Viral discovery is made difficult by the frequent inability to replicate these agents in vitro and the limitations of traditional methods requiring antigenic/serological cross-reactivity or nucleic acid hybridization. We postulate, based on our recent study of viral capsid-protected nucleic acids in symptomatic humans, that new viruses, both commensal and pathogenic, can be readily identified using a metagenomic approach. Our successes finding both new as well as a diverse mix of previously known human viruses in unprocessed biological samples using a minimal amount of sequencing indicate that a rich yield of previously unknown viruses is present in human samples. We have assembled for this nucleic acid survey a collection of samples from extensively characterized patients showing a range of symptoms including hepatitis, encephalitis and pneumonia of unexplained etiology. Samples from heavily virus-exposed (IDUs, MSM) and susceptible subjects (AIDS patients) and from humans frequently exposed to non-human primates will be similarly analyzed. Using an unbiased viral DNA and RNA amplification method, together with both traditional shotgun library sequencing and high throughput pyrosequencing, we will conduct a metagenomic survey of the human virome. Virus-specific bioinformatics methods will be developed to facilitate the detection of phylogenetically close as well as distant relatives of known viral species. Initial viral sequence similarity matches will be followed by full viral genome sequencing and phylogenetic analysis. The prevalence of newly identified viruses will then be determined using real-time PCR on different populations including healthy blood donors, IDUs and patients with identical symptoms or exposure risks. This metagenomic survey of non-human nucleic acids in humans will therefore begin the task of determining the full range of viral diversity in humans.

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Research Project (R01)
Project #
5R01HL083254-04
Application #
7778220
Study Section
Clinical Research and Field Studies of Infectious Diseases Study Section (CRFS)
Program Officer
Welniak, Lisbeth A
Project Start
2007-04-01
Project End
2012-03-31
Budget Start
2010-04-01
Budget End
2012-03-31
Support Year
4
Fiscal Year
2010
Total Cost
$400,600
Indirect Cost
Name
Blood Systems Research Institute
Department
Type
DUNS #
006902498
City
San Francisco
State
CA
Country
United States
Zip Code
94118
Phan, Tung Gia; Del Valle Mendoza, Juana; Sadeghi, Mohammadreza et al. (2017) Sera of Peruvians with fever of unknown origins include viral nucleic acids from non-vertebrate hosts. Virus Genes :
Sadeghi, Mohammadreza; Popov, Vsevolod; Guzman, Hilda et al. (2017) Genomes of viral isolates derived from different mosquitos species. Virus Res 242:49-57
Li, Linlin; Pesavento, Patricia A; Gaynor, Anne M et al. (2015) A gyrovirus infecting a sea bird. Arch Virol 160:2105-9
Linsuwanon, Piyada; Poovorawan, Yong; Li, Linlin et al. (2015) The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses. PLoS One 10:e0135573
Phan, Tung Gia; Desnues, Christelle; Switzer, William M et al. (2015) Absence of giant blood Marseille-like virus DNA detection by polymerase chain reaction in plasma from healthy US blood donors and serum from multiply transfused patients from Cameroon. Transfusion 55:1256-62
Li, Linlin; Deng, Xutao; Mee, Edward T et al. (2015) Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J Virol Methods 213:139-46
Boros, Ákos; Pankovics, Péter; Knowles, Nick J et al. (2014) Comparative complete genome analysis of chicken and Turkey megriviruses (family picornaviridae): long 3' untranslated regions with a potential second open reading frame and evidence for possible recombination. J Virol 88:6434-43
Boros, Ákos; Kiss, Tamás; Kiss, Orsolya et al. (2013) Genetic characterization of a novel picornavirus distantly related to the marine mammal-infecting aquamaviruses in a long-distance migrant bird species, European roller (Coracias garrulus). J Gen Virol 94:2029-35
Ng, Terry Fei Fan; Driscoll, Cindy; Carlos, Maria Paz et al. (2013) Distinct lineage of vesiculovirus from big brown bats, United States. Emerg Infect Dis 19:1978-80
Reuter, Gábor; Nemes, Csaba; Boros, Akos et al. (2013) Porcine kobuvirus in wild boars (Sus scrofa). Arch Virol 158:281-2

Showing the most recent 10 out of 50 publications