Schematic of the African elephant polyomavirus 1 (AelPyV-1) genome organization.

<p>Schematic of the African elephant polyomavirus 1 (AelPyV-1) genome organization.</p

Nucleotide-based maximum likelihood phylogenetic analysis of the large T antigen open-reading frame of AelPyV-1 and 61 other polyomaviruses.

<p>The numbers at the internal nodes represent significant bootstrap support values, determined from 10,000 iterations. The scale bar indicates the genetic distance in nucleotide substitutions per site.</p

Amino acid-based neighbor-joining analysis of (A) the major capsid protein VP1, (B) the minor capsid protein VP2, (C) the large T antigen, and (D) the small T antigen.

<div><p>The numbers at the internal nodes represent significant bootstrap support values determined from 10,000 iterations. The scale bar indicates the genetic distance in amino acid substitutions per site.</p> <p>Genbank accession numbers: <i>African green </i><i>monkey </i><i>polyomavirus</i>, NC_004763; <i>Bovine </i><i>polyomavirus</i>, NC_001442; <i>Cebus albifrons </i><i>polyomavirus 1</i>, NC_019854; <i>Crow </i><i>polyomavirus</i>, NC_007922; <i>Finch </i><i>polyomavirus</i>, NC_007923; <i>Hamster </i><i>polyomavirus</i>, NC_001663; <i>Human </i><i>polyomavirus 2</i> (JC), NC_001699; <i>Human </i><i>polyomavirus 3</i> (KI), NC_009238; <i>Human </i><i>polyomavirus 4</i> (WU), NC_009539; <i>Human </i><i>polyomavirus 5</i> (Merkel cell), JQ479318; <i>Human </i><i>polyomavirus 7</i>, NC_014407; <i>Human </i><i>polyomavirus 9</i>, NC_015150; <i>Murine </i><i>pneumotropic </i><i>virus</i>, NC_001505; <i>Pteronotus polyomavirus</i>, NC_020070; <i>Squirrel </i><i>monkey </i><i>polyomavirus</i>, NC_009951; <i>Vervet monkey </i><i>polyomavirus 1</i>, NC_019844.</p> <p>PyV: Polyomavirus.</p></div

Lesions found on the trunks of the elephants.

<p>(a) Nodular lesion as seen on the trunks of three elephants; (b) Protruding ulcerated fibroma, from which the biopsy was taken; (c) Interface between the fibroblastic mass and proliferative dermis; (d) Whirling fibroblasts with prominent collagen deposits.</p

A lethal disease model for New World hantaviruses using immunosuppressed Syrian hamsters

<div><p>Background</p><p>Hantavirus, the hemorrhagic causative agent of two clinical diseases, is found worldwide with variation in severity, incidence and mortality. The most lethal hantaviruses are found on the American continent where the most prevalent viruses like Andes virus and Sin Nombre virus are known to cause hantavirus pulmonary syndrome. New World hantavirus infection of immunocompetent hamsters results in an asymptomatic infection except for Andes virus and Maporal virus; the only hantaviruses causing a lethal disease in immunocompetent Syrian hamsters mimicking hantavirus pulmonary syndrome in humans.</p><p>Methodology/Principal findings</p><p>Hamsters, immunosuppressed with dexamethasone and cyclophosphamide, were infected intramuscularly with different New World hantavirus strains (Bayou virus, Black Creek Canal virus, Caño Delgadito virus, Choclo virus, Laguna Negra virus, and Maporal virus). In the present study, we show that immunosuppression of hamsters followed by infection with a New World hantavirus results in an acute disease that precisely mimics both hantavirus disease in humans and Andes virus infection of hamsters.</p><p>Conclusions/ Significance</p><p>Infected hamsters showed specific clinical signs of disease and moreover, histological analysis of lung tissue showed signs of pulmonary edema and inflammation within alveolar septa. In this study, we were able to infect immunosuppressed hamsters with different New World hantaviruses reaching a lethal outcome with signs of disease mimicking human disease.</p></div

Survival curves of golden Syrian hamsters infected with New World hantaviruses.

<p>A) Infection with New World hantaviruses (BAYV, BCCV, CDV, SNV and ANDV) leading to a mortality rate of 100%. B) Infection with New World hantaviruses leading to a mortality rate of 75% for CHOV and 50% for LNV and MAPV. BAYV, CDV, BCCV, ANDV and SNV, Log-rank: p value <0.0001, Gehan-Breslow-Wilcoxon: p value = 0.0002; LNV and MAPV, Log-rank: p value = 0.0251, Gehan-Breslow-Wilcoxon: p value = 0.0265; and CHOV; Log-rank: p value = 0.0024, Gehan-Breslow-Wilcoxon: p value = 0.0032.</p

Dexamethasone and cyclophosphamide dosing scheme.

<p>Dexamethasone and cyclophosphamide dosing scheme.</p

Histology of lung tissue from BAYV-, BCCV- and uninfected immunosuppressed hamsters.

<p>A) Lung biopsy showing a diffuse acute inflammation. Alveoli are filled with edema, mostly polymorphic inflammatory cells and fibrin (H&E x 100; Black Creek Canal virus group). B) Lung biopsy showing severe hemorrhagic edema in the alveoli, spilling over in the bronchiolar lumen (H&E x 100; Bayou virus group) C) Lung biopsy showing normal alveolar parenchyma and bronchioles (H&E x 100; Dex-Cyp control group).</p

Circulation of HRSV in Belgium: From Multiple Genotype Circulation to Prolonged Circulation of Predominant Genotypes

<div><p>Molecular surveillance of HRSV in Belgium for 15 consecutive seasons (1996–2011) revealed a shift from a regular 3-yearly cyclic pattern, into a yearly alternating periodicity where HRSV-B is replaced by HRSV-A. Phylogenetic analysis for HRSV-A demonstrated the stable circulation of GA2 and GA5, with GA2 being dominant over GA5 during 5 consecutive seasons (2006–2011). We also identified 2 new genotype specific amino acid mutations of the GA2 genotype (A122 and Q156) and 7 new GA5 genotype specific amino acid mutations (F102, I108, T111, I125, D161, S191 and L217). Several amino acid positions, all located in the second hypervariable region of HRSV-A were found to be under positive selection. Phylogenetic analysis of HRSV-B showed the circulation of GB12 and GB13, where GB13 represented 100% of the isolated strains in 4 out of 5 consecutive seasons (2007–2011). Amino acids under positive selection were all located in the aminoterminal hypervariable region of HRSV-B, except one amino acid located in the conserved region. The genotype distribution within the HRSV-B subgroup has evolved from a co-circulation of multiple genotypes to the circulation of a single predominant genotype. The Belgian GB13 strains circulating since 2006, all clustered under the BAIV branch and contained several branch specific amino acid substitutions. The demographic history of genotypes GA2, GA5 and GB13 demonstrated a decrease in the total GA2 and GA5 population size, coinciding with the global expansion of the GB13 population. The emergence of the GB13 genotype resulted in a newly established balance between the predominant genotypes.</p> </div

A Method Enabling High-Throughput Sequencing of Human Cytomegalovirus Complete Genomes from Clinical Isolates

<div><p>Human cytomegalovirus (HCMV) is a ubiquitous virus that can cause serious sequelae in immunocompromised patients and in the developing fetus. The coding capacity of the 235 kbp genome is still incompletely understood, and there is a pressing need to characterize genomic contents in clinical isolates. In this study, a procedure for the high-throughput generation of full genome consensus sequences from clinical HCMV isolates is presented. This method relies on low number passaging of clinical isolates on human fibroblasts, followed by digestion of cellular DNA and purification of viral DNA. After multiple displacement amplification, highly pure viral DNA is generated. These extracts are suitable for high-throughput next-generation sequencing and assembly of consensus sequences. Throughout a series of validation experiments, we showed that the workflow reproducibly generated consensus sequences representative for the virus population present in the original clinical material. Additionally, the performance of 454 GS FLX and/or Illumina Genome Analyzer datasets in consensus sequence deduction was evaluated. Based on assembly performance data, the Illumina Genome Analyzer was the platform of choice in the presented workflow. Analysis of the consensus sequences derived in this study confirmed the presence of gene-disrupting mutations in clinical HCMV isolates independent from <i>in vitro</i> passaging. These mutations were identified in genes RL5A, UL1, UL9, UL111A and UL150. In conclusion, the presented workflow provides opportunities for high-throughput characterization of complete HCMV genomes that could deliver new insights into HCMV coding capacity and genetic determinants of viral tropism and pathogenicity.</p></div