Nine Complete Genome Sequences of Cutaneous Human Papillomavirus Genotypes Isolated from Healthy Skin of Individuals Living in Rural He Nan Province, China

Abstract

Nine novel human papillomavirus (HPV) types were isolated from healthy skin of individuals in rural Anyang, China. All of these isolates belong to the genus Gammapapillomavirus. These data will provide us with useful information for a better understanding of PV evolution and the relationship of PV with the host.

GENOME ANNOUNCEMENT

Human papillomavirus (HPV) is one of the most important groups of the PV family, and it can be roughly divided into two tropism groups, cutaneous and mucosal HPV types, which infect the skin and mucosal tissues, respectively (4). The role of cutaneous HPV types in pathogenesis remains unclear (1). Human skin harbors a large spectrum of HPV genotypes, and most of these have previously been unknown (2). Although they show genomic organization similar to that of the mucosal types, cutaneous HPVs present milder relationships with human beings (8). Differences in the pathogenesis of HPVs are based on DNA sequence changes, and analysis of whole genomes allows for unprecedented precision in detailing sequence-level changes that are of potential evolutionary importance (3).

Nine novel HPV genotypes were isolated from normal skin of individuals who are permanent residents of the rural area of Anyang, He Nan province, China. The complete genomes of these nine novel HPV types were amplified through rolling-circle amplification of cellular DNA and subsequent long PCR amplification (6), using corresponding primers of L1 sequences which had initially been amplified from samples. All 9 HPV genomes described here were cloned into pCR-XL-TOPO vectors (Invitrogen) and then sequenced with the 3730xl DNA analyzer system (ABI). Overlapping consensus sequences were assembled with SeqMan5.00 software, and open reading frames (ORF) were predicted using the ORF Finder program.

The sizes of these 9 novel HPV genomes were 7,238 bp (KC1), 7,214 bp (KC2), 7,233 bp (KC3), 7,233 bp (KC4), 7,143 bp (KC5), 7,252 bp (KC6), 7,129 bp (KC7), 7,417 bp (KC8), and 7,212 bp (KC9). All of these genomes contain five early genes, E1, E2, E4, E6, and E7, and two late genes, L1 and L2. Five of these novel HPV genomes (KC1, KC2, KC3, KC7, KC8) do not have start codons for the putative E4 ORF and are suspected to start in the E1 ORF with subsequent splicing into the E4 gene (7). A new PV isolate is defined as containing a genome where the DNA sequence of the L1 ORF differs by more than 10% from the closest known PV type (5). All of these isolates satisfied this criterion, and the most similar PV types to KC1 to KC9 were HPV127 (63.14%), HPV135 (64.15%), HPV95 (67.46%), HPV112 (75.33%), HPV127 (70.25%), HPV126 (71.66%), HPV127 (67.86%), HPV109 (71.13%), and HPV4 (61.65%), respectively, as determined using the PASC global alignments analysis searching for the best matches within papillomavirus family (http://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi?cmdresult=main&id=247). All of these isolates belong to the genus Gammapapillomavirus.

The cloning and sequencing of nine novel HPV genotypes will improve our knowledge of the diversity of PVs which infect humans and will add to the repertoire of human Gammapapillomavirus. This will also provide useful information for research into PV evolution.

Nucleotide sequence accession numbers.

The completed genome sequences of these nine novel HPV genotypes are available in the GenBank under accession numbers JX413109 (KC1), JX413108 (KC2), JX413107 (KC3), JX413106 (KC4), JX444073 (KC5), JX413105 (KC6), JX444072 (KC7), JX413110 (KC8), and JX413104 (KC9).