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.bioinformatics ͉ nucleotide sequencing ͉ respiratory tract infection ͉ virus V irus infections impose an enormous disease burden on humanity, but our knowledge of the viruses that infect humans is still incomplete. Because of the elusive nature of viruses, most studies are limited to the investigation of already known viruses, whereas the discovery of an unknown virus and production of the first diagnostic reagent is very difficult and remains a rare occurrence. The majority of viruses known today were first identified by animal experiments or virus replication in tissue culture. We know that there are viruses that cannot be replicated in the laboratory, and some of these have been identified by molecular methods (1-4). No generally applicable method for the identification of such viruses has been available, and, in fact, a very large number of unidentified human viruses may exist (2). Thus, numerous acute and chronic diseases with unknown etiology may be caused by unidentified viruses, and the systematic search for unknown viruses is an urgent scientific task (2).Lower respiratory tract infection (LRTI) is a leading cause for hospitalization of infants and young children and accounts for Ϸ250,000 hospitalizations a year in the United States alone (5). The most important viral agent in this group of patients is respiratory syncytial virus (RSV). Other important agents are influenza viruses, parainfluenza viruses, adenoviruses, rhinoviruses, coronaviruses, and human metapneumovirus (6-8). Human metapneumovirus was cultured and characterized in 2001, and, more recently, a renewed interest in coronaviruses after the severe acute respiratory syndrome epidemic has led to the characterization of two coronavirus species associated with LRTI (9-11). In comprehensive studies of the etiology of LRTI, no etiologic agent has been found in 12-39% of cases, which suggests that additional unknown agents may be involved in the etiology of LRTI (6-8).The identification of viruses...

Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.