Non-invasive surveys of mammalian viruses using environmental DNA

ABSTRACTEnvironmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively to mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA have been applied to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent.To detect and identify known and novel mammalian viruses from eDNA/iDNA sources, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing.We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes.Our results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.

Download Full-text

Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples

10.1101/087437 ◽

2016 ◽

Cited By ~ 11

Author(s):

Shadi Shokralla ◽

Joel F. Gibson ◽

Ian King ◽

Donald J. Baird ◽

Daniel H. Janzen ◽

...

Keyword(s):

Environmental Samples ◽

High Throughput Sequencing ◽

Dna Analysis ◽

Dna Barcode ◽

Environmental Dna ◽

Amplicon Sequencing ◽

Marker Genes ◽

Hybridization Capture ◽

Sequence Capture ◽

Wide Range

ABSTRACTEnvironmental DNA analysis using PCR amplified marker genes has been a key application of high-throughput sequencing (HTS). However, PCR bias is a major drawback to gain accurate qualitative and quantitative biodiversity data. We developed a PCR-free approach using enrichment baits for species-specific mitochondrial cytochrome c oxidase 1(COI) DNA barcodes. The sequence capture was tested on species-rich bulk terrestrial and aquatic benthic samples. Hybridization capture recovered an average of 6 and 4.7 more arthropod orders than amplicon sequencing for terrestrial and benthic samples, respectively. For the terrestrial sample, the four most abundant arthropod orders comprised 94.0% of the sample biomass. These same four orders comprised 95.5% and 97.5% of the COI sequences recovered by amplification and capture, respectively. Hybridization capture recovered three arthropod orders that were detected by biomass analysis, but not by amplicon sequencing and two other insect orders that were not detected by either biomass or amplicon methods. These results indicate the advantage of using sequence capture for a more accurate analysis of biodiversity in bulk environmental samples. The protocol can be easily customized to other DNA barcode markers or gene regions of interest for a wide range of taxa or for a specific target group.

Download Full-text

Development of an environmental DNA method for monitoring fish communities: ground truthing in diverse lakes with characterised fish faunas

10.1101/394718 ◽

2018 ◽

Author(s):

Jianlong Li ◽

Tristan W. Hatton-Ellis ◽

Lori-Jayne Lawson Handley ◽

Helen S. Kimbell ◽

Marco Benucci ◽

...

Keyword(s):

Water Samples ◽

Fish Communities ◽

Environmental Dna ◽

Quantitative Information ◽

12S Rrna ◽

Similar Species ◽

List Type ◽

Large Lakes ◽

Non Invasive ◽

Wide Range

AbstractAccurate, cost-effective monitoring of fish is required to assess the quality of lakes under the European Water Framework Directive (WFD). Recent studies have shown that environmental DNA (eDNA) metabarcoding is an effective and non-invasive method, which can provide semi-quantitative information on fish communities in large lakes.This study further investigated the potential of eDNA metabarcoding as a tool for WFD status assessment by collecting and analysing water samples from eight Welsh lakes and six meres in Cheshire, England, with well described fish faunas. Water samples (N = 252) were assayed using two mitochondrial DNA regions (Cytb and 12S rRNA).eDNA sampling indicated the presence of very similar species in the lakes compared to those expected on the basis of existing and historical information. In total, 24 species were detected with a total of 111 species occurrences in the lakes studied using eDNA. Secondly, there was a significant positive correlation between expected faunas and eDNA data in terms of confidence of species occurrence (Spearman’s r = 0.74, df = 109, p <; 0.001). Thirdly, eDNA data can estimate relative abundance with the standard five-level classification scale (“DAFOR”). Lastly, four ecological fish communities were characterised using eDNA data which agrees with the pre-defined lake types according to environmental characteristics.Synthesis and applications. This study provides further evidence that eDNA metabarcoding could be a powerful and non-invasive monitoring tool for WFD purpose in a wide range of lake types, considerably outperforming other methods for community level analysis.

Download Full-text

DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION

Molecular Diagnostics and Biosafety – 2020. Russian national scientific and practical conference with international participation (October, 6–8, 2020): Conference Proceedings ◽

10.36233/978-5-9900432-9-9-42 ◽

2020 ◽

Author(s):

E.V. Korneenko ◽

◽

А.E. Samoilov ◽

I.V. Artyushin ◽

M.V. Safonova ◽

...

Keyword(s):

High Throughput ◽

Viral Genome ◽

High Throughput Sequencing ◽

Pcr Amplification ◽

Moscow Region ◽

Fecal Samples ◽

Genus Level ◽

Zoonotic Viruses ◽

Reservoir Hosts ◽

Blastn Search

In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses.

Download Full-text

Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

Scientific Reports ◽

10.1038/s41598-021-83318-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tatsuhiko Hoshino ◽

Ryohei Nakao ◽

Hideyuki Doi ◽

Toshifumi Minamoto

Keyword(s):

Fish Species ◽

High Throughput Sequencing ◽

Correlation Coefficients ◽

Environmental Dna ◽

Digital Pcr ◽

Absolute Quantification ◽

Taqman Probe ◽

Individual Species ◽

Natural Environments ◽

Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

Download Full-text

PIAS1 potentiates the anti-EBV activity of SAMHD1 through SUMOylation

Cell & Bioscience ◽

10.1186/s13578-021-00636-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Farjana Saiada ◽

Kun Zhang ◽

Renfeng Li

Keyword(s):

Lytic Replication ◽

Dependent Manner ◽

Dna Viruses ◽

Post Translational Modifications ◽

Protein Protein Interaction ◽

Barr Virus ◽

Sumo Ligase ◽

Lysine Residues ◽

Epstein Barr ◽

Rna And Dna

Abstract Background Sterile alpha motif and HD domain 1 (SAMHD1) is a deoxynucleotide triphosphohydrolase (dNTPase) that restricts the infection of a variety of RNA and DNA viruses, including herpesviruses. The anti-viral function of SAMHD1 is associated with its dNTPase activity, which is regulated by several post-translational modifications, including phosphorylation, acetylation and ubiquitination. Our recent studies also demonstrated that the E3 SUMO ligase PIAS1 functions as an Epstein-Barr virus (EBV) restriction factor. However, whether SAMHD1 is regulated by PIAS1 to restrict EBV replication remains unknown. Results In this study, we showed that PIAS1 interacts with SAMHD1 and promotes its SUMOylation. We identified three lysine residues (K469, K595 and K622) located on the surface of SAMHD1 as the major SUMOylation sites. We demonstrated that phosphorylated SAMHD1 can be SUMOylated by PIAS1 and SUMOylated SAMHD1 can also be phosphorylated by viral protein kinases. We showed that SUMOylation-deficient SAMHD1 loses its anti-EBV activity. Furthermore, we demonstrated that SAMHD1 is associated with EBV genome in a PIAS1-dependent manner. Conclusion Our study reveals that PIAS1 synergizes with SAMHD1 to inhibit EBV lytic replication through protein–protein interaction and SUMOylation.

Download Full-text

Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens

Scientific Reports ◽

10.1038/s41598-021-91956-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Komal Jain ◽

Teresa Tagliafierro ◽

Adriana Marques ◽

Santiago Sanchez-Vicente ◽

Alper Gokden ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Fold Increase ◽

The United States ◽

Genomic Research ◽

Babesia Microti ◽

Hybridization Capture ◽

Mouse Tissues ◽

Genome Analyses ◽

Capture Sequencing

AbstractInadequate sensitivity has been the primary limitation for implementing high-throughput sequencing for studies of tick-borne agents. Here we describe the development of TBDCapSeq, a sequencing assay that uses hybridization capture probes that cover the complete genomes of the eleven most common tick-borne agents found in the United States. The probes are used for solution-based capture and enrichment of pathogen nucleic acid followed by high-throughput sequencing. We evaluated the performance of TBDCapSeq to surveil samples that included human whole blood, mouse tissues, and field-collected ticks. For Borrelia burgdorferi and Babesia microti, the sensitivity of TBDCapSeq was comparable and occasionally exceeded the performance of agent-specific quantitative PCR and resulted in 25 to > 10,000-fold increase in pathogen reads when compared to standard unbiased sequencing. TBDCapSeq also enabled genome analyses directly within vertebrate and tick hosts. The implementation of TBDCapSeq could have major impact in studies of tick-borne pathogens by improving detection and facilitating genomic research that was previously unachievable with standard sequencing approaches.

Download Full-text

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

Antarctic Science ◽

10.1017/s0954102021000274 ◽

2021 ◽

pp. 1-10

Author(s):

Micheline Carvalho-Silva ◽

Luiz Henrique Rosa ◽

Otávio H.B. Pinto ◽

Thamar Holanda Da Silva ◽

Diego Knop Henriques ◽

...

Keyword(s):

High Throughput Sequencing ◽

Crater Lake ◽

Environmental Dna ◽

Food Sources ◽

South Shetland Islands ◽

Deception Island ◽

Shetland Islands ◽

Operational Taxonomic Units ◽

First Time ◽

Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

Download Full-text

Phenoxazine nucleoside derivatives with a multiple activity against RNA and DNA viruses

European Journal of Medicinal Chemistry ◽

10.1016/j.ejmech.2021.113467 ◽

2021 ◽

Vol 220 ◽

pp. 113467

Author(s):

Liubov I. Kozlovskaya ◽

Viktor P. Volok ◽

Anna A. Shtro ◽

Yulia V. Nikolaeva ◽

Alexey A. Chistov ◽

...

Keyword(s):

Dna Viruses ◽

Rna And Dna

Download Full-text

Development and performance evaluation of a Pedal Operated Seed Cleaner (POS-Cleaner)

SN Applied Sciences ◽

10.1007/s42452-021-04612-6 ◽

2021 ◽

Vol 3 (6) ◽

Author(s):

Wilber Akatuhurira ◽

Peter Tumutegyereize ◽

Isaac Oluk ◽

Emmanuel Baidhe ◽

Julia Kigozi ◽

...

Keyword(s):

Smallholder Farmers ◽

List Type ◽

Centrifugal Fan ◽

Rural And Remote ◽

Value Addition ◽

Remote Areas ◽

Individual Family ◽

Rural And Remote Areas ◽

And Performance ◽

Cleaning Methods

Abstract Traditional grain cleaning methods are labor-intensive, time-consuming, and yet very inefficient. The use of available mechanical seed cleaners is widely limited since they are expensive to own, operate, and maintain. A Pedal Operated Seed Cleaner (PoS-Cleaner) was developed and its performance evaluated. Appropriate engineering principles and methodologies were used in the sizing and construction of the machine. The cleaner consists of a bicycle-like pedaling system, hopper, a centrifugal fan, and three cleaning sieves which include two inside interlocking sieves (one sieve fixed and the other adjustable); whose meshes can be adjusted to be larger than the size of the unclean seeds by longitudinally translating the second sieve to achieve the appropriate seed size. This allows trapping of impurities larger than the seeds. Cleaning rates of 576.5 kg/h, 375.8 kg/h, and 377.4 kg/h for maize, beans, and groundnuts were obtained respectively. Maize, beans, and groundnuts had their highest cleaning efficiencies of 95.09%, 87.61%, and 81.67% at inner sieve sizes of 13 mm, 16 mm and 10 mm respectively, pedaling speed of 60 rpm. The PoS-Cleaner presents a more viable cleaning option for smallholder farmers in rural and remote areas with no access to the national grid, therefore producing high-quality seeds. This will eventually facilitate agricultural value addition and increase individual family incomes in Uganda. Article highlights A pedal operated multi-seed cleaner was developed. Achieved 5 times higher seed cleaning rates compared to traditional cleaning technologies. Attained higher separation efficiencies of seed and externalities compared to traditional technologies.

Download Full-text