Rapid Characterization of Genetic Diversity among Twelve Dengue-2 Virus Isolates by Single-Strand Conformation Polymorphism Analysis

Farfan, Jose A.; Olson, Kenneth E.; Black, William C.; Gubler, Duane J.; Beaty, Barry J.

doi:10.4269/ajtmh.1997.57.416

Cited by 15 publications

(16 citation statements)

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“…17 By use of SSCP, reliable detection of nucleotide sequence differences has been reported for RT-PCR amplicons from several arthropod-borne viruses. Sequence differences have been detected in gene fragments of up to 291 bp for dengue-2 virus isolates 15 ; 669 bp for LaCrosse, Snowshoe Hare, and Tahyna viruses 16 ; and 750 bp for St. Louis encephalitis virus strains. 17 In this study, we have described the ability of SSCP to reliably identify VEE strains that differ in their sequences of a 856-bp region of the P62 gene.…”

Section: Discussionmentioning

confidence: 99%

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Genetic diversity and relationships among Venezuelan equine encephalitis virus field isolates from Colombia and Venezuela.

Moncayo

Medina

Kalvatchev

et al. 2001

The American Journal of Tropical Medicine and Hygiene

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Abstract. During field studies of enzootic Venezuelan equine encephalitis (VEE) viruses associated with epizootic emergence, a large number of virus isolates were made in sylvatic foci of Venezuela and Colombia. To rapidly characterize these isolates, antigenic subtypes were determined by means of immunofluorescence and by single-strand conformational polymorphism (SSCP) analysis by use of an 856-bp fragment from the P62 gene, which we used to distinguish genetic variants. Representative isolates were sequenced to assess the sensitivity of SSCP to detect genetic differences. The SSCP analysis distinguished isolates differing by as little as 1 nucleotide; overall, differences of Ն 1 nucleotide were recognized 89% of the time, and the sensitivity to distinguish strains that differed by only 1 or 4 nucleotides was 17 and 57%, respectively. Phylogenetic analyses of representative sequences showed that all recent isolates from the Catatumbo region of western Venezuela and the middle Magdalena Valley of Colombia were closely related to epizootic subtype IAB and IC strains; strains from Yaracuy and Miranda States were more distantly related. Cocirculation of the same virus genotype in both Colombian and Venezuelan foci indicated that these viruses are readily transported between enzootic regions separated by Ͼ 300 km. The SSCP analysis appears to be a simple, fast, and relatively efficient method of screening VEE virus isolates to identify meaningful genetic variants.

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Section: Discussionmentioning

confidence: 99%

“…14 However, reliable detection of nucleotide differences has been reported for larger RT-PCR amplicons from several viruses. [15][16][17] Here, we report the detection of genetic diversity among VEE virus isolates from northern South America by SSCP to analyze a 856-bp fragment amplified from the P62 gene.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and relationships among Venezuelan equine encephalitis virus field isolates from Colombia and Venezuela.

Moncayo

Medina

Kalvatchev

et al. 2001

The American Journal of Tropical Medicine and Hygiene

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“…5 Molecular epidemiologic approaches have revealed extensive genetic variability within the DEN serotypes and have led to the recognition of two to five different genotypes within the respective serotypes. [9][10][11][12][13][14][15][16] Genotypes differ in their ability to cause severe DEN disease. For example in the Americas, infection with the native DEN-2 American genotype typically results in DF cases, whereas infection with recently introduced, Southeast Asian genotype more frequently results in DHF/DSS.…”

Section: Introductionmentioning

confidence: 99%

“…11 Comparison of SSCP patterns with E gene nucleotide sequences in GenBank demonstrated that SSCP analyses were reproducible and sensitive for detecting base changes within the virus RNA genome (Farfán JA, Ph.D Dissertation, Colorado State University, Fort Collins, CO, 2001). The prM locus proved to be more variable and presumably more informative for genetic analyses than loci at the E and NS5 genes.…”

Section: Introductionmentioning

confidence: 99%

“…The prM locus proved to be more variable and presumably more informative for genetic analyses than loci at the E and NS5 genes. 11 In this work, molecular epidemiologic techniques (i.e., SSCP and sequence analyses) were used to genetically characterize the DEN viruses circulating in Yucatan, Mexico during an 18 year period. The sensitivity and specificity of the SSCP technique for detecting genetic polymorphisms in the prM region of the DEN genome were estimated and phylogenetic relationships of the viruses were established.…”

Section: Introductionmentioning

confidence: 99%

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Genetic variation within the premembrane coding region of dengue viruses from the Yucatan peninsula of Mexico.

Díaz¹,

Farfán-Ale²,

Olson³

et al. 2002

The American Journal of Tropical Medicine and Hygiene

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Abstract. Single-strand conformation polymorphism (SSCP) and sequence analyses were used to characterize genetic polymorphisms and phylogenetic relationships, respectively, among dengue (DEN) viruses isolated between 1980 and 1997 from Yucatan, Mexico and surrounding states. Amplified cDNAs from the premembrane (prM) coding region of the DEN viruses were characterized by SSCP. There were six distinct haplotypes of DEN-1 viruses, four haplotypes of DEN-2, four haplotypes of DEN-3, and eight haplotypes of DEN-4. The diversity index for DEN-3 isolates was significantly lower than that of the other serotypes, probably reflecting the recent introduction of this viral serotype into Mexico. The SSCP was a sensitive (84.5%) and specific (95.5%) technique for identifying nucleotide substitutions. Sequence analyses provided insight into the phylogenetic relationships of the DEN strains isolated in Yucatan. One DEN-2 isolate from 1996 was demonstrated to cluster with viruses of the Sri Lanka genotype, none of which have been detected before in the Americas.

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Rapid investigation of hepatitis A virus outbreak by single strand conformation polymorphism analysis

Mackiewicz

Roque–Afonso

Marchadier

et al. 2005

Journal of Medical Virology

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Investigation of hepatitis A virus (HAV) outbreaks often implies nucleotide sequence analysis. As an alternative method for the identification of related strains, single strand conformation polymorphism method (SSCP) was compared to sequence analysis. Twenty-three strains from sporadic and outbreak cases were studied retrospectively. SSCP, sequence identity and phylogenetic analyses were conducted on a 267 bp fragment of the VP1-2A variable region. The results of SSCP pattern comparison and sequence identity were highly correlated (r = 0.92, P < 0.001). If SSCP showed similar patterns, the VP1-2A fragments had a high and significant probability to have a sequence identity over 99.6%. Results were concordant for outbreak strains. The only discordant result concerned a cluster of three sporadic cases evidenced by phylogenetic analysis while SSCP showed similar patterns for only two of these three cases. A prospective SSCP analysis of a recent HAV outbreak confirmed the reliability of this technique. SSCP may thus provide a rapid and cost-effective tool for preliminary investigation of HAV outbreaks, before undertaking exhaustive nucleotide sequence analysis.

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Rapid Characterization of Genetic Diversity among Twelve Dengue-2 Virus Isolates by Single-Strand Conformation Polymorphism Analysis

Cited by 15 publications

References 0 publications

Genetic diversity and relationships among Venezuelan equine encephalitis virus field isolates from Colombia and Venezuela.

Genetic diversity and relationships among Venezuelan equine encephalitis virus field isolates from Colombia and Venezuela.

Genetic variation within the premembrane coding region of dengue viruses from the Yucatan peninsula of Mexico.

Rapid investigation of hepatitis A virus outbreak by single strand conformation polymorphism analysis

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