Full mitochondrial and nuclear genome comparison confirms that Onchocerca sp. "Siisa" is Onchocerca ochengi

Potential of Onchocerca ochengi inosine-5'-monophosphate dehydrogenase (IMPDH) and guanosine-5'-monophosphate oxidoreductase (GMPR) as druggable and vaccine candidates: immunoinformatics screening

Onchocerciasis is a vector-borne disease caused by the filarial nematode Onchocerca volvulus, which is responsible for most of the visual impairments recorded in Africa, Asia and the Americas. It is known that O. volvulus has similar molecular and biological characteristics as Onchocerca ochengi in cattle. This study was designed to screen for immunogenic epitopes and binding pockets of O. ochengi IMPDH and GMPR ligands using immunoinformatic approaches. In this study, a total of 23 B cell epitopes for IMPDH and 7 B cell epitopes for GMPR were predicted using ABCpred tool, Bepipred 2.0 and Kolaskar and Tongaonkar methods. The CD4+ Th computational results showed 16 antigenic epitopes from IMPDH with strong binding affinity for DRB1_0301, DRB3_0101, DRB1_0103 and DRB1_1501 MHC II alleles while 8 antigenic epitopes from GMPR were predicted to bind DRB1_0101 and DRB1_0401 MHC II alleles, respectively. For the CD8+ CTLs analysis, 8 antigenic epitopes from IMPDH showed strong binding affinity to human leukocyte antigen HLA-A*26:01, HLA-A*03:01, HLA-A*24:02 and HLA-A*01:01 MHC I alleles while 2 antigenic epitopes from GMPR showed strong binding affinity to HLA-A*01:01 allele, respectively. The immunogenic B cell and T cell epitopes were further evaluated for antigenicity, non-alllergernicity, toxicity, IFN-gamma, IL4 and IL10. The docking score revealed favorable binding free energy with IMP and MYD scoring the highest binding affinity at -6.6 kcal/mol with IMPDH and -8.3 kcal/mol with GMPR. This study provides valuable insight on IMPDH and GMPR as potential drug targets and for the development of multiple epitope vaccine candidates.Communicated by Ramaswamy H. Sarma.

LupiQuant: A real-time PCR based assay for determining host-to-parasite DNA ratios of Onchocerca lupi and host Canis lupus from onchocercosis samples

Onchocerca lupi is a filarial nematode that causes ocular onchocercosis in canines globally including North America and areas of Europe, North Africa, and the Middle East. Reported incidence of this parasite in canines has continued to steadily escalate since the early 21st century and was more recently documented in humans. Whole genome sequencing (WGS) of this parasite can provide insight into gene content, provide novel surveillance targets, and elucidate the origin and range expansion. However, past attempts of whole genome sequencing of other Onchocerca species reported a substantial portion of their data unusable due to the variable over-abundance of host DNA in samples. Here, we have developed a method to determine the host-to-parasite DNA ratio using a quantitative PCR (qPCR) approach that relies on two standard plasmids each of which contains a single copy gene specific to the parasite genus Onchocerca (major body wall myosin gene, myosin) or a single copy gene specific to the canine host (polycystin-1 precursor, pkd1). These plasmid standards were used to determine the copy number of the myosin and pkd1 genes within a sample to calculate the ratio of parasite and host DNA. Furthermore, whole genome sequence (WGS) data for three O. lupi isolates were consistent with our host-to-parasite DNA ratio results. Our study demonstrates, despite unified DNA extraction methods, variable quantities of host DNA within any one sample which will likely affect downstream WGS applications. Our quantification assay of host-to-parasite genome copy number provides a robust and accurate method of assessing canine host DNA load in an O. lupi specimen that will allow informed sample selection for WGS. This study has also provided the first whole genome draft sequence for this species. This approach is also useful for future focused WGS studies of other parasites.

Setaria cervi (Filarioidea, Onchocercidae) undressing in ungulates: altered morphology of developmental stages, their molecular detection and complete sequence cox1 gene

This work introduces new morphological and molecular information on the filaroid nematode Setaria cervi (Rudolphi, 1819) obtained from 13 infected game ungulates out of 96 dissected. The hosts comprised the following: a single moose (Alces alces), ten red deer (Cervus elaphus) and two sika deer (Cervus nippon) originating from the western and northern regions of the Czech Republic. Based on the complete sequences of the gene encoding mitochondrial cytochrome c oxidase subunit 1 (cox1), all 20 females and four males belonged to the species S. cervi. We detected three developmental female stages (adult fertile females, juvenile L5 females and L4 female larvae) differing in size and some morphological traits as the subtle structure of peribuccal crown and shape and features of tail knob. Such differences were described in detail for the first time. The phylogenetic relationships within the family Onchocercidae have been evaluated using new information on the cox1 sequence of S. cervi (maximum likelihood method, GTR + I + G model). In accordance with the latest phylogenetic studies, the present analysis confirmed the ancient separation of the subclass Setariinae from the remaining two onchocercid lineages Dirofilariinae and Onchocerinae.

Pinworms of the red howler monkey (Alouatta seniculus) in Colombia: Gathering the pieces of the pinworm-primate puzzle

Pinworms of primates are believed to be highly host specific parasites, forming co-evolutionary associations with their hosts. In order to assess the strength and reach of such evolutionary links, we need to have a broad understanding of the pinworm diversity associated with primates. Here, we employed an integrative taxonomic approach to assess pinworm diversity in red howler monkeys in Colombia. Molecular and morphological evidence validate the presence of at least four different species of Trypanoxyuris occurring in red howler monkeys: T. minutus, a widely distributed species, and three new species, T. seunimiii n. sp., T. kemuimae n. sp. and T. kotudoi n. sp. The mitochondrial COI gene and the 28S ribosomal gene were used for phylogenetic assessments through Bayesian inference. The three new species were morphologically distinct and formed reciprocally monophyletic lineages. Further molecular lineage subdivision in T. minutus and T. kotudoi n. sp. without morphological correspondence, suggests the potential scenario for the existence of cryptic species. Phylogenetic relationships imply that the different species of Trypanoxyuris occurring in each howler monkey species were acquired through independent colonization events. On-going efforts to uncover pinworm diversity will allow us to test the degree of host specificity and the co-phylogenetic hypothesis, as well as to further unravel the primate-pinworm evolutionary history puzzle.

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Three new species of pinworms from red howler monkeys are described.

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Phylogenetic analysis suggests the potential existence of cryptic species.

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Our results agree with pinworms of primates as highly host specific parasites.

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Trypanoxyuris species occurring in each howler species are not closely related.

High genetic diversity in the Dirofilaria repens species complex revealed by mitochondrial genomes of feline microfilaria samples from Narathiwat, Thailand

Dirofilaria repens is a zoonotic, mosquito-borne filaria infecting carnivores, particularly dogs. It is expanding its range in Europe but epidemiological information is sparse for other Eurasian regions. In Hong Kong and India, the closely related species Candidatus Dirofilaria hongkongensis was proposed. Previous analysis of 2.5 kb partial mitochondrial genome sequences containing the particularly variable non-coding control region revealed low diversity in European D. repens while Asian nematodes showed high diversity. Sequences derived from feline blood samples from Narathiwat (Thailand) led to the proposal of a third potential species, Dirofilaria sp. "Thailand II". To avoid bias from rapidly evolving non-coding regions, this study aimed to compare Dirofilaria sp. "Thailand II" with D. repens and C. D. hongkongensis based on complete mitochondrial genomes. Using PCRs and Sanger sequencing, three complete mitochondrial genomes (13,651 bp) were assembled from DNA obtained from different feline blood samples. Mitochondrial genome organization was identical to other onchocercids with eleven protein-coding, two rRNA and 22 tRNA genes and no atp-8 gene. All genes were on the same strand showing an extremely high thymidine content (56.7%). Maximum-likelihood phylogenetic analysis using protein and rRNA sequences confirmed closer relationship of Dirofilaria sp. "Thailand II" to C. D. hongkongensis than to D. repens. All distances between these three putative species were considerably larger than the distance between the valid sibling species Onchocerca volvulus and Onchocerca ochengi. Sequencing of a 2.5 kb fragment containing the control region from microfilarial DNA from additional feline blood samples from Narathiwat 3-4 years later revealed that these also fell into the C. D. hongkongensis clade but were remarkably different from C. D. hongkongensis and Dirofilaria sp. "Thailand II". Since D. repens-like filaria are absent from dogs in Narathiwat, further field studies are required to confirm if these genotypes represent locally circulating cat-specific Dirofilaria genotypes or species.

Molecular marker sequences of cattle Cooperia species identify Cooperia spatulata as a morphotype of Cooperia punctata

The genus Cooperia includes important parasites of ruminants and currently contains 34 accepted species. However, even for those species infecting livestock, there is a considerable lack of molecular information and many species are only identifiable using subtle morphological traits. The present study aimed to provide molecular data to allow diagnosis of Cooperia species infecting cattle. Partial sequences of two mitochondrial (cytochrome oxidase 2, 12S rRNA gene) and two nuclear genes (isotype 1 β tubulin gene including two introns, internal transcribed spacers (ITS) were obtained from morphologically identified specimens of Cooperia pectinata, Cooperia punctata and Cooperia spatulata as well as from larvae of pure Cooperia oncophora and C. punctata laboratory isolates. Pairwise identity of ITS-2 sequences was very high and it was the only region able to identify a specimen as Cooperia sp. However, the ITS-2 was unreliable for diagnosis at the species level. All other marker sequences could not unequivocally be allocated to the genus Cooperia but allowed clear species identification with the exception of the pair C. punctata/C. spatulata for which no significant differences were found for any marker sequence. Maximum-likelihood phylogenetic analyses of individual genes as well as a multi-locus analysis covering all four sequences confirmed that specimen identified as C. spatulata were randomly distributed throughout the C. punctata cluster and formed no group of their own. In contrast, the other Cooperia species formed clearly separated and statistically supported clusters. These data indicate that C. spatulata is most likely only a morphotype of C. punctata and the name should be considered a synonym. Combinations of nuclear and mitochondrial markers should be used to identify morphotypes or cryptic species to benefit from excellent barcoding properties of the latter but allowing proper phylogenetic analyses and controlling for lineage sorting that might occur for mitochondrial genotypes within a species.