ArticlePloS one2011
A comprehensive deep sequencing strategy for full-length genomes of influenza A.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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.
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Who cites it
28 citing papers in PubMed.
- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- Article
- Genome characterization and mutation analysis of human influenza A virus in Thailand.Genomics & informatics · 2022Article
- The Bank Vole (Viruses · 2021Article
- Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017.Influenza and other respiratory viruses · 2020Article
- Genomic analysis of serologically untypable human enteroviruses in Taiwan.Journal of biomedical science · 2019Article
- A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection.Scientific reports · 2018Article
- Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing.Frontiers in microbiology · 2018Article
- Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses.Journal of clinical microbiology · 2017Article
- Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.Human cell · 2017Review
- Transstadial Transmission and Long-term Association of Crimean-Congo Hemorrhagic Fever Virus in Ticks Shapes Genome Plasticity.Scientific reports · 2016Article
- Reverse genetics in high throughput: rapid generation of complete negative strand RNA virus cDNA clones and recombinant viruses thereof.Scientific reports · 2016Article
- A Pan-HIV Strategy for Complete Genome Sequencing.Journal of clinical microbiology · 2016Article
- Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples.Journal of clinical microbiology · 2015Article
- Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing.BMC genomics · 2015Article
- Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases?Methods in molecular biology (Clifton, N.J.) · 2015Review
- Deep sequencing: becoming a critical tool in clinical virology.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2014Review
- Article
- Alternative reassortment events leading to transmissible H9N1 influenza viruses in the ferret model.Journal of virology · 2014Article
- Biased mutational pattern and quasispecies hypothesis in H5N1 virus.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Driven by the impact of influenza A viruses on human and animal health, much research is conducted on this pathogen. To support this research, we designed an all influenza A-embracing reverse transcription-PCR (RT-PCR) for the generation of DNA from influenza A virus negative strand RNA genome segments for full-length genome deep sequencing on a Genome Sequencer FLX instrument. For high reliability, the RT-PCRs are designed such that every genome segment is divided into two amplicons and for the most variable segments redundancy is included. Moreover, to minimize the risk of contamination of diagnostic real-time PCRs by sequencing amplicons, RT-PCR does not generate amplicons that are amenable to RT-qPCR detection. With the presented protocol we were able to generate virtually all amplicons (99.3% success rate) from isolates representing all so far known 16 hemagglutinin and 9 neuraminidase subtypes and from an additional 2009 pandemic influenza A H1N1 virus. Three isolates were sequenced to analyze the suitability of the DNA for sequencing. Moreover, we provide a short R script that disambiguates the sequences of the primers used. We show that using unambiguous primer sequences for read trimming prior to assembly with the genome sequencer assembler software results in higher quality of the final genome sequences. Using the disambiguated primer sequences, high quality full-length sequences for the three isolates used for sequencing trials could be established from the raw data in de novo assemblies.
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