Presence of Human G Rotavirus Genotypes Amongst Bovine Calves and its Combination with P Genotypes

2021 ◽  
Author(s):  
Vandana Gupta ◽  
Anju Nayak ◽  
Madhu Swamy ◽  
R.V. Singh ◽  
Vishnu Gupta ◽  
...  
Keyword(s):  
Economic Loss ◽  
Interspecies Transmission ◽  
Genotype Combination ◽  
Mixed Genotype ◽  
Fecal Samples ◽  
Rotavirus A ◽  
Bovine Rotavirus ◽  
Proof Reading ◽  
Two Samples ◽  
Reading Activity

Background: Bovine Rotavirus is one of the most important viral etiological agent responsible for causing neonatal diarrhea incurring severe economic loss to farmers. The presence of large genome size, segmented nature and absence of proof reading activity of RNA polymerase leads to frequent reassortment and thus emergence of new G and P types with ability of interspecies transmission. Methods: During an epidemiological study (July 2016 to July 2019) 200 diarrheic fecal samples were screened for Bovine Rotavirus A using ELISA and RNA-PAGE. Further, twenty two positive samples for RVA were subjected to molecular detection for VP6, VP4 and VP7 genes. Result: Ten (20/200) and 11(22/200) percent diarrheic fecal samples were found positive using ELISA and RNA-PAGE respectively. Twenty samples found positive in ELISA were also found positive in RNA-PAGE. Amongst which 22 (100%) samples were found positive for VP6, while 15 (68.18%) samples showed amplification for VP4 and VP7 gene. All Rotavirus A positive samples were genotyped by multiplex RT-PCR assay. G1G3 was found to be most predominant (53.33%) followed by G3 (26.66%), while one sample each showed the presence of G1G5 and G3G8 (6.66%). Ten samples showed mixed genotype (66.66%). One sample was non typeable (6.66%). Among the P types, P[11] was the most predominant (73.33%), while one sample each showed the presence of P[5] and P[5]P[11] (6.66%) and 02 samples were non typeable (13.33%). The G and P genotype combination determined in 12 samples were as follows; G3P [11] found in two samples (16.66%), G3P[5] in 01(08.33%), G1G5P[11] in 01(08.33%), G1G3P[11] in 07 (58.33%), while 01 (08.33%) sample had mixed genotype G1G3P[5]P[11] combination.

scholarly journals Comparison of Diagnostic Tests for Detection of Bovine Rotavirus a in Calf Feces

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Shama Ranjan Barua ◽  
Shariful Islam ◽  
А.М.А.М. Zonaed Siddiki ◽  
Md Masuduzzaman ◽  
Mohammad Alamgir Hossain ◽  
...  
Keyword(s):  
Diagnostic Tests ◽  
Rapid Test ◽  
Diagnostic Methods ◽  
Diagnostic Tools ◽  
Rt Pcr ◽  
Fecal Samples ◽  
Rotavirus A ◽  
Bovine Rotavirus ◽  
Test Elisa ◽  
Calf Mortality

AbstractBovine rotavirus A (BRVA) is a frequent causative agent of diarrhea in neonatal calves. Accurate and rapid diagnosis is crucial to prevent calf mortality from BRVA induced diarrhea. Currently, variety of diagnostic methods are being used to detect BRVA from calves’ feces: antibody-based rapid test and ELISA, and molecular-based RT-PCR and RT-qPCR. The aim of the study was to evaluate the accuracy (sensitivity and specificity) of the rapid test (Immunochromatography), ELISA, and RT-PCR assays, using RT-qPCR as the gold standard, in detection of BRVA in diarrheic calves’ fecal samples. One hundred (n=100) clinically diarrheic fecal samples were tested with four different diagnostic tools. The percent of samples positive by rapid test, ELISA, RT-PCR and RT-qPCR was 10%, 16%, 17%, and 33%, respectively. The agreement between different assays was 75% to 99%. The highest agreement was observed between ELISA and RT-PCR assay (99%). The lowest agreement was recorded (75%) between rapid test and RT-qPCR. The sensitivity of the rapid test, ELISA, and RT-PCR were 30%, 49%, and 52%, respectively when compared to the reference test (RT-qPCR), whereas specificity was 100% for all assays. In conclusion, none of the frequently used diagnostic tests showed a satisfactory level of sensitivity to identify BRVA in calves’ feces. Therefore, the use of a more sensitive rapid test should be used to identify infected calves in field conditions in order to prevent calf mortality from rotaviral diarrhea.

scholarly journals Molecular Epidemiology of Rotavirus in Cats in the United Kingdom

2014 ◽  
Vol 53 (2) ◽  
pp. 455-464 ◽  
Author(s):  
A. C. German ◽  
M. Iturriza-Gómara ◽  
W. Dove ◽  
M. Sandrasegaram ◽  
T. Nakagomi ◽  
...  
Keyword(s):  
United Kingdom ◽  
Epidemiological Studies ◽  
Population Based ◽  
Interspecies Transmission ◽  
Cross Sectional Survey ◽  
Cross Sectional ◽  
Fecal Samples ◽  
Rotavirus A ◽  
Reverse Transcription Pcr ◽  
The United Kingdom

Rotaviruses are leading causes of gastroenteritis in the young of many species. Molecular epidemiological studies in children suggest that interspecies transmission contributes to rotavirus strain diversity in people. However, population-based studies of rotaviruses in animals are few. We investigated the prevalence, risk factors for infection, and genetic diversity of rotavirus A in a cross-sectional survey of cats housed within 25 rescue catteries across the United Kingdom. Morning litter tray fecal samples were collected during the winter and summer in 2012 from all pens containing kittens and a random sample of those housing adult cats. Group A rotavirus RNA was detected by real-time reverse transcription-PCR, and positive samples were G and P genotyped using nested VP4 and VP7 PCR assays. A total of 1,727 fecal samples were collected from 1,105 pens. Overall, the prevalence of rotavirus was 3.0% (95% confidence interval [CI], 1.2 to 4.9%). Thirteen out of 25 (52%; 95% CI, 31.3 to 72.2%) centers housed at least one rotavirus-positive cat. The prevalence of rotavirus was associated with season (odds ratio, 14.8 [95% CI, 1.1 to 200.4];P= 0.04) but not age or diarrhea. It was higher during the summer (4.7%; 95% CI, 1.2 to 8.3%) than in winter (0.8%; 95% CI, 0.2 to 1.5%). Asymptomatic epidemics of infection were detected in two centers. G genotypes were characterized for 19 (33.3%) of the 57 rotavirus-positive samples and P genotypes for 36 (59.7%). Two rotavirus genotypes were identified, G3P[9] and G6P[9]. This is the first population-based study of rotavirus in cats and the first report of feline G6P[9], which questions the previous belief that G6P[9] in people is of bovine origin.

scholarly journals A survey on the occurrence of Brachyspira pilosicoli and Brachyspira hyodysenteriae in growing-finishing pigs

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1702
Author(s):  
Arkadiusz Dors ◽  
Ewelina Czyżewska-Dors ◽  
Grzegorz Woźniakowski
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Finishing Pigs ◽  
Lawsonia Intracellularis ◽  
Fecal Samples ◽  
Brachyspira Pilosicoli ◽  
Brachyspira Hyodysenteriae ◽  
Veterinary Research ◽  
Two Samples ◽  
Intestinal Pathogens

Background: The major pathogenic intestinal spirochetes affecting pigs during the growing- finishing stage of production include Brachyspira hyodysenteriae and Brachyspira pilosicoli. Infections by these pathogens, which affect the economics of pig production, can result in mortality, growth rate losses and substantial antibiotic costs. The aim of this study was to assess the current occurrence of B. hyodysenteriae and B. pilosicoli in Polish pig herds. Moreover, associations between the presence of diarrhea or other intestinal pathogens and occurrence of B. hyodysenteriae and B. pilosicoli in pigs were investigated. Methods: Between January 2017 and August 2019, a total of 401 samples of pig feces from 95 different herds were submitted to the National Veterinary Research Institute of Poland. These samples were obtained from pigs older than 7 weeks. All the received fecal samples were examined for the presence of B. hyodysenteriae, B. pilosicoli and Lawsonia intracellularis by real-time PCR. Results: For B. pilosicoli, 4.5% (95% CI, 2.5–7.0%) of samples and 13.7% (95% CI, 7.5–22.3%) of herds were positive. Out of 12 samples, B. pilosicoli was detected simultaneously with L. intracellularis, B. hyodysenteriae and B. pilosicoli were detected alone in two samples each. In terms of B. hyodysenteriae, 7.0% of samples (95% CI, 4.7–9.9%) from 18.9% of herds (95% CI, 11.6–28.3%) were positive in real time PCR. The presence of B. hyodysenteriae in fecal samples was associated with the presence of diarrhea in pigs. Conclusions: This study confirmed that B. pilosicoli infections occur in Polish pig herds, but the prevalence is at a low level and the presence of B. pilosicoli is not associated with the development of diarrhea in pigs. B. hyodysenteriae is still a common cause of diarrhea among pigs from Polish herds.

scholarly journals Phylogenetic Analyses of Rotavirus A from Cattle in Uruguay Reveal the Circulation of Common and Uncommon Genotypes and Suggest Interspecies Transmission

Pathogens ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 570
Author(s):  
Matías Castells ◽  
Rubén Darío Caffarena ◽  
María Laura Casaux ◽  
Carlos Schild ◽  
Samuel Miño ◽  
...  
Keyword(s):  
Dairy Products ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Economic Losses ◽  
Cattle Production ◽  
Economic Sectors ◽  
Beef Calves ◽  
Rotavirus A ◽  
P Type ◽  
Neonatal Calf Diarrhea

Uruguay is one of the main exporters of beef and dairy products, and cattle production is one of the main economic sectors in this country. Rotavirus A (RVA) is the main pathogen associated with neonatal calf diarrhea (NCD), a syndrome that leads to significant economic losses to the livestock industry. The aims of this study are to determine the frequency of RVA infections, and to analyze the genetic diversity of RVA strains in calves in Uruguay. A total of 833 samples from dairy and beef calves were analyzed through RT-qPCR and sequencing. RVA was detected in 57.0% of the samples. The frequency of detection was significantly higher in dairy (59.5%) than beef (28.4%) calves (p < 0.001), while it did not differ significantly among calves born in herds that were vaccinated (64.0%) or not vaccinated (66.7%) against NCD. The frequency of RVA detection and the viral load were significantly higher in samples from diarrheic (72.1%, 7.99 log10 genome copies/mL of feces) than non-diarrheic (59.9%, 7.35 log10 genome copies/mL of feces) calves (p < 0.005 and p = 0.007, respectively). The observed G-types (VP7) were G6 (77.6%), G10 (20.7%), and G24 (1.7%), while the P-types were P[5] (28.4%), P[11] (70.7%), and P[33] (0.9%). The G-type and P-type combinations were G6P[11] (40.4%), G6P[5] (38.6%), G10P[11] (19.3%), and the uncommon genotype G24P[33] (1.8%). VP6 and NSP1-5 genotyping were performed to better characterize some strains. The phylogenetic analyses suggested interspecies transmission, including transmission between animals and humans.

scholarly journals Human, porcine and bovine rotaviruses in Slovenia: evidence of interspecies transmission and genome reassortment

2008 ◽  
Vol 89 (7) ◽  
pp. 1690-1698 ◽  
Author(s):  
Andrej Steyer ◽  
Mateja Poljšak-Prijatelj ◽  
Darja Barlič-Maganja ◽  
Jožica Marin
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Zoonotic Transmission ◽  
Interspecies Transmission ◽  
Genotype Combination ◽  
Human Rotavirus ◽  
Group A Rotaviruses ◽  
Group A ◽  
Stool Samples ◽  
Genome Reassortment

A surveillance of human, porcine and bovine rotaviruses was carried out in Slovenia in 2004 and 2005. Stool samples were collected from a total of 406 pigs (373 from asymptomatic animals), 132 cattle (126 from asymptomatic animals) and 241 humans (all with diarrhoea), tested for group A rotaviruses using RT-PCR and analysed by sequencing. The aims of the study were to determine the incidence of asymptomatic rotavirus infection in animals, to look for evidence of zoonotic transmission and to detect reassortment among rotaviruses. The rates of asymptomatic shedding of rotaviruses in pigs and cattle were 18.0 % (67/373) and 4.0 % (5/126), respectively. Evidence for zoonotic transmission was detected in one human rotavirus strain, SI-MB6, with the G3P[6] genotype combination, as the nucleotide and predicted amino acid sequences of the VP6, VP7, VP8* and NSP4 genes of strain SI-MB6 and of porcine strains showed high nucleotide and amino acid sequence identity. Two porcine rotavirus strains carried VP7 of probable human origin, suggesting an interspecies reassortment event in the past.

Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus

2015 ◽  
Vol 160 (10) ◽  
pp. 2491-2501 ◽  
Author(s):  
Makoto Nagai ◽  
Tsutomu Omatsu ◽  
Hiroshi Aoki ◽  
Konosuke Otomaru ◽  
Takehiko Uto ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Interspecies Transmission ◽  
Full Genome ◽  
Fecal Samples ◽  
Full Genome Analysis

scholarly journals Are Human P[14] Rotavirus Strains the Result of Interspecies Transmissions from Sheep or Other Ungulates That Belong to the Mammalian Order Artiodactyla?

2009 ◽  
Vol 83 (7) ◽  
pp. 2917-2929 ◽  
Author(s):  
Jelle Matthijnssens ◽  
Christiaan A. Potgieter ◽  
Max Ciarlet ◽  
Viviana Parreño ◽  
Vito Martella ◽  
...  
Keyword(s):  
Complete Genome ◽  
Human Population ◽  
Animal Species ◽  
Genetic Relatedness ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Genome Sequences ◽  
Lama Guanicoe ◽  
Bovine Rotavirus ◽  
Genomic Relatedness

ABSTRACT A limited number of human G6P[14] rotavirus strains that cause gastroenteritis in humans have been isolated in Europe and Australia. The complete genome sequences were determined for five of these human strains—B10925-97 (isolated in Belgium in 1997), 111/05-27 (Italy, 2005), PA169 (Italy, 1987), MG6 (Australia, 1993), and Hun5 (Hungary, 1997)—and their genetic relatedness to animal rotavirus strains was evaluated by sequencing the complete genome of the sheep rotavirus OVR762 (G8P[14]; Spain, 2002), the guanaco (Lama guanicoe) rotavirus strains Arg/Chubut/99 and Arg/Río Negro/98 (G8P[14] and G8P[1], respectively; Argentina, 1999 and 1998), the sable antelope strain RC-18/08 (G6P[14]; South Africa, 2008), and the bovine rotavirus strain Arg/B383/98 (G15P[11]; Argentina, 1998). These analyses revealed an overall consensus genomic constellation (G6/G8)-P[14]-I2-(R2/R5)-C2-M2-(A3/A11)-N2-T6-(E2/E12)-H3, together with a few gene reassortments, and the phylogenetic analyses confirmed that the P[14] human strains evaluated in this study were closely related to rotavirus strains isolated from sheep, cattle, goats, guanacos, and antelopes and to rabbits (albeit to a lesser extent), suggesting that one (or more) of these animal species might be the source of the human G6P[14] strains. The main feature of the genotype and phylogenetic analyses was the close overall genomic relatedness between the five human G6P[14] rotavirus strains and the ovine and antelope rotavirus strains. Taken together, these data strongly suggest a common origin for the human P[14] strains and those of the even-toed ungulates belonging to the mammalian order Artiodactyla, with sheep probably playing a key role in the interspecies transmission responsible for the introduction of P[14] rotavirus strains into the human population.

scholarly journals The application and epidemiological research of xTAG-GPP multiplex PCR in the Diagnosis of children persistent and chronic diarrhea

2020 ◽  
Author(s):  
Chunli Wang ◽  
Xiaoying Zhou ◽  
Mengshu Zhu ◽  
Hanjun Yin ◽  
Jiamei Tang ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Chronic Diarrhea ◽  
Virus Detection ◽  
Rotavirus A ◽  
Multiplex Pcr Assay ◽  
Gastrointestinal Pathogen ◽  
Three Samples ◽  
Two Samples ◽  
Positive Rate ◽  
Medical University

Abstract Background Persistent and chronic diarrhea is difficult to treat, and infection is still the main causes. Clearly infected pathogens are essential for treatment. In this study, we investigate the application value of xTAG gastrointestinal pathogen panel (xTAG GPP) multiplex PCR in the early diagnosis of children with persistent and chronic diarrhea and understand the epidemiology of intestinal diarrhea pathogens. Methods One hundred and ninety-nine specimens were collected from Nanjing Children's Hospital Affiliated to Nanjing Medical University (Nanjing, China). Comparing the xTAG GPP multiplex PCR Assay with the traditional methods (culture, rapid enzyme immunoassay chromatography, microscopic examination) and madding the statistical analysis. Results The positive rate of 199 patients with diarrhea specimens was 72.86% (145/199). The virus detection rate was 48.7%, Rotavirus A was the most common organism detected (34.6%), concentrated in winter, popular in children. Secondly, Norovirus GI/GII (20.6%). The positive rate of bacteria was 40.2%, Campylobacter (22.11%, 44/199) was most frequently detected. With C. difficile toxins A/B and Salmonella detected 44 and 17 samples, respectively. Infections with Shigella occurred 4 times, E. coli O157 was only detected once. There were three samples with parasitic (1.51%), two samples were positive for Entamoeba histolytica, one for Cryptosporidium. Adenovirus40/41, STEC, ETEC, Giardia, Yersinia enterocolitica and Vibriocholera were not detected. Totally 86 (43.2%) infected specimens with single pathogen were detected. There were 57 co-infections (28.64% of samples) of viruses and/or bacteria and/or parasites. Co-infections involved 29 double infections (23.62%) samples, 9 triple infections (4.52%) and 2 quadruple infections (0.5%). Norovirus GI/GII was found to have the highest involvement in co-infections 30(15.08%). Conclusion xTAG GPP multiplex PCR is simple, sensitive, specific and can be used as a quick way to diagnose the children persistent and chronic diarrhea.

scholarly journals Simultaneous detection and ribotyping of Clostridioides difficile, and toxin gene detection directly on fecal samples

2021 ◽  
Author(s):  
Tessel Meike van Rossen ◽  
Joffrey van Prehn ◽  
Alex G. Koek ◽  
Marcel Jonges ◽  
Robin van Houdt ◽  
...  
Keyword(s):  
Simultaneous Detection ◽  
Rapid Test ◽  
Toxin Gene ◽  
Reference Laboratory ◽  
Fecal Dna ◽  
Fecal Samples ◽  
Toxin Genes ◽  
Clostridioides Difficile ◽  
Nosocomial Diarrhea ◽  
Two Samples

Abstract Background: Clostridioides difficile is the most common cause of nosocomial diarrhea. Ribotyping of cultured strains by a PCR-based test is used to study potential transmission between patients. We aimed to develop a rapid test that can be applied directly on fecal samples for simultaneous detection and ribotyping of C. difficile, as well as detection of toxin genes.Methods: We developed a highly specific and sensitive primer set for simultaneous detection and ribotyping of C. difficile directly on total fecal DNA. Toxin genes were detected with primers adapted from Persson et al. (CMI, 2008). Our study set comprised 130 fecal samples: 65 samples with positive qPCR for C. difficile toxin A/B genes and 65 C. difficile qPCR negative samples. PCR products were analyzed by capillary gel electrophoresis. Results: Ribosomal DNA fragment peak profiles and toxin genes were detected in all 65 C. difficile positive fecal samples and in none of the 65 C. difficile negative samples. The 65 samples were assigned to 27 ribotypes by the Dutch reference laboratory. Our peak profiles corresponded to these ribotypes, except for two samples. During a C. difficile outbreak, patients were correctly allocated to the outbreak-cluster based on the results of direct fecal ribotyping, before C. difficile isolates were cultured and conventionally typed.Conclusion: C. difficile ribotyping directly on fecal DNA is feasible, with sensitivity and specificity comparable to that of diagnostic toxin gene qPCR and with ribotype assignment similar to that obtained by conventional typing on DNA from cultured isolates. This supports simultaneous diagnosis and typing to recognize an outbreak.

scholarly journals First report of Cryptosporidium viatorum and Cryptosporidium occultus in humans in China, and of the unique novel C. viatorum subtype XVaA3h

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ning Xu ◽  
Hua Liu ◽  
Yanyan Jiang ◽  
Jianhai Yin ◽  
Zhongying Yuan ◽  
...  
Keyword(s):  
Risk Factors ◽  
Rural Areas ◽  
Cluster Sampling ◽  
Intestinal Protozoa ◽  
Fecal Samples ◽  
Exact Test ◽  
First Report ◽  
Two Samples ◽  
Epidemiological Characteristics

Abstract Background Cryptosporidium is a genus of common intestinal protozoa, members of which cause diarrhea in a wide variety of hosts. Previous studies on Cryptosporidium in China have mainly focused on diarrhea sufferers, children, and immunodeficient individuals such as HIV/AIDS patients. However, the epidemiological characteristics of Cryptosporidium in the population in rural areas remain unclear. Herein, we investigated the prevalence of, and risk factors for, Cryptosporidium in rural areas of Binyang County, Guangxi Zhuang Autonomous Region, China, and genetically characterized the Cryptosporidium isolates we obtained. Methods From August to December 2016, two villages in Binyang County, Guangxi, were sampled using a random cluster sampling method. Fresh fecal samples were collected from all eligible residents (residence time > 6 months). Molecular characterization of Cryptosporidium was carried out based on its SSU rRNA, gp60, actin and hsp70 gene sequences. Fisher’s exact test were conducted to assess the risk factors for Cryptosporidium infection. Results A total of 400 fecal samples were collected from 195 males (48.8%) and 205 females (51.2%). Two samples (0.5%) were positive for Cryptosporidium and were identified as C. viatorum and C. occultus respectively. Moreover, a new C. viatorum subtype XVaA3h was identified based on the sequence of the gp 60 gene. Conclusions To our knowledge, this is the first report of C. viatorum and C. occultus infections in humans in China and of C. viatorum subtype XVaA3h. The findings provide important information on the prevalence of Cryptosporidium in the Chinese population, and expand the range of Cryptosporidium species known to infect people in China.

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