Background: Polyomaviruses (PyV) are small, circular, non-enveloped viruses with a diameter of about 40–50 nm, and have a double-stranded DNA molecule descended from the Polyomaviridae family. Until now, about 32 PyV species have been described, where more than 10 of them have been reported to cause infection. Aim: This study aimed to identify the sequence of the complete genome of the WU polyomavirus strain and to study its phylogenetic analysis and determine variation in the WUPyV sequence. Materials and Methods: Samples (n=195) were collected to identify viral DNA by real-time and conventional PCR, respectively. One purified viral DNA sample of positive cases was used for next generation sequencing (NGS) to identify the WGS. Results: The WUPyV sequence was registered in the NCBI GenBank under the accession number LC771087. The current study showed that the WUPyV sequence has a length of 5229 bp. The WUPyV sequence was compared to the reference sequences to determine any mutations. We found many mutations, some of which were silent, and the others caused a change in the amino acid. Ten reference strains from NCBI were used to create a phylogenetic tree for the clinical sample studied. The present results revealed that the strain LC771087.1 WU Polyomavirus showed great similarity with one sequence, EU711054.1 WU Polyomavirus strain WU/ Wuerzburg/01/03. Conclusion: The current study concluded that WU polyomaviruses used in the multiple sequence alignment with our strain have the same length 5229 bp, with 99.5% similarity in DNA sequences and 99.2% identity of amino acid sequences.