Genetic variation of human papillomavirus type 16 in individual clinical specimens revealed by deep sequencing.
Viral genetic diversity within infected cells or tissues, called viral quasispecies, has been mostly studied for RNA viruses, but has also been described among DNA viruses, including human papillomavirus type 16 (HPV16) present in cervical precancerous lesions. However, the extent of HPV genetic variation in cervical specimens, and its involvement in HPV-induced carcinogenesis, remains unclear. Here, we employ deep sequencing to comprehensively analyze genetic variation in the HPV16 genome isolated from individual clinical specimens. Through overlapping full-circle PCR, approximately 8-kb DNA fragments covering the whole HPV16 genome were amplified from HPV16-positive cervical exfoliated cells collected from patients with either low-grade squamous intraepithelial lesion (LSIL) or invasive cervical cancer (ICC). Deep sequencing of the amplified HPV16 DNA enabled de novo assembly of the full-length HPV16 genome sequence for each of 7 specimens (5 LSIL and 2 ICC samples). Subsequent alignment of read sequences to the assembled HPV16 sequence revealed that 2 LSILs and 1 ICC contained nucleotide variations within E6, E1 and the non-coding region between E5 and L2 with mutation frequencies of 0.60% to 5.42%. In transient replication assays, a novel E1 mutant found in ICC, E1 Q381E, showed reduced ability to support HPV16 origin-dependent replication. In addition, partially deleted E2 genes were detected in 1 LSIL sample in a mixed state with the intact E2 gene. Thus, the methods used in this study provide a fundamental framework for investigating the influence of HPV somatic genetic variation on cervical carcinogenesis.
Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.
Iwao
I
Kukimoto
Tomohiko
T
Maehama
Tsuyoshi
T
Sekizuka
Yumiko
Y
Ogasawara
Kazunari
K
Kondo
Rika
R
Kusumoto-Matsuo
Seiichiro
S
Mori
Yoshiyuki
Y
Ishii
Takamasa
T
Takeuchi
Toshiyuki
T
Yamaji
Fumihiko
F
Takeuchi
Kentaro
K
Hanada
Makoto
M
Kuroda
D019943:Amino Acid Substitution; D001483:Base Sequence; D002460:Cell Line; D004279:DNA, Viral; D005260:Female; D023061:Gene Order; D014644:Genetic Variation; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D052162:Human papillomavirus 16 / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D059645:Mutation Rate; D009856:Oncogene Proteins, Viral / Q000235:genetics; D030361:Papillomavirus Infections / Q000821:virology; D016415:Sequence Alignment; D017384:Sequence Deletion; D002583:Uterine Cervical Neoplasms / Q000473:pathology / Q000821:virology; D014779:Virus Replication
D004279:DNA, Viral; C093478:E1 protein, Human papillomavirus 16; D009856:Oncogene Proteins, Viral