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Article: Unveiling the viral escape: Quantification of microfloc-bound viruses in precoagulation and membrane filtration.

Yasui, Midori / Katayama, Hiroyuki

2024 Volume 22, Issue 2, Page(s) 309–320

Abstract: The implementation of precoagulation before the physical removal process is expected to achieve a high virus removal rate. However, viruses may form small flocs and subsequently escape into the effluent during physical removal processes. This study ... ...

Abstract	The implementation of precoagulation before the physical removal process is expected to achieve a high virus removal rate. However, viruses may form small flocs and subsequently escape into the effluent during physical removal processes. This study evaluated how viruses in the microflocs could be quantified using conventional virus quantification methods (plaque assay and quantitative polymerase chain reaction (qPCR)) to reveal the risk of underestimating virus concentration. In this study, the microfloc dissolution phenomenon in phosphate buffer solution was employed as a floc dissolution test. Viruses in microflocs formed under the experimental conditions. assuming water treatments, were quantified before and after floc dissolution. The findings revealed that virus concentrations increased by 1.0-3.9 log plaque-forming units/mL according to the plaque assay and by 1.7-4.0 log copies/mL according to the qPCR. This increase occurred after the dissolution of microflocs that were prepared in the humic acid test water. In the case of treated wastewater, virus concentrations increased in all samples according to the plaque assay and in seven of eight samples according to the qPCR. Our results indicate the necessity of careful consideration of virus quantification after precoagulation and physical removal systems.
MeSH term(s)	Wastewater/virology ; Viruses/isolation & purification
Chemical Substances	Wastewater
Language	English
Publishing date	2024-02-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2123845-5
ISSN	1996-7829 ; 1477-8920
ISSN (online)	1996-7829
ISSN	1477-8920
DOI	10.2166/wh.2024.233
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Article ; Online: Correspondence of SARS-CoV-2 genomic sequences obtained from wastewater samples and COVID-19 patient at long-term care facilities.

Kadoya, Syun-Suke / Maeda, Hideo / Katayama, Hiroyuki

The Science of the total environment

2024 Volume 916, Page(s) 170103

Abstract: Wastewater-based epidemiology (WBE) has been in the spotlight because of applicability of early detection of virus outbreak and new variants at the catchment area. However, there has been a notable absence of research directly confirming the association ... ...

Abstract	Wastewater-based epidemiology (WBE) has been in the spotlight because of applicability of early detection of virus outbreak and new variants at the catchment area. However, there has been a notable absence of research directly confirming the association between SARS-CoV-2 in wastewater and patient specimens. In this study, we performed a quantitative and qualitative investigation with a genetic-level comparison of SARS-CoV-2 between COVID-19 patients and SARS-CoV-2 positive wastewater samples at long-term care facilities. Wastewater samples were collected via passive sampling from manholes, and SARS-CoV-2 load in wastewater was determined by qPCR. We performed correlation analysis between SARS-CoV-2 load and COVID-19 case number, which suggested that SARS-CoV-2 was detected from wastewater earlier than ascertainment of COVID-19 case. Six and six RNA samples from COVID-19 positive cases and wastewater, respectively, from two facilities were then applied for amplicon sequencing analysis. Mutation analysis revealed high sequence similarity of SARS-CoV-2 variants between wastewater and patient samples (>99 %). To the best of our knowledge, this is the first study demonstrating that WBE is also effective in predicting predominant SARS-CoV-2 variant at facility-level, which is helpful to develop early-warning system for outbreak occurrence with predominant variant.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Wastewater ; COVID-19/epidemiology ; Long-Term Care ; Genomics
Chemical Substances	Wastewater
Language	English
Publishing date	2024-01-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2024.170103
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Article: Viruses in Water Environment.

Katayama, Hiroyuki

Uirusu

2016 Volume 66, Issue 2, Page(s) 163–170

Abstract: Development of PCR method had a great impact on studies on viruses in water environment, and now it makes possible to determine various kind of viruses from river, marine water and water/wastewater treatment systems, though there are still needs to ... ...

Abstract	Development of PCR method had a great impact on studies on viruses in water environment, and now it makes possible to determine various kind of viruses from river, marine water and water/wastewater treatment systems, though there are still needs to improve accuracy of quantification. Now we know that river water may contain 1000copy/L of norovirus. The infectious risk management for recreational water has been left and not updated, hence we need develop better management system based on scientific knowledge.
Language	Japanese
Publishing date	2016
Publishing country	Japan
Document type	Journal Article
ZDB-ID	603272-2
ISSN	0042-6857
ISSN	0042-6857
DOI	10.2222/jsv.66.163
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Article ; Online: Surfactant Treatment for Efficient Gene Detection of Enteric Viruses and Indicators in Surface Water Concentrated by Ultrafiltration.

Hata, Akihiko / Meuchi, Yuno / Liu, Miaomiao / Torii, Shotaro / Katayama, Hiroyuki

Food and environmental virology

2023 Volume 15, Issue 1, Page(s) 8–20

Abstract: The hollow fiber ultrafiltration (HFUF)-based microbial concentration method is widely applied for monitoring pathogenic viruses and microbial indicators in environmental water samples. However, the HFUF-based method can co-concentrate substances that ... ...

Abstract	The hollow fiber ultrafiltration (HFUF)-based microbial concentration method is widely applied for monitoring pathogenic viruses and microbial indicators in environmental water samples. However, the HFUF-based method can co-concentrate substances that interfere with downstream molecular processes-nucleic acid extraction, reverse transcription (RT), and PCR. These inhibitory substances are assumed to be hydrophobic and, therefore, expected to be excluded by a simple surfactant treatment before the silica membrane-based RNA extraction process. In this study, the efficacy and limitations of the sodium deoxycholate (SD) treatment were assessed by quantifying a process control and indigenous viruses using 42 surface water samples concentrated with HFUF. With some exceptions, which tended to be seen in samples with high turbidity (> 4.0 NTU), virus recovery by the ultrafiltration method was sufficiently high (> 10%). RNA extraction-RT-quantitative PCR (RT-qPCR) efficiency of the process control was insufficient (10%) for 30 of the 42 HFUF concentrates without any pretreatments, but it was markedly improved for 21 of the 30 inhibitory concentrates by the SD treatment. Detection rates of indigenous viruses were also improved and no substantial loss of viral RNA was observed. The SD treatment was particularly effective in mitigating RT-qPCR inhibition, although it was not effective in improving RNA extraction efficiency. The methodology is simple and easily applied. These findings indicate that SD treatment can be a good alternative to sample dilution, which is widely applied to mitigate the effect of RT-qPCR inhibition, and can be compatible with other countermeasures.
MeSH term(s)	Ultrafiltration/methods ; Water ; Surface-Active Agents ; Enterovirus ; Viruses ; RNA ; Water Microbiology
Chemical Substances	Water (059QF0KO0R) ; Surface-Active Agents ; RNA (63231-63-0)
Language	English
Publishing date	2023-01-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2487173-4
ISSN	1867-0342 ; 1867-0334
ISSN (online)	1867-0342
ISSN	1867-0334
DOI	10.1007/s12560-022-09543-y
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Article: Effects of surface hydrophobicity on the removal of F-specific RNA phages from reclaimed water by coagulation and ceramic membrane microfiltration.

Yasui, Midori / Ikner, Luisa / Yonetani, Takashi / Liu, Miaomiao / Katayama, Hiroyuki

Water science and technology : a journal of the International Association on Water Pollution Research

2023 Volume 87, Issue 9, Page(s) 2304–2314

Abstract: Microfiltration (MF) has been widely adopted as an advanced treatment process to reduce suspended solids and turbidity in treated wastewater effluents designated for potable reuse. Although microfilter pores are much larger than viruses, the addition of ... ...

Abstract	Microfiltration (MF) has been widely adopted as an advanced treatment process to reduce suspended solids and turbidity in treated wastewater effluents designated for potable reuse. Although microfilter pores are much larger than viruses, the addition of a coagulant upstream of a microfilter system can achieve stable virus removal. Ceramic membranes have a narrow pore size distribution to achieve the high removal of contaminants. This study aims to evaluate virus log reduction using bench-scale coagulation and ceramic membrane MF. To investigate the effects of differences in net surface hydrophobicity, 18 sewage-derived F-specific RNA phages (FRNAPHs) were used for batch hydrophobicity and coagulation-MF tests. The capability of bench-scale coagulation and ceramic membrane MF under continuous automated long-term operation was tested to remove the lab reference strain MS2 and three selected FRNAPH isolates which varied by surface property. Median virus log reduction values (LRVs) exceeding 6.2 were obtained for all three isolates and MS2. Although coagulation and hydrophobicity were positively correlated, the virus isolate demonstrating the lowest level of hydrophobicity and coagulation (genogroup I) still exhibited a high LRV. Thus, coagulation and ceramic membrane MF systems may serve as viable options for virus removal during water reclamation and advanced treatment.
MeSH term(s)	RNA Phages ; Water Purification ; Viruses ; Ultrafiltration ; Ceramics/chemistry ; Membranes, Artificial
Chemical Substances	Membranes, Artificial
Language	English
Publishing date	2023-05-15
Publishing country	England
Document type	Journal Article
ZDB-ID	764273-8
ISSN	1996-9732 ; 0273-1223
ISSN (online)	1996-9732
ISSN	0273-1223
DOI	10.2166/wst.2023.133
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Article ; Online: Development of a simple and low-cost method using Moringa seeds for efficient virus concentration in wastewater.

Canh, Vu Duc / Nga, Tran Thi Viet / Lien, Nguyen Thuy / Katayama, Hiroyuki

The Science of the total environment

2023 Volume 905, Page(s) 167101

Abstract: Effective virus concentration methods are essential for detecting pathogenic viruses in environmental waters and play a crucial role in wastewater-based epidemiology. However, the current methods are often expensive, complicated, and time-consuming, ... ...

Abstract	Effective virus concentration methods are essential for detecting pathogenic viruses in environmental waters and play a crucial role in wastewater-based epidemiology. However, the current methods are often expensive, complicated, and time-consuming, which limits their practical application. In this study, a simple and low-cost method was developed using the extract of Moringa oleifera (MO) seeds (MO method) to recover both enveloped and non-enveloped viruses, including pepper mild mottle virus (PMMoV), murine norovirus (MNV), Aichivirus (AiV), murine hepatitis virus (MHV), and influenza A virus subtype H1N1[H1N1] in wastewater. The optimal conditions for the MO method were determined to be a concentration of MO extract at the UV
MeSH term(s)	Animals ; Mice ; Wastewater ; Moringa ; Influenza A Virus, H1N1 Subtype ; Viruses ; Norovirus
Chemical Substances	Wastewater
Language	English
Publishing date	2023-09-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.167101
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Article ; Online: Activity- and gene-based quantification of enteric viruses, F- specific RNA phage genogroups, pepper mild mottle virus, and Escherichia coli in surface water.

Hata, Akihiko / Meuchi, Yuno / Liu, Miaomiao / Torii, Shotaro / Katayama, Hiroyuki

The Science of the total environment

2023 Volume 904, Page(s) 166338

Abstract: Polymerase chain reaction (PCR) is widely applied for the monitoring of pathogenic viruses in water environments. To date, several pretreatments to selectively detect genes from infectious viruses via PCR have been developed. This study was aimed to ... ...

Abstract	Polymerase chain reaction (PCR) is widely applied for the monitoring of pathogenic viruses in water environments. To date, several pretreatments to selectively detect genes from infectious viruses via PCR have been developed. This study was aimed to characterize and validate methods for quantifying active viruses and indicators and to evaluate the proportion of their active fractions in surface water (n = 42). Active E. coli and F-specific RNA phage (FRNAPH) genogroups were quantified using culture assays. In addition to these microbes, norovirus genogroups I (GI) and II, Aichi virus 1, and pepper mild mottle virus (PMMoV) were quantified by (reverse transcription)-quantitative PCR (RT-qPCR) with and without cis-dichlorodiammineplatinum (CDDP) treatment to exclude genes in inactive viruses. CDDP-RT-qPCR showed concentrations and detection frequencies comparable to or higher than culture assays. Consequently, although CDDP-RT-qPCR can suggest the presence of an inactive virus, it can also overestimate the activity of the virus in the environment. Differences between culture and CDDP-RT-qPCR and between CDDP-RT-qPCR and RT-qPCR varied among the viruses. CDDP-RT-qPCR showed a concentration comparable to the culture assay (within 1 log
MeSH term(s)	Water ; Escherichia coli ; RNA Phages/genetics ; Enterovirus ; Viruses ; Genotype
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2023-08-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.166338
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Article: Inactivation of coxsackievirus B5 by free chlorine under conditions relevant to drinking water treatment.

Canh, Vu Duc / Torii, Shotaro / Singhopon, Tippawan / Katayama, Hiroyuki

Journal of water and health

2023 Volume 21, Issue 9, Page(s) 1318–1324

Abstract: Chlorine disinfection is commonly applied to inactivate pathogenic viruses in drinking water treatment plants. However, the role of water quality in chlorine disinfection of viruses has not been investigated thoughtfully. In this study, we investigated ... ...

Abstract	Chlorine disinfection is commonly applied to inactivate pathogenic viruses in drinking water treatment plants. However, the role of water quality in chlorine disinfection of viruses has not been investigated thoughtfully. In this study, we investigated the inactivation efficiency of coxsackievirus B5 (CVB5) by free chlorine using actual water samples collected from four full-scale drinking water treatment plants in Japan under strict turbidity management (less than 0.14 NTU) over a 12-month period. It was found that chlorine disinfection of CVB5 might not be affected by water quality. Japanese turbidity management might play an indirect role in controlling the efficiency of chlorine disinfection.
MeSH term(s)	Chlorine/pharmacology ; Drinking Water ; Enterovirus B, Human ; Disinfection ; Japan
Chemical Substances	Chlorine (4R7X1O2820) ; Drinking Water
Language	English
Publishing date	2023-09-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2123845-5
ISSN	1996-7829 ; 1477-8920
ISSN (online)	1996-7829
ISSN	1477-8920
DOI	10.2166/wh.2023.178
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Article ; Online: Proteomic Profiling of the Tumor Microenvironment.

Capello, Michela / Katayama, Hiroyuki / Hanash, Samir M

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2435, Page(s) 157–167

Abstract: The tumor microenvironment forms a complex pro-tumorigenic milieu constituted by extracellular matrix, surrounding stroma, infiltrating cell populations, and signaling molecules. Proteomic studies have the potential to reveal how individual cell ... ...

Abstract	The tumor microenvironment forms a complex pro-tumorigenic milieu constituted by extracellular matrix, surrounding stroma, infiltrating cell populations, and signaling molecules. Proteomic studies have the potential to reveal how individual cell populations within the tumor tissue modulate the microenvironment through protein secretion and consequently alter their protein expression and localization to adapt to this milieu. As a result, proteomic approaches have uncovered how these dynamic components communicate and promote tumor development and progression. The characterization of these mechanisms is relevant for the identification of clinically targetable pathways and for the development of diagnostic tools. Here we describe a method based on the isolation of individual cell compartments and the chromatographic fractionation of intact proteins, followed by enzymatic digestion of individual fractions, and mass-spectrometry analysis, for the profiling of tumor microenvironment cell populations.
MeSH term(s)	Extracellular Matrix/metabolism ; Mass Spectrometry ; Proteins/metabolism ; Proteomics ; Tumor Microenvironment
Chemical Substances	Proteins
Language	English
Publishing date	2022-01-07
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2014-4_11
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Article: Mining the Immunopeptidome for Antigenic Peptides in Cancer.

León-Letelier, Ricardo A / Katayama, Hiroyuki / Hanash, Sam

Cancers

2022 Volume 14, Issue 20

Abstract: Although harnessing the immune system for cancer therapy has shown success, response to immunotherapy has been limited. The immunopeptidome of cancer cells presents an opportunity to discover novel antigens for immunotherapy applications. These ... ...

Abstract	Although harnessing the immune system for cancer therapy has shown success, response to immunotherapy has been limited. The immunopeptidome of cancer cells presents an opportunity to discover novel antigens for immunotherapy applications. These neoantigens bind to MHC class I and class II molecules. Remarkably, the immunopeptidome encompasses protein post-translation modifications (PTMs) that may not be evident from genome or transcriptome profiling. A case in point is citrullination, which has been demonstrated to induce a strong immune response. In this review, we cover how the immunopeptidome, with a special focus on PTMs, can be utilized to identify cancer-specific antigens for immunotherapeutic applications.
Language	English
Publishing date	2022-10-11
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers14204968
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