Samantha Treagus
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View article: Norovirus trends in British Columbia from 2021 to 2022: the relationship between wastewater surveillance and clinical outbreak data during the COVID-19 pandemic
Norovirus trends in British Columbia from 2021 to 2022: the relationship between wastewater surveillance and clinical outbreak data during the COVID-19 pandemic Open
View article: Long Amplicon Nanopore Sequencing for Dual-Typing RdRp and VP1 Genes of Norovirus Genogroups I and II in Wastewater
Long Amplicon Nanopore Sequencing for Dual-Typing RdRp and VP1 Genes of Norovirus Genogroups I and II in Wastewater Open
Noroviruses (NoVs) are the leading cause of non-bacterial gastroenteritis with societal costs of US$60.3 billion per annum. Development of a long amplicon nanopore-based method for dual-typing the RNA-dependent RNA polymerase ( RdRp ) and …
View article: Long Amplicon Nanopore Sequencing for Dual-Typing<i>RdRp</i>and<i>VP1</i>Genes of Norovirus Genogroups I and II in Wastewater
Long Amplicon Nanopore Sequencing for Dual-Typing<i>RdRp</i>and<i>VP1</i>Genes of Norovirus Genogroups I and II in Wastewater Open
Noroviruses (NoV) are the leading cause of non-bacterial gastroenteritis across the globe with societal costs of US$60.3 billion per annum. Development of a long amplicon nanopore-based method for dual-typing the RNA-dependent RNA polymera…
View article: Pathogenesis of Rift Valley Fever Virus in a BALB/c Mouse Model Is Affected by Virus Culture Conditions and Sex of the Animals
Pathogenesis of Rift Valley Fever Virus in a BALB/c Mouse Model Is Affected by Virus Culture Conditions and Sex of the Animals Open
Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic pathogen causing disease in livestock and humans. Whilst initially restricted to the African continent, recent spread to the Arabian Peninsula has highlighted the likelihood of en…
View article: Metabarcoding of Hepatitis E Virus Genotype 3 and Norovirus GII from Wastewater Samples in England Using Nanopore Sequencing
Metabarcoding of Hepatitis E Virus Genotype 3 and Norovirus GII from Wastewater Samples in England Using Nanopore Sequencing Open
Norovirus is one of the largest causes of gastroenteritis worldwide, and Hepatitis E virus (HEV) is an emerging pathogen that has become the most dominant cause of acute viral hepatitis in recent years. The presence of norovirus and HEV ha…
View article: Evaluation of the cross reactivity of neutralising antibody response in vaccinated human and convalescent hamster sera against SARS-CoV-2 variants up to and including JN.1 using an authentic virus neutralisation assay
Evaluation of the cross reactivity of neutralising antibody response in vaccinated human and convalescent hamster sera against SARS-CoV-2 variants up to and including JN.1 using an authentic virus neutralisation assay Open
New vaccines, therapeutics and immunity elicited by natural infection create evolutionary pressure on SARS-CoV-2 to evolve and adapt to evade vaccine-induced and infection-elicited immunity. Vaccine and therapeutics developers thus find th…
View article: Supplementary data 6.2: Alignment of G3 HEV genomes
Supplementary data 6.2: Alignment of G3 HEV genomes Open
Alignment of genotype 3 genomes of hepatitis E virus, downloaded from NCBI. Genomes are from the classified genotypes and subgenotypes recommended by Smith et al 2020.
View article: Supplementary data 6.8: Norovirus reads and coverage depth data
Supplementary data 6.8: Norovirus reads and coverage depth data Open
CSV file containing reads and coverage data from the norovirus amplicon sequencing approaches
View article: Supplementary data 5.4: Sapovirus plasmid insert for DNA control
Supplementary data 5.4: Sapovirus plasmid insert for DNA control Open
A fasta file which presents the sequence for the Sapovirus insert within the pMA-T plasmid. This plasmid formed the sapovirus control.
View article: Supplementary data 3.9: HEV regions of interest for DNA controls G1-4
Supplementary data 3.9: HEV regions of interest for DNA controls G1-4 Open
Synthetic control DNA sequences for hepatitis E virus genotypes 1-4, used as controls during qRT-PCR of samples. Shown alongside the primer set used to amplify the DNA using conventional PCR, for the purposes of creating quantitative contr…
View article: Supplementary data 3.6: Sapovirus alignment file
Supplementary data 3.6: Sapovirus alignment file Open
An alignment of a genome of mengo virus alongside the primers and probe for the Jothikumar (2006) HEV assay. The primers and probe did not align successfully.
View article: Supplementary data 3.2: Coronavirus (SARS-CoV-2) alignment
Supplementary data 3.2: Coronavirus (SARS-CoV-2) alignment Open
This data shows an alignment of a Coronavirus (Sars-CoV-2) genome alongside the primers and probe for the Jothikumar (2006) HEV assay. The primers did not successfully align.
View article: Supplementary data 6.5: HEV reference genomes for sequence processing
Supplementary data 6.5: HEV reference genomes for sequence processing Open
Alignment of HEV reference genomes as published by Smith et al 2020 for sequencing pipeline processing.
View article: Supplementary data 4.5: Raw data for norovirus in effluent samples
Supplementary data 4.5: Raw data for norovirus in effluent samples Open
Raw data for norovirus in effluent samples
View article: Supplementary data 7.1: Calculated doses of HEV and norovirus from water activities and shellfish consumption
Supplementary data 7.1: Calculated doses of HEV and norovirus from water activities and shellfish consumption Open
The calculated doses of HEV and norovirus from water activities and shellfish consumption, used to assess the risk of illness to public health.
View article: Supplementary data 6.4: Norovirus GII raw reads processing pipeline (Linux)
Supplementary data 6.4: Norovirus GII raw reads processing pipeline (Linux) Open
The norovirus alignment file used for the processing of raw norovirus reads from NGS. Created using a reference genome from each genotype and polymerase type from the Human Calicivirus Typing Tool (norovirus.ng.philab.cdc.gov/names.cgi?)
View article: Supplementary data 5.9: Raw norovirus data for the retail shellfish samples by region
Supplementary data 5.9: Raw norovirus data for the retail shellfish samples by region Open
Raw norovirus data for the retail shellfish samples by region
View article: Supplementary data 3.12: HEV G3 plasmid insert for the RNA control
Supplementary data 3.12: HEV G3 plasmid insert for the RNA control Open
The sequence composition for the different parts of the hepatitis E virus genotype 3 insert. This insert was reverse transcribed to mRNA for use as an RNA control within qRT-PCR, specifically used to assess inhibition of the reverse transc…
View article: Supplementary data 7.2: Calculated probabilities of norovirus infection from water activities and shellfish consumption
Supplementary data 7.2: Calculated probabilities of norovirus infection from water activities and shellfish consumption Open
The calculated probabilities of infection by norovirus from different water activities and shellfish consumption
View article: Supplementary data 7.3: Calculated probabilities of HEV and norovirus illness from water activities and shellfish consumption
Supplementary data 7.3: Calculated probabilities of HEV and norovirus illness from water activities and shellfish consumption Open
The calculated probabilities of illness from water activities and shellfish consumption from norovirus and HEV.
View article: Supplementary data 3.1: Astrovirus alignment
Supplementary data 3.1: Astrovirus alignment Open
This figure shows an astrovirus genome aligned with the Jothikumar (2006) HEV assay primers and probe. It is clear from this FASTA file that the primers and probe do not align correctly. Aligned using a CLUSTAL multiple sequence alignment.
View article: Supplementary data 4.7: Raw data for HEV in effluent samples
Supplementary data 4.7: Raw data for HEV in effluent samples Open
Raw data for HEV in effluent samples
View article: Supplementary data 3.4: Human Betaherpes 5 alignment
Supplementary data 3.4: Human Betaherpes 5 alignment Open
An alignment file with a genome of Epstein-Barr virus alongside the primers and probes for the Jothikumar (2006) HEV assay. The primers and probe do not align successfully.
View article: Supplementary data 3.3: Epstein-Barr Virus Alignment
Supplementary data 3.3: Epstein-Barr Virus Alignment Open
An alignment file of a Epstein-Barr virus genome alongside the primers and probe for the Jothikumar (2006) HEV assay. The primers and probe do not successfully align.
View article: Supplementary data 4.4: Raw data for norovirus in influent samples
Supplementary data 4.4: Raw data for norovirus in influent samples Open
Raw data for norovirus in influent samples
View article: Supplementary data 5.1: Shellfish harvesting area pilot study raw data
Supplementary data 5.1: Shellfish harvesting area pilot study raw data Open
Shellfish harvesting area pilot study raw data
View article: Supplementary data 6.2: Alignment of G3 HEV genomes
Supplementary data 6.2: Alignment of G3 HEV genomes Open
Alignment of genotype 3 genomes of hepatitis E virus, downloaded from NCBI. Genomes are from the classified genotypes and subgenotypes recommended by Smith et al 2020.
View article: Supplementary data 4.6: Raw data for HEV in influent samples
Supplementary data 4.6: Raw data for HEV in influent samples Open
Raw data for HEV in influent samples
View article: Supplementary data 5.2: Actin control DNA sequence
Supplementary data 5.2: Actin control DNA sequence Open
DNA sequence of part of the shellfish Actin mRNA gene. This DNA was used as a control for the Actin PCR used on shellfish samples.
View article: Supplementary data 4.1: Norovirus GI and GII DNA control sequences
Supplementary data 4.1: Norovirus GI and GII DNA control sequences Open
The control DNA sequences for GI and GII norovirus which were used in qRT-PCR detection of norovirus within samples.