The clinical utility of viral-load and integration status of human papillomavirus (HPV) infection remains uncertain. We examined 75 women infected with HPV58, a worldwide rare type found to be prevalent in cervical cancers in eastern Asia. Viral load was significantly higher for cervical intraepithelial neoplasia (CIN) 1/2, but those for a normal control group and for CIN 3 or cancer overlapped substantially. A pure integrated genome was found for all lesion grades, giving a poor positive predictive value (23.1%) for cancer. The pure episomal form's negative predictive value for cancer was only 76.3%. Mixed patterns of E2 gene disruption were common and often involved the amino-terminal and hinge regions. Disruption of the whole E2 gene was rare and was restricted to high-grade lesions. The HPV58 variant E67-HK-2 was more likely to exist in the pure episomal form. Routinely collected cervical samples contain a heterogeneous population of viruses, hampering the application of viral load and integration testing in clinical settings.