Identification of a novel polyomavirus from patients with acute respiratory tract infections

Abstract

We report the identification of a novel polyomavirus present in respiratory secretions from human patients with symptoms of acute respiratory tract infection. The virus was initially detected in a nasopharyngeal aspirate from a 3-year-old child from Australia diagnosed with pneumonia. A random library was generated from nucleic acids extracted from the nasopharyngeal aspirate and analyzed by high throughput DNA sequencing. Multiple DNA fragments were cloned that possessed limited homology to known polyomaviruses. We subsequently sequenced the entire virus genome of 5,229 bp, henceforth referred to as WU virus, and found it to have genomic features characteristic of the family Polyomaviridae. The genome was predicted to encode small T antigen, large T antigen, and three capsid proteins: VP1, VP2, and VP3. Phylogenetic analysis clearly revealed that the WU virus was divergent from all known polyomaviruses. Screening of 2,135 patients with acute respiratory tract infections in Brisbane, Queensland, Australia, and St. Louis, Missouri, United States, using WU virus-specific PCR primers resulted in the detection of 43 additional specimens that contained WU virus. The presence of multiple instances of the virus in two continents suggests that this virus is geographically widespread in the human population and raises the possibility that the WU virus may be a human pathogen.

Figure 1. Schematic of WU Virus Genome Organization

ori, origin of replication.

Figure 2. Phylogenetic Analysis of WU Virus

Amino acid–based phylogenetic trees were generated using the neighbor-joining method with 1,000 bootstrap replicates. Significant bootstrap values are shown. A) STAg; B) LTAg; C) VP1; D) VP2.

Figure 3. Strain Variation of WU virus

A 250-bp fragment of the VP2 gene was aligned using ClustalX. WU indicates the original case, and strain designations correspond to patients as listed in Table 2.