Detection of enteroviruses using cDNA and synthetic oligonucleotide probes

Abstract

This study compares the detection of enterovirus RNA by cDNA probes prepared from both the 5' and 3' end of the genome of coxsackie A21 and B4 with the use of synthetic oligonucleotides prepared from short but highly conserved sequences in the 5' end non-coding region of the picornavirus genome. The cDNA probes detected enteroviruses with a variable level of sensitivity which presumably depended on the degree of genomic homology with the detecting probes. Generally probes from coxsackievirus A21 detected more enteroviruses than did similar probes from coxsackievirus B4. Probes from the 5' end of the genome of both viruses were more sensitive than 3' end probes. In contrast, synthetic oligonucleotides detected all enteroviruses efficiently suggesting that these probes could be useful as 'universal' probes to detect any enterovirus. This paper discusses the application of these probes in the diagnosis and differentiation of enteroviruses.

The 40–80 nt region in the 5′‐NCR of genome is a critical target for inactivating poliovirus by chlorine dioxide

“…The adjacent probes had an overlap of one base. Procedures for spot hybridization and 3,3′‐diaminobenzidine (DAB) testing were carried out as described previously, but with slight modifications [Hyypia et al, 1984; Chatterjee et al, 1988; Bruce et al, 1989; Ewing et al, 1996]. Poliovirus RNA suspensions were mixed with an equal volume of stationary liquids (20 µl of 100% formamide, 7 µl of 37% formaldehyde, 2 µl of 20× SSC), and incubated at 68°C for 15 min.…”

Detection of BVD viruses using synthetic oligonucleotides

“…Nucleic acid probes, both cDNA clones and synthetic oligonucleotides, are being used for detection of viral nucleic acid in an increasing number of viral systems [5,6,13,19,24,27]. In general, nucleic acid probes are advantageous because of the specificity, speed, and potential sensitivity [24,27].…”

Oligonucleotide Probes for the Specific Detection of the Wild Poliovirus Types 1 and 3 Endemic to Brazil

“…Synthetic oligodeoxynucleotides offer several advantages as hyb ridization probes, including predictability of specificities, rapid hybridization reaction rates, and the capacity to be quickly prepared in large molar quantities at comparatively low cost [13,14]. Oligonucleotide probes have been used to identify both DNA [15][16][17][18] and RNA [19,20] viruses, including enteroviruses [21][22][23].…”