Applications of Oligonucleotide Fingerprinting to the Identification of Viruses

Kew, Olen M.; Nottay, Baldev K.; Obijeski, John F.

doi:10.1016/b978-0-12-470208-0.50008-6

Cited by 25 publications

(15 citation statements)

References 140 publications

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“…The vertical lines indicate the degree of similarity of isolates or clusters of isolates to each other. DISCUSSION Two-dimensional electrophoresis of RNase Tl-resistant oligonucleotides has been used to investigate the genetic variation of flaviviruses (Trent et aL, 1981(Trent et aL, , 1983Monath et al, 1983;Hori et al, 1986) and many other RNA viruses (Kew et al, 1984). Trent et aL (1981) observed extensive variability between Saint Louis encephalitis virus (SLE) isolates from different geographical regions.…”

Section: Resultsmentioning

confidence: 99%

Genetic Variation of Murray Valley Encephalitis Virus

Coelen

Mackenzie

1988

Journal of General Virology

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Section: Resultsmentioning

confidence: 99%

Genetic Variation of Murray Valley Encephalitis Virus

Coelen

Mackenzie

1988

Journal of General Virology

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“…This may actually be an overestimate, because we chose the VP1/2A region for its relative variability compared with the VP3 and 5' non-translated regions (Brown et al, 1989). In contrast, poliovirus averages one to two substitutions/week based upon nucleic acid fingerprinting of serial samples examined during an epidemic (Nottay et al, 1981;Kew et al, 1984). Within sub-genotypes of HAV (IA, IB, IIIA or IIIB), there is less than 7.5% nucleotide diversity.…”

Section: Discussionmentioning

confidence: 99%

Genetic relatedness of hepatitis A virus strains recovered from different geographical regions

Robertson

Jansen

Khanna

et al. 1992

Journal of General Virology

436

513

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A pairwise comparison of the nucleic acid sequence of 168 bases from 152 wild-type or unique cell cultureadapted strains of hepatitis A virus (HAV) revealed that HAV strains can be differentiated genetically into seven unique genotypes (I to VII). In general, the nucleotide sequence of viruses in different genotypes differs at 15 to 25 % of positions within this segment of the genome. Viruses from four of the genotypes (I, II, III and VII) were recovered from cases of hepatitis A in humans, whereas viruses from the other three genotypes (IV, V and VI) were isolated only from simian species developing a hepatitis A-like illness during captivity. Among non-epidemiologically related human HAV strains, 81 were characterized as genotype I, and 19 as genotype III. Within each of these major genotypes, there were two distinct groups (subgenotypes), which differed in sequence at approximately 7-5 % of base positions. Each genotype and subgenotype has a characteristic amino acid sequence in this region of the polyprotein, with the most divergent genotypes differing at 10 of 56 residues. Strains recovered from some geographical regions belonged to a common (endemic) genotype, whereas strains from other regions belonged to several, probably imported, genotypes. Thus, HAV strains recovered in North America were for the most part closely related at the nucleotide sequence level, whereas in other regions, such as Japan and Western Europe, HAV strains were derived from multiple genotypes or sub-genotypes. These data indicate that patterns of endemic transmission can be differentiated from situations in which infections are imported due to travel.

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“…Direct visual comparison of the fingerprints using internal dye markers as reference points allows a quick comparison of strains having more than 50~ of their characteristic oligonucleotides in common (Kew et al, 1984). The method is highly reproducible, but a disadvantage is that it does not work well for genomes with less than 95 ~ homology (Aaronson et al, 1982).…”

Section: Discussionmentioning

confidence: 99%

Molecular Epidemiology of Infectious Bronchitis Virus in The Netherlands

Kusters

Niesters

Bleumink-Pluym

et al. 1987

Journal of General Virology

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SUMMARYTwelve Dutch isolates and the M41 strain of infectious bronchitis virus (IBV), a coronavirus of chickens, were characterized by cross-neutralization and T1 fingerprinting to elucidate their evolutionary relationship. The T1 fingerprinting showed that the Dutch isolates formed two clusters. The first cluster contained strains H52, H120, D387, V1259, V1385 and V1397; the estimated sequence homology is 99~. Cluster two comprised strains D207, D274, D212, D1466, D3128 and D3896, which have about 95~ sequence homology. The M41 virus did not belong to either cluster. The four different serotypes which arose in the/ate 1970s belonged to cluster two and appeared to be different from the vaccine strains (H52 and H120) used at that time. This indicates that the strains were newly introduced and could have arisen from a common virus. On the other hand, three recently isolated field strains were genetically closely related to the vaccine strains H 120 and H52 (cluster one), suggesting that these live vaccine strains themselves could have given rise to these serologically altered field isolates. The data are relevant to the development of new vaccine strategies.

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Applications of Oligonucleotide Fingerprinting to the Identification of Viruses

Cited by 25 publications

References 140 publications

Genetic Variation of Murray Valley Encephalitis Virus

Genetic Variation of Murray Valley Encephalitis Virus

Genetic relatedness of hepatitis A virus strains recovered from different geographical regions

Molecular Epidemiology of Infectious Bronchitis Virus in The Netherlands

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