Animal virus discovery: improving animal health, understanding zoonoses, and opportunities for vaccine development

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Highlights

► There are numerous sources of samples for animal virus discovery. ► Many simple molecular methods exist for the characterization of novel viruses. ► Some human viruses have genetically close animal counterparts. ► Future emerging human viruses may arise from any animal viral families. ► Disease association and causation studies are needed for many new animal viruses.

Abstract

The characterization of viral genomes has accelerated due to improvement in DNA sequencing technology. Sources of animal samples and molecular methods for the identification of novel viral pathogens and steps to determine their pathogenicity are listed. The difficulties for predicting future cross-species transmissions are highlighted by the wide diversity of known viral zoonoses. Recent surveys of viruses in wild and domesticated animals have characterized numerous viruses including some closely related to those infecting humans. The detection of multiple genetic lineages within viral families infecting a single host species, phylogenetically interspersed with viruses found in other host species, reflects past cross-species transmissions. Numerous opportunities for the generation of novel vaccines will arise from a better understanding of animal viromes.

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Most cited references 89

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Cloning of a human parvovirus by molecular screening of respiratory tract samples.

Tobias Allander, Martti T Tammi, Margareta Eriksson … (2005)

The identification of new virus species is a key issue for the study of infectious disease but is technically very difficult. We developed a system for large-scale molecular virus screening of clinical samples based on host DNA depletion, random PCR amplification, large-scale sequencing, and bioinformatics. The technology was applied to pooled human respiratory tract samples. The first experiments detected seven human virus species without the use of any specific reagent. Among the detected viruses were one coronavirus and one parvovirus, both of which were at that time uncharacterized. The parvovirus, provisionally named human bocavirus, was in a retrospective clinical study detected in 17 additional patients and associated with lower respiratory tract infections in children. The molecular virus screening procedure provides a general culture-independent solution to the problem of detecting unknown virus species in single or pooled samples. We suggest that a systematic exploration of the viruses that infect humans, "the human virome," can be initiated.

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Host phylogeny constrains cross-species emergence and establishment of rabies virus in bats.

Daniel G Streicker, Amy Turmelle, Maarten J. Vonhof … (2010)

For RNA viruses, rapid viral evolution and the biological similarity of closely related host species have been proposed as key determinants of the occurrence and long-term outcome of cross-species transmission. Using a data set of hundreds of rabies viruses sampled from 23 North American bat species, we present a general framework to quantify per capita rates of cross-species transmission and reconstruct historical patterns of viral establishment in new host species using molecular sequence data. These estimates demonstrate diminishing frequencies of both cross-species transmission and host shifts with increasing phylogenetic distance between bat species. Evolutionary constraints on viral host range indicate that host species barriers may trump the intrinsic mutability of RNA viruses in determining the fate of emerging host-virus interactions.

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Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia

Charles Runckel, Michelle L. Flenniken, Juan Engel … (2011)

Honey bees (Apis mellifera) play a critical role in global food production as pollinators of numerous crops. Recently, honey bee populations in the United States, Canada, and Europe have suffered an unexplained increase in annual losses due to a phenomenon known as Colony Collapse Disorder (CCD). Epidemiological analysis of CCD is confounded by a relative dearth of bee pathogen field studies. To identify what constitutes an abnormal pathophysiological condition in a honey bee colony, it is critical to have characterized the spectrum of exogenous infectious agents in healthy hives over time. We conducted a prospective study of a large scale migratory bee keeping operation using high-frequency sampling paired with comprehensive molecular detection methods, including a custom microarray, qPCR, and ultra deep sequencing. We established seasonal incidence and abundance of known viruses, Nosema sp., Crithidia mellificae, and bacteria. Ultra deep sequence analysis further identified four novel RNA viruses, two of which were the most abundant observed components of the honey bee microbiome (∼1011 viruses per honey bee). Our results demonstrate episodic viral incidence and distinct pathogen patterns between summer and winter time-points. Peak infection of common honey bee viruses and Nosema occurred in the summer, whereas levels of the trypanosomatid Crithidia mellificae and Lake Sinai virus 2, a novel virus, peaked in January.

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Contributors

Eric Delwart

Journal

Journal ID (nlm-ta): Curr Opin Virol

Journal ID (iso-abbrev): Curr Opin Virol

Title: Current Opinion in Virology

Publisher: Elsevier

ISSN (Print): 1879-6257

ISSN (Electronic): 1879-6265

Publication date PMC-release: 15 March 2012

Publication date (Print): June 2012

Publication date (Electronic): 15 March 2012

Volume: 2

Issue: 3

Pages: 344-352

Affiliations

Blood Systems Research Institute and University of California, San Francisco, United States

Article

Publisher ID: S1879-6257(12)00039-9

DOI: 10.1016/j.coviro.2012.02.012

PMC ID: 3378828

PubMed ID: 22463981

SO-VID: 0f2fdfd4-fe37-4d44-88ed-bca2d33c7bc9

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Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

Animal virus discovery: improving animal health, understanding zoonoses, and opportunities for vaccine development

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Zoonoses

Most cited references 89

Cloning of a human parvovirus by molecular screening of respiratory tract samples.

Host phylogeny constrains cross-species emergence and establishment of rabies virus in bats.

Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia

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