Sequence, assembly and count datasets of viruses associated to the pine processionary moth Thaumetopoea pityocampa (Denis & Schiffermüller) (Lepidoptera, Notodontidae) identified from transcriptomic high-throughput sequencing.

The pine processionary moth Thaumetopoea pityocampa is a Lepidopteran pest species occurring in the Western Mediterranean. It causes heavy pine defoliations and it is a public and animal health concern because of its urticating caterpillars. Very little is known about the viruses associated to this species, as only two viruses were described so far. We here present a dataset corresponding to 34 viral transcripts, among which 27 could be confidently assigned to 9 RNA and DNA viral families (Iflaviridae, Reoviridae, Partitiviridae, Permutotetraviridae, Flaviviridae, Rhabdoviridae, Parvoviridae, Baculoviridae and PolyDNAviridae). These transcripts were identified from an original transcriptome assembled for the insect host, using both blast search and phylogenetic approaches. The data were acquired from 2 populations in Portugal and 2 populations in Italy. The transcripts were de novo assembled and used to identify viral sequences by homology searches. We also provide information about the populations and life stages in which each virus was identified. The data produced will allow to enrich the virus taxonomy in Lepidopteran hosts, and to develop PCR-based diagnostic tools to screen colonies across the range and determine the distribution and prevalence of the identified viral species.

SILVI, an open-source pipeline for T-cell epitope selection.

High-throughput screening of available genomic data and identification of potential antigenic candidates have promoted the development of epitope-based vaccines and therapeutics. Several immunoinformatic tools are available to predict potential epitopes and other immunogenicity-related features, yet it is still challenging and time-consuming to compare and integrate results from different algorithms. We developed the R script SILVI (short for: from in silico to in vivo), to assist in the selection of the potentially most immunogenic T-cell epitopes from Human Leukocyte Antigen (HLA)-binding prediction data. SILVI merges and compares data from available HLA-binding prediction servers, and integrates additional relevant information of predicted epitopes, namely BLASTp alignments with host proteins and physical-chemical properties. The two default criteria applied by SILVI and additional filtering allow the fast selection of the most conserved, promiscuous, strong binding T-cell epitopes. Users may adapt the script at their discretion as it is written in open-source R language. To demonstrate the workflow and present selection options, SILVI was used to integrate HLA-binding prediction results of three example proteins, from viral, bacterial and parasitic microorganisms, containing validated epitopes included in the Immune Epitope Database (IEDB), plus the Human Papillomavirus (HPV) proteome. Applying different filters on predicted IC50, hydrophobicity and mismatches with host proteins allows to significantly reduce the epitope lists with favourable sensitivity and specificity to select immunogenic epitopes. We contemplate SILVI will assist T-cell epitope selections and can be continuously refined in a community-driven manner, helping the improvement and design of peptide-based vaccines or immunotherapies. SILVI development version is available at: github.com/JoanaPissarra/SILVI2020 and https://doi.org/10.5281/zenodo.6865909.

Coding-Complete Genome Sequences of an Iteradensovirus and an Alphapermutotetra-Like Virus Identified from the Pine Processionary Moth (Thaumetopoea pityocampa) in Portugal.

The coding-complete genome sequences of an iteradensovirus (family Parvoviridae) and an alphapermutotetra-like virus (family Permutotetraviridae) were discovered from transcriptomic data sets obtained from Thaumetopoea pityocampa larvae collected in Portugal. Each of the coding-complete genome sequences of these viruses contains three main open reading frames (ORFs).

Coding-Complete Genome Sequence of a Partitivirus Isolated from Pine Processionary Moth Eggs.

Two coding-complete nucleotide sequences of a partitivirus (family Partitiviridae) were discovered in transcriptomic data sets obtained from eggs of the Lepidoptera Thaumetopoea pityocampa Each segment encodes a single open reading frame, and these two segments are predicted to encode an RNA-dependent RNA polymerase and a coat protein, respectively.

Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools.

Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. Nevertheless, assigning ancient DNA at the species level is a challenging process. Recently, the gut microbiome analysis of three pre-Columbian Andean mummies (Santiago-Rodriguez et al., 2016) has called into question the identification of Leishmania in South America. The accurate assignment would be important because it will provide some key elements that are linked to the evolutionary scenario for visceral leishmaniasis agents in South America. Here, we recovered the metagenomic data filed in the metagenomics RAST server (MG-RAST) to identify the different members of the Trypanosomatidae family that have infected these ancient remains. For this purpose, we used the ultrafast metagenomic sequence classifier, based on an exact alignment of k-mers (Kraken) and Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The analyses, which have been conducted on the most exhaustive genomic database possible on Trypanosomatidae, show that species assignments could be biased by a lack of some genomic sequences of Trypanosomatidae species (strains). Nevertheless, our work raises the issue of possible co-infections by multiple members of the Trypanosomatidae family in these three pre-Columbian mummies. In the three mummies, we show the presence of DNA that is reminiscent of a probable co-infection with Leptomonas seymouri, a parasite of insect's gut, and Lotmaria.

Immunodetection and molecular determination of visceral and cutaneous Leishmania infection using patients' urine.

The diagnosis of leishmaniasis relies mainly on the use of invasive processes, to collect the biological material for detecting Leishmania parasites. Body fluids, which can be collected by non-invasive process, would greatly facilitate the leishmaniasis diagnosis. In the present study, we investigated the potency of urine immunoblotting to diagnose cutaneous and visceral leishmaniasis and we compared with routine molecular methods. A total of 80 samples, including 40 sera and their 40 corresponding urine samples were collected from 37 suspected patients with cutaneous and visceral leishmaniasis, and 3 healthy individuals (as control), in Ilam and Ardabil provinces of Iran. All sera and urine samples were analyzed, using immunoblotting. The confirmation of leishmaniasis infection was performed, using conventional and quantitative PCRs as well as by sequencing the amplicons. Among 37 suspected patients, 23 patients presented cutaneous lesions (CL) and 14 exhibited clinical symptoms reminiscent of visceral leishmaniasis (L. infantum). Among cutaneous patients, 15 were positive for zoonotic cutaneous leishmaniasis (L. major), and eight for anthroponotic cutaneous leishmaniasis (L. tropica). Molecular quantification of Leishmania parasites was performed on sera, urines and cutaneous biopsies of CL and VL patients, demonstrating that parasite load is lower in urines, compared to sera or biopsy. DNA can be detected in 20 out of 23 (86.9%) CL urine samples and in 13 out of 14 (92.8%) VL urine samples. Immunodetection analysis demonstrates that 22 out of 23 (95.6%) sera from CL patients and all patients suspected with VL are positive. For urine samples, 18 out of 23 (78.2%) urine of CL patients and 13 out of 14 (92.8%) urine of VL patients were positive, using Western blot. Therefore, immunodetection and molecular analysis using urine samples can be used as a diagnostic tool for surveying cutaneous and visceral leishmaniasis.

What pre-Columbian mummies could teach us about South American leishmaniases?

A recent report on the taxonomic profile of the human gut microbiome in pre-Columbian mummies (Santiago-Rodriguez et al. 2016) gives for the first time evidence of the presence of Leishmania DNA (sequences similar to Leishmania donovani according to the authors) that can be reminiscent of visceral leishmaniasis during the pre-Columbian era. It is commonly assumed that Leishmania infantum, the etiological agent of American visceral leishmaniasis (AVL) was introduced into the New World by the Iberian conquest. This finding is really surprising and must be put into perspective with what is known from an AVL epidemiological and historical point of view. Beside L. infantum, there are other species that are occasionally reported to cause AVL in the New World. Among these, L. colombiensis is present in the region of pre-Columbian mummies studied. Other explanations for these findings include a more ancient introduction of a visceral species of Leishmania from the Old World or the existence of a yet unidentified endemic species causing visceral leishmaniasis in South America. Unfortunately, very few molecular data are known about this very long pre-Columbian period concerning the circulating species of Leishmania and their diversity in America.

An integrated overview of the midgut bacterial flora composition of Phlebotomus perniciosus, a vector of zoonotic visceral leishmaniasis in the Western Mediterranean Basin.

BACKGROUND: The Leishmania developmental life cycle within its sand fly vector occurs exclusively in the lumen of the insect's digestive tract in the presence of symbiotic bacteria. The composition of the gut microbiota and the factors that influence its composition are currently poorly understood. A set of factors, including the host and its environment, may influence this composition. It has been demonstrated that the insect gut microbiota influences the development of several human pathogens, such as Plasmodium falciparum. For sand flies and Leishmania, understanding the interactions between the parasite and the microbial environment of the vector midgut can provide new tools to control Leishmania transmission. METHODOLOGY/PRINCIPAL FINDINGS: The midguts of female Phlebotomus perniciosus from laboratory colonies or from the field were collected during the months of July, September and October 2011 and dissected. The midguts were analyzed by culture-dependent and culture-independent methods. A total of 441 and 115 cultivable isolates were assigned to 30 and 11 phylotypes from field-collected and colonized P. perniciosus, respectively. Analysis of monthly variations in microbiota composition shows a species diversity decline in October, which is to the end of the Leishmania infantum transmission period. In parallel, a compilation and a meta-analysis of all available data concerning the microbiota of two Psychodidae genera, namely Phlebotomus and Lutzomyia, was performed and compared to P. perniciosus, data obtained herein. This integrated analysis did not reveal any substantial divergences between Old and New world sand flies with regards to the midgut bacterial phyla and genera diversity. But clearly, most bacterial species (>76%) are sparsely distributed between Phlebotominae species. CONCLUSION/SIGNIFICANCE: Our results pinpoint the need for a more exhaustive understanding of the bacterial richness and abundance at the species level in Phlebotominae sand flies in order to capture the role of midgut bacteria during Leishmania development and transmission. The occurrence of Bacillus subtilis in P. perniciosus and at least two other sand fly species studied so far suggests that this bacterial species is a potential candidate for paratransgenic or biolological approaches for the control of sand fly populations in order to prevent Leishmania transmission.

Assessing species distribution using Google Street View: a pilot study with the Pine Processionary Moth.

Mapping species spatial distribution using spatial inference and prediction requires a lot of data. Occurrence data are generally not easily available from the literature and are very time-consuming to collect in the field. For that reason, we designed a survey to explore to which extent large-scale databases such as Google maps and Google Street View could be used to derive valid occurrence data. We worked with the Pine Processionary Moth (PPM) Thaumetopoea pityocampa because the larvae of that moth build silk nests that are easily visible. The presence of the species at one location can therefore be inferred from visual records derived from the panoramic views available from Google Street View. We designed a standardized procedure allowing evaluating the presence of the PPM on a sampling grid covering the landscape under study. The outputs were compared to field data. We investigated two landscapes using grids of different extent and mesh size. Data derived from Google Street View were highly similar to field data in the large-scale analysis based on a square grid with a mesh of 16 km (96% of matching records). Using a 2 km mesh size led to a strong divergence between field and Google-derived data (46% of matching records). We conclude that Google database might provide useful occurrence data for mapping the distribution of species which presence can be visually evaluated such as the PPM. However, the accuracy of the output strongly depends on the spatial scales considered and on the sampling grid used. Other factors such as the coverage of Google Street View network with regards to sampling grid size and the spatial distribution of host trees with regards to road network may also be determinant.