Frequent detection of highly diverse variants of cardiovirus, cosavirus, bocavirus, and circovirus in sewage samples collected in the United States

Abstract

Untreated sewage samples from 12 cities in the United States were screened for the presence of recently characterized RNA and DNA viruses found at high prevalence in the stool specimens of South Asian children. Genetic variants of human cosaviruses and cardioviruses in the Picornaviridae family and of DNA circoviruses and human bocaviruses were detected, expanding the known genetic diversity and geographic range of these newly identified viruses. All four virus groups were detected in sewage samples of less than a milliliter from multiple U.S. cities. PCR screening of particle-protected viral nucleic acid in sewage samples could therefore rapidly establish the presence and determine the diversity of four newly described enteric viruses in large urban populations. More frequent and deeper sampling of viral nucleic acids in sewage samples could be used to monitor changes in the prevalence and genetic composition of these and other novel enteric viruses.

FIG. 1.

Phylogenetic analysis of amplicons derived from untreated sewage waters. (A) Human cardioviruses (SAFV) based on partial helicase sequences, available genotypes based on VP1 are included in parentheses in the figure (gt). TMEV, Theiler's murine encephalomyelitis virus. (B) Human cosaviruses (HCoSV) based on partial 5′UTR sequences. (C) Human bocaviruses (HBoV) based on partial VP1 sequences. (D) Circoviruses based on partial replicase sequences. Circovirus sequences from sewage samples (SewCV) are indicated by solid black circles. GenBank accession numbers of non-sewage-derived sequences are included in taxon names. Taxa are labeled with name of virus followed by letter or number of the species (for HCoSV and HBoV) and then by the country (Canada [Can], Pakistan [Pak], Afghanistan [Afg]) or U.S. state (shown in postal state abbreviations), location within state (location 1 or 2), time points (FL1-1 to FL1-3 and FL2-1 to FL2-7 only), and origin of sequences (P for direct PCR sequencing and C for plasmid clone). Bootstrap values greater than 70 are shown. Scales represent percent divergence between taxa.