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Increasing Clinical Severity during a Dengue Virus Type 3 Cuban Epidemic: Deep Sequencing of Evolving Viral Populations.

Rodriguez-Roche R, Blanc H, Bordería AV, Díaz G, Henningsson R, Gonzalez D, Santana E, Alvarez M, Castro O, Fontes M, Vignuzzi M, Guzman MG - J. Virol. (2016)

Bottom Line: In conclusion, greater variability was detected during the epidemic's progression in terms of significant minority variants, particularly in the nonstructural genes.We concluded that greater variability in significant minor populations occurred as the epidemic progressed, particularly in the nonstructural genes, with higher variability observed in secondary infection cases.Remarkably, for the first time significant intrahost genetic variation was demonstrated within the same patient during the course of secondary infection with DENV-1/DENV-3, including changes in structural proteins.

View Article: PubMed Central - PubMed

Affiliation: Virology Department, Pedro Kouri Institute of Tropical Medicine, PAHO/WHO Collaborating Center for the Study of Dengue and Its Vector, Havana, Cuba rosmari@ipk.sld.cu.

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Synonymous variant allele rate per 10,000 bases at the complete-genome level according to time of sample collection during the 2001-2002 epidemic. Data sets a and b correspond to two different DNA libraries processed for each acute-phase sample through deep sequencing. For the synonymous variant allele rate in data set a (syna), R2 = 0.547, and for data set b (synb), R2 = 0,693; for the linear tendency for data set a, P = 1.94e−4, and for data set b, P = 5.19e−6.
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Figure 2: Synonymous variant allele rate per 10,000 bases at the complete-genome level according to time of sample collection during the 2001-2002 epidemic. Data sets a and b correspond to two different DNA libraries processed for each acute-phase sample through deep sequencing. For the synonymous variant allele rate in data set a (syna), R2 = 0.547, and for data set b (synb), R2 = 0,693; for the linear tendency for data set a, P = 1.94e−4, and for data set b, P = 5.19e−6.

Mentions: Synonymous and nonsynonymous variant allele rates per 10,000 bases at the complete-genome level were calculated according to time of isolation. An increasing trend toward the end of the epidemic was observed only for synonymous variant allele rates (Fig. 2). Interestingly, in terms of nonsynonymous variant alleles, the viral population analysis indicated that at position 4380 in the NS2B gene, a significant minor population (A, 0.875%; T, 0.0%; C, 0.0%; G, 99.111%) present in the first isolate collected during the epidemic (Cuba_15_2001) was selected and became predominant (A, 99.943%; T, 0.0%; C, 0.0%; G, 0.664%) at the end of the epidemic. Taking into account this pattern, variants at low frequency (<1%) were considered relevant; therefore, unique significant minority variants (>0.1%) that appeared with the epidemic's progression were analyzed using the first isolate (Cuba_15_2001) as a reference.


Increasing Clinical Severity during a Dengue Virus Type 3 Cuban Epidemic: Deep Sequencing of Evolving Viral Populations.

Rodriguez-Roche R, Blanc H, Bordería AV, Díaz G, Henningsson R, Gonzalez D, Santana E, Alvarez M, Castro O, Fontes M, Vignuzzi M, Guzman MG - J. Virol. (2016)

Synonymous variant allele rate per 10,000 bases at the complete-genome level according to time of sample collection during the 2001-2002 epidemic. Data sets a and b correspond to two different DNA libraries processed for each acute-phase sample through deep sequencing. For the synonymous variant allele rate in data set a (syna), R2 = 0.547, and for data set b (synb), R2 = 0,693; for the linear tendency for data set a, P = 1.94e−4, and for data set b, P = 5.19e−6.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836355&req=5

Figure 2: Synonymous variant allele rate per 10,000 bases at the complete-genome level according to time of sample collection during the 2001-2002 epidemic. Data sets a and b correspond to two different DNA libraries processed for each acute-phase sample through deep sequencing. For the synonymous variant allele rate in data set a (syna), R2 = 0.547, and for data set b (synb), R2 = 0,693; for the linear tendency for data set a, P = 1.94e−4, and for data set b, P = 5.19e−6.
Mentions: Synonymous and nonsynonymous variant allele rates per 10,000 bases at the complete-genome level were calculated according to time of isolation. An increasing trend toward the end of the epidemic was observed only for synonymous variant allele rates (Fig. 2). Interestingly, in terms of nonsynonymous variant alleles, the viral population analysis indicated that at position 4380 in the NS2B gene, a significant minor population (A, 0.875%; T, 0.0%; C, 0.0%; G, 99.111%) present in the first isolate collected during the epidemic (Cuba_15_2001) was selected and became predominant (A, 99.943%; T, 0.0%; C, 0.0%; G, 0.664%) at the end of the epidemic. Taking into account this pattern, variants at low frequency (<1%) were considered relevant; therefore, unique significant minority variants (>0.1%) that appeared with the epidemic's progression were analyzed using the first isolate (Cuba_15_2001) as a reference.

Bottom Line: In conclusion, greater variability was detected during the epidemic's progression in terms of significant minority variants, particularly in the nonstructural genes.We concluded that greater variability in significant minor populations occurred as the epidemic progressed, particularly in the nonstructural genes, with higher variability observed in secondary infection cases.Remarkably, for the first time significant intrahost genetic variation was demonstrated within the same patient during the course of secondary infection with DENV-1/DENV-3, including changes in structural proteins.

View Article: PubMed Central - PubMed

Affiliation: Virology Department, Pedro Kouri Institute of Tropical Medicine, PAHO/WHO Collaborating Center for the Study of Dengue and Its Vector, Havana, Cuba rosmari@ipk.sld.cu.

Show MeSH
Related in: MedlinePlus