Viral metagenomics updated the prevalence of human papillomavirus types in anogenital warts.

To investigate the composition of human papillomavirus (HPV) types in anogenital warts (AGWs), viral nucleic acid in 110 AGWs, pooled into 11 specimen pools, were subjected to viral metagenomic analysis. After finding HPV7 in AGWs, conventional PCR screening was performed for HPV7 in other 190 individual AGW specimens. Viral metagenomic results indicated that 29 different types of HPV were recovered, with HPV11 and HPV6 showing the highest proportion of sequence reads. HPV7 was detected in 7 of 11 pools, 5 of which contained abundant HPV7 sequence reads. 24 complete genomes of HPV were acquired in viral metagenomic analysis, including 5 HPV7 genomes, based on which phylogenetic analysis and pairwise sequence comparison were conducted. PCR screening for HPV7 in other 190 individual AGW specimens revealed 25 positive cases (13.16%), of which the amplified fragments were sequenced and confirmed to be HPV7 sequences. Although HPV7 was generally found in hand warts and recently also in warts in toe webs, our data suggested that the role of HPV7 in AGW should be considered in the future clinical test and vaccine development for AGWs.

A novel phage from periodontal pockets associated with chronic periodontitis.

Bacteriophages often constitute the majority of periodontal viral communities, but phages that infect oral bacteria remain uncharacterized. Here, we present the genetic analysis of the genome of a novel siphovirus, named Siphoviridae_29632, which was isolated from a patient with periodontitis using a viral metagenomics-based approach. Among 43 predicted open reading frames (ORFs) in the genome, the viral genes encoding structural proteins were distinct from the counterparts of other viruses, although a distant homology is shared among viral morphogenesis proteins. A total of 28 predicted coding sequences had significant homology to other known phage ORF sequences. In addition, the prevalence of Siphoviridae_29632 in a cohort of patients with chronic periodontitis was 41.67%, which was significantly higher than that in the healthy group (4.55%, P < 0.001), suggesting that this virus as well as its hosts may contribute to the ecological environment favored for chronic periodontitis.

Detection of a new species of torque teno mini virus from the gingival epithelium of patients with periodontitis.

We describe a novel species of torque teno mini virus called TTMV-204, which was isolated from the gingival epithelium of patients with periodontitis and characterized using viral metagenomics. The sequence of the full genome is 2824 nt in length. Phylogenetic analysis and genetic analyses show classic Betatorquevirus species organization with less than 40% amino acid similarity in ORF1. The prevalence of TTMV-204 in the periodontitis patient population was 18.75% (15/80), which was higher than in periodontally healthy individuals (10.00%, 10/80). However, the difference of the TTMV-204 prevalence between two groups was not statistically significant (p = 0.115). Further investigation is required to determine whether this new virus is associated with inflammation.

Determination of bone size of hip, spine, and wrist in human pedigrees by genetic and lifestyle factors.

Osteoporosis is a major public health problem defined as a loss of bone strength, of which bone size is an important determinant. Compared with extensive studies on bone mass, studies on the importance of factors determining variation in bone size are relatively few. In particular, the significance of genetic factors is largely unknown. In 49 pedigrees with 703 subjects bone sizes of the hip, spine, and wrist were measured by dual X-ray absorptiometry. We evaluated the contribution of genetic factors in determining variation in bone size of the hip, spine, and wrist while studying age, sex, weight, height, exercise, smoking, alcohol consumption, and the interaction among these factors as covariates for their effects on bone size. We found that, on average, males have larger bone sizes. Male bone sizes at the spine and hip increased with age; however, the effect of age in our female subjects was nonsignificant. Height invariably affected bone size at all the sites studied. Alcohol consumption and exercise generally had significant effects in increasing bone size at the spine and/or hip in both males and females. After adjusting for sex, age, weight, height, lifestyle factors, and the significant interactions among these factors, heritabilities (+/-SE) were, respectively, 0.48 (0.09), 0.64 (0.08), and 0.60 (0.09) for bone size at the hip, spine, and wrist.