Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing

• Published in: Proceedings of the National Academy of Sciences - PNAS 2013-06, Vol.110 (25), p.10264-10269
• Main Authors: Xu, Baoyan, Zhi, Ning, Hu, Gangqing, Wan, Zhihong, Zheng, Xiaobin, Liu, Xiaohong, Wong, Susan, Kajigaya, Sachiko, Zhao, Keji, Mao, Qing, Young, Neal S.
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Aged; Amino acids; Anemia, Aplastic - epidemiology; Anemia, Aplastic - virology; Asian Continental Ancestry Group - statistics & numerical data; Biological Sciences; Child; China - epidemiology; Circoviridae - genetics; Deoxyribonucleic acid; DNA; DNA, Viral - genetics; Evolution, Molecular; Female; Genomes; Hepatitis; Hepatitis Antibodies - blood; Hepatitis, Viral, Human - epidemiology; Hepatitis, Viral, Human - virology; High-Throughput Nucleotide Sequencing; Humans; Infections; Male; Middle Aged; Molecular Sequence Data; Parvoviridae; Parvoviridae - genetics; Parvovirus; Phylogenetics; Phylogeny; Polymerase chain reaction; Prevalence; Proteins; Risk Factors; Seroepidemiologic Studies; Viruses; Young Adult
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1303744110

Seronegative hepatitis—non-A, non-B, non-C, non-D, non-E hepatitis—is poorly characterized but strongly associated with serious complications. We collected 92 sera specimens from patients with non-A–E hepatitis in Chongqing, China between 1999 and 2007. Ten sera pools were screened by Solexa deep sequencing. We discovered a 3,780-bp contig present in all 10 pools that yielded BLASTx E scores of 7e-05–0.008 against parvoviruses. The complete sequence of the in silico -assembled 3,780-bp contig was confirmed by gene amplification of overlapping regions over almost the entire genome, and the virus was provisionally designated NIH-CQV. Further analysis revealed that the contig was composed of two major ORFs. By protein BLAST, ORF1 and ORF2 were most homologous to the replication-associated protein of bat circovirus and the capsid protein of porcine parvovirus, respectively. Phylogenetic analysis indicated that NIH-CQV is located at the interface of Parvoviridae and Circoviridae . Prevalence of NIH-CQV in patients was determined by quantitative PCR. Sixty-three of 90 patient samples (70%) were positive, but all those from 45 healthy controls were negative. Average virus titer in the patient specimens was 1.05 e4 copies/µL. Specific antibodies against NIH-CQV were sought by immunoblotting. Eighty-four percent of patients were positive for IgG, and 31% were positive for IgM; in contrast, 78% of healthy controls were positive for IgG, but all were negative for IgM. Although more work is needed to determine the etiologic role of NIH-CQV in human disease, our data indicate that a parvovirus-like virus is highly prevalent in a cohort of patients with non-A–E hepatitis.