scholarly journals Metagenomic Analysis of Viral Diversity and a Novel Astroviruse of Forest Rodent

2021 ◽  
Author(s):  
Hai Yin ◽  
Li Zhao ◽  
Hong Chen
Keyword(s):  
Rna Virus ◽  
Insect Virus ◽  
Dna Virus ◽  
Fecal Samples ◽  
Animal Pathogens ◽  
Significant Difference ◽  
Natural Hosts ◽  
Forest Rodents ◽  
Human Viruses ◽  
Genome Arrangement

Abstract Background: Rodents are important virus reservoirs and natural hosts for multiple viruses. They are one of the wild animals that are extremely threatening to the spread of human viruses. Therefore, research on rodents carrying viruses and identifying new viruses that rodents carry is of great significance for preventing and controlling viral diseases.Methods: In this study, fecal samples from six species of forest rodents in Northeast China were sequenced using metagenomics, and an abundance of virome information was acquired.Results: Among the top 10 most abundant viral families, RNA virus include Orthomyxoviridae, Picornaviridae, Bunyaviridae and Arenaviridae, DNA virus include Herpesviridae, Insect virus include Nodaviridae and Baculoviridae, Plant virus Tombusviridae and Phage (Myoriviridae). Except for Myoviridae, there was no significant difference in the abundance of virus families in the feces of each rodent species. In addition, a new strain of astrovirus was discovered, with an ORF and genome arrangement comparable to other rodent astroviruses.The newly identified astrovirus had the highest similarity with the rodent astrovirus isolate, CHN/100.Conclusions: The data obtained in this study provided an overview of the viral community present in these rodent fecal samples, revealing some rodent-associated viruses closely related to known human or animal pathogens. Strengthening our understanding of unclassified viruses harbored by rodents present in the natural environment could provide scientific guidance for preventing and controlling new viral outbreaks that can spread via rodents.

scholarly journals Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam

2017 ◽  
Vol 3 (2) ◽  
Author(s):  
Bas B. Oude Munnink ◽  
My V.T. Phan ◽  
Peter Simmonds ◽  
Marion P.G. Koopmans ◽  
Paul Kellam ◽  
...  
Keyword(s):  
Amino Acid ◽  
Rna Virus ◽  
Amino Acid Identity ◽  
Nucleotide Composition ◽  
Composition Analysis ◽  
Fecal Samples ◽  
Acid Identity ◽  
Single Location ◽  
Human Viruses ◽  
Virus Genomes

Abstract Porcine stool-associated RNA virus (posavirus), and Human stool-associated RNA virus (husavirus) are viruses in the order Picornavirales recently described in porcine and human fecal samples. The tentative group (Posa and Posa-like viruses: PPLVs) also includes fish stool-associated RNA virus (fisavirus) as well as members detected in insects (Drosophila subobscura and Anopheles sinensis) and parasites (Ascaris suum). As part of an agnostic deep sequencing survey of animal and human viruses in Vietnam, we detected three husaviruses in human fecal samples, two of which share 97–98% amino acid identity to Dutch husavirus strains and one highly divergent husavirus with only 25% amino acid identity to known husaviruses. In addition, the current study found forty-seven complete posavirus genomes from pigs, ten novel rat stool-associated RNA virus genomes (tentatively named rasavirus), and sixteen novel bat stool-associated RNA virus genomes (tentatively named basavirus). The five expected Picornavirales protein domains (helicase, 3C-protease, RNA-dependent RNA polymerase, and two Picornavirus capsid domain) were found to be encoded by all PPLV genomes. In addition, a nucleotide composition analysis revealed that the PPLVs shared compositional properties with arthropod viruses and predicted non-mammalian hosts for all PPLV lineages. The study adds seventy-six genomes to the twenty-nine PPLV genomes currently available and greatly extends our sequence knowledge of this group of viruses within the Picornavirales order.

scholarly journals Metagenomic Analysis of the Virome in Lung Tissues and Guts of Wild Mice

2020 ◽  
Author(s):  
Hai chang Yin ◽  
Hong yan Chen ◽  
Li li Zhao ◽  
Tao feng Lu
Keyword(s):  
Prevention And Control ◽  
Plant Viruses ◽  
Dna Virus ◽  
Wild Mice ◽  
Animal Pathogens ◽  
Significant Difference ◽  
Outdoor Environments ◽  
And Control ◽  
Old Mice ◽  
Insect Viruses

Abstract Background Mice, as host animals of a variety of pathogens, can spread 60 kinds of human diseases including more than ten families of viruses including Poxviridae, Herpesviridae, and so on. Methods In this study, lung tissues and gut samples of 7-week-old mice from outdoor environments were sequenced using metagenomics, and an abundance of virome information was acquired. Results A total of 82 families of mammalian viruses, plant viruses, insect viruses, and phages were detected. Among the top 10 most abundant families were the RNA viruses Orthomyxoviridae, Picornaviridae, Bunyaviridae, and Arenaviridae, the DNA virus Herpesviridae, the insect viruses Nodaviridae and Baculoviridae, the plant virus Tombusviridae, and the phage Myoviridae. Except for Myoviridae, whose abundance in guts was higher than in lung tissues, the abundance of viruses in the lung tissues and guts showed no significant difference. Conclusions The data obtained in this study provided an overview of the viral community present in these mice samples, revealing some mouse-associated viruses closely related to known human or animal pathogens. Strengthening our understanding of unclassified viruses in mice in the natural environment could provide scientific guidance for the prevention and control of new viral outbreaks that can spread via rodents.

scholarly journals Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Tao Zuo ◽  
Qin Liu ◽  
Fen Zhang ◽  
Yun Kit Yeoh ◽  
Yating Wan ◽  
...  
Keyword(s):  
Disease Severity ◽  
Rna Virus ◽  
Host Immunity ◽  
Virus Species ◽  
Human Gut ◽  
Dna Virus ◽  
Dna Viruses ◽  
Fecal Samples ◽  
Cell Counts ◽  
Rna And Dna

Abstract Background Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need. Methods We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had fecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial fecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the fecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters. Results Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in fecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Fecal virome in SARS-CoV-2 infection harbored more stress-, inflammation-, and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells, and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects. Conclusions Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether, our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19.

scholarly journals Detection of Alpha- and Betacoronaviruses in Miniopterus fuliginosus and Rousettus leschenaultii, two species of Sri Lankan Bats

Vaccines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 650
Author(s):  
Therese Muzeniek ◽  
Thejanee Perera ◽  
Sahan Siriwardana ◽  
Dilara Bas ◽  
Fatimanur Kaplan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sanger Sequencing ◽  
Rectal Swab ◽  
Sri Lankan ◽  
Rna Dependent Rna Polymerase ◽  
Fecal Samples ◽  
Natural Hosts ◽  
Pathogenic Viruses ◽  
Miniopterus Fuliginosus ◽  
Important Basis

Bats are known to be potential reservoirs of numerous human-pathogenic viruses. They have been identified as natural hosts for coronaviruses, causing Severe Acute Respiratory Syndrome (SARS) in humans. Since the emergence of SARS-CoV-2 in 2019 interest in the prevalence of coronaviruses in bats was newly raised. In this study we investigated different bat species living in a sympatric colony in the Wavul Galge cave (Koslanda, Sri Lanka). In three field sessions (in 2018 and 2019), 395 bats were captured (Miniopterus, Rousettus, Hipposideros and Rhinolophus spp.) and either rectal swabs or fecal samples were collected. From these overall 396 rectal swab and fecal samples, the screening for coronaviruses with nested PCR resulted in 33 positive samples, 31 of which originated from Miniopterus fuliginosus and two from Rousettus leschenaultii. Sanger sequencing and phylogenetic analysis of the obtained 384-nt fragment of the RNA-dependent RNA polymerase revealed that the examined M. fuliginosus bats excrete alphacoronaviruses and the examined R. leschenaultii bats excrete betacoronaviruses. Despite the sympatric roosting habitat, the coronaviruses showed host specificity and seemed to be limited to one species. Our results represent an important basis to better understand the prevalence of coronaviruses in Sri Lankan bats and may provide a basis for pursuing studies on particular bat species of interest.

Small mammal mycophagy in hemiboreal forest communities of Lithuania

2011 ◽  
Vol 6 (3) ◽  
pp. 446-456 ◽  
Author(s):  
Marija Kataržytė ◽  
Ernestas Kutorga
Keyword(s):  
Small Mammals ◽  
Small Mammal ◽  
Fungal Spores ◽  
Seasonal Effects ◽  
Deciduous Tree ◽  
Myodes Glareolus ◽  
Mammal Species ◽  
Hypogeous Fungi ◽  
Fecal Samples ◽  
Significant Difference

AbstractThe diets of small mammals in different hemiboreal spruce-dominated, oak-dominated and mixed forests in western part of Lithuania were studied by examination of fungal spores in fresh fecal pellets of caught animals. In the diets of mice (Apodemus spp.), bank voles (Myodes glareolus), and common and pygmy shrews (Sorex araneus and S. minutus), 22 different fungal taxa were identified, 15 of which were hypogeous fungi. The sporocarp abundance and the spores in fecal samples of Elaphomyces fungi prevailed in study area during this investigation. Although most of the captured individuals consumed fungi, the consumption varied among small mammal species. The data show that the fungi were more frequent and taxonomically diverse in Myodes glareolus than in Apodemus spp. diets. The study provided evidence that the fungal component in the diets of insectivorous Sorex species is more diverse than previously known. The availability of sporocarps and the fungal component in the diets of small mammals showed seasonal effects. Annual hypogeous and epigeous sporocarp abundances did not vary significantly across forest types. The significant difference in mycophagy was observed across all forest cover types, with the greatest fungal diversity in fecal samples collected in mixed coniferous-deciduous tree stands.

scholarly journals Characteristics of Gut Microbiota in Children With Biliary Atresia After Liver Transplantation

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Song ◽  
Li-Ying Sun ◽  
Zhi-Jun Zhu ◽  
Lin Wei ◽  
Wei Qu ◽  
...  
Keyword(s):  
Liver Transplantation ◽  
Gut Microbiota ◽  
Biliary Atresia ◽  
Control Level ◽  
Control Group ◽  
Metagenomic Sequencing ◽  
Polyamine Biosynthesis ◽  
Fecal Samples ◽  
Linear Discriminant ◽  
Significant Difference

Background and AimsBiliary atresia (BA) is an idiopathic neonatal cholestasis and is the most common indication in pediatric liver transplantation (LT). Previous studies have suggested that the gut microbiota (GM) in BA is disordered. However, the effect of LT on gut dysbiosis in patients with BA has not yet been elucidated.MethodsPatients with BA (n = 16) and healthy controls (n = 10) were recruited. In the early life of children with BA, Kasai surgery is a typical procedure for restoring bile flow. According to whether BA patients had previously undergone Kasai surgery, we divided the post-LT patients into the with-Kasai group (n = 8) and non-Kasai group (n = 8). Fecal samples were collected in both the BA and the control group; among BA patients, samples were obtained again 6 months after LT. A total of 40 fecal samples were collected, of which 16 were pre-LT, 14 were post-LT (8 were with-Kasai, 6 were non-Kasai), and 10 were from the control group. Metagenomic sequencing was performed to evaluate the GM.ResultsThe Kruskal-Wallis test showed a statistically significant difference in the number of genes between the pre-LT and the control group, the pre-LT and the post-LT group (P < 0.05), but no statistical difference between the post-LT and the control group. Principal coordinate analysis also showed that the microbiome structure was similar between the post-LT and control group (P > 0.05). Analysis of the GM composition showed a significant decrease in Serratia, Enterobacter, Morganella, Skunalikevirus, and Phifllikevirus while short chain fatty acid (SCFA)-producing bacteria such as Roseburia, Blautia, Clostridium, Akkermansia, and Ruminococcus were increased after LT (linear discriminant analysis > 2, P < 0.05). However, they still did not reach the normal control level. Concerning functional profiles, lipopolysaccharide metabolism, multidrug resistance, polyamine biosynthesis, GABA biosynthesis, and EHEC/EPEC pathogenicity signature were more enriched in the post-LT group compared with the control group. Prior Kasai surgery had a specific influence on the postoperative GM.ConclusionLT partly improved the GM in patients with BA, which provided new insight into understanding the role of LT in BA.

scholarly journals The Diversity of the Intestinal Flora Disturbed After Feeding Intolerance Recovery in Preterm Twins

2021 ◽  
Vol 9 ◽  
Author(s):  
Ying Li ◽  
Chunhong Jia ◽  
Xiaojun Lin ◽  
Lili Lin ◽  
Lizhen Li ◽  
...  
Keyword(s):  
Acid Metabolism ◽  
Intestinal Flora ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Feeding Intolerance ◽  
Fecal Samples ◽  
Kegg Pathways ◽  
Intestinal Bacterial Community ◽  
Β Diversity ◽  
Significant Difference

Background: Feeding intolerance (FI) is a common condition in premature infants that results in growth retardation and even necrotizing enterocolitis. The gut microbiome is linked to FI occurrence; however, the outcome after FI recovery is unclear.Methods: Fecal samples were collected from 11 pairs of premature twins/triplets for 16S rRNA gene sequencing. Initial fecal samples were collected shortly after admission, and then every other week until 7 weeks or discharge.Results: After FI recovery, there was no significant difference in the β-diversity of the intestinal flora between the FI group and the feeding tolerance (FT) group. By contrast, there was a significant difference in the β-diversity. Proteobacteria was the predominant phylum in the microbiome of the FI group, whereas Firmicutes was the predominant phylum in the microbiome of the FT group. The predominant bacteria with LDA >4 between the two groups at 13–15 days after birth, 19–28 days after birth, and at discharge were different, with the proportions of Bacillus, Clostridium butyricum, and Clostridium being highest in the FT group and Firmicutes, unidentified_Clostridiales, and Proteobacteria being highest in the FI group. Similarly, there were significant differences in the relative abundances of KEGG pathways, such as fatty acid metabolism, DNA repair and recombination proteins, energy metabolism, and amino acid metabolism, between the two groups (P < 0.01).Conclusions: There was a significant difference in diversity of the intestinal flora after feeding intolerance recovery. Feeding intolerance may disturb the succession of the intestinal bacterial community.

scholarly journals Characterization of SARS-CoV-2 Genetic Material in Wastewater

2021 ◽  
Author(s):  
Carolyn A Robinson ◽  
Hsin-yeh Hsieh ◽  
Shu Yu Hsu ◽  
Yang Wang ◽  
Braxton Salcedo ◽  
...  
Keyword(s):  
Rna Virus ◽  
Genetic Material ◽  
Temperature Changes ◽  
Cytopathic Effects ◽  
Significant Difference ◽  
Before And After ◽  
Control Virus ◽  
Wastewater Samples ◽  
Matrix Control ◽  
Raw Wastewater

SARS-CoV-2 genetic material has been detected in raw wastewater around the world throughout the COVID-19 pandemic and has served as a useful tool for monitoring community levels of SARS-CoV-2 infections. SARS-CoV-2 genetic material is highly detectable in a patient feces and the household wastewater for several days before and after a positive COVID-19 qPCR test from throat or sputum samples. Here, we characterize genetic material collected from raw wastewater samples and determine recovery efficiency during a concentration process. We find that pasteurization of raw wastewater samples did not reduce SARS-CoV-2 signal if RNA is extracted immediately after pasteurization. On the contrary, we find that signal decreased by approximately half when RNA was extracted 24-36 hours post-pasteurization and ~90% when freeze-thawed prior to concentration. As a matrix control, we use an engineered enveloped RNA virus. Surprisingly, after concentration, the recovery of SARS-CoV-2 signal is consistently higher than the recovery of the control virus leading us to question the nature of the SARS-CoV-2 genetic material detected in wastewater. We see no significant difference in signal after different 24-hour temperature changes; however, treatment with detergent decreases signal ~100-fold. Furthermore, the density of the samples is comparable to enveloped retrovirus particles, yet, interestingly, when raw wastewater samples were used to inoculate cells, no cytopathic effects were seen indicating that wastewater samples do not contain infectious SARS-CoV-2. Together, this suggests that wastewater contains fully intact enveloped particles.

scholarly journals Comparison of anticoagulant rodenticide concentrations in liver and feces from apparently healthy red foxes

2020 ◽  
Vol 32 (4) ◽  
pp. 560-564 ◽  
Author(s):  
Kristin O. Seljetun ◽  
Morten Sandvik ◽  
Vigdis Vindenes ◽  
Elin Eliassen ◽  
Elisabeth L. Øiestad ◽  
...  
Keyword(s):  
Detection Methods ◽  
Fecal Analysis ◽  
Red Foxes ◽  
Fecal Samples ◽  
Significant Difference ◽  
Liquid Chromatography Tandem Mass ◽  
Residue Levels ◽  
Good Concordance ◽  
Lethal Means ◽  
Apparently Healthy

Exposure of wildlife and domestic animals to anticoagulant rodenticides (ARs) is a worldwide concern, but few methods exist to determine residue levels in live animals. Traditional liver detection methods preclude determining exposure in live wildlife. To determine the value of assessing AR exposure by fecal analysis, we compared fecal and liver residues of ARs in the same animals. We collected liver and fecal samples from 40 apparently healthy red foxes ( Vulpes vulpes) potentially exposed to ARs, and quantified brodifacoum, bromadiolone, coumatetralyl, difenacoum, difethialone, and flocoumafen residues by liquid chromatography–tandem mass spectrometry. Residues of ARs were detected in 53% of the fecal samples and 83% of the liver samples. We found good concordance between AR residues in feces and liver for coumatetralyl, difenacoum, and difethialone. Bromadiolone occurred in significantly greater frequency in livers compared to feces, but no significant difference in concentration between feces and liver in individual foxes could be detected. Brodifacoum displayed a significant difference in concentration and occurrence of positive samples between liver and feces. Our findings demonstrate that fecal analysis of ARs provides a feasible and valuable non-lethal means of determine AR exposure in live wildlife.

scholarly journals An Analysis of Clostridium difficile Environmental Contamination During and After Treatment for C difficile Infection

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Kerrie Davies ◽  
Damian Mawer ◽  
A Sarah Walker ◽  
Claire Berry ◽  
Timothy Planche ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Environmental Contamination ◽  
Environmental Samples ◽  
Transmission Risk ◽  
Fecal Samples ◽  
Treatment Groups ◽  
End Of Treatment ◽  
Significant Difference ◽  
Time Point

Abstract Background Lower Clostridium difficile spore counts in feces from C difficile infection (CDI) patients treated with fidaxomicin versus vancomycin have been observed. We aimed to determine whether environmental contamination is lower in patients treated with fidaxomicin compared with those treated with vancomycin/metronidazole. Methods The CDI cases were recruited at 4 UK hospitals (Leeds, Bradford, and London [2 centers]). Environmental samples (5 room sites) were taken pretreatment and at 2–3, 4–5, 6–8, and 9–12 days of treatment, end of treatment (EOT), and post-EOT. Fecal samples were collected at diagnosis and as often as produced thereafter. Swabs/feces were cultured for C difficile; percentage of C difficile-positive samples and C difficile bioburden were compared between different treatment arms at each time point. Results Pre-EOT (n = 244), there was a significant reduction in environmental contamination (≥1 site positive) around fidaxomicin versus vancomycin/metronidazole recipients at days 4–5 (30% vs 50% recipients, P = .04) and at days 9–12 (22% vs 49%, P = .005). This trend was consistently seen at all other timepoints, but it was not statistically significant. No differences were seen between treatment groups post-EOT (n = 76). Fidaxomicin-associated fecal positivity rates and colony counts were consistently lower than those for vancomycin/metronidazole from days 4 to 5 of treatment (including post-EOT); however, the only significant difference was in positivity rate at days 9–12 (15% vs 55%, P = .03). Conclusions There were significant reductions in C difficile recovery from both feces and the environment around fidaxomicin versus vancomycin/metronidazole recipients. Therefore, fidaxomicin treatment may lower the C difficile transmission risk by reducing excretion and environmental contamination.

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