Erika Bujáki
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View article: Tiled PCR Amplification for Poliovirus Whole-Genome Sequencing v1
Tiled PCR Amplification for Poliovirus Whole-Genome Sequencing v1 Open
This protocol describes the amplification and whole-genome sequencing of poliovirus from clinical or environmental RNA extracts using an overlapping tiled amplicon strategy. Four overlapping PCR products are generated from viral RNA via RT…
View article: Evolution of the live-attenuated novel oral poliovirus type 2 (nOPV2) vaccine: detection of a double recombinant strain in Uganda.
Evolution of the live-attenuated novel oral poliovirus type 2 (nOPV2) vaccine: detection of a double recombinant strain in Uganda. Open
The novel oral poliovirus vaccine type 2 (nOPV2) was developed to reduce the risk of circulating vaccine-derived poliovirus outbreaks by incorporating genetic modifications to enhance genetic stability and reduce reversion to virulence whi…
View article: DDNS Data analysis and quality control checks v2
DDNS Data analysis and quality control checks v2 Open
This standard operating procedure indicates how to perform data analysis, quality control checks, and data reporting for DDNS and provides guidance on best practice for ensuring relevant sequencing run data are recorded. The document is st…
View article: DDNS Data analysis and quality control checks v1
DDNS Data analysis and quality control checks v1 Open
This standard operating procedure indicates how to perform data analysis, quality control checks, and data reporting for DDNS and provides guidance on best practice for ensuring relevant sequencing run data are recorded. The document is st…
View article: DDNS Data analysis and quality control checks v3
DDNS Data analysis and quality control checks v3 Open
This standard operating procedure indicates how to perform data analysis, quality control checks, and data reporting for DDNS and provides guidance on best practice for ensuring relevant sequencing run data are recorded. The document is st…
View article: Guidelines for in-house verification of the DDNS method for poliovirus direct detection v2
Guidelines for in-house verification of the DDNS method for poliovirus direct detection v2 Open
This document describes a pragmatic approach to conducting in-house verification of the DDNS method for detection of polioviruses from stool samples, evaluating and verifying technical performance of each process. Laboratories should condu…
View article: Guidelines for verification of the DDNS method for poliovirus direct detection v1
Guidelines for verification of the DDNS method for poliovirus direct detection v1 Open
This document describes a pragmatic approach to conduct in-house verification of the DDNS method for detection of polioviruses. A laboratory should conduct an in-house verification on the entire DDNS method to confirm that the required per…
View article: Guidelines for in-house verification of the DDNS method for poliovirus direct detection v2
Guidelines for in-house verification of the DDNS method for poliovirus direct detection v2 Open
This document describes a pragmatic approach to conducting in-house verification of the DDNS method for detection of polioviruses from stool samples, evaluating and verifying technical performance of each process. Laboratories should condu…
View article: Preparation, storage and use of the positive and negative controls for DDNS v2
Preparation, storage and use of the positive and negative controls for DDNS v2 Open
This protocol describes the laboratory process for the use of run controls (positive and negative controls)for performing direct detection of poliovirus by nanopore sequencing (DDNS assay). The protocol outlines the key steps of how and wh…
View article: Preparation, storage and use of the positive and negative controls for DDNS v1
Preparation, storage and use of the positive and negative controls for DDNS v1 Open
This protocol describes the laboratory process for the use of run controls (positive and negative controls)for performing direct detection of poliovirus by nanopore sequencing (DDNS assay). The protocol outlines the key steps of how and wh…
View article: Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Environmental Samples v1
Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Environmental Samples v1 Open
This protocol covers amplification of poliovirus nucleic acid from concentrated sewage samples and the subsequent sequencing of barcoded VP1 amplicons. The protocol was successfully tested on concentrates prepared with two-phase separation…
View article: Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v2
Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v2 Open
This protocol is an update from the protocol described in the paper "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing" by Shaw et al in the Jo…
View article: Détection Directe du poliovirus par Séquencage Nanopore (DDNS) - Selle v1
Détection Directe du poliovirus par Séquencage Nanopore (DDNS) - Selle v1 Open
Ce protocole est une mise à jour du protocole décrit dans l'article "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing" par Shaw et al dans le …
View article: Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v6
Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v6 Open
This protocol is an update from the protocol described in the paper "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing" by Shaw et al in the Jo…
View article: Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v2
Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v2 Open
This protocol is an update from the protocol described in the paper "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing" by Shaw et al in the Jo…
View article: Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v2
Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v2 Open
This protocol is an update from the protocol described in the paper "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing" by Shaw et al in the Jo…
View article: Small volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v2
Small volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v2 Open
This protocol describes the viral nucleic acid recovery and purification from stool suspensions. The method utilises the magnetic bead based MagMAX ‱ Viral RNA Isolation Kit to purify nucleic acid from 300 µL of sample. To perform manual e…
View article: Small volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v1
Small volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v1 Open
This protocol describes the viral nucleic acid recovery and purification from stool suspensions. The method utilises the magnetic bead based MagMAX ‱ Viral RNA Isolation Kit to purify nucleic acid from 300 µL of sample. To perform manual e…
View article: Purification of viral RNA from cell culture isolates or FTA cards using MagMAX Viral RNA Isolation Kit v2
Purification of viral RNA from cell culture isolates or FTA cards using MagMAX Viral RNA Isolation Kit v2 Open
This protocol describes the viral nucleic acid recovery and purification from poliovirus isolates either in their original liquid form or spotted onto FTA cards. The method utilises the magnetic bead based MagMAX ‱ Viral RNA Isolation Kit.…
View article: Purification of viral RNA from cell culture isolates or FTA cards using MagMAX Viral RNA Isolation Kit v1
Purification of viral RNA from cell culture isolates or FTA cards using MagMAX Viral RNA Isolation Kit v1 Open
This protocol describes the viral nucleic acid recovery and purification from poliovirus isolates either in their original liquid form or spotted onto FTA cards. The method utilises the magnetic bead based MagMAX ‱ Viral RNA Isolation Kit.…
View article: Séquençage nanopore d'isolats de poliovirus v1
Séquençage nanopore d'isolats de poliovirus v1 Open
ABSTRAIT Ce protocole est adapté du protocole "Détection directe du poliovirus par séquençage nanopore - les échantillons de selles" pour le rendre adapté à une utilisation avec des isolats sous forme liquide ou qui ont été transportés au …
View article: Nanopore Sequencing of poliovirus isolates v2
Nanopore Sequencing of poliovirus isolates v2 Open
This protocol is adapted from "Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool" to make it suitable for use with cell culture isolates in either a liquid form or that have been transported to the lab via FTA card. The…
View article: Nanopore Sequencing of poliovirus isolates v1
Nanopore Sequencing of poliovirus isolates v1 Open
This protocol is adapted from "Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool" to make it suitable for use with cell culture isolates in either a liquid form or that have been transported to the lab via FTA card. The…
View article: Nanopore Sequencing of poliovirus isolates v2
Nanopore Sequencing of poliovirus isolates v2 Open
This protocol is adapted from "Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool" to make it suitable for use with cell culture isolates in either a liquid form or that have been transported to the lab via FTA card. The…
View article: Large volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v2
Large volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v2 Open
This method describes large volume nucleic acid purification from sewage concentrates starting with 1.2 mL of sample using MagMAX ‱ Viral RNA Isolation Kit. Start by preparing the reagents required for the number of samples extracted, incl…
View article: Large volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v1
Large volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v1 Open
This method describes large volume nucleic acid purification from sewage concentrates starting with 1.2 mL of sample using MagMAX ‱ Viral RNA Isolation Kit. To perform automated extraction, follow steps in Workflow A, and for manual extrac…
View article: Large volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v2
Large volume viral RNA extraction using MagMAX Viral RNA Isolation Kit v2 Open
This method describes large volume nucleic acid purification from sewage concentrates starting with 1.2 mL of sample using MagMAX ‱ Viral RNA Isolation Kit. Start by preparing the reagents required for the number of samples extracted, incl…
View article: Laptop setup and piranhaGUI install v2
Laptop setup and piranhaGUI install v2 Open
This protocol provides step-by-step guidance on installing MiKNOW, piranhaGUI and its dependency Docker Desktop.
View article: Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v2
Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool v2 Open
This protocol is an update from the protocol described in the paper "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing" by Shaw et al in the Jo…
View article: Automated detection and classification of polioviruses from nanopore sequencing reads using piranha
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha Open
Widespread surveillance, rapid detection, and appropriate intervention will be critical for successful eradication of poliovirus. Using deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies’ MinION, t…