Dataset Information

Analysis of Environmental DNA and Edaphic Factors for the Detection of the Snail Intermediate Host Oncomelania hupensis quadrasi.

ABSTRACT: BACKGROUND:The perpetuation of schistosomiasis japonica in the Philippines depends to a major extent on the persistence of its intermediate host Oncomelania hupensis quadrasi, an amphibious snail. While the malacological survey remains the method of choice in determining the contamination of the environment as evidenced by snails infected with schistosome larval stages, an emerging technology known as environmental DNA (eDNA) detection provides an alternative method. Previous reports showed that O. hupensis quadrasi eDNA could be detected in water, but no reports have been made on its detection in soil. METHODS:This study, thus focused on the detection of O. hupensis quadrasi eDNA from soil samples collected from two selected schistosomiasis-endemic barangays in Gonzaga, Cagayan Valley using conventional and TaqMan-quantitative (qPCR) PCRs. RESULTS:The results show that qPCR could better detect O. hupensis quadrasi eDNA in soil than the conventional method. In determining the possible distribution range of the snail, basic edaphic factors were measured and correlated with the presence of eDNA. The eDNA detection probability increases as the pH, phosphorous, zinc, copper, and potassium content increases, possibly indicating the conditions in the environment that favor the presence of the snails. A map was generated to show the probable extent of the distribution of the snails away from the body of the freshwater. CONCLUSION:The information generated from this study could be used to determine snail habitats that could be possible hotspots of transmission and should, therefore, be targeted for snail control or be fenced off from human and animal contact or from the contamination of feces by being a dumping site for domestic wastes.

SUBMITTER: Calata FIC

PROVIDER: S-EPMC6963648 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Publications

Analysis of Environmental DNA and Edaphic Factors for the Detection of the Snail Intermediate Host <i>Oncomelania hupensis quadrasi</i>.

Calata Fritz Ivy C FIC Caranguian Camille Z CZ Mendoza Jillian Ela M JEM Fornillos Raffy Jay C RJC Tabios Ian Kim B IKB Fontanilla Ian Kendrich C IKC Leonardo Lydia R LR Sunico Louie S LS Kawai Satoru S Chigusa Yuichi Y Kikuchi Mihoko M Sato Megumi M Minamoto Toshifumi T Baoanan Zenaida G ZG Sato Marcello Otake MO

Pathogens (Basel, Switzerland) 20190923 4

<h4>Background</h4>The perpetuation of schistosomiasis japonica in the Philippines depends to a major extent on the persistence of its intermediate host <i>Oncomelania hupensis quadrasi,</i> an amphibious snail. While the malacological survey remains the method of choice in determining the contamination of the environment as evidenced by snails infected with schistosome larval stages, an emerging technology known as environmental DNA (eDNA) detection provides an alternative method. Previous repo ...[more]

PMID: 31547610

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Project description:BackgroundSchistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia. Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host of S. japonicum. A complete genome sequence of O. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite. Assembling a high-quality reference genome of O. hupehensis will provide data for further research on the snail biology and controlling the spread of S. japonicum.MethodsThe draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences.ResultsA total length of 1.46 Gb high-quality O. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed that O. hupensis was separated from a common ancestor of Pomacea canaliculata and Bellamya purificata approximately 170 million years ago. Comparing the genome of O. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity.ConclusionsIntegrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level of O. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.

Project description:BACKGROUND:Oncomelania hupensis robertsoni is the sole intermediate host for Schistosoma japonicum in western China. Given the close co-evolutionary relationships between snail host and parasite, there is interest in understanding the distribution of distinct snail phylogroups as well as regional population structures. Therefore, this study focuses on these aspects in a re-emergent schistosomiasis area known to harbour representatives of two phylogroups - the Deyang-Mianyang area in Sichuan Province, China. Based on a combination of mitochondrial and nuclear DNA, the following questions were addressed: 1) the phylogeography of the two O. h. robertsoni phylogroups, 2) regional and local population structure in space and time, and 3) patterns of local dispersal under different isolation-by-distance scenarios. RESULTS:The phylogenetic analyses confirmed the existence of two distinct phylogroups within O. h. robertsoni. In the study area, phylogroups appear to be separated by a mountain range. Local specimens belonging to the respective phylogroups form monophyletic clades, indicating a high degree of lineage endemicity. Molecular clock estimations reveal that local lineages are at least 0.69-1.58 million years (My) old and phylogeographical analyses demonstrate that local, watershed and regional effects contribute to population structure. For example, Analyses of Molecular Variances (AMOVAs) show that medium-scale watersheds are well reflected in population structures and Mantel tests indicate isolation-by-distance effects along waterways. CONCLUSIONS:The analyses revealed a deep, complex and hierarchical structure in O. h. robertsoni, likely reflecting a long and diverse evolutionary history. The findings have implications for understanding disease transmission. From a co-evolutionary standpoint, the divergence of the two phylogroups raises species level questions in O. h. robertsoni and also argues for future studies relative to the distinctness of the respective parasites. The endemicity of snail lineages at the regional level supports the concept of endemic schistosomiasis areas and calls for future geospatial analyses for a better understanding of respective boundaries. Finally, local snail dispersal mainly occurs along waterways and can be best described by using cost distance, thus potentially enabling a more precise modelling of snail, and therefore, parasite dispersal.

Project description:BackgroundSchistosomiasis japonica is a chronic parasitic disease that seriously harms people's health. Oncomelania hupensis is the only intermediate host of Schistosoma japonicum. The micro-environmental factors surrounding the snail have a great impact on the survival, growth and reproduction of O. hupensis, but there are few relevant systematic analyses until the present. This scoping review aims to identify and summarize the micro-environmental factors that greatly affect O. hupensis, and to find gaps in research thus to provide directions for future in-depth studies.Main bodyThis scoping review searched databases with search terms of the combinations of "Micro(-)environment", "Oncomelania" and their expanded aspects. A total of 133 original articles were recruited. Predefined data fields were extracted including research methods, influencing factors, and their effects on O. hupensis. Most studies focused on vegetation factors (54.1%), and other factors noted were soil composition (27.8%), water environmental factors (24.1%), and predator (3.0%), respectively. The factors with positive impacts included water level, pH value, soil temperature, soil humidity, the coverage and height of vegetation at suitable levels. This could provide more detailed information for O. hupensis habitat identification and prediction. The factors with negative impacts included plant extracts, snail control and disease prevention forests, and microorganisms with molluscicidal activities. It revealed a potential application as ecological molluscicides in the future. Factors such as physico-chemical properties of water, soil chemistry showed a gap in scientific studies, thus required further extensive research.ConclusionsMicro-environmental factors including water quality, soil composition as well as the technology and application of biomolluscicides (plant extracts and microorganisms) deserve more attention. Relative study findings on micro-environment have good potentials in snail control applications. Further studies should be implemented to investigate the impact of micro-environmental factors on snails and close the research gaps.

Project description:BackgroundOncomelania hupensis is the exclusive intermediate host of Schistosoma japonicum in China. Snail control is an essential component of schistosomiasis elimination programme. With 70 years of continuous efforts, the range of O. hupensis had reduced significantly, but slowed down in last decades. A large number of levees against flooding were constructed along Yangtze River and its affiliated lakes in the middle and lower reaches, which influenced the hydrology and ecology in the alluvial plains. The purpose of this study was to assess the impact of levees on the distribution of O. hupensis in the middle and lower reaches of the Yangtze River.MethodsThe snail habitats were digitalised by hand-held GPS system. The years for discovery and elimination of snail habitats were extracted from historical records. The accumulated snail-infested range for each habitat was calculated on the basis of annual reports. The current distribution of O. hupensis was determined by systematic and environmental sampling. The geographical distribution of levees was obtained from satellite imagery. To assess the impact of levees, the data pertaining to O. hupensis were divided into two parts: inside and outside the Yangtze River. Joinpoint regression was utilised to divide the study time span and further characterise the regression in each period. The 5-year-period moving averages of eliminated area infested by snails were calculated for the habitats inside and outside Yangtze River. The moving routes of corresponding geographical median centres were simulated in ArcGIS. Hotspot analysis was used to determine the areas with statistical significance clustering of O. hupensis density.ResultsThree periods were identified according to Joinpoint regression both inside and outside Yangtze River. The area infested by O. hupensis increased in the first two periods. It decreased rapidly outside Yangtze River year over year after 1970, while that inside the Yangtze River did not change significantly. Furthermore, the latter was significantly higher than the former. It was observed that the present density of O. hupensis inside Yangtze River was lower than outside the Yangtze River. The median centre for eliminated ranges inside Yangtze River wavered between the east (lower reach) and the west (middle reach). In contrast, the median centre for eliminated ranges continuously moved from the east to the west.ConclusionsOur findings indicated that the levees had a considerable negative impact on the distribution of O. hupensis outside Yangtze River. Some hotspots observed in the irrigation areas need a sluice system at the inlet of branch for snail control. The major distribution of O. hupensis located in Hubei might be caused by severe waterlogging. The intensive surveillance should be implemented there. The biggest two freshwater lakes, the major endemic regions historically, were identified as cold spots. The long-term impact of Three Gorges Dam on the distribution of O. hupensis in the lakes should be monitored and evaluated.

Dataset Information

Analysis of Environmental DNA and Edaphic Factors for the Detection of the Snail Intermediate Host Oncomelania hupensis quadrasi.

Publications

Analysis of Environmental DNA and Edaphic Factors for the Detection of the Snail Intermediate Host <i>Oncomelania hupensis quadrasi</i>.

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