Comprehensive viral oligonucleotide probe design using conserved protein regions

Jabado, Omar J.; Liu, Yang; Conlan, Sean; Quan, P. Lan; Hegyi, Hédi; Lussier, Yves; Briese, Thomas; Palacios, Gustavo; Lipkin, W. I.

The capacity of DNA microarrays to simultaneously screen for hundreds of viral agents makes them an attractive supplement to traditional methods in microbiology. Their utility has been demonstrated through detection of papilloma virus in cervical lesions (1) , SARS coronavirus in tissue culture (2) , parainfluenza virus 4 in nasopharyngeal aspirates (3) , influenza from nasal wash and throat swabs (4, 5) , gammaretrovirus in prostate tumors (6) , coronaviruses and rhinoviruses from nasal lavage (7) , metapneumovirus from bronchoalveolar lavage (8) , filoviruses and malarial parasites in blood in hemorrhagic fever (9) , and a wide variety of respiratory pathogens in nasal swabs and lung tissue (10) . Viral microarrays have increased in density and strain coverage as fabrication technologies have improved. cDNA pathogen arrays derived from reference strain nucleic acids (11, 12) have been replaced by oligonucleotide arrays due to their increased flexibility. Oligonucleotide design strategies have focused on pairwise sequence comparisons to identify conserved regions within a variety of viral pathogens (13) (14) (15) . Multiple alignments have been used to design probes for clinically important virus genera, e.g. rotaviruses (16) , orthopoxviruses (17) or influenzaviruses (18) . Viral resequencing arrays have recently been introduced that allow single nucleotide resolution (4, (19) (20) (21) . Although such tiling arrays enable accurate typing, the number of probes required to build a resequencing array for all viral sequences exceeds current art.