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Molecular epidemiology of human rhinovirus infections in Kilifi, coastal Kenya.

Onyango CO, Welch SR, Munywoki PK, Agoti CN, Bett A, Ngama M, Myers R, Cane PA, Nokes DJ - J. Med. Virol. (2012)

Bottom Line: Most HRV-C clusters were distinct from reference sequences downloaded from GenBank.In contrast, most HRV-A and HRV-B sequences clustered with either known serotypes or strains from elsewhere within Africa and other regions of the world.This first molecular epidemiological study of HRV in the region defines species distribution in accord with reports from elsewhere in the world, shows considerable strain diversity and does not identify an association between any species and disease severity.

View Article: PubMed Central - PubMed

Affiliation: KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya. conyango@kilifi.kemri-wellcome.org

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A phylogenetic analysis of HRV-A sequences from Kilifi and reference sequences from Genbank. Sequences with closed circles denote known serotypes, while those with open circles denote previously described strains. Bootstrap values are (2,000 replicates) shown on the branches, with values <90% omitted from the tree. The tree was drawn to scale, with branch lengths in the same units (p-distance) used to infer the phylogenetic tree. Kilifi sequences are designated K-number (KI for inpatient sequences and KO for outpatient sequences).
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fig03: A phylogenetic analysis of HRV-A sequences from Kilifi and reference sequences from Genbank. Sequences with closed circles denote known serotypes, while those with open circles denote previously described strains. Bootstrap values are (2,000 replicates) shown on the branches, with values <90% omitted from the tree. The tree was drawn to scale, with branch lengths in the same units (p-distance) used to infer the phylogenetic tree. Kilifi sequences are designated K-number (KI for inpatient sequences and KO for outpatient sequences).

Mentions: The Kilifi sequences for each of the species formed numerous unique clusters with mean nucleotide identity of 76.4% (range 52.2%–97.6%) for HRV-A, 74.2% (range 44.5–99.7%) for HRV-B, and 68% (range 51.0–98.9%) for HRV-C, suggesting considerable diversity in strains/serotypes present in the population. In the cases of HRV-A and HRV-B most sequences clustered with known serotypes or strains from around the world (Figs. 3 and 4). In contrast, many of the sequences of HRV-C identified in circulation in Kilifi (Fig. 5) did not cluster with any published strains that also are based on sequencing of the VP4/VP2 junction. The Kilifi sequences (most easily seen for HRV-A and HRV-B) showed reasonable genetic deviation from nearest known strains/serotypes, generally with mean nucleotide differences of 25% (range 15.1–48.0%) for all the three HRV species.


Molecular epidemiology of human rhinovirus infections in Kilifi, coastal Kenya.

Onyango CO, Welch SR, Munywoki PK, Agoti CN, Bett A, Ngama M, Myers R, Cane PA, Nokes DJ - J. Med. Virol. (2012)

A phylogenetic analysis of HRV-A sequences from Kilifi and reference sequences from Genbank. Sequences with closed circles denote known serotypes, while those with open circles denote previously described strains. Bootstrap values are (2,000 replicates) shown on the branches, with values <90% omitted from the tree. The tree was drawn to scale, with branch lengths in the same units (p-distance) used to infer the phylogenetic tree. Kilifi sequences are designated K-number (KI for inpatient sequences and KO for outpatient sequences).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3500870&req=5

fig03: A phylogenetic analysis of HRV-A sequences from Kilifi and reference sequences from Genbank. Sequences with closed circles denote known serotypes, while those with open circles denote previously described strains. Bootstrap values are (2,000 replicates) shown on the branches, with values <90% omitted from the tree. The tree was drawn to scale, with branch lengths in the same units (p-distance) used to infer the phylogenetic tree. Kilifi sequences are designated K-number (KI for inpatient sequences and KO for outpatient sequences).
Mentions: The Kilifi sequences for each of the species formed numerous unique clusters with mean nucleotide identity of 76.4% (range 52.2%–97.6%) for HRV-A, 74.2% (range 44.5–99.7%) for HRV-B, and 68% (range 51.0–98.9%) for HRV-C, suggesting considerable diversity in strains/serotypes present in the population. In the cases of HRV-A and HRV-B most sequences clustered with known serotypes or strains from around the world (Figs. 3 and 4). In contrast, many of the sequences of HRV-C identified in circulation in Kilifi (Fig. 5) did not cluster with any published strains that also are based on sequencing of the VP4/VP2 junction. The Kilifi sequences (most easily seen for HRV-A and HRV-B) showed reasonable genetic deviation from nearest known strains/serotypes, generally with mean nucleotide differences of 25% (range 15.1–48.0%) for all the three HRV species.

Bottom Line: Most HRV-C clusters were distinct from reference sequences downloaded from GenBank.In contrast, most HRV-A and HRV-B sequences clustered with either known serotypes or strains from elsewhere within Africa and other regions of the world.This first molecular epidemiological study of HRV in the region defines species distribution in accord with reports from elsewhere in the world, shows considerable strain diversity and does not identify an association between any species and disease severity.

View Article: PubMed Central - PubMed

Affiliation: KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya. conyango@kilifi.kemri-wellcome.org

Show MeSH
Related in: MedlinePlus