Complete genome characterization and phylogenetic analysis of WU polyomavirus in Thai pediatric patients with respiratory tract infections in 2013.

Chanchaem, Prangwalai; Poovorawan, Yong; Payungporn, Sunchai

BACKGROUND The WU polyomavirus (WUPyV) is a small DNA virus (family Polyomaviridae) that contains a circular double-stranded DNA genome, approximately 5 kb in length. WUPyV was first discovered in the respiratory tract of children with acute respiratory symptoms. OBJECTIVE This study focuses on the complete genome characterization and phylogenetic analysis of WUPyV obtained from Thai patients with respiratory diseases in 2013. MATERIAL AND METHOD DNA was extracted from nasopharyngeal (NP) suction specimens (n = 614) from patients with respiratory tract infections. WUPyV was detected by using semi-nested PCR and then characterized by whole genome sequencing. The nucleotides and deduced amino acid sequences were analyzed by multiple sequences alignment and phylogenetic tree. RESULTS Analysis revealed that 0.16% (1/614) of the sample was positive for WUPyV. Phylogenetic trees demonstrated that WUPyV(isolate CU_Chonburi 3) was closely related to previously described WUPyV. Moreover, whole genome sequences alignment of WUPyV showed several nucleotide variations within non-coding regions and amino acid changes in VP1 (position S347T); VP2 (positions L40V, G120R, Y121I, P123R, G127S, L137F, Q287R, and A327V); LTAg (positions Q357P, V369E, E377K, D378V, A381T, R382E, R383G, and D389G); and, STAg (positions R139S, K141E, R148K, and W153C). CONCLUSION Nucleotide variations within non-coding regions and critical amino acid substitutions in viral proteins may affect the rate of viral replication and viral adaptation; factors that may be linked to the susceptibility and severity of viral infection. Data obtained from this study may be useful in better understanding the genetic characterization and mutation patterns of WUPyV.