scholarly journals Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2412
Author(s):  
Jose L. Huaman ◽  
Carlo Pacioni ◽  
Subir Sarker ◽  
Mark Doyle ◽  
David M. Forsyth ◽  
...  
Keyword(s):  
Red Deer ◽  
High Throughput Sequencing ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Fallow Deer ◽  
Potential Threat ◽  
Pathogenic Potential ◽  
Reading Frame ◽  
Faecal Samples ◽  
Eastern Australia

The use of high-throughput sequencing has facilitated virus discovery in wild animals and helped determine their potential threat to humans and other animals. We report the complete genome sequence of a novel picornavirus identified by next-generation sequencing in faeces from Australian fallow deer. Genomic analysis revealed that this virus possesses a typical picornavirus-like genomic organisation of 7554 nt with a single open reading frame (ORF) encoding a polyprotein of 2225 amino acids. Based on the amino acid identity comparison and phylogenetic analysis of the P1, 2C, 3CD, and VP1 regions, this novel picornavirus was closely related to but distinct from known bopiviruses detected to date. This finding suggests that deer/bopivirus could belong to a novel species within the genus Bopivirus, tentatively designated as “Bopivirus C”. Epidemiological investigation of 91 deer (71 fallow, 14 sambar and 6 red deer) and 23 cattle faecal samples showed that six fallow deer and one red deer (overall prevalence 7.7%, 95% confidence interval [CI] 3.8–15.0%) tested positive, but deer/bopivirus was undetectable in sambar deer and cattle. In addition, phylogenetic and sequence analyses indicate that the same genotype is circulating in south-eastern Australia. To our knowledge, this study reports for the first time a deer-origin bopivirus and the presence of a member of genus Bopivirus in Australia. Further epidemiological and molecular studies are needed to investigate the geographic distribution and pathogenic potential of this novel Bopivirus species in other domestic and wild animal species.

scholarly journals Observations on autochtonous liver flukes in wild ruminants in Slovakia

2017 ◽  
Vol 54 (4) ◽  
pp. 307-313
Author(s):  
A. Iglódyová ◽  
P. Lazar ◽  
J. Čurlík ◽  
R. Karolová ◽  
J. Ciberej ◽  
...  
Keyword(s):  
Cervus Elaphus ◽  
Red Deer ◽  
Roe Deer ◽  
Fasciola Hepatica ◽  
Slovak Republic ◽  
Capreolus Capreolus ◽  
Fallow Deer ◽  
Wild Ruminants ◽  
Faecal Samples ◽  
Liver Flukes

SummaryThe aim of the study was monitoring of liver flukes in wild ruminants including red deer (Cervus elaphus), roe deer (Capreolus capreolus), fallow deer (Dama dama) and mouflon (Ovis musimon) in selected regions of Slovak Republic. Between 2014 – 2016 we examined 782 faecal samples from selected wild ruminants using coprological techniques and serological methods (ELISA detection ofF. hepaticacoproantigens). None of the samples was positive for the presence ofFasciola hepatica, 5.89 % of faecal samples were positive forDicrocoelium dendriticum. Higher prevalence was recorded in mouflon (30.83 %), lower in red deer (1.49 %).D. dendriticuminfection was not determined in fallow deer and roe deer. The seasonal distribution of dicrocoeliosis indicated a highest prevalence in autumn. Significantly higher prevalence was recorded in fenced rearing when compared with open hunting grounds, suggesting that animal agglomeration, constant use of the same areas and possible stress are the main risk factors. Parasitological examination of livers of hunted wild ruminants revealed dicrocoeliosis in mouflon.

scholarly journals Completion of Maize Stripe Virus Genome Sequence and Analysis of Diverse Isolates

2021 ◽  
Vol 12 ◽  
Author(s):  
Stephen Bolus ◽  
Kathryn S. Braithwaite ◽  
Samuel C. Grinstead ◽  
Irazema Fuentes-Bueno ◽  
Robert Beiriger ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Reference Genome ◽  
Rice Stripe Virus ◽  
The United States ◽  
Amino Acid Identity ◽  
Virus Genome ◽  
Tropical Regions ◽  
Reading Frame ◽  
Putative Protein ◽  
Insight Into

Maize stripe virus is a pathogen of corn and sorghum in subtropical and tropical regions worldwide. We used high-throughput sequencing to obtain the complete nucleotide sequence for the reference genome of maize stripe virus and to sequence the genomes of ten additional isolates collected from the United States or Papua New Guinea. Genetically, maize stripe virus is most closely related to rice stripe virus. We completed and characterized the RNA1 sequence for maize stripe virus, which revealed a large open reading frame encoding a putative protein with ovarian tumor-like cysteine protease, endonuclease, and RNA-dependent RNA polymerase domains. Phylogenetic and amino acid identity analyses among geographically diverse isolates revealed evidence for reassortment in RNA3 that was correlated with the absence of RNA5. This study yielded a complete and updated genetic description of the tenuivirus maize stripe virus and provided insight into potential mechanisms underpinning its diversity.

scholarly journals Identification and complete genome characterization of a novel picornavirus in turkey (Meleagris gallopavo)

2012 ◽  
Vol 93 (10) ◽  
pp. 2171-2182 ◽  
Author(s):  
Ákos Boros ◽  
Csaba Nemes ◽  
Péter Pankovics ◽  
Beatrix Kapusinszky ◽  
Eric Delwart ◽  
...  
Keyword(s):  
Amino Acid ◽  
Complete Genome ◽  
Bird Species ◽  
Entry Site ◽  
Pathogenic Potential ◽  
Genome Characterization ◽  
Genome Region ◽  
Faecal Samples ◽  
The Usa

Members of the family Picornaviridae are important pathogens of humans and animals, although compared with the thousands of known bird species (>10 000), only a few (n = 11) picornaviruses have been identified from avian sources. This study reports the metagenomic detection and complete genome characterization of a novel turkey picornavirus from faecal samples collected from eight turkey farms in Hungary. Using RT-PCR, both healthy (two of three) and affected (seven of eight) commercial turkeys with enteric and/or stunting syndrome were shown to be shedding viruses in seven (88 %) of the eight farms. The viral genome sequence (turkey/M176/2011/HUN; GenBank accession no. JQ691613) shows a high degree of amino acid sequence identity (96 %) to the partial P3 genome region of a picornavirus reported recently in turkey and chickens from the USA and probably belongs to the same species. In the P1 and P2 regions, turkey/M176/2011/HUN is related most closely to, but distinct from, the kobuviruses and turdivirus 1. Complete genome analysis revealed the presence of characteristic picornaviral amino acid motifs, a potential type II-like 5′ UTR internal ribosome entry site (first identified among avian-origin picornaviruses) and a conserved, 48 nt long ‘barbell-like’ structure found at the 3′ UTR of turkey/M176/2011/HUN and members of the picornavirus genera Avihepatovirus and Kobuvirus. The general presence of turkey picornavirus – a novel picornavirus species – in faecal samples from healthy and affected turkeys in Hungary and in the USA suggests the worldwide occurrence and endemic circulation of this virus in turkey farms. Further studies are needed to investigate the aetiological role and pathogenic potential of this picornavirus in food animals.

scholarly journals Glycolytic potential and ultimate muscle pH values in red deer (Cervus elaphus) and fallow deer (Dama dama)

Rangifer ◽  
2004 ◽  
Vol 24 (2) ◽  
pp. 87-94 ◽  
Author(s):  
Eva Wiklund ◽  
Timothy R. Manley ◽  
Roger P. Littlejohn
Keyword(s):  
Cervus Elaphus ◽  
Muscle Glycogen ◽  
Red Deer ◽  
Glycogen Content ◽  
Biceps Femoris ◽  
Fallow Deer ◽  
Dama Dama ◽  
Triceps Brachii ◽  
Total Glucose ◽  
The Relationship

The ultimate pH value of meat (measured at approx. 24 hours post slaughter) gives information about the technological quality, i.e. shelf life, colour, water-holding properties and tenderness and is a direct consequence of muscle glycogen (energy) levels at slaughter. It may therefore also indicate whether or not the animal has been exposed to stressful energy depleting events prior to slaughter. In the present study, 141 animals (130 red deer (Cervus elaphus) and 11 fallow deer (Dama dama) were included to investigate the relationship between ultimate pH and residual glycogen concentration in red deer and fallow deer M. longissimus. In addition, the muscle glycogen content and ultimate pH values in three red deer muscles (Mm. triceps brachii, longissimus and biceps femoris) were studied. M. triceps brachii had higher ultimate pH and lower glycogen content compared with the other two studied muscles. The frequency of intermediate DFD (5.8≤ pH<6.2) was 5.4% in red deer M. longissimus, compared with 9.1% in fallow deer, while the frequency of DFD (pH≥ 6.2) was much lower in red deer (3.8%) than in fallow deer (54.5%). A curvilinear relationship between ultimate pH and total glucose concentration (glycogen and glucose) 30 min post slaughter in red deer and fallow deer M. longissimus was found. The relationship between muscle pH and lactic acid concentration however, was indicated to be linear. A significant variation in total glucose concentration at ultimate pH below 5.80 was observed, including values in the range from 18 to 123 mmol/kg wet tissue. It was concluded that further studies are needed to further explore the relationship between muscle glycogen content and technological and sensory quality attributes of meat from different deer species.Abstract in Swedish / Sammanfattning:Köttets pH-värde (mätt ca 24 timmar efter slakt) har stor betydelse för den teknologiska kvaliteten som t. ex. hållbarhet, färg, vattenhållande förmåga och mörhet. Glykogenförrådet (energinivån) i djurens muskulatur vid slakt är helt avgörande för köttets slutliga pH-värde. Därför kan pH-värdet också indikera om hanteringen av slaktdjur varit skonsam eller om stora mängder muskelenergi har förbrukats vid stress. I vår undersökning ingick 141 hjortar (130 kronhjortar (Cervus elaphus) och 11 dovhjortar (Dama dama) för att studera sambandet mellan köttets pH-värde och glykogeninnehållet i M. longissimus. Glykogeninnehåll och pH-värden i 3 muskler från kronhjort (Mm. triceps brachii, longissimus och biceps femoris) undersöktes också. M. triceps brachii hade högre pH-värde och lägre glykogeninnehåll jämfört med de två andra musklerna. Det var inte så stor skillnad i frekvensen av intermediär DFD (pH-värden mellan 5,8 og 6,2) mellan de två hjortarterna (5,4% för kronhjort och 9,1% för dovhjort), däremot var frekvensen av DFD (pH-värden över 6,2) mycket låg hos kronhjort (3,8%) jämfört med dovhjort (54,5%). Det fanns ett kurvlinjärt samband mellan slutligt pH-värde i köttet och total glukoskoncentration (glykogen + glukos) mätt i M. longissimus 30 min efter slakt för både kron- och dovhjort. Ett linjärt samband mellan pH-värde och koncentration av mjölksyra i M. longissimus kunde också visas. Vi fann en mycket stor varitation i glukoskoncentration (18−123 mmol/kg våtvikt) när köttets pH-värdet var 5,8 eller lägre. Det behövs fler undersökningar för att vidare klargöra sambanden mellan glykogeninnehåll i muskulaturen och teknologisk och sensorisk kvalitet i olika typer av hjortkött.

scholarly journals Detection of Chlamydia psittaci and Chlamydia ibidis in the Endangered Crested Ibis (Nipponia nippon)

2020 ◽  
Vol 148 ◽  
Author(s):  
Zhaocai Li ◽  
Ping Liu ◽  
Jia Hou ◽  
Guanglan Xu ◽  
Junfeng Zhang ◽  
...  
Keyword(s):  
Avian Species ◽  
Chlamydia Psittaci ◽  
Potential Threat ◽  
High Genetic Diversity ◽  
Obligate Intracellular ◽  
Nipponia Nippon ◽  
Crested Ibis ◽  
Faecal Samples ◽  
First Time ◽  
Avian Chlamydiosis

Abstract Chlamydia spp. are a group of obligate intracellular pathogens causing a number of diseases in animals and humans. Avian chlamydiosis (AC), caused by Chlamydia psittaci (C. psittaci) as well as new emerging C. avium, C. gallinacea and C. ibidis, have been described in nearly 500 avian species worldwidely. The Crested Ibis (Nipponia nippon) is a world endangered avian species with limited population and vulnerable for various infections. To get a better understanding of the prevalence of Chlamydia spp. in the endangered Crested Ibis, faecal samples were collected and analysed. The results confirmed that 20.20% (20/99) of the faecal samples were positive for Chlamydiaceae and were identified as C. ibidis with co-existence of C. psittaci in one of the 20 positive samples. In addition, ompA sequence of C. psittaci obtained in this study was classified into the provisional genotype Matt116, while that of C. ibidis showed high genetic diversity, sharing only 77% identity with C. ibidis reference strain 10-1398/6. We report for the first time the presence of C. ibidis and C. psittaci in the Crested Ibis, which may indicate a potential threat to the endangered birds and should be aware of the future protection practice.

scholarly journals Heterogeneity of penicillin-non-susceptible group B streptococci isolated from a single patient in Germany

2019 ◽  
Vol 75 (2) ◽  
pp. 296-299 ◽  
Author(s):  
Mark van der Linden ◽  
Rafael Mamede ◽  
Natascha Levina ◽  
Peter Helwig ◽  
Pedro Vila-Cerqueira ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Analysis ◽  
Amino Acid Sequences ◽  
Capsular Type ◽  
Group B Streptococci ◽  
The Us ◽  
Type Ia ◽  
The Usa ◽  
Group B ◽  
Host Evolution

Abstract Objectives Streptococcus agalactiae [group B streptococci (GBS)] have been considered uniformly susceptible to penicillin. However, increasing reports from Asia and North America are documenting penicillin-non-susceptible GBS (PRGBS) with mutations in pbp genes. Here we report, to the best of our knowledge, the first two PRGBS isolates recovered in Europe (AC-13238-1 and AC-13238-2), isolated from the same patient. Methods Two different colony morphologies of GBS were noted from a surgical abscess drainage sample. Both were serotyped and antimicrobial susceptibility testing was performed by different methodologies. High-throughput sequencing was done to compare the isolates at the genomic level, to identify their capsular type and ST, to evaluate mutations in the pbp genes and to compare the isolates with the genomes of other PRGBS isolates sharing the same serotype and ST. Results Isolates AC-13238-1 and AC-13238-2 presented MICs above the EUCAST and CLSI breakpoints for penicillin susceptibility. Both shared the capsular type Ia operon and ST23. Genomic analysis uncovered differences between the two isolates in seven genes, including altered pbp genes. Deduced amino acid sequences revealed critical substitutions in PBP2X in both isolates. Comparison with serotype Ia clonal complex 23 PRGBS from the USA reinforced the similarity between AC-13238-1 and AC-13238-2, and their divergence from the US strains. Conclusions Our results support the in-host evolution of β-lactam-resistant GBS, with two PRGBS variants being isolated from one patient.

Some Remarks on Deer (Cervidae) in Ancient Egypt

1987 ◽  
Vol 73 (1) ◽  
pp. 238-243
Author(s):  
Patrick F. Houlihan
Keyword(s):  
Cervus Elaphus ◽  
Red Deer ◽  
Fallow Deer ◽  
Ancient Egypt ◽  
Dama Dama ◽  
Naturally Occurring ◽  
Dama Mesopotamica ◽  
In The Wild

The evidence for deer (Cervidae) in ancient Egypt is reviewed briefly. The question of whether deer ever existed in the wild as an element of the Egyptian fauna, or were only known from rare exotic imports, cannot be conclusively answered yet. It is quite likely, however, based upon the records of the Egyptians themselves, that deer were native, whether naturally occurring or introduced. While the identification of the species depicted as the Persian Fallow Deer (Dama dama mesopotamica) is probably correct, the Barbary Red Deer (Cervus elaphus) remains a possibility.

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