS-CoV)
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Thus, genomic sequencing led to identification of the source of human infection and mutations that facilitated human infection. Ebola Virus The power of genomic epidemiology to shape the response to an infectious disease outbreak became increasingly evident during the Ebola virus epidemic in West Africa (Gardy and Loman, 2018; Ladner et al., 2019)
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. Zika Virus During the 2015–2016 epidemic of the Zika virus in the Americas, whole genome sequencing, phylogenetic molecular clock analysis, and epidemiological data for this mosquito-borne virus revealed that viral strains in the Americas share a common ancestor with strains in French Polynesia and that the virus was likely circulating in Brazil more than 1 year earlier than initially believed (Faria et al., 2016, 2017; Metsky et al., 2017)
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Because annual seasonal influenza vaccines are developed and produced ahead of flu season based on expert predictions, ongoing data collection is critical for rapidly identifying the major strain(s) circulating in humans during influenza season and assessing the antigenic properties of new strains.
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. The ARMoR Program is an enterprise-wide initiative, consisting of epidemiologists, bioinformaticists, microbiology researchers, policy makers, hospital-based infection preventionists, and health care providers, that implemented next-generation sequencing across the DoD health care system and surveillance network to gain insight into the molecular epidemiology of carbapenemase-producing bacteria to elicit more accurate and actionable data for infection control (see Figure 2-1)
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24 FIGURE 2-1 Customized database for the Antimicrobial Resistance Monitoring and Research (ARMoR) Program.
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and provide a richer and more nuanced picture of the epidemiological landscape of an infectious disease outbreak, enabling the investigation and potential confirmation of hypotheses that would be difficult to pursue without the integration of genomic information into the approach. An instructive example is the surveillance framework developed to evaluate the circumstances of mosquito-borne transmission of yellow fever virus (Faria et al., 2018)
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coli example described above, foodborne disease outbreaks can benefit from genomic analysis to allow the linking of cases to a point source of infection. The genomic data asso ciated with the outbreaks, however, must be combined with relevant epidemiological data to identify risk that allow for specific interventions to be meaningful (Hill et al., 2017)
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2017. Functional charac terization of adaptive mutations during the West African Ebola virus outbreak.
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2017. Establishment and cryptic transmission of Zika virus in Brazil and the Americas.
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2018. Genomic and epidemiological monitoring of yellow fever virus transmission potential.
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2008. Persistent replication of severe acute respiratory syndrome coronavirus in human tubular kidney cells selects for adaptive mutations in the membrane protein.
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2016. Human adaptation of Ebola virus during the West African outbreak.
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