1
|
Hussein MA, Al-zaban MI, Mahmoud YA, Al-Doaiss AA, Bahshwan SM, El-Dougdoug KA, EL-Shanshory MR. How does a Saccharomyces cerevisiae extract influence the components of isolated rotavirus particles from stool samples collected in a clinical setting from children? Saudi J Biol Sci 2024; 31:104031. [PMID: 38946847 PMCID: PMC11214517 DOI: 10.1016/j.sjbs.2024.104031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 07/02/2024] Open
Abstract
Human Rotavirus (HRV) is the causative pathogen of severe acute enteric infections that cause mortality among children worldwide. This study focuses on developing a new and effective treatment for rotavirus infection using an extract from Saccharomyces cerevisiae, aiming to make this treatment easily accessible to everyone. 15 antigens and 26 antibodies were detected in serum and stool using ELISA. The titers of HRVq1, HRVq2, HRVC1, and HRVC2 on Vero cells were determined to be 1.2x106, 3.0x106, 4.2x106, and 7.5x105 (Plaque forming unit, PFU/ml) four days after infection, respectively. The HRVq1 isolate induced cytopathic effects, i.e., forming multinucleated, rounded, enlarged, and expanding gigantic cells. RT-PCR identified this isolate, and the accession number 2691714 was assigned to GeneBank. The molecular docking analysis revealed that nonstructural proteins (NSPs) NSP1, NSP2, NSP3, NSP4, NSP5, and NSP6 exhibited significant binding with RNA. NSP2 demonstrated the highest binding affinity and the lowest binding energy (-8.9 kcal/mol). This affinity was maintained via hydrophobic interactions and hydrogen bonds spanning in length from 1.12 Å to 3.11 Å. The ADMET and bioactivity predictions indicated that the yeast extract possessed ideal solubility, was nontoxic, and did not cause cancer. The inhibitory constant values predicted for the S. cerevisiae extract in the presence of HRV vital proteins varied from 5.32 to 7.45 mM, indicating its potential as a viable drug candidate. Saccharomyces cerevisiae extract could be utilized as a dietary supplement to combat HRV as an alternative dietary supplement.
Collapse
Affiliation(s)
- Mona A.M. Hussein
- Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Mayasar I. Al-zaban
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Yahia A.G. Mahmoud
- Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Amin A. Al-Doaiss
- Biology Department, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Safia M.A. Bahshwan
- Biological Sciences Department, College of Science and Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Khalid A. El-Dougdoug
- Microbiology Department, Faculty of Agriculture, Ain Shams University, PO Box 68, Hadayek Shobra 11241, Cairo, Egypt
| | | |
Collapse
|
2
|
Rupprom K, Thongpanich Y, Sukkham W, Utrarachkij F, Kittigul L. Recovery and Quantification of Norovirus in Air Samples from Experimentally Produced Aerosols. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:216-224. [PMID: 38512560 PMCID: PMC11186938 DOI: 10.1007/s12560-024-09590-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/13/2024] [Indexed: 03/23/2024]
Abstract
Norovirus is the leading cause of acute gastroenteritis in humans across all age groups worldwide. Norovirus-infected patients can produce aerosolized droplets which play a role in gastroenteritis transmission. The study aimed to assess bioaerosol sampling in combination with a virus concentrating procedure to facilitate molecular detection of norovirus genogroup (G) II from experimentally contaminated aerosols. Using a nebulizer within an experimental chamber, aerosols of norovirus GII were generated at known concentrations. Air samples were then collected in both 5 mL and 20 mL water using the SKC BioSampler at a flow rate of 12.5 L/min, 15 min. Subsequently, the virus in collected water was concentrated using speedVac centrifugation and quantified by RT-qPCR. The optimal distances between the nebulizer and the SKC BioSampler yielded high recoveries of the virus for both 5 and 20 mL collections. Following nebulization, norovirus GII RNA was detectable up to 120 min in 5 mL and up to 240 min in 20 mL collection. The concentrations of norovirus GII RNA recovered from air samples in the aerosol chamber ranged from 102 to 105 genome copies/mL, with average recoveries of 25 ± 12% for 5 mL and 22 ± 19% for 20 mL collections. These findings provide quantitative data on norovirus GII in aerosols and introduce a novel virus concentrating method for aerosol collection in water, thus enhancing surveillance of this virus.
Collapse
Affiliation(s)
- Kitwadee Rupprom
- Department of Clinical Pathology, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Yuwanda Thongpanich
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
| | - Woravat Sukkham
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
| | - Fuangfa Utrarachkij
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
| | - Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand.
| |
Collapse
|
3
|
Mostafa-Hedeab G, Allayeh AK, Elhady HA, Eledrdery AY, Mraheil MA, Mostafa A. Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19137707. [PMID: 35805367 PMCID: PMC9265447 DOI: 10.3390/ijerph19137707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 12/17/2022]
Abstract
Enteric viruses (EVs) occurrence within aquatic environments varies and leads to significant risk on public health of humans, animals, and diversity of aquatic taxa. Early and efficacious recognition of cultivable and fastidious EVs in aquatic systems are important to ensure the sanitary level of aquatic water and implement required treatment strategies. Herein, we provided a comprehensive overview of the conventional and up-to-date eco-genomic tools for aquatic biomonitoring of EVs, aiming to develop better water pollution monitoring tools. In combination with bioinformatics techniques, genetic tools including cloning sequencing analysis, DNA microarray, next-generation sequencing (NGS), and metagenomic sequencing technologies are implemented to make informed decisions about the global burden of waterborne EVs-associated diseases. The data presented in this review are helpful to recommend that: (1) Each viral pollution detection method has its own merits and demerits; therefore, it would be advantageous for viral pollution evaluation to be integrated as a complementary platform. (2) The total viral genome pool extracted from aquatic environmental samples is a real reflection of pollution status of the aquatic eco-systems; therefore, it is recommended to conduct regular sampling through the year to establish an updated monitoring system for EVs, and quantify viral peak concentrations, viral typing, and genotyping. (3) Despite that conventional detection methods are cheaper, it is highly recommended to implement molecular-based technologies to complement aquatic ecosystems biomonitoring due to numerous advantages including high-throughput capability. (4) Continuous implementation of the eco-genetic detection tools for monitoring the EVs in aquatic ecosystems is recommended.
Collapse
Affiliation(s)
- Gomaa Mostafa-Hedeab
- Pharmacology Department and Health Research Unit, Medical College, Jouf University, Skaka 11564, Saudi Arabia
- Correspondence: (G.M.-H.); (M.A.M.); (A.M.)
| | - Abdou Kamal Allayeh
- Water Pollution Department, Virology Laboratory, National Research Centre, Dokki, Giza 12622, Egypt;
| | | | - Abozer Y. Eledrdery
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 11564, Saudi Arabia;
| | - Mobarak Abu Mraheil
- German Center for Infection Research (DZIF), Institute of Medical Microbiology, Justus-Liebig University, 35392 Giessen, Germany
- Correspondence: (G.M.-H.); (M.A.M.); (A.M.)
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
- Correspondence: (G.M.-H.); (M.A.M.); (A.M.)
| |
Collapse
|
4
|
Omatola CA, Olaniran AO. Epidemiological significance of the occurrence and persistence of rotaviruses in water and sewage: a critical review and proposal for routine microbiological monitoring. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:380-399. [PMID: 35174845 DOI: 10.1039/d1em00435b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Globally, waterborne gastroenteritis attributable to rotaviruses is on the increase due to the rapid increase in population growth, poor socioeconomic conditions, and drastic changes in climatic conditions. The burden of diarrhea is quite alarming in developing nations where the majority of the populations still rely on untreated surface water that is usually polluted for their immediate water needs. Humans and animals of all ages are affected by rotaviruses. In humans, the preponderance of cases occurs in children under 5 years. Global efforts in advancing water/wastewater treatment technologies have not yet realized the objective of complete viral removal from wastewater. Most times, surface waters are impacted heavily by inadequately treated wastewater run-offs thereby exposing people or animals to preventable health risks. The relative stability of rotaviruses in aquatic matrices during wastewater treatment, poor correlation of bacteriological indicators with the presence of rotaviruses, and their infectiousness at a low dose informed the proposal for inclusion in the routine microbiological water screening panel. Environmental monitoring data have been shown to provide early warnings that can complement clinical data used to monitor the impact of current rotavirus vaccination in a community. This review was therefore undertaken to critically appraise rotavirus excretion and emission pathways, and the existence, viability and persistence in the receiving aquatic milieu. The efficiency of the current wastewater treatment modality for rotavirus removal, correlation of the current bacteriological water quality assessment strategy, public health risks and current laboratory methods for an epidemiological study were also discussed.
Collapse
Affiliation(s)
- Cornelius A Omatola
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, Republic of South Africa.
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, Republic of South Africa.
| |
Collapse
|
5
|
Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
Collapse
|
6
|
Osuolale O, Okoh A. Human enteric bacteria and viruses in five wastewater treatment plants in the Eastern Cape, South Africa. J Infect Public Health 2017; 10:541-547. [DOI: 10.1016/j.jiph.2016.11.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/10/2016] [Accepted: 11/18/2016] [Indexed: 11/24/2022] Open
|
7
|
Qiao Y, Sui Z, Hu G, Cao H, Yang G, Li Y, Lei Y, Zhao L, Chen Q. Comparison of concentration methods for detection of hepatitis A virus in water samples. Virol Sin 2016; 31:331-8. [PMID: 27535067 DOI: 10.1007/s12250-016-3786-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/01/2016] [Indexed: 11/30/2022] Open
Abstract
Hepatitis A virus is a pathogen associated with water pollution. Contaminated drinking water can cause hepatitis A outbreaks, lead to economic losses, and even threaten human lives. It is difficult to detect low levels of hepatitis A virus in water, so the virus must be concentrated in order to quantify it accurately. Here, we present a simple, rapid, efficient technique for the concentration and detection of hepatitis A virus in water. Our data showed that adding phosphate-buffered saline to the water, pre-filtering the water, and adding Trizol reagent directly to the filtration membrane can significantly improve concentration efficiency. Of three types of filtration membranes studied (mixed cellulose ester membrane, polyvinylidene fluoride membrane, and nylon membrane), the concentration efficiency using mixed cellulose ester membrane with a 0.1-μm pore size was the highest, reaching 92.62 ± 5.17%. This method was used to concentrate hepatitis A virus in water samples from Donghu Lake. Using SYBR Green real-time reverse transcription polymerase chain reaction analysis, the detection sensitivity of this method reached 10(1) copies/μL and its concentration efficiency reached 79.45 ± 9.88%.
Collapse
Affiliation(s)
- Yuting Qiao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,College of Animal Science and Technology, Institute of Animal Population Health, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhiwei Sui
- National Institute of Metrology, Beijing, 100013, China
| | - Guoliang Hu
- College of Animal Science and Technology, Institute of Animal Population Health, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huabin Cao
- College of Animal Science and Technology, Institute of Animal Population Health, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Guoxiang Yang
- Hubei Wildlife Epidemic Focus and Disease Surveillance Center, Wuhan, 430075, China
| | - Yong Li
- Hubei Wildlife Epidemic Focus and Disease Surveillance Center, Wuhan, 430075, China
| | - Yongsong Lei
- Hubei Wildlife Epidemic Focus and Disease Surveillance Center, Wuhan, 430075, China
| | - Lihua Zhao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Quanjiao Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| |
Collapse
|
8
|
Sakudo A, Baba K, Ikuta K. Capturing and concentrating adenovirus using magnetic anionic nanobeads. Int J Nanomedicine 2016; 11:1847-57. [PMID: 27274228 PMCID: PMC4869635 DOI: 10.2147/ijn.s104926] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We recently demonstrated how various enveloped viruses can be efficiently concentrated using magnetic beads coated with an anionic polymer, poly(methyl vinyl ether-maleic anhydrate). However, the exact mechanism of interaction between the virus particles and anionic beads remains unclear. To further investigate whether these magnetic anionic beads specifically bind to the viral envelope, we examined their potential interaction with a nonenveloped virus (adenovirus). The beads were incubated with either adenovirus-infected cell culture medium or nasal aspirates from adenovirus-infected individuals and then separated from the supernatant by applying a magnetic field. After thoroughly washing the beads, adsorption of adenovirus was confirmed by a variety of techniques, including immunochromatography, polymerase chain reaction, Western blotting, and cell culture infection assays. These detection methods positively identified the hexon and penton capsid proteins of adenovirus along with the viral genome on the magnetic beads. Furthermore, various types of adenovirus including Types 5, 6, 11, 19, and 41 were captured using the magnetic bead procedure. Our bead capture method was also found to increase the sensitivity of viral detection. Adenovirus below the detectable limit for immunochromatography was efficiently concentrated using the magnetic bead procedure, allowing the virus to be successfully detected using this methodology. Moreover, these findings clearly demonstrate that a viral envelope is not required for binding to the anionic magnetic beads. Taken together, our results show that this capture procedure increases the sensitivity of detection of adenovirus and would, therefore, be a valuable tool for analyzing both clinical and experimental samples.
Collapse
Affiliation(s)
- Akikazu Sakudo
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | | | - Kazuyoshi Ikuta
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka, Suita, Osaka, Japan; Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kanonji, Kagawa, Japan
| |
Collapse
|
9
|
Kittigul L, Singhaboot Y, Chavalitshewinkoon-Petmitr P, Pombubpa K, Hirunpetcharat C. A comparison of virus concentration methods for molecular detection and characterization of rotavirus in bivalve shellfish species. Food Microbiol 2014; 46:161-167. [PMID: 25475280 DOI: 10.1016/j.fm.2014.07.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/09/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
The objectives of this study were to develop a method for concentrating rotavirus, to assess the detection rate, and to characterize the genotype of naturally occurring rotavirus in bivalve shellfish species; including oysters (Saccostrea forskali), cockles (Anadara nodifera), and mussels (Perna viridis). The results demonstrated that an adsorption-twice elution-extraction method was less-time consuming method of concentrating the spiked rotavirus, yielding high sensitivity of 1.14 genome copies/g of digestive tissues from all three shellfish species, as detected using an RT-nested PCR. In seeding experiments, rotavirus as low as 1.39 genome copies was able to be detected in 4 g of digestive tissues or per sample. In the period of August 2011 to July 2012, of the 300 bivalve shellfish samples collected and tested, 24 (8.0%) were found to be contaminated with rotavirus, the figures being: oysters, 13/100 samples; mussels, 10/100 samples; and cockles, 1/100 samples. By DNA sequencing of the RT-nested PCR products and phylogenetic analysis, the rotaviruses detected were classified into G1, lineage II (4 samples); G3 (10 samples): lineage I (3 samples), lineage IIIc (3 samples), lineage IIId (3 samples), lineage IV (1 sample); G9 (6 samples); and G12, lineage III (1 sample). These findings suggest that this virus concentration method provides high sensitivity for the detection of rotavirus from the three bivalve shellfish species. The prevalence of rotavirus and the identified genotypes contribute to the molecular epidemiology of rotavirus in different shellfish species.
Collapse
Affiliation(s)
- Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand.
| | - Yutatirat Singhaboot
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
| | | | - Kannika Pombubpa
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
| | - Chakrit Hirunpetcharat
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
| |
Collapse
|
10
|
Kittigul L, Panjangampatthana A, Rupprom K, Pombubpa K. Genetic diversity of rotavirus strains circulating in environmental water and bivalve shellfish in Thailand. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2014; 11:1299-311. [PMID: 24469269 PMCID: PMC3945539 DOI: 10.3390/ijerph110201299] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/12/2014] [Accepted: 01/15/2014] [Indexed: 12/22/2022]
Abstract
Rotavirus is a common cause of acute diarrhea in young children worldwide. This study investigated the prevalence and molecular characterization of rotavirus in environmental water and oyster samples in Thailand. A total of 114 water samples and 110 oyster samples were collected and tested for group A rotavirus using RT-nested PCR. Rotavirus genotype was identified by phylogenetic analysis of the VP7 genetic sequences. Group A rotavirus was detected in 21 water samples (18.4%) and six oyster samples (5.4%). Twenty five rotavirus strains were successfully sequenced and classified into four genotypes; G1, G2, G3, and G9. Rotavirus G1 (three strains), G2 (three strains), and G9 (two strains) demonstrated the genetic sequences similar to human strains (90%-99% nucleotide identity), whereas G3 (17 strains) was closely related to animal strains (84%-98% nucleotide identity). G1 strains belonged to lineages I (sub-lineage c) and II. G2 strains belonged to lineage II. G9 strains belonged to lineages III (sub-lineage b) and IV. G3 strains belonged to lineages I, III (sub-lineage c), and IV with a predominance of lineage I. The present study provides important information on the rotavirus strains circulating in the environment.
Collapse
Affiliation(s)
- Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok 10400, Thailand.
| | - Apinya Panjangampatthana
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok 10400, Thailand.
| | - Kitwadee Rupprom
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok 10400, Thailand.
| | - Kannika Pombubpa
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok 10400, Thailand.
| |
Collapse
|
11
|
Vecchia AD, Kluge M, dos Santos da Silva JV, Comerlato J, Rodrigues MT, Fleck JD, da Luz RB, Teixeira TF, Roehe PM, Capalonga R, Oliveira AB, Spilki FR. Presence of Torque teno virus (TTV) in tap water in public schools from Southern Brazil. FOOD AND ENVIRONMENTAL VIROLOGY 2013; 5:41-45. [PMID: 23412718 DOI: 10.1007/s12560-012-9096-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
Torque teno virus (TTV) was surveyed in tap water collected in schools from three municipalities located in the south of Brazil. TTV genomes were found in 11.7 % (4/34) of the samples. TTV DNA was detected in 10.5 % (2/19) of the samples collected at the city of Caxias do Sul and in 25 % (2/8) of the samples from Pelotas. Those cities have a low rate of sewage treatment. All samples from Santa Cruz do Sul, which has nearly 92 % of its sewage treated, were negative. These results suggest that the amount of sewage treated may have an effect on the detection rates of TTV DNA in drinking water in a given urban area, showing a mild negative correlation (r = -0.76), when comparing the percentage of sewage treatment to the detection of TTV genomes. The detection rate of TTV was also compared with Escherichia coli, showing a strong correlation (r = 0.97), indicating that TTV may be a suitable marker of fecal contamination.
Collapse
Affiliation(s)
- Andréia Dalla Vecchia
- Molecular Microbiology Laboratory, Institute of Health Sciences, Universidade Feevale, RS-239 2755, Novo Hamburgo, RS, 93352-000, Brazil
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Pang XL, Lee BE, Pabbaraju K, Gabos S, Craik S, Payment P, Neumann N. Pre-analytical and analytical procedures for the detection of enteric viruses and enterovirus in water samples. J Virol Methods 2012; 184:77-83. [DOI: 10.1016/j.jviromet.2012.05.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 04/17/2012] [Accepted: 05/15/2012] [Indexed: 01/14/2023]
|
13
|
SAKUDO AKIKAZU, IKUTA KAZUYOSHI. A technique for capturing broad subtypes and circulating recombinant forms of HIV-1 based on anionic polymer-coated magnetic beads. Int J Mol Med 2012; 30:437-42. [DOI: 10.3892/ijmm.2012.1009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/23/2012] [Indexed: 11/06/2022] Open
|
14
|
Biosensors for the detection of waterborne pathogens. Anal Bioanal Chem 2011; 402:117-27. [DOI: 10.1007/s00216-011-5407-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/30/2011] [Accepted: 09/08/2011] [Indexed: 11/26/2022]
|
15
|
Cell surface display of poliovirus receptor on Escherichia coli, a novel method for concentrating viral particles in water. Appl Environ Microbiol 2011; 77:5141-8. [PMID: 21622793 DOI: 10.1128/aem.00071-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The lack of efficient methods for concentrating viruses in water samples leads to underreporting of viral contamination in source water. A novel strategy for viral concentration was developed using the expression of target virus receptors on bacterial cells. Poliovirus type 1, the most studied enterovirus, was used as a surrogate for enteric viruses. The human poliovirus receptor (hPVR) gene was expressed on the surface of Escherichia coli cells by using the ice nucleation protein (INP) gene. The hPVR gene was ligated to the 3' end of the INP gene after the removal of the stop codon. The resulting open reading frame (ORF) was used for the projection of hPVR onto the outer membrane of E. coli. Gene expression was tested by SDS-PAGE, Western blot, and dot blot analyses, and virion capture ability was confirmed by transmission electron microscopy. The application of engineered E. coli cells for capturing viruses in 1-liter samples of source and drinking water resulted in 75 to 99% procedural recovery efficiency. Cell surface display of viral receptors on bacterial cells opens a new prospect for an efficient and inexpensive alternative tool for capturing and concentrating waterborne viruses in water samples.
Collapse
|
16
|
Grassi T, Bagordo F, Idolo A, Lugoli F, Gabutti G, De Donno A. Rotavirus detection in environmental water samples by tangential flow ultrafiltration and RT-nested PCR. ENVIRONMENTAL MONITORING AND ASSESSMENT 2010; 164:199-205. [PMID: 19357978 DOI: 10.1007/s10661-009-0885-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 03/10/2009] [Indexed: 05/27/2023]
Abstract
Environmental monitoring was conducted in Otranto (Italy), from January 2006 to April 2007, to monitor the circulation of rotaviruses in various water matrices (raw and treated sewage, surface waters and seawater) and to identify any correlation with the traditional bacteriological indices (faecal coliforms). The viruses were detected using tangential flow ultrafiltration and reverse transcriptase-nested polymerase chain reaction, whilst detection of feaecal coliform was performed according to standard methods. The results showed widespread viral contamination, particularly in spring, of the matrices tested, with the exception of seawater, which at all times tested negative for the presence of rotaviruses. The typing of the rotavirus strains identified the circulation in the studied area of only two genotypes: G1 (22%) and G2 (78%). The bacterial recoveries confirmed the presence of faecal pollution indicators in all examined samples, sometimes with high values. A very weak correlation was found between the presence of faecal coliforms and the circulation of rotaviruses in the environment. The presence of rotaviruses in the environmental water samples may constitute a potential health risk for the local population.
Collapse
Affiliation(s)
- Tiziana Grassi
- Department of Biological and Environmental Science and Technology, Laboratory of Hygiene, University of the Salento, via Prov.le Lecce-Monteroni, 73100, Lecce, Italy.
| | | | | | | | | | | |
Collapse
|
17
|
Sakudo A, Baba K, Tsukamoto M, Ikuta K. Use of anionic polymer, poly(methyl vinyl ether-maleic anhydride)-coated beads for capture of respiratory syncytial virus. Bioorg Med Chem Lett 2009; 19:4488-91. [DOI: 10.1016/j.bmcl.2009.05.127] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 05/01/2009] [Accepted: 05/02/2009] [Indexed: 11/26/2022]
|
18
|
Abstract
Viruses in water are usually present in concentrations too low for detection by direct analysis. Virological investigation of water samples is always a multi-stage process involving concentration of viruses present followed by an appropriate detection procedure. There are several approaches to detection of viruses. Part or all of the concentrate may be inoculated into cell cultures to detect infectious cytopathogenic virus, and if this is done in a quantitative fashion the virus can be enumerated, the count being reported as plaque-forming units, the tissue culture infectious dose, or most probable number units. The virus may be isolated and identified from the cell cultures. Viruses that multiply without producing an identifiable cytopathic effect in culture may sometimes be detected by immunoperoxidase or immunofluorescence staining. The concentrate may also be analyzed by molecular biological procedures (usually polymerase chain reaction (PCR) or real-time-PCR). The problem then is that such techniques do not usually detect the infectious virus, and novel approaches have been made recently to meet this challenge.
Collapse
Affiliation(s)
- Peter Wyn-Jones
- Institute of Geography and Earth Sciences, University of Wales, Aberystwyth, UK
| |
Collapse
|
19
|
Villar LM, de Paula VS, Diniz-Mendes L, Lampe E, Gaspar AMC. Evaluation of methods used to concentrate and detect hepatitis A virus in water samples. J Virol Methods 2006; 137:169-76. [PMID: 16887200 DOI: 10.1016/j.jviromet.2006.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 05/30/2006] [Accepted: 06/08/2006] [Indexed: 10/24/2022]
Abstract
Two adsorption-elution concentration methods, both involving negatively charged membranes, were evaluated in order to monitor hepatitis A virus (HAV) contamination in tap, river, mineral and coastal water samples: elution with urea-arginine phosphate buffer/reconcentration with magnesium chloride (method 1); and sodium hydroxide elution/reconcentration with a commercial concentrator (method 2). Nested (qualitative) reverse transcriptase PCR (RT-PCR) and real-time (quantitative) RT-PCR were used to detect and quantify HAV RNA in concentrated water samples. For concentrating HAV, method 1 was found to be the most suitable for tap water and method 2 most suitable for mineral water. HAV inoculated experimentally was detected in river water samples by both methods and in coastal water samples by neither method. The detection limits were 6 x 10(9) g equiv./ml for qualitative PCR and 60 g equiv./ml for quantitative PCR. In a field application study, HAV was detected in 20% of river and tap water samples but not in coastal or mineral water samples. River water samples contained subgenotype IA, and tap water samples contained subgenotype IB. It is concluded that, although influencing qualitative PCR, the concentration method does not affect quantitative PCR, which could therefore be used for all types of water samples. Both techniques are recommended for detecting HAV in environmental water samples.
Collapse
Affiliation(s)
- Livia Melo Villar
- Department of Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brazil 4365, 21045-900 Rio de Janeiro, RJ, Brazil.
| | | | | | | | | |
Collapse
|
20
|
Kittigul L, Uthaisin A, Ekchaloemkiet S, Utrarachkij F, Luksamijarulkul P. Detection and characterization of hepatitis A virus in water samples in Thailand. J Appl Microbiol 2006; 100:1318-23. [PMID: 16696679 DOI: 10.1111/j.1365-2672.2006.02876.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Outbreaks of hepatitis A in Thailand have been reported continuely and associated with water supply. However, the genetic analysis of hepatitis A virus (HAV) in water is limited. This study described the application of virus concentration method and reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) to detect HAV RNA and analyse the genetic sequence of the virus in environmental water samples. METHODS AND RESULTS The HAV from water samples was concentrated by using a developed virus concentration method (adsorption-elution and subsequent speedVac reconcentration) and the viral RNA was detected by RT-nested PCR followed by sequencing of the amplified DNA products. Detection limit of HAV determined by the RT-nested PCR was 1.29 radioimmunofocus assay (RIFA) units ml(-1). The DNA band appeared at 183 basepairs. No cross-reactivity was observed in the presence of other enteric viruses (poliovirus and rotavirus). A total of 180 water samples were collected, concentrated, and detected for HAV. The HAV was found in 6/40 (15%) of water samples collected from a swamp and 3/30 (10%) collected from a canal. Ten river samples and 100 tap water samples stored in containers for drinking and domestic uses were negative for HAV. In sequence analysis of the DNA products and alignment with the HAV sequence deposited in the GenBank, six water samples showed the nucleotide sequence associated with HAV. The 120 nucleotides in the N-terminal VP1 region obtained from two swamp samples showed 95 and 96.7% identity to HAV genotype IA. In nearly all water samples where HAV was present bacterial indicators (faecal coliforms and Escherichia coli) were found for faecal contamination. CONCLUSIONS A coupled virus concentration method and RT-nested PCR was successfully applied to examine HAV in water samples collected from various sources. DNA sequencing of nested PCR products showed the genotype IA associated with HAV that is predominate in Thailand. SIGNIFICANCE AND IMPACT OF THE STUDY This research is the first study of genetic sequence of HAV in water samples in Thailand. The presence of naturally occurring HAV might pose a potential health risk for people.
Collapse
Affiliation(s)
- L Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand.
| | | | | | | | | |
Collapse
|
21
|
Chen Z, Hsu FC, Battigelli D, Chang HC. Capture and release of viruses using amino-functionalized silica particles. Anal Chim Acta 2006. [DOI: 10.1016/j.aca.2006.03.103] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
22
|
Brassard J, Seyer K, Houde A, Simard C, Trottier YL. Concentration and detection of hepatitis A virus and rotavirus in spring water samples by reverse transcription-PCR. J Virol Methods 2005; 123:163-9. [PMID: 15620398 DOI: 10.1016/j.jviromet.2004.09.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Accepted: 09/27/2004] [Indexed: 11/28/2022]
Abstract
Every year, enteric viruses such as hepatitis A virus (HAV), rotaviruses, and noroviruses are responsible for viral gastro-enteritis and hepatitis reported worldwide. These viruses are mostly transmitted via the faecal-oral route, from direct contact between people, or by ingestion of contaminated food and water. Since only a few viral particles may cause disease, detection of low concentration of these viruses in food matrices is usually complex. The development of methods to concentrate viruses from food matrices is crucial in collecting data for the development of control strategies or for diagnostic purposes. In the present study, samples of bottled spring water were inoculated with known amounts of HAV (strain HM-175), and rotaviruses (strain Wa) viral particles and filtered through positively charged membranes. Elution of viruses attached to the membranes was achieved with a tryptose phosphate broth-glycine buffer. Eluates were further concentrated using Microsep 100. Finally, RNA was extracted using the Qiagen RNeasy kit followed by an evaporation step with a SpeedVac instrument. The detection limit by reverse-transcription (RT-PCR) was at least 10(-1) TCID50%/ml and at least 10(-3) TCID50%/ml for HAV and rotavirus, respectively.
Collapse
Affiliation(s)
- Julie Brassard
- Canadian Food Inspection Agency, Saint-Hyacinthe Laboratory, 3400 Casavant Blvd. West, Saint-Hyacinthe, Que., Canada J2S 8E3
| | | | | | | | | |
Collapse
|
23
|
Kittigul L, Ekchaloemkiet S, Utrarachkij F, Siripanichgon K, Sujirarat D, Pungchitton S, Boonthum A. An efficient virus concentration method and RT-nested PCR for detection of rotaviruses in environmental water samples. J Virol Methods 2005; 124:117-22. [PMID: 15664059 DOI: 10.1016/j.jviromet.2004.11.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Accepted: 11/15/2004] [Indexed: 11/20/2022]
Abstract
Water samples were concentrated by the modified adsorption-elution technique followed by speedVac reconcentration of the filter eluates. Reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) was used to detect rotavirus RNA in concentrates of the water. The detection limit of the rotavirus determined by RT-nested PCR alone was about 1.67 plaque forming units (PFU) per RT-PCR assay and that by RT-nested PCR combined with concentration from 1l seeded tap water sample was 1.46 plaque forming units per assay. Water samples were collected from various sources, concentrated, and determined rotavirus RNA. Of 120 water samples, rotavirus RNA was detected in 20 samples (16.7%); 2/10 (20%) of the river samples, 8/30 (26.7%) of the canal samples, and 10/40 (25%) of the sewage samples but was not found in any tap water samples (0/40). Only three water samples were positive for rotavirus antigen determined using an enzyme-linked immunosorbent assay (ELISA). Alignment analysis of the sequenced PCR product (346-bp fragment) was performed in eight rotavirus-positive samples using the rotavirus sequence deposited in the GenBank. All samples gave the correct VP7 sequence. Results of analysis showed two samples similar to human rotavirus (97-98%), five similar to rotavirus G9 sequence (94-99%), and one sample similar to animal rotavirus (97%). PCR inhibitors were not observed in any concentrated water samples. In all 20 (of 120) samples where rotaviruses were found, fecal coliforms including Escherichia coli were also found, but of the samples testing negative for rotaviruses, 76 were fecal coliforms positive and 69 were E. coli positive. The combination of the virus concentration method and RT-nested PCR described below made it possible to effectively detect rotaviruses in environmental water samples.
Collapse
Affiliation(s)
- Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Rajvithi Road, Bangkok 10400, Thailand.
| | | | | | | | | | | | | |
Collapse
|
24
|
Uchida E, Sato K, Iwata A, Ishii-Watabe A, Mizuguchi H, Hikata M, Murata M, Yamaguchi T, Hayakawa T. An improved method for detection of replication-competent retrovirus in retrovirus vector products. Biologicals 2004; 32:139-46. [PMID: 15536044 DOI: 10.1016/j.biologicals.2004.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Accepted: 08/19/2004] [Indexed: 11/16/2022] Open
Abstract
Contamination by replication-competent retrovirus (RCR) is one of the most important safety issues of retrovirus vector products for gene therapy clinical research. To improve the sensitivity of RCR detection and to shorten the assay period, we have developed a novel RCR detection method (infectivity RT-PCR method) based on real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) in combination with virus infection and a novel virus concentration method using polyethyleneimine (PEI)-conjugated magnetic beads. In this method, permissive cells were infected with RCR samples, and amplified RCR in the culture supernatants was adsorbed by PEI-beads. Then RCR RNA extracted from PEI-beads was quantified by real-time RT-PCR. We demonstrated that 1 infectious unit (iu) of RCR spiked in 10(6) cfu/ml of vector products could be detected within 3 days, and the sensitivity for viral detection was increased 3- to 10-fold compared with the direct S+L- assay. By this method, the presence of retroviral vector interfered with RCR detection only slightly. In conclusion, infectivity RT-PCR conducted in conjunction with virus concentration using PEI-beads can detect RCR more sensitively and rapidly than the conventional infectivity assay.
Collapse
Affiliation(s)
- Eriko Uchida
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Iwata A, Satoh K, Murata M, Hikata M, Hayakawa T, Yamaguchi T. Virus concentration using sulfonated magnetic beads to improve sensitivity in nucleic acid amplification tests. Biol Pharm Bull 2003; 26:1065-9. [PMID: 12913251 DOI: 10.1248/bpb.26.1065] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To enhance the sensitivity of virus detection by polymerase chain reaction (PCR) and reverse-transcriptional (RT)-PCR, we developed a novel virus-concentration method using sulfonated (SO-) magnetic beads in the presence of divalent cations. In the presence of either Zn(2+) or Cu(2+) ions, we showed that SO-magnetic beads were able to concentrate non-enveloped model viruses, such as porcine parvovirus (PPV) and poliovirus, which were not concentrated by polyethyleneimine (PEI)-magnetic beads.(1)) Using the SO-magnetic beads, the sensitivity of virus genome detection by PCR or RT-PCR can be enhanced. Therefore, an efficient virus concentration method using either SO-magnetic beads or PEI-magnetic beads enhances the sensitivity of virus detection by PCR or RT-PCR.
Collapse
Affiliation(s)
- Akiko Iwata
- The National Institute of Health Sciences, Tokyo, Japan
| | | | | | | | | | | |
Collapse
|
26
|
Abstract
A simple and improved protocol for the isolation and detection of noroviruses ('Norwalk-like viruses', NLVs) and enteroviruses in ground- and drinking water is described. An improved procedure was developed for concentration of enteric viruses from water, whereby viruses are directly lysed after filtration on a negatively charged membrane. As the method is free from possible recovery losses during usual rinsing, elution, flocculation or concentration steps prior to RNA extraction, a high sensitivity and reliability is achieved. Detection was carried out by using a modified reverse-transcription polymerase chain reaction described previously and agarose gel electrophoresis. The overall detection sensitivity of our method by spiking 1 l of water was 0.1 PFU for polioviruses (Sabine 1). For Norwalk-like viruses ggII (Lordsdale), the detection limit is clearly lower compared to older protocols with elution and concentration steps (concentration of viral particles in positive stool samples were not known). Another simple protocol was used to isolate NLVs from contaminated stool samples.
Collapse
Affiliation(s)
- Christian Beuret
- Cantonal Food Laboratory of Solothurn, Werkhofstrasse 5, CH-4500 Solothurn, Switzerland.
| |
Collapse
|