Journal: Food and Environmental Virology

Article Title: Assessing the Removal Efficiency of Murine Norovirus 1, Hepatitis A Virus, and Human Coronavirus 229E on Dish Surfaces Through General Wash Program of Household Dishwasher

doi: 10.1007/s12560-022-09546-9

Figure Lengend Snippet: Changes in viral RNA on dish surface before and after the general wash program by RT-qPCR

Article Snippet: Quantification was executed using the standard quantitative genomic viral RNA from ATCC (MNV-1, VR-3255SD; HAV, VR-3257SD; HCoV-229E, VR-740DQ), in which the slope and intercept of MNV-1, HAV, and HCoV-229E were shown in Fig. , respectively.

Techniques: Control

Journal: Foods

Article Title: Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

doi: 10.3390/foods11213348

Figure Lengend Snippet: Overview of the different samples and methods of preparation of the genetic material tested in the study, starting from the total RNA extracted from the food sample following ISO 15216-2. Raspberries were spiked with norovirus GI at a concentration of 10 5 genome copies per 25 g (hunov, Cq 33), norovirus GV at a concentration of 10 7 (munov, Cq 26), or kept as a blank (Bk, not detected by qPCR). The spiking was repeated twice. A naturally contaminated bivalve sample (bivalve, Cq 34) was also investigated. Each method is explained in detail in (Materials and Methods). Three methods were based on the total RNA (methods A-B-C) and three methods were based on the whole transcriptome amplification of the total RNA (methods D-E-F). The theoretical read outputs after sequencing are displayed for each method. The methods are classified per openness of the approach with a color code (orange least open, blue most open). The blue RNA/cDNA/reads represent the genetic material from norovirus in the sample while the other colors represent genetic materials from other origins, as indicated in the figure.

Article Snippet: One kilogram of frozen raspberries was bought at a local store and was divided in parts of 25 g that were used for extraction (bk, ) or spiked with 5 lenticule discs of human norovirus GI.7 (Public Health England culture collection, Salisbury, UK, mean concentration of 1.9 × 10 4 genome copies per lenticule disc), or with 100 μL of murine norovirus GV from the VIRSeek Murine Norovirus kit (Eurofins Genescan Technologies GmbH, Freiburg, Germany, mean concentration of 10 8 genome copies per mL).

Techniques: Concentration Assay, Amplification, Sequencing

Journal: Foods

Article Title: Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

doi: 10.3390/foods11213348

Figure Lengend Snippet: Results of data analysis of samples of raspberries spiked with murine norovirus (munov) in biological duplicates (munov1 and munov2), human norovirus (hunov) in biological duplicates (hunov1 and hunov2), a blank of raspberries (bk), and a naturally contaminated sample of bivalve positive for norovirus in qPCR (bivalve). Shotgun cDNA: complementary DNA after reverse transcription (method C). Shotgun WTA: cDNA after whole transcriptome amplification (Method D). WTA hybrid capture: cDNA after whole transcriptome amplification with target enrichment for norovirus using SureSelect (method F). WTA adaptive sampling: cDNA after whole transcriptome amplification, sequenced with adaptive sampling (Method E). All reads: all reads sequenced during adaptive sampling. Stop receiving: only reads matching to the database of norovirus and hepatitis A virus reference genomes during adaptive sampling. n/a: not applicable because norovirus not detected in the profiling step.

Article Snippet: One kilogram of frozen raspberries was bought at a local store and was divided in parts of 25 g that were used for extraction (bk, ) or spiked with 5 lenticule discs of human norovirus GI.7 (Public Health England culture collection, Salisbury, UK, mean concentration of 1.9 × 10 4 genome copies per lenticule disc), or with 100 μL of murine norovirus GV from the VIRSeek Murine Norovirus kit (Eurofins Genescan Technologies GmbH, Freiburg, Germany, mean concentration of 10 8 genome copies per mL).

Techniques: Reverse Transcription, Amplification, Sampling, Virus, Sequencing

Journal: Foods

Article Title: Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

doi: 10.3390/foods11213348

Figure Lengend Snippet: Phylogenetic tree of consensus sequences of all norovirus strains from metagenomics datasets and several reference strains as background. SRR535XXX: norovirus strains obtained from metagenomics samples of spiked celery . Munov: in biological duplicates (1,2), norovirus strain obtained from raspberries spiked with murine norovirus GV. Hunov: in biological duplicates (1,2), norovirus strain obtained from raspberries spiked with human norovirus GI. Shotgun cDNA: complementary DNA after reverse transcription (method C). Shotgun wta: cDNA after whole transcriptome amplification (Method D). Wta hybrid capture: cDNA after whole transcriptome amplification with target enrichment for norovirus using SureSelect (Method F). Wta adaptive sampling: cDNA after whole transcriptome amplification, sequenced with adaptive sampling (Method E). All: all reads sequenced. Stop: only “stop receiving” reads after adaptive sampling of whole transcriptome amplification cDNA. Background strains obtained from NCBI . The scale represents the distance of 20% genetic variation.

Article Snippet: One kilogram of frozen raspberries was bought at a local store and was divided in parts of 25 g that were used for extraction (bk, ) or spiked with 5 lenticule discs of human norovirus GI.7 (Public Health England culture collection, Salisbury, UK, mean concentration of 1.9 × 10 4 genome copies per lenticule disc), or with 100 μL of murine norovirus GV from the VIRSeek Murine Norovirus kit (Eurofins Genescan Technologies GmbH, Freiburg, Germany, mean concentration of 10 8 genome copies per mL).

Techniques: Reverse Transcription, Amplification, Sampling

Journal: Foods

Article Title: Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

doi: 10.3390/foods11213348

Figure Lengend Snippet: Results of data analysis of samples of celery spiked with norovirus (NOV) and/or HAV [ 18 ]. -1: first biological replicate. -2: second biological replicate. When two viruses were spiked, the best mash hit of each species was presented along with the result of the mapping and typing for each strain. n/a: not applicable (analysis was not continued because only 1 strain detected when 2 strains were spiked). Sequence read lengths: 35–100 bp.

Article Snippet: One kilogram of frozen raspberries was bought at a local store and was divided in parts of 25 g that were used for extraction (bk, ) or spiked with 5 lenticule discs of human norovirus GI.7 (Public Health England culture collection, Salisbury, UK, mean concentration of 1.9 × 10 4 genome copies per lenticule disc), or with 100 μL of murine norovirus GV from the VIRSeek Murine Norovirus kit (Eurofins Genescan Technologies GmbH, Freiburg, Germany, mean concentration of 10 8 genome copies per mL).

Techniques: Sequencing

Journal: Foods

Article Title: Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

doi: 10.3390/foods11213348

Figure Lengend Snippet: Overview of the different samples and methods of preparation of the genetic material tested in the study, starting from the total RNA extracted from the food sample following ISO 15216-2. Raspberries were spiked with norovirus GI at a concentration of 10 5 genome copies per 25 g (hunov, Cq 33), norovirus GV at a concentration of 10 7 (munov, Cq 26), or kept as a blank (Bk, not detected by qPCR). The spiking was repeated twice. A naturally contaminated bivalve sample (bivalve, Cq 34) was also investigated. Each method is explained in detail in (Materials and Methods). Three methods were based on the total RNA (methods A-B-C) and three methods were based on the whole transcriptome amplification of the total RNA (methods D-E-F). The theoretical read outputs after sequencing are displayed for each method. The methods are classified per openness of the approach with a color code (orange least open, blue most open). The blue RNA/cDNA/reads represent the genetic material from norovirus in the sample while the other colors represent genetic materials from other origins, as indicated in the figure.

Article Snippet: The presence of norovirus in the RNA pools was analyzed with qPCR ( , ) using NovGI/GII @ceeramTools food kit multiplex (Biomérieux, Marcy-l’Etoile, France) to detect the human norovirus in accordance with the specifications of the ISO 15216-2, or using the VIRSeek Murine Norovirus kit (Eurofins Genescan Technologies GmbH, Freibourg, Germany) to detect the murine norovirus.

Techniques: Concentration Assay, Amplification, Sequencing

Journal: Foods

Article Title: Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

doi: 10.3390/foods11213348

Figure Lengend Snippet: Results of data analysis of samples of raspberries spiked with murine norovirus (munov) in biological duplicates (munov1 and munov2), human norovirus (hunov) in biological duplicates (hunov1 and hunov2), a blank of raspberries (bk), and a naturally contaminated sample of bivalve positive for norovirus in qPCR (bivalve). Shotgun cDNA: complementary DNA after reverse transcription (method C). Shotgun WTA: cDNA after whole transcriptome amplification (Method D). WTA hybrid capture: cDNA after whole transcriptome amplification with target enrichment for norovirus using SureSelect (method F). WTA adaptive sampling: cDNA after whole transcriptome amplification, sequenced with adaptive sampling (Method E). All reads: all reads sequenced during adaptive sampling. Stop receiving: only reads matching to the database of norovirus and hepatitis A virus reference genomes during adaptive sampling. n/a: not applicable because norovirus not detected in the profiling step.

Article Snippet: The presence of norovirus in the RNA pools was analyzed with qPCR ( , ) using NovGI/GII @ceeramTools food kit multiplex (Biomérieux, Marcy-l’Etoile, France) to detect the human norovirus in accordance with the specifications of the ISO 15216-2, or using the VIRSeek Murine Norovirus kit (Eurofins Genescan Technologies GmbH, Freibourg, Germany) to detect the murine norovirus.

Techniques: Amplification, Sampling, Sequencing

Journal: Foods

Article Title: Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

doi: 10.3390/foods11213348

Figure Lengend Snippet: Phylogenetic tree of consensus sequences of all norovirus strains from metagenomics datasets and several reference strains as background. SRR535XXX: norovirus strains obtained from metagenomics samples of spiked celery . Munov: in biological duplicates (1,2), norovirus strain obtained from raspberries spiked with murine norovirus GV. Hunov: in biological duplicates (1,2), norovirus strain obtained from raspberries spiked with human norovirus GI. Shotgun cDNA: complementary DNA after reverse transcription (method C). Shotgun wta: cDNA after whole transcriptome amplification (Method D). Wta hybrid capture: cDNA after whole transcriptome amplification with target enrichment for norovirus using SureSelect (Method F). Wta adaptive sampling: cDNA after whole transcriptome amplification, sequenced with adaptive sampling (Method E). All: all reads sequenced. Stop: only “stop receiving” reads after adaptive sampling of whole transcriptome amplification cDNA. Background strains obtained from NCBI . The scale represents the distance of 20% genetic variation.

Article Snippet: The presence of norovirus in the RNA pools was analyzed with qPCR ( , ) using NovGI/GII @ceeramTools food kit multiplex (Biomérieux, Marcy-l’Etoile, France) to detect the human norovirus in accordance with the specifications of the ISO 15216-2, or using the VIRSeek Murine Norovirus kit (Eurofins Genescan Technologies GmbH, Freibourg, Germany) to detect the murine norovirus.

Techniques: Amplification, Sampling

Journal: Foods

Article Title: Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

doi: 10.3390/foods11213348

Figure Lengend Snippet: Results of data analysis of samples of celery spiked with norovirus (NOV) and/or HAV [ 18 ]. -1: first biological replicate. -2: second biological replicate. When two viruses were spiked, the best mash hit of each species was presented along with the result of the mapping and typing for each strain. n/a: not applicable (analysis was not continued because only 1 strain detected when 2 strains were spiked). Sequence read lengths: 35–100 bp.

Article Snippet: The presence of norovirus in the RNA pools was analyzed with qPCR ( , ) using NovGI/GII @ceeramTools food kit multiplex (Biomérieux, Marcy-l’Etoile, France) to detect the human norovirus in accordance with the specifications of the ISO 15216-2, or using the VIRSeek Murine Norovirus kit (Eurofins Genescan Technologies GmbH, Freibourg, Germany) to detect the murine norovirus.

Techniques: Sequencing

Journal: Food Technology and Biotechnology

Article Title: Investigation of SARS-CoV-2 Detection Method Applicability and Virus Occurrence in Food and Food Packaging

doi: 10.17113/ftb.61.02.23.8018

Figure Lengend Snippet: Presentation of the results of the efficiency test (E) of the three extraction kits tested by real-time RT-PCR detection of a double series of 10-fold dilution of the murine norovirus standard (MNV): a) kit 1 (ethanol), b) kit 1 (isopropanol), c) kit 2 (ethanol), d) kit 2 (isopropanol), e) kit 3 (ethanol) and f) kit 3 (isopropanol). C q =number of cycles at which the target analyte (after the RT-PCR reaction) curve intersects the threshold line

Article Snippet: The standard is integral to VIR Seek Murine Norovirus (MNV), a quantitative real-time RT-PCR kit for food and environmental samples (EuroFins GeneScan Technologies, Freiburg, Germany).

Techniques: Extraction, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction