Cloning and characterization of an Onchocerca volvulus specific DNA sequence

Duplex Real-Time PCR Assay for Clinical Differentiation of Onchocerca lupi and Onchocerca volvulus

In the United States and Europe, human onchocerciasis is a rare disease caused by zoonotic or anthropophilic parasites in the genus Onchocerca. The zoonotic species identified in focal areas of Europe and United States is Onchocerca lupi, and Onchocerca volvulus, the anthroponotic species, may be found among people who had lived in endemic areas of Africa, the Arabian Peninsula, or Latin America. Onchocerciasis due to O. lupi is an emergent parasitic disease, with limited diagnostic methods, in addition to the lack of information on its biology, transmission, and epidemiology. Cutaneous nodules are the disease's most prevalent manifestation but lack diagnostic specificity. To address the diagnosis of onchocerciasis at reference laboratories, we developed a duplex TaqMan real-time PCR (qPCR) method, targeting the cytochrome oxidase subunit I locus which has species-specific probes to identify and differentiate O. lupi from O. volvulus. We determined the performance of the duplex with a panel of 45 samples: 11 positives for O. lupi, six for O. volvulus, five samples with negative results for Onchocerca spp., and 23 non-Onchocerca nematodes. The duplex qPCR correctly detected 10 of 11 O. lupi- and six of six O. volvulus-positive specimens. The new duplex assay allowed the simultaneous detection and discrimination of O. lupi and O. volvulus in clinical specimens, expediting and facilitating the clinical diagnosis of O. lupi in non-endemic settings where the disease is an infrequent finding.

The insufficiency of circulating miRNA and DNA as diagnostic tools or as biomarkers of treatment efficacy for Onchocerca volvulus

Skin snip evaluation for onchocerciasis has insufficient sensitivity when skin microfilarial (mf) densities are low, such as following ivermectin treatment. Mf density is suitable for assessing microfilaricidal efficacy but only serves as an indirect indicator of macrofilaricidal activity. We assessed circulating nucleic acids from Onchocerca volvulus as an alternative to skin snips. We screened a plasma sample set of infected individuals followed up at four, 12 and 21 months after microfilaricidal (ivermectin, n = four), macrofilaricidal (doxycycline, n = nine), or combination treatment (n = five). Two parasite-derived miRNAs, cel-miR-71-5p and bma-lin-4, and O-150 repeat DNA were assessed. Highly abundant DNA repeat families identified in the O. volvulus genome were also evaluated. miRNAs were detected in two of 72 plasma samples (2.8%) and two of 47 samples (4.3%) with microfilaridermia using RT-qPCR. O-150 DNA was detected in eight (44.4%) baseline samples by qPCR and the number of positives declined post-treatment. One doxycycline-treated individual remained O-150 positive. However, only 11 (23.4%) samples with microfilaridermia were qPCR-positive. Analysis by qPCR showed novel DNA repeat families were comparatively less abundant than the O-150 repeat. Circulating parasite-derived nucleic acids are therefore insufficient as diagnostic tools or as biomarkers of treatment efficacy for O. volvulus.

A Case for Using Genomics and a Bioinformatics Pipeline to Develop Sensitive and Species-Specific PCR-Based Diagnostics for Soil-Transmitted Helminths

The balance of expense and ease of use vs. specificity and sensitivity in diagnostic assays for helminth disease is an important consideration, with expense and ease often winning out in endemic areas where funds and sophisticated equipment may be scarce. In this review, we argue that molecular diagnostics, specifically new assays that have been developed with the aid of next-generation sequence data and robust bioinformatic tools, more than make up for their expense with the benefit of a clear and precise assessment of the situation on the ground. Elimination efforts associated with the London Declaration and the World Health Organization (WHO) 2020 Roadmap have resulted in areas of low disease incidence and reduced infection burdens. An accurate assessment of infection levels is critical for determining where and when the programs can be successfully ended. Thus, more sensitive assays are needed in locations where elimination efforts are approaching a successful conclusion. Although microscopy or more general PCR targets have a role to play, they can mislead and cause study results to be confounded. Hyper-specific qPCR assays enable a more definitive assessment of the situation in the field, as well as of shifting dynamics and emerging diseases.

Entomological assessment of the transmission following recrudescence of onchocerciasis in the Comoé Valley, Burkina Faso

Background

Onchocerciasis, or river blindness, is a dermal filariasis caused by infection with the nematode parasite Onchocerca volvulus, transmitted to humans through the bites of blackflies of the genus Simulium. Despite the decade-long West African Regional Programme for the Elimination of Onchocerciasis, involving the mass administration of ivermectin to populations in endemic areas, recrudescence has occurred. An example is in the Cascades Region of south-west Burkina Faso where the resumption of transmission had resulted in infection prevalences of up to 70% in some villages. In 2011, a strategy for community-directed distribution of ivermectin (CDTI) was set up to respond to this worrying re-emergence.

Here, we report on a study of Onchocerca spp. transmission in the affected area carried out from January to December 2012. Every month, host-seeking adult females of the S. damnosum complex were collected at sites on the River Comoé near the four villages (Bodadiougou, Bolibana, Badara Karaboro and Badara Dogossè) that had recorded the highest prevalences in 2010. Collected blackflies were dissected and infective larvae were identified using the O-150 PCR method.

Results

A total of 9114 S. damnosum (s.l.) adult females were collected, of which 5142 were parous (56.4%) and 78 (1.51%) were infective carrying a total of 137 infective larvae. The annual transmission potential (ATP) was calculated as 0, 30, 255 and 771 infective larvae/man/year in Badara Dogossè, Bolibana, Badara Karaboro and Bodadiougou, respectively. Transmission levels in the latter two are of particular concern as they were higher than 100 infective larvae/person/year, the designated minimum threshold required for elimination of severe pathology, including damage to vision.

Conclusions

These results confirm that recrudescence of onchocerciasis has occurred, and that transmission of O. volvulus was active at sites on the Comoé River in the Cascades region in 2012. In accordance with WHO recommendations, CDTI should be continued and the situation in the Cascades region should be closely monitored if further spread of this outbreak is to be avoided.

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3290-5) contains supplementary material, which is available to authorized users.

Innovative Surveillance Strategies to Support the Elimination of Filariasis in Africa

Lymphatic filariasis (LF) and onchocerciasis are two neglected tropical diseases (NTDs) of public health significance targeted for global elimination. The World Health Organization (WHO) African Region is a priority region, with the highest collective burden of LF and onchocerciasis globally. Coendemic loiasis further complicates elimination due to the risk of adverse events associated with ivermectin treatment. A public health framework focusing on health-related data, systematic collection of data, and analysis and interpretation of data is used to highlight the range of innovative surveillance strategies required for filariasis elimination. The most recent and significant developments include: rapid point-of-care test (POCT) diagnostics; clinical assessment tools; new WHO guidelines; open-access online data portals; mHealth platforms; large-scale prevalence maps; and the optimisation of mathematical models.

O-5S quantitative real-time PCR: a new diagnostic tool for laboratory confirmation of human onchocerciasis

Background

Onchocerciasis is a parasitic disease caused by the filarial nematode Onchocerca volvulus. In endemic areas, the diagnosis is commonly confirmed by microscopic examination of skin snip samples, though this technique is considered to have low sensitivity. The available melting-curve based quantitative real-time PCR (qPCR) using degenerated primers targeting the O-150 repeat of O. volvulus was considered insufficient for confirming the individual diagnosis, especially in elimination studies. This study aimed to improve detection of O. volvulus DNA in clinical samples through the development of a highly sensitive qPCR assay.

Methods

A novel hydrolysis probe based qPCR assay was designed targeting the specific sequence of the O. volvulus O-5S rRNA gene. A total of 200 clinically suspected onchocerciasis cases were included from Goma district in South-west Ethiopia, from October 2012 through May 2013. Skin snip samples were collected and subjected to microscopy, O-150 qPCR, and the novel O-5S qPCR.

Results

Among the 200 individuals, 133 patients tested positive (positivity rate of 66.5%) and 67 negative by O-5S qPCR, 74 tested positive by microscopy (37.0%) and 78 tested positive by O-150 qPCR (39.0%). Among the 133 O-5S qPCR positive individuals, microscopy and O-150 qPCR detected 55.6 and 59.4% patients, respectively, implying a higher sensitivity of O-5S qPCR than microscopy and O-150 qPCR. None of the 67 individuals who tested negative by O-5S qPCR tested positive by microscopy or O-150 qPCR, implying 100% specificity of the newly designed O-5S qPCR assay.

Conclusions

The novel O-5S qPCR assay is more sensitive than both microscopic examination and the existing O-150 qPCR for the detection of O. volvulus from skin snip samples. The newly designed assay is an important step towards appropriate individual diagnosis and control of onchocerciasis.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2382-3) contains supplementary material, which is available to authorized users.

The Current Status of Molecular Xenomonitoring for Lymphatic Filariasis and Onchocerciasis

The capacity of vector insect surveillance to provide estimates of pathogen prevalence and transmission potential has long been recognized within the global communities tasked with eliminating lymphatic filariasis (LF), the underlying cause of elephantiasis and hydrocele, and onchocerciasis (river blindness). Initially restricted to the practice of dissection, the potential of vector monitoring has grown due to the advent of molecular methods capable of increasing the sensitivity and throughput of testing. However, despite such advancement, operational research gaps remain. If insufficiently addressed, these gaps will reduce the utility of molecular xenomonitoring (MX) for onchocerciasis as elimination efforts expand into Africa. Similarly, such shortcomings will limit the programmatic usefulness of MX for LF, resulting in this technique's significant underutilization.

Colorimetric tests for diagnosis of filarial infection and vector surveillance using non-instrumented nucleic acid loop-mediated isothermal amplification (NINA-LAMP)

Accurate detection of filarial parasites in humans is essential for the implementation and evaluation of mass drug administration programs to control onchocerciasis and lymphatic filariasis. Determining the infection levels in vector populations is also important for assessing transmission, deciding when drug treatments may be terminated and for monitoring recrudescence. Immunological methods to detect infection in humans are available, however, cross-reactivity issues have been reported. Nucleic acid-based molecular assays offer high levels of specificity and sensitivity, and can be used to detect infection in both humans and vectors. In this study we developed loop-mediated isothermal amplification (LAMP) tests to detect three different filarial DNAs in human and insect samples using pH sensitive dyes for enhanced visual detection of amplification. Furthermore, reactions were performed in a portable, non-instrumented nucleic acid amplification (NINA) device that provides a stable heat source for LAMP. The efficacy of several strand displacing DNA polymerases were evaluated in combination with neutral red or phenol red dyes. Colorimetric NINA-LAMP assays targeting Brugia Hha I repeat, Onchocerca volvulus GST1a and Wuchereria bancrofti LDR each exhibit species-specificity and are also highly sensitive, detecting DNA equivalent to 1/10-1/5000^th of one microfilaria. Reaction times varied depending on whether a single copy gene (70 minutes, O. volvulus) or repetitive DNA (40 min, B. malayi and W. bancrofti) was employed as a biomarker. The NINA heater can be used to detect multiple infections simultaneously. The accuracy, simplicity and versatility of the technology suggests that colorimetric NINA-LAMP assays are ideally suited for monitoring the success of filariasis control programs.

25 Years of the Onchocerca ochengi Model

Although of limited veterinary significance, Onchocerca ochengi has become famous as a natural model or 'analogue' of human onchocerciasis (river blindness), which is caused by Onchocerca volvulus. On the basis of both morphological and molecular criteria, O. ochengi is the closest extant relative of O. volvulus and shares several key natural history traits with the human pathogen. These include exploitation of the same group of insect vectors (blackflies of the Simulium damnosum complex) and formation of collagenous nodules with a similar histological structure to human nodules. Here, we review the contribution of this natural system to drug and vaccine discovery efforts, as well as to our basic biological understanding of Onchocerca spp., over the past quarter-century.

Conventional parasitology and DNA-based diagnostic methods for onchocerciasis elimination programmes

Commonly used methods for diagnosing Onchocerca volvulus infections (microscopic detection of microfilariae in skin snips and nodule palpation) are insensitive. Improved methods are needed for monitoring and evaluation of onchocerciasis elimination programmes and for clinical diagnosis of individual patients. A sensitive probe-based qPCR assay was developed for detecting O. volvulus DNA, and this was tested with samples collected from an endemic area in eastern Côte d'Ivoire. The new test was evaluated with dried skin snip pairs from 369 subjects and compared to routine skin snip microscopy and nodule palpation results from the same individuals. Onchocerciasis prevalence for these samples by qPCR, skin snip microscopy, and nodule palpation were 56.9%, 26.0%, and 37.9%, respectively. Furthermore, the combination of all three tests produced an infection prevalence of 72.9%, which was significantly higher than 53.1% detected by microscopy plus nodule palpation without qPCR. However, the qPCR assay was negative for 54 of 229 individuals with palpable nodules. qPCR could be a useful tool for detecting residual O. volvulus infections in human populations as prevalence decreases in areas following community-directed treatment with ivermectin.

Analysis of Polymorphism of 18S rRNA Gene inWuchereria bancroftiMicrofilariae

The polymorphism of the 18S rRNA gene in Wuchereria bancrofti microfilariae (mf) collected from three different zones in India was analyzed by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). The RFLPs of the amplified products obtained after digestion with restriction enzymes Ssp I, Msp I and Hha I showed no difference in the banding patterns among the mf isolates from different endemic zones. Further the sequencing of PCR products did not show any difference in the nucleotide sequence either. The phylogenetic analysis of the sequences of W. bancrofti mf isolates from different endemic zones has shown branching with the earlier reported sequences of W. bancrofti and its close relative Brugia malayi.

Assessment and monitoring of onchocerciasis in Latin America

Onchocerciasis has historically been one of the leading causes of infectious blindness worldwide. It is endemic to tropical regions both in Africa and Latin America and in the Yemen. In Latin America, it is found in 13 foci located in 6 different countries. The epidemiologically most important focus of onchocerciasis in the Americas is located in a region spanning the border between Guatemala and Mexico. However, the Amazonian focus straddling the border of Venezuela and Brazil is larger in overall area because the Yanomami populations are scattered over a very large geographical region. Onchocerciasis is caused by infection with the filarial parasite Onchocerca volvulus. The infection is spread through the bites of an insect vector, black flies of the genus Simulium. In Africa, the major vectors are members of the S. damnosum complex, while numerous species serve as vectors of the parasite in Latin America. Latin America has had a long history of attempts to control onchocerciasis, stretching back almost 100 years. The earliest programmes used a strategy of surgical removal of the adult parasites from affected individuals. However, because many of the adult parasites lodge in undetectable and inaccessible areas of the body, the overall effect of this strategy on the prevalence of infection was relatively minor. In 1988, a new drug, ivermectin, was introduced that effectively killed the larval stage (microfilaria) of the parasite in infected humans. As the microfilaria is both the stage that is transmitted by the vector fly and the cause of most of the pathologies associated with the infection, ivermectin opened up a new strategy for the control of onchocerciasis. Concurrent with the use of ivermectin for the treatment of onchocerciasis, a number of sensitive new diagnostic tools were developed (both serological and nucleic acid based) that provided the efficiency, sensitivity and specificity necessary to monitor the decline and eventual elimination of onchocerciasis as a result of successful control. As a result of these advances, a strategy for the elimination of onchocerciasis was developed, based upon mass distribution of ivermectin to afflicted communities for periods lasting long enough to ensure that the parasite population was placed on the road to local elimination. This strategy has been applied for the past decade to the foci in Latin America by a programme overseen by the Onchocerciasis Elimination Program for the Americas (OEPA). The efforts spearheaded by OEPA have been very successful, eliminating ocular disease caused by O. volvulus, and eliminating and interrupting transmission of the parasite in 8 of the 13 foci in the region. As onchocerciasis approaches elimination in Latin America, several questions still need to be addressed. These include defining an acceptable upper limit for transmission in areas in which transmission is thought to have been suppressed (e.g. what is the maximum value for the upper bound of the 95% confidence interval for transmission rates in areas where transmission is no longer detectable), how to develop strategies for conducting surveillance for recrudescence of infection in areas in which transmission is thought to be interrupted and how to address the problem in areas where the mass distribution of ivermectin seems to be unable to completely eliminate the infection.

The role of Onchocerca volvulus in the development of epilepsy in a rural area of Tanzania

INTRODUCTION

Several reports indicate high prevalences of both onchocerciasis and epilepsy in some regions of Africa. This raises the question of whether these diseases are associated. We therefore investigated people with epilepsy and/or onchocerciasis living in an area in Tanzania endemic for Onchocerca volvulus (O. volvulus).

METHODS

We collected clinical information, skin snips, and blood from 300 individuals, and cerebrospinal fluid (CSF) from 197. Participants were allocated to 4 groups consisting of people with epilepsy and onchocerciasis (n=135), those with either epilepsy (n=61) or onchocerciasis only (n=35), and healthy individuals (n=69). Samples were evaluated for microfilaria, IgG4 antibodies against O. volvulus, O. volvulus antibody index (CSF/serum), and CSF routine parameters. Polymerase chain reaction (PCR) was performed on skin snips and CSF.

RESULTS

No difference was found in microfilarial density between participants with and without epilepsy (P=0.498). The antibody index was raised in 2 participants. CSF PCR was negative in all samples tested.

DISCUSSION

Our results do not give evidence of a relationship between O. volvulus and epilepsy. Despite the fact that 2 participants had raised antibody index, the existence of cerebral onchocerciasis caused by migration of microfilariae into the CSF appears unlikely. However, to date unexplored reactions to the infestation with O. volvulus causing epilepsy cannot be excluded.

Detection of Onchocerca volvulus (Nematoda: Onchocercidae) infection in vectors from Amazonian Brazil following mass Mectizan™ distribution

Detection of Onchocerca volvulus in Simulium populations is of primary importance in the assessment of the effectiveness of onchocerciasis control programs. In Brazil, the main focus of onchocerciasis is in the Amazon region, in a Yanomami reserve. The main onchocerciasis control strategy in Brazil is the semi-annually mass distribution of the microfilaricide ivermectin. In accordance with the control strategy for the disease, polymerase chain reaction (PCR) was applied in pools of simuliids from the area to detect the helminth infection in the vectors, as recommended by the Onchocerciasis Elimination Program for the Americas and the World Health Organization. Systematic sampling was performed monthly from September 1998 to October 1999, and a total of 4942 blackflies were collected from two sites (2576 from Balawaú and 2366 from Toototobi). The molecular methodology was found to be highly sensitive and specific for the detection of infected and/or infective blackflies in pools of 50 blackflies. The results from the material collected under field conditions showed that after the sixth cycle of distribution of ivermectin, the prevalence of infected blackflies with O. volvulus had decreased from 8.6 to 0.3% in Balawaú and from 4 to 0.1% in Toototobi.

Molecular studies of Onchocerca volvulus isolates from Mexico

DNA from Onchocerca volvulus from Oaxaca and Chiapas, Mexico were used as templates to amplify members of the O-150 Onchocerca specific repeat sequence family. The resulting PCR amplicons all hybridized with OVS2, an oligonucleotide that has been previously shown to recognize amplicons derived from O. volvulus with 100% sensitivity. However, when PCR products amplified from the O. volvulus specific plasmid pOVS134 were used as a probe, most samples did not hybridize. Similarly, when PCR products amplified from DNA isolated from adult O. volvulus from Oaxaca were used as a probe, amplicons from adult worms from both Oaxaca and Chiapas were recognized, but PCR products from infected black flies from Chiapas were not recognized. Amplicons derived from an adult worm from Chiapas hybridized with PCR products produced from adult parasites from both Oaxaca and Chiapas and to PCR products derived from the DNA of infected black flies from Chiapas. These data, when taken together, suggest that differences exist among the repeat sequence populations of parasites from Oaxaca and Chiapas in Mexico, suggesting that the O-150 repeat sequence family may be a useful tool for biogeographic studies of O. volvulus in the Americas.

Control of Onchocerciasis

Onchocerciasis is a filarial infection which causes blindness and debilitating skin lesions. The disease occurs in 37 countries, of which 30 are found in Africa (the most affected in terms of the distribution and the severity of the clinical manifestations of the disease), six in the Americas and one in the Arabian Peninsula. The latest WHO Expert Committee on Onchocerciasis estimated that in 1995 around 17.7 million persons were infected, about 270,000 of whom were blind and another 500,000 severely visually impaired. The disease is responsible for 1 million DALYs. Eye disease from onchocerciasis accounts for 40% of DALYs annually although severe skin disease is also recognized as of public health significance. Great progress has been made in the last thirty years in the control of onchocerciasis, both in Africa and the Americas, and this progress has been due largely to international public-private partnerships, sustained funding regional programmes, and new tools and technology. Landmarks in the global control of river blindness include the significant success of the Onchocerciasis Control Programme of West Africa (1975-2002), and the donation of ivermectin (Mectizan) by Merck & Co. Inc., in 1988, a medicine that is distributed to millions free of charge each year. Future major technical challenges of onchocerciasis control include ivermectin mass administration in areas co-endemic for the parasite Loa loa in the light of possible severe adverse reactions, ivermectin treatment in hypoendemic areas hitherto excluded from African control programmes, sustainability of ivermectin distribution, post-control surveillance for recrudescence detection, surveillance for emergence of resistance, and decisions of when to stop mass ivermectin treatments. There is the need to develop the appropriate information systems and diagnostic tools to help in accomplishing many of these tasks. A search for a second-line treatment or as an additional drug to ivermectin as well as a search for a macrofilaricide are issues that need to be addressed in the future.

Onchocerca ochengi: Mimic, model or modulator of O. volvulus?

The cattle parasite, Onchocerca ochengi, is widely distributed in West Africa. Significantly, Simulium darnnosum, the vector o f the important human parasite, O. volvulus, the cause o f river blindness, also appears to be the vector of O. ochengi. For epidemiological reasons it is therefore vital to be able to distinguish the infective larvae o f these filoriae. Here, Sandy Trees also describes other features of the cattle parasite that make it of significance to investigations of human filariases.

Variation and polymorphism in helminth parasites

There are strong biological, evolutionary and immunological arguments for predicting extensive polymorphism among helminth parasites, but relatively little data and few instances from which the selective forces acting on parasite diversity can be discerned. The paucity of information on intraspecific variation stands in contrast to the fine detail with which helminth species have been delineated by morphological techniques, accentuating a trend towards considering laboratory strains as representative of a relatively invariant organism. However, in the fast-moving evolutionary race between host and parasite one would predict a monomorphic species would be driven to extinction. We review the arena of intraspecific variation for the major helminth parasites, ranging from biological properties such as host or vector preference, to biochemical and immunological characteristics, as well as molecular markers such as DNA sequence variants. These data are summarized, before focusing in more detail on polymorphisms within protein-coding genes of potential relevance to the host-parasite relationship, such as vaccine candidates. In particular, we discuss the available data on a number of major antigens from the filarial nematode Brugia malayi. Information is currently too sparse to answer the question of whether there is antigenic variation in filariasis, but the indications are that proteins from the blood-borne microfilarial stage show significant intraspecific variability. Future work will define whether polymorphisms in these antigens may be driven by exposure to the host immune response or reflect some other facet of parasite biology.

DNA-based detection of onchocerca volvulus

During the 1980s, the idea of using deoxyribonucleic acid probes for specific identification and diagnosis of infectious agents became very fashionable. There was therefore an explosion in the development of these tools and one particular group of organisms which received much attention was the parasitic nematodes. This review traces the development and use of such probes with the filarial nematode Onchocerca volvulus, with emphasis on their application to resolving certain 'problems' associated with this parasite, e.g. whether or not strains exist and difficulties in distinguishing the infective larval stage morphologically from related species.

Onchocerca volvulus: genetic diversity of parasite isolates from Sudan

Onchocerciasis in Sudan exists in three distinct foci which exhibit differing clinical presentations. Previous studies have demonstrated that a tandemly repeated Onchocerca sequence family with a unit repeat length of 150 bp (the O-150 family) is a useful marker for deducing relationships among different O. volvulus populations. In the current study, the O-150 repeat families of O. volvulus from Sudan were analyzed and compared to each other and to those of parasites from West Africa. Similar to West African and American O. volvulus, the O-150 families of the Sudanese parasites could be divided into clusters within which little or no intracluster variation was evident, suggesting that the O-150 family in these parasites was subject to the forces of concerted evolution. Statistical analysis of the O-150 families from the different Sudanese parasite isolates, employing a nested algorithm based on an analysis of variance, revealed that O. volvulus endemic to the northern focus at Abu Hamed were significantly different from all other O. volvulus populations examined to date. In contrast, parasites from the southern and eastern foci of Sudan were indistinguishable from those endemic to the West African savanna. The significance of these data are discussed in light of knowledge of the biogeography and biology of transmission of O. volvulus in Africa.

The genomes of Onchocerca volvulus

Onchocerca volvulus, the filarial parasite that causes onchocerciasis or river blindness, contains three distinct genomes. These include the nuclear genome, the mitochondrial genome and the genome of an intracellular endosymbiont of the genus Wolbachia. The nuclear genome is roughly 1.5x10(8) bp in size, and is arranged on four chromosome pairs. Analysis of expressed sequence tags from different life-cycle stages has resulted in the identification of transcripts from roughly 4000 O. volvulus genes. Several of these transcripts are highly abundant, including those encoding collagen and cuticular proteins. Analysis of several gene sequences from O. volvulus suggests that the nuclear genes of O. volvulus are relatively compact and are interrupted relatively frequently by small introns. The intron-exon boundaries of these genes generally follow the GU-AG rule characteristic of the splice donor and acceptors of other vertebrate organisms. The nuclear genome also contains at least one repeated sequence family of a 150 bp repeat which is arranged in tandem arrays and appears subject to concerted evolution. The mitochondrial genome of O. volvulus is remarkably compact, only 13747 bp in size. Consistent with the small size of the genome, four gene pairs overlap, eight contain no intergenic regions and the remaining gene pairs are separated by small intergenic domains ranging from 1 to 46 bp. The protein-coding genes of the O. volvulus mitochondrial genome exhibit a striking codon bias, with 15/20 amino acids having a single codon preference greater than 70%. Intraspecific variation in both the nuclear and mitochondrial genomes appears to be quite limited, consistent with the hypothesis that O. volvulus has suffered a genetic bottleneck in the recent past.

The filarial genome project: analysis of the nuclear, mitochondrial and endosymbiont genomes of Brugia malayi

The Filarial Genome Project (FGP) was initiated in 1994 under the auspices of the World Health Organisation. Brugia malayi was chosen as the model organism due to the availability of all life cycle stages for the construction of cDNA libraries. To date, over 20000 cDNA clones have been partially sequenced and submitted to the EST database (dbEST). These ESTs define approximately 7000 new Brugia genes. Analysis of the EST dataset provides useful information on the expression pattern of the most abundantly expressed Brugia genes. Some highly expressed genes have been identified that are expressed in all stages of the parasite's life cycle, while other highly expressed genes appear to be stage-specific. To elucidate the structure of the Brugia genome and to provide a basis for comparison to the Caenorhabditis elegans genome, the FGP is also constructing a physical map of the Brugia chromosomes and is sequencing genomic BAC clones. In addition to the nuclear genome, B. malayi possesses two other genomes: the mitochondrial genome and the genome of a bacterial endosymbiont. Eighty percent of the mitochondrial genome of B. malayi has been sequenced and is being compared to mitochondrial sequences of other nematodes. The bacterial endosymbiont genome found in B. malayi is closely related to the Wolbachia group of rickettsia-like bacteria that infects many insect species. A set of overlapping BAC clones is being assembled to cover the entire bacterial genome. Currently, half of the bacterial genome has been assembled into four contigs. A consortium has been established to sequence the entire genome of the Brugia endosymbiont. The sequence and mapping data provided by the FGP is being utilised by the nematode research community to develop a better understanding of the biology of filarial parasites and to identify new vaccine candidates and drug targets to aid the elimination of human filariasis.

Satellite DNA sequences as taxonomic markers in nematodes of agronomic interest

The success of alternative crop protection practices against plant-parasitic nematodes using host resistance genes depends fundamentally upon identification of the species and pathotypes effectively controlled by these genes. In the same way, biological control of insects by entomopathogenic nematodes will work only if the nematode strains used are indeed active against the pests to be eliminated. For these applications, the accurate interspecific and/or intraspecific identification of nematodes is thus of outstanding importance. Here, Eric Grenier, Philippe Castagnone-Sereno and Pierre Abad discuss the recent use of satellite DNA sequences in nematode taxonomic diagnostics.

Evaluation of serological assays for diagnosis of onchocercosis

Microscopic analysis of skin snips is the most widely used diagnostic technique for onchocercosis in endemic countries. The invasive nature and low sensitivity of that procedure has called for alternative diagnostic methods for this disease. Presently, serological assays detecting filariosis in general are available for routine analysis. However, serological assays specific for onchocercosis are still not universally available. We have evaluated the performance of a dot blot assay (DBA) as a potential method for specific detection of onchocercosis. The DBA, which detects IgG, as compared with 2 IgG4-immunoblot assays, all employing Onchocerca volvulus antigen. Furthermore, an enzyme-linked immunosorbent assay (ELISA) and an immunofluorescence assay (IFA) based on antigens from Acanthocheilonema viteae and Brugia malayi, respectively, were included in the comparison. Samples from microfilariae-positive patients and negative controls from the onchocercosis-endemic country Ghana were analysed. The DBA was significantly more sensitive and specific than the IgG4-assays and the ELISA, respectively. Furthermore, the anti-filarial Ig was increased in patients 1 month post-ivermectin treatment. Sera from patients with suspected filariosis from different parts of the world were analysed using DBA, ELISA and IFA. Patients responding positively in the DBA (12%) had clinical symptoms compatible with onchocercosis whereas those positive in ELISA and IFA (53% and 48%, respectively) had various clinical symptoms. These results indicate that the DBA is more specific than and as sensitive as the ELISA and the IFA presently used for the diagnosis of onchocercosis.

Rapid delineation of closely-related filarial parasites using genetic markers in spacer rDNA

Two closely-related species of filarial parasite, Litomosoides galizai and L. sigmodontis, were characterised using a polymerase chain reaction-linked restriction fragment length polymorphism (PCR-RFLP) technique. The rDNA region spanning the first and second internal transcribed spacers as well as the 5.8S gene (ITS+) was amplified by PCR from each of the species using conserved primers to the 18S and 28S ribosomal genes, digested separately with a range of restriction endonucleases and the fragments separated by agarose gel electrophoresis. PCR-RFLP of ITS+ using endonucleases Alu I, Cfo I, Dra I, Rsa I and Vsp I produced characteristic patterns for each species. No variation in RFLP patterns was detected among different DNA sample preparations or the sexes of each species. The present study demonstrates that the ITS+ provides genetic markers for the differentiation of L. galizai from L sigmodontis and suggests that internal transcribed spacer rDNA may provide species markers for other filarioid nematodes. Such markers have implications for diagnosis and for studying the biology, pathogenesis and systematics of filarial parasites.

Molecular characterization of two species-specific tandemly repeated DNAs from entomopathogenic nematodes Steinernema and Heterorhabditis (Nematoda:Rhabditida)

Two AluI tandemly repeated DNAs were cloned from two entomopathogenic nematodes: the first one from Steinernema glaseri and the second one from Heterorhabditis bacteriophora. The monomeric units of these two satellite DNAs have a repeat length of 174 and 168 bp, respectively. These AluI repeated element families appear to constitute 5.5% of the S. glaseri genome and 5% of the H. bacteriophora genome. Their A + T contents were estimated at 55% and 57%. Moreover, the monomers of these two families are quite homogeneous in sequence, showing, on average, 3.9% and 2.7% divergence from their respective consensus sequence. These results suggest that some mechanism is acting to maintain the homogeneity of these repeated DNAs despite their abundance. We have also shown that these two DNA families are species-specific and therefore could be used for the identification of Steinernema and Heterorhabditis entomopathogenic nematode species.

Polymerase chain reaction for detecting Onchocerca volvulus in pools of blackflies

The detection of Onchocerca volvulus infected simuliids or blackflies is routinely done by dissection and microscopic examination of individual flies, but this method is tedious and time consuming. Here we describe a method of detecting single O. volvulus infected blackflies in pools of uninfected blackflies. Using a PCR with Onchocerca specific primers it is possible to reproducibly detect one heavily infected blackfly in a pool of 80 flies, or to detect one blackfly inoculated with one microfilaria in a pool of 20 flies. With the method described large numbers of blackflies can be rapidly screened for the presence of O. volvulus infected flies.

Sensitivity of a polymerase chain reaction-based assay to detect Onchocerca volvulus DNA in skin biopsies

A polymerase chain reaction (PCR) of a 150-bp tandem repeat of Onchocerca volvulus (O-150) combined with Southern-blot hybridization to species-specific DNA probes was employed for DNA detection. O-150 was amplified from parasites originating from Uganda, Benin, Cameroon, Liberia, Ghana, Burkina Faso, Mali, and Zaire and was successfully hybridized to digoxigenin-labeled oligonucleotides. To investigate the sensitivity of the PCR, 2 skin biopsies were taken from each of 227 persons from Uganda with proven O. volvulus infections but with low microfilaria (mf) densities due to ivermectin treatment. One biopsy was tested by PCR and the other was digested using collagenase to assess the total number of mf. The PCR revealed 76.2% of the samples to be positive, and the collagenase method showed that 78.9% were positive, indicating similar sensitivity for the two methods. It is probable that for both techniques the biopsy must contain at least one live mf or fragments of a dead mf. In this study, no free or circulating O. volvulus DNA could be detected in skin biopsies by PCR.

Strain differentiation of Onchocerca volvulus from Uganda using DNA probes

Polymerase chain reaction (PCR) combined with non-radioactive DNA hybridization was applied for the detection and characterization of a 150 bp tandem repeat of Onchocerca volvulus. DNA of worms from western Uganda was amplified and then probed with a digoxygenin-labelled oligonucleotide, specific for the forest form of O. volvulus and compared to samples from various African countries. Hybridization was only observed with PCR products from the forest in Liberia, south-eastern Ghana, Benin and southern Cameroon, but not with worms from Uganda or the savannah in Burkina Faso and northern Ghana. A nested PCR using primers derived form the forest form-specific DNA sequence confirmed these results. Morphometric studies revealed length differences between the microfilariae of Ugandan O. volvulus to those of West Africa, especially to those of the savannah in Burkina Faso. It is concluded that the forest/savannah classification of O. volvulus from West Africa is not suitable for Simulium neavei-transmitted O. volvulus from Uganda.

Characterization of genes encoding members of the nuclear hormone receptor superfamily from Onchocerca volvulus

Several lines of evidence suggest that molting in parasitic nematodes is controlled through the action of steroid molting hormones, or ecdysones. In other organisms, the central mediator of steroid hormone action is the hormone receptor. These receptor molecules are members of a superfamily of proteins called the nuclear hormone receptor family. Using an oligonucleotide derived from the amino-acid sequence of the Drosophila melanogaster ecdysone receptor, genes encoding homologues of the nuclear hormone receptor family were identified in the genome of the human filarial parasite Onchocerca volvulus. The O. volvulus genome contains at least three genes that encode putative members of the nuclear hormone receptor superfamily. A complete cDNA for one of these genes, designated OvNHR-1, has been isolated and characterized. The OvNHR-1 cDNA was 2378 bp in length, and contained a single open reading frame of 1104 bp. The open reading frame encoded a peptide with all of the features characteristic of a member of the nuclear hormone receptor superfamily of proteins. OVNHR-1 appeared to be encoded by a single-copy gene. Expression of the mRNA corresponding to OvNHR-1 was developmentally regulated, with maximal expression occurring during early embryogenesis. The polypeptide encoded by the OvNHR-1 open reading frame is antigenic in a minority of individuals exposed to O. volvulus.

The Onchocerca volvulus homologue of the multifunctional polypeptide protein disulfide isomerase

Protein disulfide isomerase (PDI) functions to catalyze the formation of correct disulfide bonds in nascent proteins, and also acts as one of the subunits of prolyl-4 hydroxylase, the enzyme responsible for the oxidative maturation of procollagen. Since the cuticle of parasitic nematodes consists primarily of a network of collagen molecules which are connected through intermolecular disulfide bonds, PDI might be expected to be involved in the process of cuticle biosynthesis. The isolation and characterization of a cDNA encoding the PDI homologue of Onchocerca volvulus is described. This cDNA contains a single, long open reading frame that encodes sequence motifs identical to the two known active sites of PDI for isomerase activity. The O. volvulus PDI appears to be encoded by a single copy gene. Both in situ hybridization and immunolocalization data suggest that PDI is both spatially and temporally regulated in O. volvulus. The pattern of spatial and temporal regulation is consistent with the involvement of PDI in the biosynthesis of the parasite cuticle. The parasite protein appears to be an antigen recognized by a minority of individuals exposed to O. volvulus.

A middle-repetitive DNA sequence element in the sheep parasitic nematode, Trichostrongylus colubriformis

A novel repetitive DNA sequence in the sheep parasitic nematode Trichostrongylus colubriformis was cloned and sequenced. A 1.1 kb repetitive sequence (Tc15) which hybridized with DNA from T. colubriformis but not with DNA from two other parasitic nematodes, Haemonchus contortus and Ostertagia circumcincta, or sheep was further characterized. Southern blot analysis showed that the repeat hybridized to a range of fragments in restriction digested T. colubriformis DNA and existed in multiple copy number tandem arrays. However, to define clearly the repetitive monomeric unit further screening of phagemid libraries containing BamH I restriction fragments using a subclone of Tc15 as a probe was carried out. Restriction map and sequence data were compiled for 3 clones containing a 145 bp highly repetitive sequence (designated TcREP) which shared homology with the original pTc15 clone. TcREP hybridized to a tandemly repeating sequence monomer of 145 bp in T. colubriformis DNA which was cloned from various genetic environments in the T. colubriformis genome. TcREP homologous sequences were also found in the genomes of two other species of the same genus (Trichostrongylus axei and Trichostrongylus vitrinus) but not in a fourth species (Trichostrongylus rugatus).

Characterization of a species-specific satellite DNA family of Dolichopoda schiavazzii (Orthoptera, Rhaphidophoridae) cave crickets

The satellite DNA family pDoP102 is species specific for the cave cricket Dolichopoda schiavazzii, an endemic species of mainland and insular Tuscany. It consists of numerous tandemly arranged repeats, 102 bp in length, and evolved most probably after cladogenesis of D. schiavazzii from the D. baccettii-aegilion group within the last 2.3 +/- 0.8 million years. A sequence comparison of 31 clones (53 repetition units) from three isolated populations reveals a very high degree of sequence homogeneity within the species with no evidence for any specific population features. This appears to be in contrast to the results of allozyme analyses which account for a relatively old evolutionary divergence of the Elba island population from the mainland ones. Since the assumption of actual gene flow and recent colonization is rejected, the observed sequence homogeneity is hypothesized to be maintained by recombination processes preventing fixation of newly introduced mutations on pDoP102 sequence clusters.

A universally applicable diagnostic approach to filarial and other infections

Antibody-based assays for the diagnosis of filarial and other infections cannot reliably distinguish between past and current infection, nor can they be used to assess the efficacy of chemotherapy. In this article, Thomas Nutmon, Peter Zimmerman, Joseph Kubofcik and Donna Kostyu discuss how the detection of parasite-specific PCR products using on ELISA-based assay may overcome these problems.

DNA-based methods for the identification of insect vectors

Many insect vectors are members of complexes composed of morphologically identical sibling species. The identification of individual species, a requirement of epidemiological studies and control programmes, has traditionally relied upon techniques such as chromosomal analysis or isoenzyme typing. Owing to the limitations of these techniques, the last few years have seen many developments in DNA-based technologies for identification. DNA-based protocols have advantages over the other techniques utilized, in that they may identify all insect stages of both sexes using alcohol-preserved, dried, fresh or frozen specimens. The methods ultimately rely upon either DNA probe hybridization or the polymerase chain reaction (PCR). This review describes a number of approaches taken towards the development of these techniques. The aim of these approaches, whether directed or random, is to produce a methodology that is cheap, accurate and easy to use. In this review, the DNA-based techniques developed for the identification of Anopheles gambiae complex mosquitoes are used to illustrate the power of these methods, although, as the review demonstrates, the technology is directly applicable to many other mosquito or insect vectors. In addition, the methods discussed may be utilized for generating additional epidemiological data, such as identification of parasites within the vector or origin of the bloodmeal. A comprehensive survey of the probe systems available for the identification of insect vectors and the disease-causing organisms they transmit to the human population is therefore included. Given further advances in this technology, it may be anticipated that DNA-based approaches to identification may eventually supersede more traditional methodologies in the fields of tropical medicine and parasitology.

Characterization of a tandemly repetitive DNA sequence from Haemonchus contortus

Genomic DNA from the sheep parasitic nematode Haemonchus contortus was shotgun cloned in the plasmid vector pUC18. Recombinants which gave the strongest hybridization signals to 32P-radiolabelled genomic DNA were selected as representatives of the repetitive component of the parasite DNA. One repetitive sequence which hybridized only with DNA from H. contortus and not with DNA from two other sheep nematodes (Trichostrongylus colubriformis and Ostertagia circumcincta) was further characterized by sequencing and dot blot analysis. A related repeat was found in the closely related species Haemonchus placei. Experiments to determine the genomic organization of the repeat showed that it existed in a multi-copy number tandem array. This is the first report on the characterization of repetitive DNA in sheep parasite nematodes.

Molecular variation in Onchocerca spp

Over the past two decades there has been an upsurge of interest in defining morphological, immunological, biochemical, biological and genetic differences between species of Onchocerca to provide solutions to practical problems associated with finding models and epidemiological tools to assist with control of human onchocerciasis. The information gathered has confirmed the close relationship between species of Onchocerca and provided highly sensitive and specific probes to distinguish species and even strains of the same species. It has also identified pathways, especially using sequences from common DNA repeat units, that may lead to a better understanding of the progression of divergence of species of this genus than has previously been possible.

Design of Onchocerca DNA probes based upon analysis of a repeated sequence family

Repeated DNA sequences have been instrumental in the development of DNA probes for many different parasites. Isolation of such DNA probes has generally been accomplished by differential screening of genomic libraries with total genomic DNA preparations. In the current work, a rational design strategy is presented for the development of oligonucleotide probes based upon repeated sequence families. A repeated sequence family present in the genome of Onchocerca parasites, designated O-150, has been amplified from various samples of genomic DNA using PCR. DNA sequence analysis of the resulting PCR products demonstrated that the sequences may be arranged into clusters within which the individual sequences are identical or nearly identical. Differences among the cluster consensus sequences have been exploited to explain the specificities of previously isolated O-150 based probes and to develop two new oligonucleotide probes. One of these probes hybridizes specifically to Onchocerca volvulus O-150 PCR products, while the second hybridizes specifically to O-150 PCR products from the closely related bovine parasite O. ochengi. These oligonucleotide probes have been used to characterize Onchocerca infective larvae isolated from wild caught infected flies in West Africa. Because repeated sequence families are a common feature of most genomes, including those of parasites, this method should be applicable to the rational design of oligonucleotide probes for other parasitic infections.

Deforestation: effects on vector-borne disease

This review addresses changes in the ecology of vectors and epidemiology of vector-borne diseases which result from deforestation. Selected examples are considered from viral and parasitic infections (arboviruses, malaria, the leishmaniases, filariases, Chagas Disease and schistosomiasis) where disease patterns have been directly or indirectly influenced by loss of natural tropical forests. A wide range of activities have resulted in deforestation. These include colonisation and settlement, transmigrant programmes, logging, agricultural activities to provide for cash crops, mining, hydropower development and fuelwood collection. Each activity influences the prevalence, incidence and distribution of vector-borne disease. Three main regions are considered--South America, West & Central Africa and South-East Asia. In each, documented changes in vector ecology and behaviour and disease pattern have occurred. Such changes result from human activity at the forest interface and within the forest. They include both deforestation and reafforestation programmes. Deforestation, or activities associated with it, have produced new habitats for Anopheles darlingi mosquitoes and have caused malaria epidemics in South America. The different species complexes in South-East Asia (A. dirus, A. minimus, A. balabacensis) have been affected in different ways by forest clearance with different impacts on malaria incidence. The ability of zoophilic vectors to adapt to human blood as an alternative source of food and to become associated with human dwellings (peridomestic behaviour) have influenced the distribution of the leishmaniases in South America. Certain species of sandflies (Lutzomyia intermedia, Lu. longipalpis, Lu. whitmani), which were originally zoophilic and sylvatic, have adapted to feeding on humans in peridomestic and even periurban situations. The changes in behaviour of reservoir hosts and the ability of pathogens to adapt to new reservoir hosts in the newly-created habitats also influence the patterns of disease. In anthroponotic infections, such as Plasmodium, Onchocerca and Wuchereria, changes in disease patterns and vector ecology may be more difficult to detect. Detailed knowledge of vector species and species complexes is needed in relation to changing climate associated with deforestation. The distributions of the Anopheles gambiae and Simulium damnosum species complexes in West Africa are examples. There have been detailed longitudinal studies of Anopheles gambiae populations in different ecological zones of West Africa. Studies on Simulium damnosum cytoforms (using chromosome identification methods) in the Onchocerciasis Control Programme were necessary to detect changes in distribution of species in relation to changed habitats. These examples underline the need for studies on the taxonomy of medically-important insects in parallel with long-term observations on changing habitats.(ABSTRACT TRUNCATED AT 400 WORDS)

Cloning and characterization of a Loa loa-specific repetitive DNA

A Loa loa EcoRI genomic library in lambda gt11 was screened with 32P-labeled L. loa DNA and 1 repetitive clone, LL20, was isolated. An 800-bp Rsa I fragment of LL20, which is L. loa specific, was subcloned into pUC19 and the recombinant plasmid was designated pRsa4. While the 3.8-kb Eco RI fragment of LL20 cross-hybridized to other filarial DNA under low stringency conditions, the 800-bp fragment of pRsa4 was L. loa specific under the same conditions. Further characterization of the insert of pRsa4 was therefore carried out. Its lower limit of detection is 800 pg of L. loa genomic DNA, it has a low copy number (50-100) and an interspersed distribution in the genome. As a probe it does not distinguish between simian and human L. loa DNA. The nucleotide sequence contains 69% A + T and 31% G + C and shows no notable internal repeats.

[Molecular biological techniques in the diagnosis of tropical parasitic diseases]

Recent advances in the development of molecular biological techniques have resulted in their supplementary application for improved diagnosis of tropical parasitic diseases. The main areas of interest are the production of recombinant antigens for immunodiagnosis, and the detection of parasites by hybridization of nucleic acids and by DNA amplification (PCR) in vitro.

Identification of filarial larvae in vectors by DNA hybridization

Infectivity rates of insect vectors are the best criteria by which to assess the transmission of filarial parasites and the efficacy of filariasis control programs. Currently available DNA probes can be used to estimate the proportion of vectors containing larvae of a given filarial species but provide no information on three other important variables in the transmission dynamics of filarial nematodes: the developmental stage, the location and the actual number of larvae that are present in the vector, all of which can be reliably determined by microscopy. However, species identification is often difficult and sometimes impossible by conventional microscopy, which requires morphologically intact specimens. DNA is tough and DNA probing can identify worms that are dead and that have lost morphologic integrity; it also permits multiple analyses of the same specimen with different probes and has the potential for simultaneous processing of very large numbers of samples. Here, Senaroth Dissonoyake and Willy Piessens outline the route to the development of species- and life cycle stage-specific DNA/RNA probing reagents, and simple, reliable and quantitative technologies that can supplement and ultimately replace microscopic dissection.

Morphometric differentiation of Onchocerca volvulus and O. ochengi infective larvae

By microinjection of cryopreserved microfilariae (mf) into nulliparous flies, a comparison of the lengths of the infective larvae (L3) of Onchocerca volvulus and O. ochengi from the head of Simulium damnosum s.l. (presumed S. sirbanum) has been made. The suitability of S. sirbanum as a host was similar for both Onchocerca spp. The mean length +/- standard deviation of O. ochengi infective larvae measured in aqueous medium after storage of infected flies in liquid nitrogen was 762 +/- 63 microns (n = 39), significantly longer (P much less than 0.0001) than those of a savanna isolate of O. volvulus (676 +/- 56 microns, n = 26). Although the frequency distributions of the lengths of larvae of the 2 species overlapped, a critical value for discrimination of 719 microns applied to normally distributed populations with means and standard deviations of these samples would result in correct classification of 78% of true O. volvulus and 75% of true O. ochengi. A discriminant function analysis incorporating width measurements did not usefully improve the level of accuracy of discrimination. Larvae from flies stored in 70% ethanol and stained with acid haemalum were about 10% shorter, but O. ochengi infective larvae were still proportionately longer than those of O. volvulus (693 +/- 40 microns, n = 45 compared to 580 +/- 38 microns, n = 6, respectively). These data show that the infective L3 of O. volvulus and O. ochengi differ morphologically. Although the population length distributions overlap, by classifying larvae greater than 719 microns long as O. ochengi and those less than 719 microns long as O. volvulus a more accurate estimation of true O. volvulus infection rates in S. damnosum s.l. can be derived than is currently possible.