Discovery of a Novel Polyomavirus in Acute Diarrheal Samples from Children

Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
PLoS ONE (Impact Factor: 3.23). 11/2012; 7(11):e49449. DOI: 10.1371/journal.pone.0049449
Source: PubMed


Polyomaviruses are small circular DNA viruses associated with chronic infections and tumors in both human and animal hosts. Using an unbiased deep sequencing approach, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. The ∼5.0 kB viral genome exhibits little overall homology (<46% amino acid identity) to known polyomaviruses, and, due to phylogenetic variation among its individual proteins, cannot be placed in any existing taxonomic group. PCR-based screening detected MXPyV in 28 of 834 (3.4%) fecal samples collected from California, Mexico, and Chile, and 1 of 136 (0.74%) of respiratory samples from Mexico, but not in blood or urine samples from immunocompromised patients. By quantitative PCR, the measured titers of MXPyV in human stool at 10% (weight/volume) were as high as 15,075 copies. No association was found between the presence of MXPyV and diarrhea, although girls were more likely to shed MXPyV in the stool than boys (p = 0.012). In one child, viral shedding was observed in two stools obtained 91 days apart, raising the possibility of chronic infection by MXPyV. A multiple sequence alignment revealed that MXPyV is a closely related variant of the recently reported MWPyV and HPyV10 polyomaviruses. Further studies will be important to determine the association, if any, of MXPyV with disease in humans.

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    • "Reference databases of host and pathogen sequences range in size from 2 Gb for viruses to 3.1 Gb for the human genome to 42 Gb for all nucleotide sequences in the National Center for Biotechnology Information (NCBI) nucleotide (nt) collection (NCBI nt DB) as of January 2013. Second, only a small fraction of short NGS reads in clinical metagenomic data typically correspond to pathogens (a ''needle-in-a-haystack'' problem) (Kostic et al. 2012; Wylie et al. 2012; Yu et al. 2012), and such sparse reads often do not overlap sufficiently to permit de novo assembly into longer contiguous sequences (contigs) (Kostic et al. 2011). Thus, individual reads, typically only 100–300 nucleotides (nt) in length, must be classified to a high degree of accuracy. "
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