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Recent metagenomics studies have revealed several tick species to host a variety of previously undiscovered RNA viruses. Ixodes ricinus, which is known to be a vector for many viral, bacterial and protozoan pathogens, is the most prevalent tick species in Europe. For this study, we decided to investigate the virosphere of Belgian I. ricinus ticks. High-throughput sequencing of tick pools collected from six different sampling sites revealed the presence of viruses belonging to many different viral orders and families, including Mononegavirales, Bunyavirales, Partitiviridae and Reoviridae. Of particular interest was the detection of several new reoviruses, two of which cluster together with members of the genus Coltivirus. This includes a new strain of Eyach virus, a known causative agent of tick-borne encephalitis. All genome segments of this new strain are highly similar to those of previously published Eyach virus genomes, except for the fourth segment, encoding VP4, which is markedly more dissimilar, potentially indicating the occurrence of a genetic reassortment. Further PCR-based screening of over 230 tick pools for 14 selected viruses showed that most viruses could be found in all six sampling sites, indicating the wide spread of these viruses throughout the Belgian tick population. Taken together, these results illustrate the role of ticks as important virus reservoirs, highlighting the need for adequate tick control measures.

Common or European hedgehogs can be found throughout Western Europe. They are known carriers of a variety of parasitic and bacterial pathogens, and have also been shown to carry several viruses, including morbilli-like paramyxoviruses, although the pathogenic and zoonotic potential of some of these viruses has yet to be determined. We report here the discovery of a novel paramyxovirus in Belgian hedgehogs, named Belerina virus. The virus was detected by nanopore sequencing of RNA isolated from hedgehog tissue. Out of 147 animals screened in this study, 57 tested positive for Belerina virus (39%), indicating a high prevalence of this virus in the Belgian hedgehog population. Based on its divergence from other known paramyxovirus species, Belerina virus is thought to represent a new species in the family Paramyxoviridae. Phylogenetic analysis groups Belerina virus together with the bat-borne Shaan virus within the genus Jeilongvirus, although expanding the tree with partial genomes shows Belerina virus forming a separate subclade within this genus, alongside a yet-unnamed paramyxovirus isolated from a greater tube-nosed bat. In summary, we discuss the complete genome sequence of Belerina virus, a putative new paramyxovirus species commonly found in Belgian hedgehogs.

Recent metagenomics studies have revealed several arthropod species to be major reservoirs for RNA viruses. One of these reservoirs is Ixodes ricinus, the most prevalent tick species in Europe, which is known to be a vector for many viral and bacterial pathogens. For this study, we decided to investigate the virosphere of Belgian Ixodes ricinus ticks. High-throughput sequencing of tick pools collected from six different sampling sites revealed the presence of viruses belonging to many different viral orders and families, including Mononegavirales, Bunyavirales, Partitiviridae, and Reoviridae. Of particular interest was the detection of several putative human pathogens, including members of the families Nairoviridae and Phenuiviridae as well as three new reoviruses, two of which cluster together with members of the genus Coltivirus. One of these two viruses represents a new strain of Eyach virus, a known causative agent of tick-borne encephalitis. All genome segments of this new strain are highly similar to those of previously published Eyach virus genomes, except for the fourth segment, encoding VP4, which is markedly more dissimilar, potentially indicating the occurrence of an antigenic shift. Further PCR-based screening of over 200 tick pools for 11 selected viruses showed that most viruses could be found in all six sampling sites, indicating the wide spread of these viruses throughout the Belgian tick population. Taken together, these results illustrate the role of ticks as important virus reservoirs, highlighting the need for adequate tick control measures.

Because of the enormous variation in their genome sequence, genotyping enteroviruses by standard methods can prove to be quite challenging. Nanopore sequencing offers the potential to overcome the limitations of older techniques, but thus far, only amplicon-based strategies have been used to sequence complete enterovirus genomes. By combining a sequence-independent, single primer amplification (SISPA) for cDNA generation with next-generation sequencing using the Oxford Nanopore MinION, complete enterovirus genomes can be obtained in an easy-to-use, sequence-independent manner. To demonstrate its usability, we applied this technique to determine the complete genome sequence of an enterovirus C104 strain, representing the first documented occurrence of this uncommon enterovirus strain in Belgium.

Background Diagnostic procedures for the diagnosis of infection with the nematode parasite Onchocerca volvulus are currently based on the microscopic detection of microfilariae in skin biopsies. Alternative approaches based on amplification of parasitic DNA in these skin biopsies are currently being explored. Mostly this is based on the detection of the O-150 repeat sequence using PCR based techniques. Methods An isothermal, loop-mediated amplification method has been designed using the mitochondrial O. volvulus cox1 gene as a target. Results Analysis of dilution series of synthetic DNA containing the targeted sequence show a non-linear dose-response curve, as is usually the case for isothermal amplification methods. Evaluation of cross-reactivity with the heterologous sequence from the closely related parasites Wuchereria bancrofti, Loa loa and Brugia malayi demonstrated strong specificity, as none of these sequences was amplified. The assay however amplified both O. volvulus and O. ochengi DNA, but with a different melting point that can be used to discriminate between the species. Evaluation of this assay in a set of skin snip biopsies collected in an endemic area in Ghana showed a high correlation with O-150 qPCR and also demonstrated a similar sensitivity. Compared to qPCR, LAMP had a sensitivity of 88.2% and a specificity of 99.2%. Conclusions We have developed a sensitive and specific loop-mediated amplification method for detection of O. volvulus DNA in skin biopsies that is capable of providing results within 30 min. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1913-7) contains supplementary material, which is available to authorized users.

In SIV-infected adult Macaca mulatta, increases in monocyte turnover indicates death of short-lived tissue macrophages and predicts SAIDS. Increased turnover also correlates with infection, not death, of long-lived tissue macrophages. Higher baseline monocyte turnover is measured in neonates, and faster disease progression. Our data shows increase in monocyte turnover and tissue macrophage infection is associated with rapid SAIDS progression in infants. We hypothesize early and high infection of macrophages results in establishment of viral reservoir in long-lived subsets, in infants not controlling viral load despite antiretroviral therapy (ART). In rhesus infants infected with SIVmac251, cell turnover is measured using BrdU uptake. Flow cytometry and confocal imaging allow phenotypic characterization of cells in blood and tissues. PCR and in situ hybridization are used to quantify SIV. Plasma cytokine analysis is performed using Milliplex bead panel. Infant macaques euthanized post-infection (no ART) are used to quantify macrophage infection. Animals euthanized after various lengths of ART provide data on reservoir seeding, viral persistence and immune activation status. ART-treated infants with discordant viral loads are evaluated to identify the source of viral replication. In treated animals, regardless of viral load, no differences are observed in activation status, absolute number, or kinetics of CD4 and CD8 T cells. Confocal imaging and viral RNA and DNA analysis of tissues and sorted cells should confirm that viral replication during ART is due to infected macrophages. Ongoing works suggest magnitude of long-lived macrophage infection may dictate effectiveness of ART in pediatric SIV infection.