Genomic Analysis of Viral Outbreaks

Wohl, Shirlee; Schaffner, Stephen F.; Sabeti, Pardis C.

doi:10.1146/annurev-virology-110615-035747

Cited by 60 publications

(54 citation statements)

References 147 publications

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“…Molecular clock phylogenetic analyses can be used to infer the emergence times of pathogens and the timescales of outbreaks (38). Some of these tools are particularly applicable to heterochronous data sets, in which sequences from rapidly evolving populations have been sampled longitudinally through time.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary Dynamics of Oropouche Virus in South America

Gutierrez

Wise

Pullan

et al. 2020

J Virol

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The Amazon basin is home to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the genus Orthobunyavirus, family Peribunyaviridae, that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the OROV genome remain poorly understood. Here, we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genome sequences obtained from patients in Ecuador, representing the first set of genomes from this country. Our results show differing evolutionary processes on the three segments that comprise the viral genome. We infer differing times of the most recent common ancestors of the genome segments and propose that this can be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, as well as codons that evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of OROV through a combined phylogenetic and structural approach. IMPORTANCE The emergence and reemergence of pathogens such as Zika virus, chikungunya virus, and yellow fever virus have drawn attention toward other cocirculating arboviruses in South America. Oropouche virus (OROV) is a poorly studied pathogen responsible for over a dozen outbreaks since the early 1960s and represents a public health burden to countries such as Brazil, Panama, and Peru. OROV is likely underreported since its symptomatology can be easily confounded with other febrile illnesses (e.g., dengue fever and leptospirosis) and point-of-care testing for the virus is still uncommon. With limited data, there is a need to optimize the information currently available. Analysis of OROV genomes can help us understand how the virus circulates in nature and can reveal the evolutionary forces that shape the genetic diversity of the virus, which has implications for molecular diagnostics and the design of potential vaccines.

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Section: Discussionmentioning

confidence: 99%

Evolutionary Dynamics of Oropouche Virus in South America

Gutierrez

Wise

Pullan

et al. 2020

J Virol

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“…An excellent method to assess differential evolution of host and pathogen is through characterization of gene flow patterns, which can be measured at many temporal scales. For example, viral gene flow, manifested as past transmission events, is often inferred by phylogenetic techniques, such as transmission trees and discrete trait analysis with host state reconstruction (Wohl et al 2016). In comparison, host gene flow is generally assessed using population genetic distance measures, such as F ST , proportion of shared alleles, or relatedness.…”

Section: Inferring Host and Pathogen Gene Flowmentioning

confidence: 99%

The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise

Fitak

Antonides

Baitchman

et al. 2019

Journal of Heredity

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The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of biodiversity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented "Big Data" tools in disease research; however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural "Genomics of Disease in Wildlife" workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed 5 themes considered to be the most pressing to the application of genomics in wildlife disease research: 1) "Improving communication, " 2) "Methodological and analytical advancements, " 3) "Translation into practice, " 4) "Integrating landscape ecology and genomics, " and 5) "Emerging new questions. " Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.

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“…Availability of microbe species genome sequences and application of system biology to the field of vaccinology have provided new ways for identification and evaluation of potential vaccine candidates. Phylogenetic analysis is one of the best tools for studying the adaptive evolution of pathogens, and it is used to investigate outbreaks or endemic diseases and the history of the pandemics, including the pattern (when, where, and how) of disease spreading throughout the world …”

Section: Role Of Phylogenetic Analysis In Vaccine Strategiesmentioning

confidence: 99%

“…Phylogenetic analysis is one of the best tools for studying the adaptive evolution of pathogens, and it is used to investigate outbreaks or endemic diseases and the history of the pandemics, including the pattern (when, where, and how) of disease spreading throughout the world. 216,217 Despite the wide use of vaccines, vaccination failure is possible due to the emergence of variants that escape vaccination. Thus, it is pivotal to determine the genetic diversity between circulating field strains and the currently used vaccine strains.…”

Section: Role Of Phylogenetic Analysis In Vaccine Strategiesmentioning

confidence: 99%

The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review

Ciccozzi

Lai

Zehender

et al. 2019

Journal of Medical Virology

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In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing “phylogeny” or “epidemiology AND phylogeny” only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.

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Genomic Analysis of Viral Outbreaks

Cited by 60 publications

References 147 publications

Evolutionary Dynamics of Oropouche Virus in South America

Evolutionary Dynamics of Oropouche Virus in South America

The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise

The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review

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