EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. Part III. Virus Detection by RT-qPCR

Fout, G. Shay; Cashdollar, Jennifer L.; Griffin, Shannon M.; Brinkman, Nichole E.; Varughese, Eunice A.; Parshionikar, Sandhya U.

doi:10.3791/52646

Cited by 26 publications

(33 citation statements)

References 34 publications

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“…As one of the virus that is generally transmitted by the fecal‐oral route, PV surveillance in the stool specimens cannot be ignored. Some of environmental surveillances of PV in water and sewage have been described previously in Brazil, Israel, Japan, Poland, Spain, and USA [Bosch et al, ; Sinclair et al, ; Nakamura et al, ; de et al, ; Fout et al, ] and the detection rates of PV varied from 2.0% to 5.7%. The prevalence of PV in environmental water in Thailand was comparable to that obtained in other countries at 2.0% [Kittigul et al, ; Tansuphasiri et al, ].…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, environmental surveillance of PV is an additional choice for monitoring PV strains circulating in the population [Kuryk et al, ]. Epidemiological study of PV infection has been focused mainly on the AFP cases and only few studies have been investigated for the PV in environmental sources [Kittigul et al, ; Tansuphasiri et al, ; Bosch et al, ; Sinclair et al, ; Kuryk et al, ; Nakamura et al, ; de et al, ; Fout et al, ]. In Thailand, only few reports of PV detection in environmental water and sewage have been described [Kittigul et al, ; Tansuphasiri et al, ] and there is no data available for PV surveillance in children with diarrhea.…”

Section: Introductionmentioning

confidence: 99%

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Detection of poliovirus infection in children with acute gastroenteritis in Chiang Mai, Thailand

Khamrin

Maneekarn

2016

J. Med. Virol.

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Poliovirus (PV) is typically transmitted by the fecal-oral route, which means that the risk of infection and virus distribution could be achieved by exposure to the virus contaminated in food and water. The aim of this study was to determine the occurrence of PV strains by detecting the virus in pediatric patients who admitted to the hospitals with diarrhea in Chiang Mai, Thailand during 2010-2015. By applying a reverse transcription-polymerase chain reaction and nucleotide sequencing analysis of 1,300 stool specimens collected from pediatric patients, PVs were detected at 0.61% (8 out of 1,300 specimens). Among eight PV positive samples, mixed infection with norovirus or human bocavirus was detected in one each out of eight cases. All PV strains detected in this study were characterized further by phylogenetic analysis of 343 bp of the 5' UTR and 315 bp of the partial VP1 sequences. The results revealed that eight PV strains detected in the present study two of each were PV1 and PV2, and four were PV3 serotypes of the Sabin vaccine strains. The data demonstrated the presence of PV1, PV2, and PV3 Sabin vaccine strains in children with acute gastroenteritis in Chiang Mai, Thailand. J. Med. Virol. 89:775-781, 2017. © 2016 Wiley Periodicals, Inc.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Detection of poliovirus infection in children with acute gastroenteritis in Chiang Mai, Thailand

Khamrin

Maneekarn

2016

J. Med. Virol.

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“…Reactions were processed in a 7900HT Fast real-time PCR system (Life Technologies, Inc.) at 95°C for 10 min followed by 40 cycles of 95°C for 15 s and 60°C for 1 min. To enumerate EV in wastewater samples, custom-made Armored RNA (Asuragen, Austin, TX), described in EPA method 1615 (57), was used to generate a standard curve. The custom Armored RNA was made from a construct described previously (44) containing a 195-nucleotide (nt) sequence of the 5= untranslated region that is amplified by the primer and probe assay, along with 96-nt and 89-nt sequences of the norovirus ORF1-ORF2 region.…”

Section: Methodsmentioning

confidence: 99%

“…The quantities of target sequences extracted at each dilution were determined by RT-droplet digital PCR (RT-ddPCR; described below). Linear regression analysis of the standard curve was used to determine concentrations of EV in wastewater samples; standard curves exhibited amplification efficiency of at least 80% and R 2 values of Ն0.97 (57).…”

Section: Methodsmentioning

confidence: 99%

Retrospective Surveillance of Wastewater To Examine Seasonal Dynamics of Enterovirus Infections

Brinkman

Fout

Keely

2017

mSphere

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Enteroviruses are RNA viruses that are responsible for both mild gastroenteritis and mild respiratory illnesses as well as debilitating diseases such as meningitis and myocarditis. The disease burden of enteroviruses in the United States is difficult to assess because most infections are not recorded. Since infected individuals shed enterovirus in feces and urine, surveillance of municipal wastewater can reveal the diversity of enteroviruses circulating in human populations. Therefore, monthly municipal wastewater samples were collected for 1 year and enteroviruses were quantified by reverse transcriptase quantitative PCR and identified by next-generation, high-throughput sequencing. Enterovirus concentrations ranged from 3.8 to 5.9 log equivalent copies/liter in monthly samples. From the mean monthly concentration, it can be estimated that 2.8% of the contributing population was shedding enterovirus daily. Sequence analysis showed that and alternate in predominance, with comprising over 80% of the reads during the summer and fall months and accounting for >45% of the reads in spring. was observed throughout the year, while was present intermittently. Principal-component analysis further supported the date corresponding to enterovirus seasonal trends as CVA6 () was predominant in the spring months; CVB3, CVB5, and E9 () were predominant in the summer and fall months; and CVA1, CVA19, and CVA22 () and EV97 () were predominant in winter. Rhinoviruses were also observed. Wastewater monitoring of human enterovirus provided improved insight into the seasonal patterns of enteroviruses circulating in communities and can contribute to understanding of enterovirus disease burden. Enterovirus infections are often not tracked or reported to health officials. This makes it hard to know how many people in a community are infected with these viruses at any given time. Here, we explored enterovirus in municipal wastewater to look at this issue. We show that enteroviruses are present year-round in municipal wastewater at levels of up to 800,000 genomic copies per liter. We estimate that, on average, 2.8% of the people contributing to the wastewater shed enterovirus daily. Sequence analysis of the viral capsid protein 4 gene shows that 8 enterovirus types are key drivers of seasonal trends. Populations of members peak in the spring, while types are most prevalent during the summer and fall months and members influence the winter months. was observed sporadically and did not influence seasonal trends.

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“…These, along with those located in limestone and crystalline (fractured bedrock) settings are likely to have higher virus concentrations than in other settings 8,15,16 . USEPA virus methods specify sampling volumes of 200 L (ICR) to 300 L (Method 1615) of surface water and 1,000 L (ICR) to 1,500 L (Method 1615) of groundwater 17,18 . However, even with the use of large sample volumes, most surface and ground water samples are negative for virus 8,11,19,20 .…”

Section: Introductionmentioning

confidence: 99%

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. I. Collection of Virus Samples

Fout¹,

Cashdollar²,

Varughese³

et al. 2015

JoVE

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EPA Method 1615 was developed with a goal of providing a standard method for measuring enteroviruses and noroviruses in environmental and drinking waters. The standardized sampling component of the method concentrates viruses that may be present in water by passage of a minimum specified volume of water through an electropositive cartridge filter. The minimum specified volumes for surface and finished/ ground water are 300 L and 1,500 L, respectively. A major method limitation is the tendency for the filters to clog before meeting the sample volume requirement. Studies using two different, but equivalent, cartridge filter options showed that filter clogging was a problem with 10% of the samples with one of the filter types compared to 6% with the other filter type. Clogging tends to increase with turbidity, but cannot be predicted based on turbidity measurements only. From a cost standpoint one of the filter options is preferable over the other, but the water quality and experience with the water system to be sampled should be taken into consideration in making filter selections.

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EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. Part III. Virus Detection by RT-qPCR

Cited by 26 publications

References 34 publications

Detection of poliovirus infection in children with acute gastroenteritis in Chiang Mai, Thailand

Detection of poliovirus infection in children with acute gastroenteritis in Chiang Mai, Thailand

Retrospective Surveillance of Wastewater To Examine Seasonal Dynamics of Enterovirus Infections

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. I. Collection of Virus Samples

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