Genotypes of human polyomaviruses in urine samples of pregnant women in Taiwan

The viral DNA of human polyomaviruses JC virus (JCV) and BK virus (BKV) was detected by the polymerase chain reaction (PCR) in urine samples from 31 pregnant women in Taiwan. A pair of appropriate primers amplified both JCV and BKV DNA of the regulatory region simultaneously in PCR. An oligonucleotide probe homologous to both JCV and BKV regulatory region was used subsequently to detect the viral DNA by Southern blotting after PCR amplification. Approximately 36% of the examined urine samples were human polyomavirus positive. The genotypes of JCV and BKV were determined by DNA sequencing of their regulatory regions. Besides CY archetype, a new strain (Taiwan‐1) of JCV with a pentanucleotide (GGGAA) deletion and a new strain (Taichung‐1) of BKV with two nucleotide alterations within the regulatory region were found in the urine samples. Eight of the examined samples were JCV infected, one was BKV infected, and two were JCV and BKV mix‐infected. The JCV positive individuals were infected by CY archetype and Taiwan‐1 strain equally. However, Taichung‐1 strain was the only BKV strain found in the BKV positive individuals. © 1996 Wiley‐Liss, Inc.