12 research outputs found
Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences
Local transmission of chikungunya virus (CHIKV) was first
detected in the Americas in December 2013, after which it spread
rapidly throughout the Caribbean islands and American mainland,
causing a major chikungunya fever epidemic. Previous
phylogenetic analysis of CHIKV from a limited number of
countries in the Americas suggests that an Asian genotype strain
was responsible, except in Brazil where both Asian and
East/Central/South African (ECSA) lineage strains were detected.
In this study, we sequenced thirty-three complete CHIKV genomes
from viruses isolated in 2014 from fourteen Caribbean islands,
the Bahamas and two mainland countries in the Americas.
Phylogenetic analyses confirmed that they all belonged to the
Asian genotype and clustered together with other Caribbean and
mainland sequences isolated during the American outbreak,
forming an 'Asian/American' lineage defined by two amino acid
substitutions, E2 V368A and 6K L20M, and divided into two
well-supported clades. This lineage is estimated to be evolving
at a mean rate of 5 x 10-4 substitutions per site per year (95%
higher probability density, 2.9-7.9 x 10-4) and to have arisen
from an ancestor introduced to the Caribbean (most likely from
Oceania) in about March 2013, 9 months prior to the first report
of CHIKV in the Americas. Estimation of evolutionary rates for
individual gene regions and selection analyses indicate that (in
contrast to the Indian Ocean Lineage that emerged from the ECSA
genotype followed by adaptive evolution and with a significantly
higher substitution rate) the evolutionary dynamics of the
Asian/American lineage are very similar to the rest of the Asian
genotype and natural selection does not appear to have played a
major role in its emergence. However, several codon sites with
evidence of positive selection were identified within the
non-structural regions of Asian genotype sequences outside of
the Asian/American lineage
Phylogeography and population dynamics of dengue viruses in the Americas.
Changes in Dengue virus (DENV) disease patterns in the Americas over recent decades have been attributed, at least in part, to repeated introduction of DENV strains from other regions, resulting in a shift from hypoendemicity to hyperendemicity. Using newly sequenced DENV-1 and DENV-3 envelope (E) gene isolates from 11 Caribbean countries, along with sequences available on GenBank, we sought to document the population genetic and spatiotemporal transmission histories of the four main invading DENV genotypes within the Americas and investigate factors that influence the rate and intensity of DENV transmission. For all genotypes, there was an initial invasion phase characterized by rapid increases in genetic diversity, which coincided with the first confirmed cases of each genotype in the region. Rapid geographic dispersal occurred upon each genotype's introduction, after which individual lineages were locally maintained, and gene flow was primarily observed among neighboring and nearby countries. There were, however, centers of viral diversity (Barbados, Puerto Rico, Colombia, Suriname, Venezuela, and Brazil) that were repeatedly involved in gene flow with more distant locations. For DENV-1 and DENV-2, we found that a "distance-informed" model, which posits that the intensity of virus movement between locations is inversely proportional to the distance between them, provided a better fit than a model assuming equal rates of movement between all pairs of countries. However, for DENV-3 and DENV-4, the more stochastic "equal rates" model was preferred
Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences
Local transmission of chikungunya virus (CHIKV) was first
detected in the Americas in December 2013, after which it spread
rapidly throughout the Caribbean islands and American mainland,
causing a major chikungunya fever epidemic. Previous
phylogenetic analysis of CHIKV from a limited number of
countries in the Americas suggests that an Asian genotype strain
was responsible, except in Brazil where both Asian and
East/Central/South African (ECSA) lineage strains were detected.
In this study, we sequenced thirty-three complete CHIKV genomes
from viruses isolated in 2014 from fourteen Caribbean islands,
the Bahamas and two mainland countries in the Americas.
Phylogenetic analyses confirmed that they all belonged to the
Asian genotype and clustered together with other Caribbean and
mainland sequences isolated during the American outbreak,
forming an 'Asian/American' lineage defined by two amino acid
substitutions, E2 V368A and 6K L20M, and divided into two
well-supported clades. This lineage is estimated to be evolving
at a mean rate of 5 x 10-4 substitutions per site per year (95%
higher probability density, 2.9-7.9 x 10-4) and to have arisen
from an ancestor introduced to the Caribbean (most likely from
Oceania) in about March 2013, 9 months prior to the first report
of CHIKV in the Americas. Estimation of evolutionary rates for
individual gene regions and selection analyses indicate that (in
contrast to the Indian Ocean Lineage that emerged from the ECSA
genotype followed by adaptive evolution and with a significantly
higher substitution rate) the evolutionary dynamics of the
Asian/American lineage are very similar to the rest of the Asian
genotype and natural selection does not appear to have played a
major role in its emergence. However, several codon sites with
evidence of positive selection were identified within the
non-structural regions of Asian genotype sequences outside of
the Asian/American lineage
Phylogeography and population dynamics of dengue viruses in the Americas
Changes in Dengue virus (DENV) disease patterns in the Americas over recent decades have been attributed, at least in part, to repeated introduction of DENV strains from other regions, resulting in a shift from hypoendemicity to hyperendemicity. Using newly sequenced DENV-1 and DENV-3 envelope (E) gene isolates from 11 Caribbean countries, along with sequences available on GenBank, we sought to document the population genetic and spatiotemporal transmission histories of the four main invading DENV genotypes within the Americas and investigate factors that influence the rate and intensity of DENV transmission. For all genotypes, there was an initial invasion phase characterized by rapid increases in genetic diversity, which coincided with the first confirmed cases of each genotype in the region. Rapid geographic dispersal occurred upon each genotype's introduction, after which individual lineages were locally maintained, and gene flow was primarily observed among neighboring and nearby countries. There were, however, centers of viral diversity (Barbados, Puerto Rico, Colombia, Suriname, Venezuela, and Brazil) that were repeatedly involved in gene flow with more distant locations. For DENV-1 and DENV-2, we found that a "distance-informed" model, which posits that the intensity of virus movement between locations is inversely proportional to the distance between them, provided a better fit than a model assuming equal rates of movement between all pairs of countries. However, for DENV-3 and DENV-4, the more stochastic "equal rates" model was preferre