scholarly journals Application of Cation-Coated Filter Method to Detection of Noroviruses, Enteroviruses, Adenoviruses, and Torque Teno Viruses in the Tamagawa River in Japan

2005 ◽  
Vol 71 (5) ◽  
pp. 2403-2411 ◽  
Author(s):  
Eiji Haramoto ◽  
Hiroyuki Katayama ◽  
Kumiko Oguma ◽  
Shinichiro Ohgaki
Keyword(s):  
Surface Water ◽  
Filter Method ◽  
Genotype 1 ◽  
Direct Pcr ◽  
Hepatitis Viruses ◽  
Total Coliforms ◽  
Positive Ratio ◽  
Three Samples ◽  
Genotype 2 ◽  
Taqman Pcr

ABSTRACT The occurrence of human enteric viruses in surface water in the Tamagawa River, Japan, was surveyed for 1 year, from April 2003 to March 2004. Sixty-four samples were collected from six sites along the river, and 500 ml of the sample was concentrated using the cation-coated filter method, which was developed in our previous study. This method showed recovery yields of 56% ± 32% (n = 37) for surface water samples inoculated with polioviruses. More than one kind of tested virus was detected in 43 (67%) of 64 samples by TaqMan PCR. Noroviruses and adenoviruses were detected in a high positive ratio; 34 (53%), 28 (44%), and 29 (45%) of 64 samples were positive for norovirus genotype 1 and genotype 2 and adenoviruses, respectively. The mean concentrations of norovirus genotype 1 or genotype 2 determined by real-time PCR were 0.087 and 0.61 genome/ml, respectively, showing much higher values in winter (0.21 genome/ml for genotype 1 and 2.3 genomes/ml for genotype 2). Enteroviruses were detected by both direct PCR (6 of 64 samples; 9%) and cell culture PCR (2 of 64 samples; 3%). Torque teno viruses, emerging hepatitis viruses, were also isolated in three samples (5%). The concentration of total coliforms and the presence of F-specific phages showed a high correlation with the presence of viruses, which suggested that the simultaneous use of total coliforms and F-specific phages as indicators of surface water may work to monitor viral contamination.

Seasonal profiles of human noroviruses and indicator bacteria in a wastewater treatment plant in Tokyo, Japan

2006 ◽  
Vol 54 (11-12) ◽  
pp. 301-308 ◽  
Author(s):  
E. Haramoto ◽  
H. Katayama ◽  
K. Oguma ◽  
H. Yamashita ◽  
A. Tajima ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Wastewater Treatment Plant ◽  
Treatment Plant ◽  
Genotype 1 ◽  
Human Noroviruses ◽  
Total Coliforms ◽  
Epidemic Season ◽  
Genotype 2 ◽  
One Year ◽  
Final Effluent

The seasonal profiles of microorganisms in raw sewage, secondary-treated sewage, and final effluent at a wastewater treatment plant in Tokyo, Japan, were quantitatively determined each month for one year, from July 2003 to June 2004. Human noroviruses, which were determined by real-time PCR, in raw sewage varied from 0.17–260 copies/mL for genotype 1 and from 2.4–1900 copies/mL for genotype 2, showing much higher values in winter, the epidemic season. The concentration of total coliforms, Escherichia coli, or F-specific phages in raw sewage was almost constant throughout the year. Human noroviruses of genotype 2 were removed most effectively (3.69 log10 on average) at the wastewater treatment plant, followed by E. coli (3.37 log10), total coliforms (3.05 log10), F-specific phages (2.81 log10), and human noroviruses of genotype 1 (2.27 log10). The removal ratio of human noroviruses was almost constant, independent of the initial concentration of the viruses in raw sewage, which led to the increasing concentration of human noroviruses in final effluent in winter. None of the tested bacteria was judged to be a reliable indicator of human noroviruses in final effluent.

scholarly journals crAssphage is not associated with diarrhoea and has high genetic diversity

2016 ◽  
Vol 144 (16) ◽  
pp. 3549-3553 ◽  
Author(s):  
Y. Y. LIANG ◽  
W. ZHANG ◽  
Y. G. TONG ◽  
S. P. CHEN
Keyword(s):  
Genetic Diversity ◽  
Molecular Epidemiology ◽  
Healthy Adults ◽  
Infants And Children ◽  
Chinese Patients ◽  
Genotype 1 ◽  
High Genetic Diversity ◽  
Viral Loads ◽  
Positive Ratio ◽  
Genotype 2

SUMMARYcrAssphage is a newly discovered gut bacteriophage. However, its pathogenicity and molecular epidemiology in humans are as yet unclear. In this study, we investigated the association between crAssphage and diarrhoea, as well as the molecular epidemiology of crAssphage in Chinese patients from our hospital. Our results indicated that there were no significant differences in the crAssphage-positive ratio and viral loads in faecal supernatants between adults with diarrhoea and healthy adults. Of infants and children with diarrhoea, 2·8% were found to be crAssphage-positive, including two infants aged <1 month. Markedly, of all confirmed crAssphage-positive strains, 100% had the ORF00039 deletion and 77·8% had low identity of ORF00018 compared to crAssphage (GenBank accession no. NC_024711, designated genotype 1). Thus, crAssphage was not associated with diarrhoea and most strains of crAssphage in Chinese patients (designated genotype 2) were characterized by the ORF00039 deletion and low identity of ORF00018.

Epstein - Barr virus epidemiology in HIV infected transsexuals

2021 ◽  
pp. 1-11
Author(s):  
Sadia Salahuddin ◽  
Joharia Azhar ◽  
Hasham Akhtar ◽  
Jabbar Khan ◽  
Noor Muhammad
Keyword(s):  
Human Immunodeficiency Virus ◽  
Epstein Barr Virus ◽  
Qualitative Assessment ◽  
Genotype 1 ◽  
Virus Genotype ◽  
Blood Samples ◽  
Barr Virus ◽  
Genotype 2 ◽  
Immunodeficiency Virus ◽  
Epstein Barr

Abstract Objectives: To molecularly characterise the relationship between Epstein-Barr virus genotypes and Pashtun ethnicity. Method: The cross-sectional study was conducted from November 2018 to December 2019 after approval from the Gomal University, Dera Ismail Khan, Pakistan, and comprised blood samples from transgender sex workers who were seropositive for human immunodeficiency virus-1 and seronegative for human immunodeficiency virus residing in two cities of Khyber Pakhtunkhwa province and Islamabad, the federal capital. Formalin-fixed paraffin-embedded samples were collected retrospectively, but collection of blood samples from the study subjects was purely on the basis of physical availability. ?-globin gene and EBER-1 were amplified for qualitative assessment and existence of Epstein-Barr virus. Characterisation of EBNA-2 was done through nested polymerase chain reaction. Results: Of the 80 subjects, 40(50%) each were seropositive and seronegative individuals. The overall mean age was 28±6.917 years. Among the seropositive group, 38(95%) were homosexual and 2(5%) were heterosexual. Among the seropositive group, 16(40%) had Epstein-Barr virus genotype 1 and 6(15%) had genotype 2, while co-infections were found in 2(5%) subjects. In the seronegative group, 36(90%) subjects had Epstein-Barr virus genotype 1, while there was no case of genotype 2 or co-infection. EBV-2 genotypes with HIV seropositivity showed strong association (p=0.005). Amplification for the EBER-1 gene was done in all the 80(100%) samples. Conclusion: Epstein-Barr virus EBV genotype 1 was found to be the most frequent type, while genotype 2 and co-infections were detected only seropositive samples. Continuous...

scholarly journals High SVR-Rates in Patients With HCV Genotype 1-Infection, Who Are Dually Infected With Either Genotype 2 or 3 and Treated With PEG-IFNα-2B and Ribavirin

2011 ◽  
Vol 140 (5) ◽  
pp. S-948
Author(s):  
Stefan Mauss ◽  
Gerlinde Teuber ◽  
Elmar Zehnter ◽  
Michael P. Manns ◽  
Tarek Dahhan ◽  
...  
Keyword(s):  
Genotype 1 ◽  
Hcv Genotype ◽  
Genotype 2 ◽  
Hcv Genotype 1

scholarly journals Tuberculous lesions in pig lymph nodes caused by kaolin fed as a supplement

2012 ◽  
Vol 49 (No. 10) ◽  
pp. 379-388 ◽  
Author(s):  
L. Matlova ◽  
L. Dvorska ◽  
M. Bartos ◽  
J. Docekal ◽  
M. Trckova ◽  
...  
Keyword(s):  
Surface Water ◽  
Lymph Nodes ◽  
Mesenteric Lymph Nodes ◽  
Mesenteric Lymph ◽  
Three Samples ◽  
Potential Sources ◽  
Sources Of Infection ◽  
On Farm ◽  
Slaughtered Pigs

An increased incidence of tuberculous lesions in head and mesenteric lymph nodes from slaughtered pigs weighing about 115 kg was recorded in a herd of pigs kept in two farms A and B in the CzechRepublic. Tuberculous lesions were more frequently (P &lt; 0.01) diagnosed in pigs from Farm A (10.4%) than from Farm B (1.1%). The follow-up investigation of potential sources of infection on Farm A revealed that the piglets were fed kaolin from a nearby mine as a supplement. Among 20 samples from the pigs&rsquo; environment, atypical conditionally pathogenic mycobacteria (ACPM) were detected in four samples as follows: dust (n = 2), pig faeces (n = 1) and kaolin fed as a supplement (n = 1). Mycobacterium avium subsp. hominissuis of genotype IS901&ndash; and IS1245+ and serotype 8 was isolated from kaolin and pig lymph nodes, M. fortuitum from stable dust and pig faeces and other ACPM from stable dust. When kaolin feeding to piglets ceased, the incidence of tuberculous lesions in these pigs at slaughter 5&ndash;6 months later decreased from 16.1% to 3.4%. No ACPM was detected on Farm B in 27 samples from the environment. An investigation of surface kaolin mines did not detect mycobacteria in non-extracted kaolin. However, surface water (three isolates among 13 samples) from the pond used for kaolin levigation and 23 batches of the final product of kaolin (10 samples from each batch, i.e. a total of 230 samples were examined) were contaminated with ACPM. Among the latter, ACPM were isolated from three samples originating from three different batches. ACPM were likely to survive during transport of the kaolin, as a suspension through the pipeline, and during its further processing to the final product (sedimentation, addition of colloid substances, drying and other procedures).

scholarly journals Successful Kidney Transplantation in a Recipient Coinfected with Hepatitis C Genotype 2 and HIV from a Donor Infected with Hepatitis C Genotype 1 in the Direct-Acting Antiviral Era

2020 ◽  
Vol 2020 ◽  
pp. 1-6
Author(s):  
Dimitrios Farmakiotis ◽  
Zoe Weiss ◽  
Amy L. Brotherton ◽  
Paul Morrissey ◽  
Reginald Gohh ◽  
...  
Keyword(s):  
Kidney Transplantation ◽  
Hepatitis C ◽  
Antiviral Treatment ◽  
Holistic Approach ◽  
Kidney Graft ◽  
Genotype 1 ◽  
Direct Acting Antiviral ◽  
First Case ◽  
Genotype 2 ◽  
Transplant Candidates

Despite significant advances in transplantation of HIV-infected individuals, little is known about HIV coinfected patients with hepatitis C virus (HCV) genotypes other than genotype 1, especially when receiving HCV-infected organs with a different genotype. We describe the first case of kidney transplantation in a man coinfected with hepatitis C and HIV in our state. To our knowledge, this is also the first report of an HIV/HCV/HBV tri-infected patient with non-1 (2a) HCV genotype who received an HCV-infected kidney graft with the discordant genotype (1a), to which he converted after transplant. Our case study highlights the following: (1) transplant centers need to monitor wait times for an HCV-infected organ and regularly assess the risk of delaying HCV antiviral treatment for HCV-infected transplant candidates in anticipation of the transplant from an HCV-infected donor; (2) closer monitoring of tacrolimus levels during the early phases of anti-HCV protease inhibitor introduction and discontinuation may be indicated; (3) donor genotype transmission can occur; (4) HIV/HCV coinfected transplant candidates require a holistic approach with emphasis on the cardiovascular risk profile and low threshold for cardiac catheterization as part of their pretransplant evaluation.

Toxoplasmosis among cancer patients undergoing chemotherapy: a population study based on the serological, molecular and epidemiological aspects

2020 ◽  
Author(s):  
Seyed Abdollah Hosseini ◽  
Mehdi Sharif ◽  
Shahabeddin Sarvi ◽  
Ghasem Janbabai ◽  
Shahrbanoo Keihanian ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Fragment Length Polymorphism ◽  
Type I ◽  
Type Ii ◽  
Genotype 1 ◽  
Serum Samples ◽  
Northern Iran ◽  
Patients With Cancer ◽  
Genotype 2 ◽  
High Prevalence

Abstract Background Toxoplasmosis is highly prevalent in northern Iran and immunocompromised individuals are more susceptible to this infection. The present study aimed to determine the seroprevalence, parasitism and genetic diversity of Toxoplasma gondii among patients with cancer undergoing chemotherapy in northern Iran. Methods A total of 350 serum samples obtained from cancer patients were collected from laboratory centers in northern Iran. Immunodiagnosis and DNA detection were accomplished by ELISA and PCR. Thereafter, multiplex-nested PCR-restriction fragment length polymorphism was used for the genotyping of T. gondii. Results In general, out of 350 patients, 264 (75.4%) and 9 (2.57%) cases were positive for anti-T. gondii IgG and IgM, respectively. Moreover, 19 (5.43%) samples contained T. gondii DNA. From 19 positive samples, 10 high-quality samples with sharp and non-smear bands were selected to determine the genotypes of T. gondii. Accordingly, the samples were classified as genotype #1 (type II clonal; n=4, 40%), genotype #2 (type III clonal; n=3, 30%), genotype #10 (type I clonal; n=2, 20%) and genotype #27 (type I variant; n=1, 10%). Conclusions As evidenced by the results, due to the high prevalence of T. gondii, cancer patients in northern Iran are at serious risk of severe toxoplasmosis and its complications. Therefore, oncologists need to regard this critical health problem as a matter requiring urgent attention.

scholarly journals Preclinical Characterization of BMS-791325, an Allosteric Inhibitor of Hepatitis C Virus NS5B Polymerase

2014 ◽  
Vol 58 (6) ◽  
pp. 3485-3495 ◽  
Author(s):  
Julie A. Lemm ◽  
Mengping Liu ◽  
Robert G. Gentles ◽  
Min Ding ◽  
Stacey Voss ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Nucleoside Analogs ◽  
Synergistic Activity ◽  
Genotype 1 ◽  
Allosteric Inhibitor ◽  
Genotype 2 ◽  
Hcv Genotype 1 ◽  
Ns3 Protease

ABSTRACTBMS-791325 is an allosteric inhibitor that binds to thumb site 1 of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase. BMS-791325 inhibits recombinant NS5B proteins from HCV genotypes 1, 3, 4, and 5 at 50% inhibitory concentrations (IC50) below 28 nM. In cell culture, BMS-791325 inhibited replication of HCV subgenomic replicons representing genotypes 1a and 1b at 50% effective concentrations (EC50s) of 3 nM and 6 nM, respectively, with similar (3 to 18 nM) values for genotypes 3a, 4a, and 5a. Potency against genotype 6a showed more variability (9 to 125 nM), and activity was weaker against genotype 2 (EC50, 87 to 925 nM). Specificity was demonstrated by the absence of activity (EC50s of >4 μM) against a panel of mammalian viruses, and cytotoxic concentrations (50%) were >3,000-fold above the HCV EC50. Resistance substitutions selected by BMS-791325 in genotype 1 replicons mostly mapped to a single site, NS5B amino acid 495 (P495A/S/L/T). Additive or synergistic activity was observed in combination studies using BMS-791325 with alfa interferon plus ribavirin, inhibitors of NS3 protease or NS5A, and other classes of NS5B inhibitor (palm site 2-binding or nucleoside analogs). Plasma and liver exposuresin vivoin several animal species indicated that BMS-791325 has a hepatotropic disposition (liver-to-plasma ratios ranging from 1.6- to 60-fold across species). Twenty-four hours postdose, liver exposures across all species tested were ≥10-fold above the inhibitor EC50s observed with HCV genotype 1 replicons. These findings support the evaluation of BMS-791325 in combination regimens for the treatment of HCV. Phase 3 studies are ongoing.

Contamination of coagulation factor concentrates with human parvovirus B19 genotype 1 and 2

2004 ◽  
Vol 92 (10) ◽  
pp. 838-845 ◽  
Author(s):  
Beate Schneider ◽  
Maria Becker ◽  
Hans-Hermann Brackmann ◽  
Anna Eis-Hübinger
Keyword(s):  
Parvovirus B19 ◽  
Simultaneous Detection ◽  
Coagulation Factor ◽  
Nucleic Acid Amplification ◽  
Clotting Factor ◽  
Human Parvovirus B19 ◽  
Genotype 1 ◽  
Viral Inactivation ◽  
Genotype 2 ◽  
Coagulation Factor Concentrates

SummaryHuman parvovirus B19 (B19) DNA has frequently been detected in plasma-derived coagulation factor concentrates. Furthermore, transmission of B19 infection was observed, indicating presence of the infectious virus despite routine viral inactivation/removal procedures during the manufacturing process. Recently, human parvovirus DNA isolates, variant from B19, have been identified resulting in classification of B19 virus into three distinct genotypes, with all viruses previously classified as B19 belonging to genotype 1. So far, there is no information available on contamination of clotting factor concentrates with genotype 2. Therefore, we analysed 202 different factor concentrate lots for genotype 1 and 2 DNA by PCR. Analysis of one hundred eighty-one lots representing 13 different products, administered over the last three years, was compared to 21 lots (8 products) used until the early 1980s which had not been treated by viral inactivation procedures. Genotype 1 DNA was detected in 77/181 (42.5%) currently administered lots, and 17/21 (81%) previously used lots. The level of genotype 1 DNA contamination was similar in currently and previously administered concentrates. Genotype 2 DNA was found in 5/202 (2.5%) lots, all of which were co-contaminated with genotype 1 DNA. DNA sequence analysis showed that the PCR-double positive concentrates contained typical genotype 1 and genotype 2 DNA. Because genotype 2 appears to cause a similar spectrum of diseases as genotype 1, simultaneous detection of genotype 2 by nucleic acid amplification testing (NAT), now widely applied to plasma pools for genotype 1, would give an added level of safety to blood products.

Potentially pathogenic bacteria isolated from different tropical waters in Sri Lanka

2013 ◽  
Vol 13 (6) ◽  
pp. 1463-1469 ◽  
Author(s):  
W. M. G. C. K. Mannapperuma ◽  
C. L. Abayasekara ◽  
G. B. B. Herath ◽  
D. R. I. B. Werellagama
Keyword(s):  
Surface Water ◽  
Sri Lanka ◽  
Water Samples ◽  
Pathogenic Bacteria ◽  
Water Sources ◽  
Bottled Water ◽  
Well Water ◽  
Faecal Coliforms ◽  
Total Coliforms ◽  
Source Waters

This study investigated the bacteriological contamination of different water sources in Sri Lanka. Source waters (n = 74) including bottled water, well water and surface water were assessed for enumerating total coliforms and faecal coliforms using the membrane filtration method. The results showed that 18.5 and 14.8% of bottled water samples were contaminated with total coliforms and faecal coliforms, respectively. All the well water and surface water samples exceeded the WHO permitted levels for total coliforms and faecal coliforms. Bacteriological identification using biochemical tests and api 20E identification tests revealed the presence of potentially pathogenic bacteria in all water sources tested. Bottled water mainly contained three Enterobacter species, while well water samples showed the broadest spectrum of bacteria including eleven coliform species belonging to the genera Klebsiella, Escherichia, Enterobacter, Citrobacter, Kluyvera, Pantoea, Rautella, and 10 non-coliform species in the genera Pseudomonas, Aeromonas, Salmonella and Acinetobacter. Surface waters contained seven coliform species belonging to the genera Klebsiella, Escherichia, Citrobacter, Rautella and Serratia, and eight non-coliform species in the genera Pseudomonas, Aeromonas and Acinetobacter. Detection of higher bacteriological counts and identification of potentially pathogenic bacteria in different source waters suggest a potential health risk of the water sources used in Sri Lanka.

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