Performance comparison of fiveextraction kits for SARS-CoV-2 RNA extraction
Notice bibliographique
Résumé
A new type of coronavirus, SARS-CoV-2, was identified in January 2020 Its associated disease, COVID-19, wasannounced as a pandemic by the World Health Organization in March 2020 The Ontario Institute for CancerResearch quickly engaged to support viral sequencing, not only in frontline health care workers but in cancerpatients A key deliverable was the selection of an extraction methodology that would not impact the supply ofapproved diagnostic testing reagents This consideration was in response to reports of possible shortages predictedearly in the pandemic and as indicated by the Public Health Agency of Canada (PHAC), through their call forreagents in April 2020 Five commercially available kits for automated nucleic acid extraction were compared TheKingFisher Flex Purification System (ThermoFisher, 5400610) was used for nucleic acid extraction Four kits wereselected based on availability, system compatibility, and exclusion from PHAC's call for COVID-19 testing reagents The MagMAX CORE Nucleic Acid Purification Kit (CORE;ThermoFisher, A32702), MagMAX Total Nucleic AcidIsolation Kit (Total NA;ThermoFisher, AM1840), MagMAX Total RNA Isolation Kit (Total RNA;ThermoFisher, AM1830), and Mag-Bind Viral DNA/RNA 96 Kit (Omega;Omega BioTek, M6246-03) were evaluated The MagMAXViral/Pathogen Kit (MVP;ThermoFisher, A42352), approved by the Food and Drug Administration of Canada fordiagnostic testing, was used as a benchmark Test samples were prepared using Universal Human RNA (Agilent,740000), lambda DNA solution (Sigma Aldrich, ERMAD442K), SARS-CoV-2 RNA (ATCC, VR1986D) and heat-inactivated virus (ATCC, VR-1986HK) Extractions were performed by two operators on replicate samples Protocols were assessed on reproducibility, yield, reagent availability, run time, and ease of use The top two kits were validated with nasopharyngeal swab samples from SARS-CoV-2-positive patients Four of five kits demonstratedreproducible yields, while yields from the Total RNA kit were inconsistent The CORE and Omega kits possessedthe best overall extraction efficiencies (both 70%) The MVP kit and Total NA kit were 59% and 44% efficient inrecovery, respectively The CORE and Omega kits ranked best after overall assessment Patient samples weresubsequently extracted using both kits and successfully sequenced Extraction kits do not all perform to the samespecification In our hands, we found the MVP kit did not perform as well as others, despite being approved fordiagnostic use, and the Total RNA kit showed inconsistent results Many reagents are commercially available andshould be explored as alternatives to the approved SARS-CoV-2 diagnostic reagents, particularly during a globalcrisis Interestingly, following our validation testing, supply of the CORE kit became limited with unknown futureavailability This illustrated the need to validate multiple methods during uncertain times in order to maintain criticaltesting
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,010 | 0,019 |
| Méta-épidémiologie (sens strict) | 0,003 | 0,002 |
| Méta-épidémiologie (sens large) | 0,002 | 0,002 |
| Bibliométrie | 0,004 | 0,002 |
| Études des sciences et des technologies | 0,001 | 0,002 |
| Communication savante | 0,003 | 0,002 |
| Science ouverte | 0,002 | 0,003 |
| Intégrité de la recherche | 0,003 | 0,002 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,003 | 0,004 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».