1. Epidemiology and Global Health
  2. Genetics and Genomics
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Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa

  1. Eme Ekeng
  2. Serges Tchatchouang
  3. Blaise Akenji
  4. Bassira Boubacar Issaka
  5. Ifeoluwa Akintayo
  6. Christopher Chukwu
  7. Ibrahim Dan Dano
  8. Sylvie Melingui
  9. Sani Ousmane
  10. Michael Oladotun Popoola
  11. Ariane Nzouankeu
  12. Yap Boum
  13. Francisco Luquero
  14. Anthony Ahumibe
  15. Dhamari Naidoo
  16. Andrew Azman
  17. Justin Lessler
  18. Shirlee Wohl  Is a corresponding author
  1. Nigeria Centre for Disease Control, Nigeria
  2. Centre Pasteur du Cameroun, Cameroon
  3. National Public Health Laboratory, Cameroon
  4. Centre de Recherche Médicale et Sanitaire, Niger
  5. Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Nigeria
  6. Epicentre, France
  7. World Health Organization Nigeria, Nigeria
  8. Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, United States
Short Report
Cite this article as: eLife 2021;10:e65159 doi: 10.7554/eLife.65159
2 figures and 3 additional files

Figures

Cholera cases and sequenced isolates.

(A) Weekly suspected cholera cases for Cameroon (orange), Niger (blue), and Nigeria (green) from 2010 through 2019 (‘Regional Cholera Platform in West and Central Africa,’ n.d.) (Figure 1—source data 1). Suspected cases are defined as recommended by the World Health Organization (Global Task Force on Cholera Control Surveillance Working Group, 2017). Red points: weeks with no more than five suspected cases reported across all three countries. Arrows: collection dates of isolates sequenced. Collection dates provided as year only (n=2) are plotted on January 1 of their given year. (B) Map of Cameroon, Niger, and Nigeria. Colors are as in (A). White points: location of sequenced isolates collected in 2018 and 2019 (Figure 1—source data 2). Black crosses: location of sequenced isolates collected prior to 2018. One isolate with unknown sub-country location is not shown.

Figure 1—source data 1

Case counts by epidemiological week in Niger, Nigeria, and Cameroon, 2010 to 2019.

https://cdn.elifesciences.org/articles/65159/elife-65159-fig1-data1-v1.zip
Figure 1—source data 2

Sample metadata for isolates sequenced in this study.

https://cdn.elifesciences.org/articles/65159/elife-65159-fig1-data2-v1.zip
Figure 2 with 2 supplements
Phylogenetic tree of V. cholerae O1 sequences.

Left: maximum likelihood tree of global V. cholerae isolates. Samples generated in this study are shown in blue (see also, Figure 2—source data 1). Right: zoom view of a portion of the T12 lineage containing V. cholerae genomes generated in this study. Country codes: TGO, Togo; NER, Niger; GHA, Ghana; CMR, Cameroon; NGA, Nigeria; TCD, Chad. Scale bar unit: nucleotide substitutions per site.

Figure 2—source data 1

Table of sequencing metrics for V. cholerae O1 genomes.

https://cdn.elifesciences.org/articles/65159/elife-65159-fig2-data1-v1.xlsx
Figure 2—source data 2

Summary table of published V. cholerae O1 genomes included in this study.

https://cdn.elifesciences.org/articles/65159/elife-65159-fig2-data2-v1.xlsx
Figure 2—source data 3

Accession numbers, references, and basic metadata for sequences included in global phylogeny.

The majority of these data were compiled by Weill et al., and the majority of background sequences were originally published in Weill et al., 2017, Weill et al., 2017, Irenge et al., 2020, and Bwire et al., 2018, among others.

https://cdn.elifesciences.org/articles/65159/elife-65159-fig2-data3-v1.zip
Figure 2—source data 4

Cases reported to the World Health Organization by decade, continent, and African subregion (where applicable), compiled from weekly epidemiological records (World Health Organization, 2019).

https://cdn.elifesciences.org/articles/65159/elife-65159-fig2-data4-v1.zip
Figure 2—figure supplement 1
Proportion of reported cholera cases and V. cholerae sequences by continent.

For each decade, the proportion of cholera cases reported to the World Health Organization from each continent (blue bars) and proportion of V. cholerae sequences included in this study from each continent (gray bars).

Figure 2—figure supplement 2
Proportion of reported cholera cases and V. cholerae sequences by African region.

For each decade, the proportion of cholera cases reported to the World Health Organization from each African subregion (blue bars) and proportion of V. cholerae sequences included in this study from each African subregion (gray bars).

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