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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Timed phylogeny for 6,335 SNPs in 260 genomes from the seventh pandemic.The vertical order is the same as in S1A Table. Branches are colored according to inferred location as shown in the legend at the lower left, with the exception of branches for which the location was uncertain which are shown in gray. Isolates from China are subdivided into isolates from Xinjiang (black dot), inland provinces (red dot) and coastal provinces (no dot). Selected clades of multiple, closely related isolates are indicated by grey boxes next on the left of the clade designations (1.A, 1.B, etc). Inset: Maximum likelihood tree of the same data with significantly longer branches according to S3 Fig indicated in red.
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pgen.1005072.g003: Timed phylogeny for 6,335 SNPs in 260 genomes from the seventh pandemic.The vertical order is the same as in S1A Table. Branches are colored according to inferred location as shown in the legend at the lower left, with the exception of branches for which the location was uncertain which are shown in gray. Isolates from China are subdivided into isolates from Xinjiang (black dot), inland provinces (red dot) and coastal provinces (no dot). Selected clades of multiple, closely related isolates are indicated by grey boxes next on the left of the clade designations (1.A, 1.B, etc). Inset: Maximum likelihood tree of the same data with significantly longer branches according to S3 Fig indicated in red.

Mentions: We now focus on the seventh pandemic based on 260 genomes from lineage L2. A maximum likelihood tree based on the 6,335 SNPs in their non-repetitive, core genomes (Fig. 3 inset; S3A Fig) confirmed that they are all genetically related, and clustered in three successive groups of decreasing diversity, which correspond to the three waves that were previously described [6]. The root-to-tip distances in the phylogeny correlated strongly with the dates of isolation of the individual strains (S3B Fig; R2 = 0.932; p-value = 2.56x10-142) with the exception of 17 of the 260 genomes which were significant outliers to this linear regression. They were located on long terminal branches (red in Fig. 3 inset and S3 Fig), as previously noted for strain A4 [6].


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)

Timed phylogeny for 6,335 SNPs in 260 genomes from the seventh pandemic.The vertical order is the same as in S1A Table. Branches are colored according to inferred location as shown in the legend at the lower left, with the exception of branches for which the location was uncertain which are shown in gray. Isolates from China are subdivided into isolates from Xinjiang (black dot), inland provinces (red dot) and coastal provinces (no dot). Selected clades of multiple, closely related isolates are indicated by grey boxes next on the left of the clade designations (1.A, 1.B, etc). Inset: Maximum likelihood tree of the same data with significantly longer branches according to S3 Fig indicated in red.
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005072.g003: Timed phylogeny for 6,335 SNPs in 260 genomes from the seventh pandemic.The vertical order is the same as in S1A Table. Branches are colored according to inferred location as shown in the legend at the lower left, with the exception of branches for which the location was uncertain which are shown in gray. Isolates from China are subdivided into isolates from Xinjiang (black dot), inland provinces (red dot) and coastal provinces (no dot). Selected clades of multiple, closely related isolates are indicated by grey boxes next on the left of the clade designations (1.A, 1.B, etc). Inset: Maximum likelihood tree of the same data with significantly longer branches according to S3 Fig indicated in red.
Mentions: We now focus on the seventh pandemic based on 260 genomes from lineage L2. A maximum likelihood tree based on the 6,335 SNPs in their non-repetitive, core genomes (Fig. 3 inset; S3A Fig) confirmed that they are all genetically related, and clustered in three successive groups of decreasing diversity, which correspond to the three waves that were previously described [6]. The root-to-tip distances in the phylogeny correlated strongly with the dates of isolation of the individual strains (S3B Fig; R2 = 0.932; p-value = 2.56x10-142) with the exception of 17 of the 260 genomes which were significant outliers to this linear regression. They were located on long terminal branches (red in Fig. 3 inset and S3 Fig), as previously noted for strain A4 [6].

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