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Rapid Diagnosis of Avian Influenza Virus in Wild Birds: Use of a Portable rRT-PCR and Freeze-dried Reagents in the Field
Published on: August 2, 2011
Identifying errors in avian influenza virus gene sequences and implications for data usage of public databases
Jinling Li1, Heinrich zu Dohna, Joy Miller
1School of Veterinary Medicine, University of California, Davis, CA, USA. jlli@ucdavis.edu <jlli@ucdavis.edu>
Genomics
|September 22, 2009
Summary
Misclassified avian influenza virus (AIV) gene sequences in public databases were identified using novel tests. Approximately 0.8% of sequences may be inaccurate, potentially affecting research conclusions.
Area of Science:
- Virology
- Bioinformatics
- Genomics
Background:
- Public gene sequence databases are crucial for understanding viruses and other organisms.
- Concerns exist regarding the accuracy of sequence identification information in these databases.
Purpose of the Study:
- To develop and apply tests for identifying misclassified avian influenza virus (AIV) hemagglutinin and neuraminidase gene sequences in public databases.
- To assess the potential impact of misclassified sequences on published research findings.
Main Methods:
- Developed two novel tests to analyze published AIV gene sequences.
- Test 1: Identified highly similar nucleotide sequences with significantly different sampling dates.
- Test 2: Detected sequences with greater nucleotide differences to themselves than to their closest relatives, applied to re-sequenced samples.
Main Results:
- Examined 4040 published AIV gene sequences.
- Identified approximately 0.8% of sequences as potentially misclassified.
- Traced misclassified sequences to publications, assessing contamination risks and impact on conclusions.
- Found increased risk of contamination with laboratory-adapted strains and simultaneous sample handling.
Conclusions:
- A small but significant proportion of published AIV gene sequences in public databases may be misclassified.
- Misclassified sequences can lead to inaccurate statements in scientific publications.
- The developed tests can aid in screening new sequence submissions to public databases.
- Laboratory practices, such as using adapted strains and handling multiple samples, increase contamination risks.
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