New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban <i>Rattus norvegicus</i> Using Circular DNA Enrichment and Metagenomics

<div><p><i>Rattus norvegicus</i> (<i>R</i>. <i>norvegicus</i>) are ubiquitous and their presence has several effects on the human populations in our urban areas on a global scale. Both historically and presently, this close interaction has facilitated the dissemination of many pathogens to humans, making screening for potentially zoonotic and emerging viruses in rats highly relevant. We have investigated faecal samples from <i>R</i>. <i>norvegicus</i> collected from urban areas using a protocol based on metagenomic enrichment of circular DNA genomes and subsequent sequencing. We found a new type of papillomavirus, with a L1 region 82% identical to that of the known <i>R</i>. <i>norvegicus</i> Papillomavirus 2. Additionally, we found 20 different circular replication associated protein (Rep)-encoding single stranded DNA (CRESS-DNA) virus-like genomes, one of which has homology to the replication-associated gene of Beak and feather disease virus. Papillomaviruses are a group of viruses known for their carcinogenic potential, and although they are known to infect several different vertebrates, they are mainly studied and characterised in humans. CRESS-DNA viruses are found in many different environments and tissue types. Both papillomaviruses and CRESS-DNA viruses are known to have pathogenic potential and screening for novel and known viruses in <i>R</i>. <i>norvegicus</i> could help identify viruses with pathogenic potential.</p></div

Subset of phylogenetic relationship among the papillomavirus L1 genes and L1 genes from the RnPV3 and RnPV2-variants identified in this study.

<p>The bootstraps values presented were inferred from 1000 bootstrap replicates. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141952#pone.0141952.s002" target="_blank">S2 Fig</a> for a complete tree of 289 L1 genes, the RnPV3 L1 gene and the RnpV2 type variant L1 genes.</p

Additional file 2: Table S2. of Cancer associated fibroblasts (CAFs) are activated in cutaneous basal cell carcinoma and in the peritumoural skin

The list contains the 65 genes coding for extracellular matrix components or enzymes involved in matrix metabolism that were found upregulated in BCC. (DOCX 18 kb

Additional file 1: Table S1. of Cancer associated fibroblasts (CAFs) are activated in cutaneous basal cell carcinoma and in the peritumoural skin

The number of reads in the mRNA sequencing analysis and the following reads that were actually mapped. Whereas approximately 97% of all reads mapped to the human genome, duplicate reads constituted a significant fraction leaving only around 48 million unique reads. (DOCX 33 kb

Illumina MiSeq data ITS2 Vascular plants

Contains 12 fastq files corresponding to R1 and R2 data from 6 Illumina MiSeq 250 bp PE sequencing libraries. 130 soil samples from Denmark were amplified with tagged primers (S2F and ITS4) and build into TruSeq PCR free libraries. Each sample was amplified in triplicates. Fastq files R1A and R1B contain reads from the first replicates, R2A and R2B from the second, etc. Data were produced as part of the Biowide (Biodiversity in width and depth), carryied out in Denmark from 2014-2018) supported by the Villum foundation. The vascular plant data included here was used in the validation of the LULU algorithm for post-clustering curation of OTU tables for reliable biodiversity metrics, as described in the publication. Tagging scheme and other information needed to demultiplex and analyse the data are accessible on the GitHub repository accompanying the publication/r-package

Quantity of virus in complex control sample material.

<p>HIV-1; Human Immunodeficiency Virus type-1, HPV-18; Human papillomavirus type 18, HAdV; Human Adenovirus C, EV; Enterovirus B Coxsackievirus B3, MeV; Measles virus, aRNA; armored RNA.</p><p>Quantity of virus in complex control sample material.</p

Rarefaction analysis showing the covered proportion of the EV genome as a function of the total number of sequence reads from each sample for RNA shotgun sequencing.

<p>Numbers provided for each sample are given as copies/μl in the test sample.</p

Expected and observed proportion of reads in RNA shotgun libraries.

<p>ND: None detected.</p><p>* Proportions expressed in ppm.</p><p>^# Value defined by the observed.</p><p>Expected and observed proportion of reads in RNA shotgun libraries.</p

Sequencing required to reach threshold coverage of viral target genomes.

<p>Sequencing required to reach threshold coverage of viral target genomes.</p

Expected and observed proportion of reads in DNA shotgun libraries.

<p>* Proportions expressed in ppm.</p><p>Expected and observed proportion of reads in DNA shotgun libraries.</p