Limits...
The role of China in the global spread of the current cholera pandemic.

Didelot X, Pang B, Zhou Z, McCann A, Ni P, Li D, Achtman M, Kan B - PLoS Genet. (2015)

Bottom Line: We sequenced the genomes of 71 strains isolated in China between 1961 and 2010, as well as eight from other sources, and compared them with 181 published genomes.The results indicated that outbreaks in China between 1960 and 1990 were associated with wave 1 whereas later outbreaks were associated with wave 2.We therefore suggest replacing them by a series of tightly delineated clades.

View Article: PubMed Central - PubMed

Affiliation: Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.

ABSTRACT
Epidemics and pandemics of cholera, a severe diarrheal disease, have occurred since the early 19th century and waves of epidemic disease continue today. Cholera epidemics are caused by individual, genetically monomorphic lineages of Vibrio cholerae: the ongoing seventh pandemic, which has spread globally since 1961, is associated with lineage L2 of biotype El Tor. Previous genomic studies of the epidemiology of the seventh pandemic identified three successive sub-lineages within L2, designated waves 1 to 3, which spread globally from the Bay of Bengal on multiple occasions. However, these studies did not include samples from China, which also experienced multiple epidemics of cholera in recent decades. We sequenced the genomes of 71 strains isolated in China between 1961 and 2010, as well as eight from other sources, and compared them with 181 published genomes. The results indicated that outbreaks in China between 1960 and 1990 were associated with wave 1 whereas later outbreaks were associated with wave 2. However, the previously defined waves overlapped temporally, and are an inadequate representation of the shape of the global genealogy. We therefore suggest replacing them by a series of tightly delineated clades. Between 1960 and 1990 multiple such clades were imported into China, underwent further microevolution there and then spread to other countries. China was thus both a sink and source during the pandemic spread of V. cholerae, and needs to be included in reconstructions of the global patterns of spread of cholera.

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Related in: MedlinePlus

Phylogeny of 19 genomes from both El Tor and classical V. cholerae.The phylogeny is based exclusively on mutational SNPs (as identified using ClonalFrame), and the two numbers above each branch are the estimated numbers of SNPs caused by mutation and recombination, respectively. Lineage designations are indicated within circles. Strain designations (cf S1B Table) are indicated at the tips of the branches, and the source and date of isolation of each strain are shown at the right.
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pgen.1005072.g002: Phylogeny of 19 genomes from both El Tor and classical V. cholerae.The phylogeny is based exclusively on mutational SNPs (as identified using ClonalFrame), and the two numbers above each branch are the estimated numbers of SNPs caused by mutation and recombination, respectively. Lineage designations are indicated within circles. Strain designations (cf S1B Table) are indicated at the tips of the branches, and the source and date of isolation of each strain are shown at the right.

Mentions: In order to clarify these issues, we re-examined the core genomic sequences of lineages L3, L5, L6 and L8, comparing them with genomes from classical strains as well as the earliest L2 strains isolated from Indonesia, China and Bangladesh. We used ClonalFrame [15] to estimate for each SNP the probability of having arisen by mutation or recombination, and calculated a maximum likelihood tree based exclusively on mutational SNPs (Fig. 2). Interestingly, only 336 mutational SNPs separated the root of all El Tor lineages from the most closely related classical genome (SN372). Furthermore, the MRCA of L2 only differed by 76 mutational SNPs from the MRCA of L5 (Sulawesi, 1937) and L8 (Australia, 1986), suggesting that their common ancestor existed quite recently. That ancestor differed by 31 mutational SNPs from the MRCA of L6 (Saudi Arabia, 1910), L3 (Gulf strains) and a closely related Chinese isolate from 1977. The L2 lineage encompassed not only the early seventh pandemic isolates but also the slightly earlier isolate from Sulawesi (1957). Individual L2 genomes differed from each other by 36–105 mutational SNPs, which is similar to the pairwise differences between El Tor lineages.


The role of China in the global spread of the current cholera pandemic.

Didelot X, Pang B, Zhou Z, McCann A, Ni P, Li D, Achtman M, Kan B - PLoS Genet. (2015)

Phylogeny of 19 genomes from both El Tor and classical V. cholerae.The phylogeny is based exclusively on mutational SNPs (as identified using ClonalFrame), and the two numbers above each branch are the estimated numbers of SNPs caused by mutation and recombination, respectively. Lineage designations are indicated within circles. Strain designations (cf S1B Table) are indicated at the tips of the branches, and the source and date of isolation of each strain are shown at the right.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4358972&req=5

pgen.1005072.g002: Phylogeny of 19 genomes from both El Tor and classical V. cholerae.The phylogeny is based exclusively on mutational SNPs (as identified using ClonalFrame), and the two numbers above each branch are the estimated numbers of SNPs caused by mutation and recombination, respectively. Lineage designations are indicated within circles. Strain designations (cf S1B Table) are indicated at the tips of the branches, and the source and date of isolation of each strain are shown at the right.
Mentions: In order to clarify these issues, we re-examined the core genomic sequences of lineages L3, L5, L6 and L8, comparing them with genomes from classical strains as well as the earliest L2 strains isolated from Indonesia, China and Bangladesh. We used ClonalFrame [15] to estimate for each SNP the probability of having arisen by mutation or recombination, and calculated a maximum likelihood tree based exclusively on mutational SNPs (Fig. 2). Interestingly, only 336 mutational SNPs separated the root of all El Tor lineages from the most closely related classical genome (SN372). Furthermore, the MRCA of L2 only differed by 76 mutational SNPs from the MRCA of L5 (Sulawesi, 1937) and L8 (Australia, 1986), suggesting that their common ancestor existed quite recently. That ancestor differed by 31 mutational SNPs from the MRCA of L6 (Saudi Arabia, 1910), L3 (Gulf strains) and a closely related Chinese isolate from 1977. The L2 lineage encompassed not only the early seventh pandemic isolates but also the slightly earlier isolate from Sulawesi (1957). Individual L2 genomes differed from each other by 36–105 mutational SNPs, which is similar to the pairwise differences between El Tor lineages.

Bottom Line: We sequenced the genomes of 71 strains isolated in China between 1961 and 2010, as well as eight from other sources, and compared them with 181 published genomes.The results indicated that outbreaks in China between 1960 and 1990 were associated with wave 1 whereas later outbreaks were associated with wave 2.We therefore suggest replacing them by a series of tightly delineated clades.

View Article: PubMed Central - PubMed

Affiliation: Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.

ABSTRACT
Epidemics and pandemics of cholera, a severe diarrheal disease, have occurred since the early 19th century and waves of epidemic disease continue today. Cholera epidemics are caused by individual, genetically monomorphic lineages of Vibrio cholerae: the ongoing seventh pandemic, which has spread globally since 1961, is associated with lineage L2 of biotype El Tor. Previous genomic studies of the epidemiology of the seventh pandemic identified three successive sub-lineages within L2, designated waves 1 to 3, which spread globally from the Bay of Bengal on multiple occasions. However, these studies did not include samples from China, which also experienced multiple epidemics of cholera in recent decades. We sequenced the genomes of 71 strains isolated in China between 1961 and 2010, as well as eight from other sources, and compared them with 181 published genomes. The results indicated that outbreaks in China between 1960 and 1990 were associated with wave 1 whereas later outbreaks were associated with wave 2. However, the previously defined waves overlapped temporally, and are an inadequate representation of the shape of the global genealogy. We therefore suggest replacing them by a series of tightly delineated clades. Between 1960 and 1990 multiple such clades were imported into China, underwent further microevolution there and then spread to other countries. China was thus both a sink and source during the pandemic spread of V. cholerae, and needs to be included in reconstructions of the global patterns of spread of cholera.

Show MeSH
Related in: MedlinePlus