Virus identification in unknown tropical febrile illness cases using deep sequencing.
Nathan L. Yozwiak,Peter Skewes-Cox,Mark D. Stenglein,Angel Balmaseda,Eva Harris,Joseph L. DeRisi +5 more
TLDR
The utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness is demonstrated.Abstract:
Dengue virus is an emerging infectious agent that infects an estimated 50-100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human Herpesvirus 6 sequences. Other samples contained sequences with similarity to sequences from viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known viruses, and in others they diverged, suggesting that they may derive from novel viruses. These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness.read more
Citations
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Drivers, dynamics, and control of emerging vector-borne zoonotic diseases
TL;DR: Challenges inherent in the control of vector-borne zoonotic diseases and some emerging non-traditional strategies that could be effective in the long term are described.
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An introduction to the analysis of shotgun metagenomic data.
TL;DR: This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use and documents how metagenomes can be analyzed to quantify community structure and diversity.
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African swine fever virus replication and genomics
TL;DR: African swine fever virus (ASFV) is a large icosahedral DNA virus which replicates predominantly in the cytoplasm of infected cells and a similar mechanism of replication to Poxviruses has been proposed for ASFV.
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Going viral: next-generation sequencing applied to phage populations in the human gut.
TL;DR: How work characterizing phage diversity and lifestyles in the human gut is changing the authors' view of ourselves as supra-organisms is explored and how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of their gut microbiomes is discussed.
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Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults
Charles Langelier,Katrina Kalantar,Farzad Moazed,Michael R. Wilson,Emily D. Crawford,Thomas Deiss,Annika Belzer,Samaneh Bolourchi,Saharai Caldera,Monica Fung,Alejandra Jauregui,Katherine Malcolm,Amy Lyden,Lillian M. Khan,Kathryn Vessel,Jenai Quan,Matt S. Zinter,Charles Y. Chiu,Eric D. Chow,Jenny L. Wilson,Steve Miller,Michael A. Matthay,Katherine S. Pollard,Katherine S. Pollard,Stephanie A. Christenson,Carolyn S. Calfee,Joseph L. DeRisi +26 more
TL;DR: It is suggested that a single streamlined protocol offering an integrated genomic portrait of pathogen, microbiome, and host transcriptome may hold promise as a tool for LRTI diagnosis.
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