Comparison of Skimmed Milk and Lanthanum Flocculation for Concentration of Pathogenic Viruses in Water

Borgmästars, Emmy; Persson, Sofia; Hellmér, Maria; Simonsson, Magnus; Eriksson, Ronnie

doi:10.1007/s12560-021-09477-x

Cited by 5 publications

(4 citation statements)

References 35 publications

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“…Regarding recovery rates of MgV, used as a model on non-enveloped viruses, higher recoveries were obtained when the TNA method was used. These recovery rates (mean 33.7 %) were similar to the ones obtained by Borgmästars et al (2021) for MgV and human enteric viruses (Norovirus GI and GII, and HAV) with skimmed milk flocculation (SMF). However, with the SMF technique, 10 L were used for sample concentration, while with the TNA method only 40 mL were processed, simplifying the whole procedure.…”

Section: Discussionsupporting

confidence: 81%

Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing

Girón-Guzmán

Díaz-Reolid

Cuevas-Ferrando

et al. 2023

Science of The Total Environment

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Section: Discussionsupporting

confidence: 81%

Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing

Girón-Guzmán

Díaz-Reolid

Cuevas-Ferrando

et al. 2023

Science of The Total Environment

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“…recovery used in this study was determined by the authors that designed this viral concentration method and it has been used by several authors worldwide (Assis et al, 2018;Borgmästars et al, 2021;Calgua et al, 2013;Gonzales-Gustavson et al, 2017;Shubo et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…We did not perform experiments in order to calculate the recovery efficiency of the protocol used in this study. However, the recovery efficiency used in this study was determined by the authors that designed this viral concentration method and it has been used by several authors worldwide (Assis et al, 2018; Borgmästars et al, 2021; Calgua et al, 2013; Gonzales‐Gustavson et al, 2017; Shubo et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Comparison of the risk of infection of human rotavirus and astrovirus according to fishing and swimming activities at Las Cañas beach, Uruguay

Bortagaray

Gamazo

Castro

et al. 2022

Journal of Applied Microbiology

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Aims:To estimate the risk of human rotavirus (RV) and astrovirus (HAstV) infections for swimmers and fishers at Las Cañas beach, Uruguay. Methods and Results: Surface water samples were collected monthly for 1 year.The dose-response models used were β-Poisson and 1 F 1 hypergeometric for RV and HAstV, respectively. The probabilities of infection were calculated using a kernel density estimate to fitting the data and then sampling from this distribution (Monte Carlo simulation). The probability of RV infection for fishers was between 0 and 65% and for swimmers was between 0 and 50% (<18 years old) and between 0 and 38% (>18 years old). For HAstV, the probability of infection for fishers was between 0% and 45% and for swimmers was between 0 and 38% (<18 years old) and between 0 and 18% (>18 years old). Conclusions:This study suggests that fishers are at higher risk of infection for both viruses compared with swimmers mainly due to higher viral frequency and concentration at the site for fishing activities.

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“…RT-qPCR was performed with RT at 50 °C for 15 min, inactivation of the reverse transcriptase and activation of the DNA polymerase at 95 °C for 2 min, followed by 45 cycles of denaturation at 95 °C for 3 s, annealing and elongation at 60 °C for 30 s. Cycle of quantification (Cq) values were determined by the LightCycler 96 software, version 1.1 (Roche). Quantification was performed using a tenfold dilution series of linearised plasmid DNA with a norovirus GI insert, as previously described [ 27 ]. The standard curve ranged from 5·10 5 to 50 plasmid equivalents per reaction.…”

Section: Case Study: Materials and Methodsmentioning

confidence: 99%

rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses

et al. 2022

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Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development.

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Comparison of Skimmed Milk and Lanthanum Flocculation for Concentration of Pathogenic Viruses in Water

Cited by 5 publications

References 35 publications

Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing

Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing

Comparison of the risk of infection of human rotavirus and astrovirus according to fishing and swimming activities at Las Cañas beach, Uruguay

rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses

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