Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm

Abstract

BackgroundA resequencing microarray called PathogenID v2.0 has been developed and used to explore various strategies of sequence selection for its design. The part dedicated to influenza viruses was based on consensus sequences specific for one gene generated from global alignments of a large number of influenza virus sequences available in databanks.ResultsFor each HA (H1, H2, H3, H5, H7 and H9) and NA (N1, N2 and N7) molecular type chosen to be tested, 1 to 3 consensus sequences were computed and tiled on the microarray. A total of 12 influenza virus samples from different host origins (humans, pigs, horses and birds) and isolated over a period of about 50 years were used in this study. Influenza viruses were correctly identified, and in most cases with the accurate information of the time of their emergence.ConclusionsPathogenID v2.0 microarray demonstrated its ability to type and subtype influenza viruses, often to the level of viral variants, with a minimum number of tiled sequences. This validated the strategy of using consensus sequences, which do not exist in nature, for our microarray design. The versatility, rapidity and high discriminatory power of the PathogenID v2.0 microarray could prove critical to detect and identify viral genome reassortment events resulting in a novel virus with epidemic or pandemic potential and therefore assist health authorities to make efficient decisions about patient treatment and outbreak management.

Recurrent Breast Abscesses due toCorynebacterium kroppenstedtii, a Human Pathogen Uncommon in Caucasian Women

“…A resequencing microarray was used in parallel to the bacteriological methods. This molecular tool was developed for the detection of a massive panel of viral and bacterial agents as well as more than 600 genes involved in pathogenicity or antibiotic resistance [ 6 – 9 ]. Bacterial signatures obtained from the isolate confirmed the bacterial identification.…”

DNA Microarrays for Pathogen Detection

“…The method does not require the design of specific primers for all potential targets and the setting up of the corresponding PCRs. This technology was applied for the identification of influenza viruses of different host origins (humans, pigs, horses, and birds) [114], highly pathogenic viruses causing hemorrhagic fever [115], and viruses causing arboviral diseases [116]. The microarray was shown to identify sequences having 13-14% of divergence with the tiled sequence, or stretches of 20 consecutive nucleotides identical to the tiled sequence.…”

Resequencing Microarray Technology for Genotyping Human Papillomavirus in Cervical Smears

“…We have previously used RMAs for the detection of a large panel of viral and bacterial pathogens by resequencing the hybridised DNA. This approach has been successfully applied to diverse clinical situations such as the establishment of a rapid laboratory diagnostic test for pandemic influenza viruses [11] , [12] , the characterization of different strains of the monkeypox virus [13] , [14] , the genotyping of several members of the Rhabdoviridae family [8] and the identification and characterization of arboviruses and hemorrhagic fever viruses in biological samples [15] , [16] .…”