Extension of the viral ecology in humans using viral profile hidden Markov models

<div><p>When human samples are sequenced, many assembled contigs are “unknown”, as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, “vFam”. We used HMMER3 analysis of “unknown” human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family). In summary, we find that analysis using the HMMER3 algorithm and the “vFam” database greatly extended the detection of viruses in biospecimens from humans.</p></div

Number of contigs, classified as virus-related by HMM, stratified by related virus family and types of samples.

<p>FFPE: Formalin-fixed paraffin-embedded tissue specimens.</p

Maximum likelihood phylogenetic tree (PhyML v3.0 www.atgc-montpellier.fr/phyml/) based on the RCR Rep proteins from genbank and 21 previously not described Rep proteins related to <i>Circoviridae</i>, that were found in the present study (shown in black color with the prefix SE).

<p>Maximum likelihood phylogenetic tree (PhyML v3.0 <a href="http://www.atgc-montpellier.fr/phyml/" target="_blank">www.atgc-montpellier.fr/phyml/</a>) based on the RCR Rep proteins from genbank and 21 previously not described Rep proteins related to <i>Circoviridae</i>, that were found in the present study (shown in black color with the prefix SE).</p

Number of contigs classified into different taxonomy groups by blastn and blastx.

<p>Number of contigs classified into different taxonomy groups by blastn and blastx.</p

Factors associated with detection of human papillomavirus (HPV) in the male urethra and expressed prostate secretions (EPS): Multivariate Analysis.

<p>Factors associated with detection of human papillomavirus (HPV) in the male urethra and expressed prostate secretions (EPS): Multivariate Analysis.</p

Human papillomavirus types showing significant excess or deficit in 2-type co-infections, Sweden.

<p>N: number; HPV: human papillomavirus; O: observed; E: expected.</p>a<p>Two thresholds of significance are considered: one based on the Bonferroni method, i.e, 0.0004, and 0.01;</p>b<p>Results are displayed if statistically significant in either women or men;</p>c<p>Urine, urine+genital or vagina, cervix, cervix+urethra, urethra;</p>d<p>Urine, urine+genital, urethra;</p>e<p>As estimated by the Full model.</p

Distribution of background characteristics among 314 women with ASCUS/LSIL index cytologies.

<p>*13 HR types: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68</p><p>**Excluding types 16 and 18</p><p>***24 non-HR types: 6, 11, 26, 40, 42, 53, 54, 55, 61, 62, 64, 66, 67, 69, 70, 71, 72, 73 (MM9), 81, 82 (MM4), 83 (MM7), 84 (MM8), IS39, and CP6108.</p><p>ASCUS: atypical squamous cells of undetermined significance, LSIL: low-grade squamous intraepithelial lesions, HPV: human papillomavirus.</p><p>Distribution of background characteristics among 314 women with ASCUS/LSIL index cytologies.</p

Observed <i>versus</i> expected occurrence for 2-type human papillomavirus infections, 9,949 samples from men, Sweden.

<p>Plus signs represent occurrences of HPV pairs. HPV pairs located in the upper triangle indicate positive clustering, while those located in the lower triangle represent negative clustering between the HPV types involved. There were no significant p-values for joint HPV infections at the chosen significance level of 0.0004.</p

Cumulative incidence of CIN2+ by baseline test result and HR HPV status.

<p>CIN2+: cervical intraepithelial neoplasia grade 2 or worse, ASCUS: atypical squamous cells of undetermined significance, LSIL: low-grade squamous intraepithelial lesions, HR HPV: high-risk human papillomavirus. Log rank p-value: <0.0001</p

Observed <i>versus</i> expected occurrence for 2-type human papillomavirus infections, 31,717 samples from women, Sweden.

<p>Plus signs represent occurrences of HPV pairs. HPV pairs located in the upper triangle indicate positive clustering, while those located in the lower triangle represent negative clustering between the HPV types involved. Three of the p-values for joint HPV infections were significant at the chosen significance level of 0.0004: one positive clustering involving HPV6 with 18; two negative clustering involving the following pairs: HPV51/68, and HPV6/68. Overlaid on the main figure are the occurrences relative to HPV68 (small box on the bottom-right, scaled from 0 to 70) and to HPV6 (small box on the top-left, scaled from 0 to 300). To note, the significant negative cluster involving HPV6/68 appears on both small boxes. HPV68 showed a general tendency to be involved in negative clustering with all other types. The same behaviour was not observed for any other HPV type, including HPV6 that was also involved in 2 significant co-infections, but in opposite directions.</p