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

Sebastian Maurer-Stroh; Charlie W H Lee; Champa Patel; Marilla Lucero; Hanna Nohynek; Wing-Kin Sung; Chrysanti Murad; Jianmin Ma; Martin L Hibberd; Christopher W Wong; Eric A F Simões

doi:10.1016/j.diagmicrobio.2015.11.003

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

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

Authors

Affiliations

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.

PMID: 26658310
DOI: 10.1016/j.diagmicrobio.2015.11.003

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Child, Preschool
Disease Outbreaks
Genome, Viral*
Humans
Indonesia / epidemiology
Infant
Influenza A virus / classification*
Influenza A virus / genetics*
Influenza, Human / epidemiology
Influenza, Human / virology
Oligonucleotide Array Sequence Analysis
Philippines / epidemiology
Phylogeny*
Poliomyelitis / epidemiology
Poliomyelitis / virology
Poliovirus / classification
Poliovirus / genetics
Poliovirus Vaccines / classification*
Poliovirus Vaccines / genetics*

Substances

Poliovirus Vaccines