The global threat of (re)emerging infectious viruses requires a more effective approach regarding virus surveillance and diagnostic assays, as current diagnostics are often virus species specific and not able to detect highly divergent or unknown viruses. A systematic exploration of viruses that infect humans is the key to effectively counter the potential public health threat caused by new and emerging infectious diseases. The human gut is a known reservoir of a wide variety of microorganisms, including viruses. In this study, Dutch clinical diarrhea samples for which no etiological agent could be identified by available cell culture, serological, or nucleic acid-based tests were gathered. Large-scale molecular RNA virus screening based on host nucleic acid depletion, sequence-independent amplification, and sequencing of partially purified viral RNA from a limited number of clinical diarrhea samples revealed four eukaryotic virus species. Among the detected viruses were a rhinovirus and a new picobirnavirus variant. In total, ϳ20% of clinical diarrhea samples contained human picobirnavirus sequences. The Dutch picobirnaviruses belonged to different phylogenetic clades and did not group with other picobirnaviruses according to year of isolation or host species. Interestingly, the average age of patients infected with picobirnavirus was significantly higher than that of uninfected patients. Our data show that sequence-independent amplification of partially purified viral RNA is an efficient procedure for identification of known and highly divergent new RNA viruses in clinical diarrhea samples.Infectious diseases, both emerging and reemerging, pose a continuous health threat and a burden to humans. Since the 1980s, an increased frequency of infectious outbreaks in humans and animals has been observed. Over 50 (re)emerging pathogens have been identified during the last 40 years, among which are human immunodeficiency virus, hepatitis C virus, H5N1 avian influenza A virus, and severe acute respiratory syndrome (SARS) coronavirus (12). In addition, during the last 5 years, the World Health Organization has verified more than 1,100 epidemic events worldwide (http://www.who.int/whr/en/index.html). Yet, our knowledge of viruses that infect humans is still incomplete, and many acute and chronic diseases with unknown etiology may be caused by as-yet-unidentified viruses.The majority of viruses known today were first identified by animal experiments, virus replication in tissue culture, or molecular detection methods. For virus identification in clinical samples, laboratories nowadays perform largely viral-speciesspecific assays to increase the sensitivity of detection and reduce the time needed for diagnosis. Although these diagnostic assays are successful, failure rates in determining the etiological cause can vary significantly (11,19,31) because of limited detection of divergent viruses due to the high specificity of the assays. The discovery of new viruses with these assays remains rare. New technologies are currently...

A thorough understanding of the diversity of viruses in wildlife provides epidemiological baseline information about potential pathogens. Metagenomic analysis of the enteric viral flora revealed a new anellovirus and bocavirus species in pine martens and a new circovirus-like virus and geminivirus-related DNA virus in European badgers. In addition, sequences with homology to viruses from the families Paramyxo-and Picornaviridae were detected.

Sequence-independent amplification and specific reverse transcription PCRs identified genogroup I and II picobirnaviruses in respiratory tracts of pigs. These data expand knowledge of picobirnavirus diversity and tropism. Genetic relationships between porcine respiratory and human enteric picobirnaviruses suggest cross-species transmission of picobirnaviruses between pigs and humans.

The threat of emerging infectious viruses in humans requires a more effective approach regarding virus surveillance. A thorough understanding of virus diversity in wildlife provides epidemiological baseline information about pathogens and may lead to the identification of newly emerging pathogens in the future. In this study, diarrhoea samples from an outbreak of gastrointestinal illness in a Danish population of European roe deer were gathered for which no aetiological agent could be identified. Large-scale molecular RNA virus screening, based on host nucleic acid depletion, sequence-independent amplification and sequencing of partially purified viral RNA, revealed the presence of novel astroviruses, CcAstV-1 and CcAstV-2, in two of ten diarrhoea samples. Whether these viruses were responsible for causing diarrhoea remains to be determined. Phylogenetic analyses on amplified sequences showed that these viruses were most closely related to each other, were a novel species in the genus Mamastrovirus and may represent two different serotypes.

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