ArticleVirology2019
A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43.
Article in Virology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 38 citations in OpenAlex.
- Dengue virus surveillance in Nepal yields the first on-site whole genome sequences of isolates from the 2022 outbreak.BMC genomics · 2024Article
- Development and application of a whole genome amplicon sequencing method for infectious salmon anemia virus (ISAV).Frontiers in microbiology · 2024Article
- Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia.Microbial genomics · 2023Article
- Review
- Interference reduction isothermal nucleic acid amplification strategy for COVID-19 variant detection.Sensors and actuators. B, Chemical · 2023Article
- Sub genomic analysis of SARS-CoV-2 using short read amplicon-based sequencing.Frontiers in genetics · 2023Article
- Rapid genotyping of targeted viral samples using Illumina short-read sequencing data.PloS one · 2022Article
- Phage T7 as a Potential Platform for Vaccine Development.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Rapid and sensitive amplicon-based genome sequencing of SARS-CoV-2.Frontiers in microbiology · 2022Article
- Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene.Diagnostics (Basel, Switzerland) · 2021Article
- On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study.Viruses · 2021Review
- Nucleic Acid Testing of SARS-CoV-2.International journal of molecular sciences · 2021Review
- Current methods for diagnosis of human coronaviruses: pros and cons.Analytical and bioanalytical chemistry · 2021Review
- Review
- Article
- Laboratory diagnosis of coronavirus disease-2019 (COVID-19).Clinica chimica acta; international journal of clinical chemistry · 2020Review
- Molecular Characterization of Hemorrhagic Enteritis Virus (HEV) Obtained from Clinical Samples in Western Canada 2017-2018.Viruses · 2020Article
- Article
- Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome sequencing of virus has become a useful tool for better understanding of virus pathogenicity and epidemiological surveillance. Obtaining virus genome sequence directly from clinical samples is still a challenging task due to the low load of virus genetic material compared to the host DNA, and to the difficulty to get an accurate genome assembly. Here we introduce a complete sequencing and analyzing protocol called V-ASAP for Virus Amplicon Sequencing Assembly Pipeline. Our protocol is able to generate the viral dominant genome sequence starting from clinical samples. It is based on a multiplex PCR amplicon sequencing coupled with a reference-free analytical pipeline. This protocol was applied to 11 clinical samples infected with coronavirus OC43 (HcoV-OC43), and led to seven complete and two nearly complete genome assemblies. The protocol introduced here is shown to be robust, to produce a reliable sequence, and could be applied to other virus.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.