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Diagn Microbiol Infect Dis. 2016 Mar;84(3):203-6. doi: 10.1016/j.diagmicrobio.2015.11.003. Epub 2015 Nov 6.

Comparison of microarray-predicted closest genomes to sequencing for poliovirus vaccine strain similarity and influenza A phylogeny.

Author information

1
Bioinformatics Institute (BII), A*STAR, 30 Biopolis St, #07-01 Matrix, 138671, Singapore; School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, 637551, Singapore. Electronic address: sebastianms@bii.a-star.edu.sg.
2
Genome Institute Singapore (GIS), A*STAR, 60 Biopolis St, #02-01 Genome, 138672, Singapore.
3
University of Colorado School of Medicine, 13001 E 17th Place, Aurora, CO 80045, USA.
4
Medical Department, Research Institute for Tropical Medicine, Alabang, Muntinlupa City, Philippines.
5
KTL National Public Health Institute, Helsinki, Finland.
6
Microbiology Department, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.
7
Bioinformatics Institute (BII), A*STAR, 30 Biopolis St, #07-01 Matrix, 138671, Singapore.
8
University of Colorado School of Medicine, 13001 E 17th Place, Aurora, CO 80045, USA; Center for Global Health, Colorado School of Public Health, and Children's Hospital Colorado, 13001 E 17th Place, Aurora, CO 80045, USA.

Abstract

We evaluate sequence data from the PathChip high-density hybridization array for epidemiological interpretation of detected pathogens. For influenza A, we derive similar relative outbreak clustering in phylogenetic trees from PathChip-derived compared to classical Sanger-derived sequences. For a positive polio detection, recent infection could be excluded based on vaccine strain similarity.

KEYWORDS:

Diagnostics; Epidemiology; Hybridization array; Infectious disease; Influenza; PCR; Poliovirus

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