1. Microbiology and Infectious Disease
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Unravelling the history of hepatitis B virus genotypes A and D infection using a full-genome phylogenetic and phylogeographic approach

  1. Evangelia-Georgia Kostaki
  2. Timokratis Karamitros
  3. Garyfallia Stefanou
  4. Ioannis Mamais
  5. Konstantinos Angelis
  6. Angelos Hatzakis
  7. Anna Kramvis
  8. Dimitrios Paraskevis  Is a corresponding author
  1. National and Kapodistrian University of Athens, Greece
  2. University of Oxford, United Kingdom
  3. European University of Cyprus, Cyprus
  4. University of the Witwatersrand, South Africa
Research Article
Cite this article as: eLife 2018;7:e36709 doi: 10.7554/eLife.36709
4 figures, 4 tables and 7 additional files

Figures

Figure 1 with 3 supplements
Midpoint rooted phylogeographic tree estimated by RAxML v8.0.20.

HBV genotype D sequences (N = 916) categorized according to the geographic region of sampling were used in the analysis. Monophyletic clusters are indicated as triangles. Major clusters are indicated in Roman numerals.

https://doi.org/10.7554/eLife.36709.004
Figure 1—figure supplement 1
Midpoint rooted phylogeographic tree on 916 HBV genotype D sequences categorized according to the country/geographic region of sampling.
https://doi.org/10.7554/eLife.36709.005
Figure 1—figure supplement 2
Midpoint rooted phylogeographic tree on HBV genotype D sequences after the inclusion of RS-D5.
https://doi.org/10.7554/eLife.36709.006
Figure 1—figure supplement 3
Phylogenetic analysis of genotype D including the RS-D5 in two non-overlapping subgenomic areas (1–2000 nts) and (2001–3078 nts). RS-D5 sequences are shown in red.
https://doi.org/10.7554/eLife.36709.007
Figure 2 with 1 supplement
Putative major dispersal pathways of genotype D as estimated by phylogeographic analysis.

The origin is depicted with dotted line. Subgenotypes and their corresponding dispersal routes are shown with different colors. Colored circles depict the geographic areas where subgenotypes are the most prevalent.

https://doi.org/10.7554/eLife.36709.010
Figure 2—figure supplement 1
Putative major dispersal pathways of genotype D as estimated by phylogeographic analysis after the inclusion of RS-D5.
https://doi.org/10.7554/eLife.36709.011
Figure 3 with 1 supplement
Midpoint rooted phylogeographic tree estimated by RAxML v8.0.20.

HBV genotype A sequences (N = 493) categorized according to the geographic region of sampling were used in the analysis. Monophyletic clusters are indicated as triangles. Major clusters are indicated in Roman numerals.

https://doi.org/10.7554/eLife.36709.014
Figure 3—figure supplement 1
Midpoint rooted phylogeographic tree on 493 HBV genotype A sequences categorized according to the country/geographic region of sampling.
https://doi.org/10.7554/eLife.36709.015
Putative major dispersal pathways for genotype A as revealed by the phylogeographic analysis.

The putative geographic origin of genotype A is in the Middle East/Central Asia. Subgenotypes and their corresponding dispersal routes are shown with different colors. Colored circles depict the geographic areas where subgenotypes are the most prevalent. Dotted lines represent the source and sinks for distant dispersal pathways.

https://doi.org/10.7554/eLife.36709.016

Tables

Table 1
Sampling of HBV* genotype D sequences from different geographic regions.
https://doi.org/10.7554/eLife.36709.003
Region of samplingCountries (N)Sequences (N, %)
North Africa/Middle East5394 (43.0)
South Asia2151 (16.5)
Western Europe970 (7.6)
Central Asia444 (4.8)
Australasia240 (4.4)
Asia-Pacific136 (3.9)
East Asia235 (3.8)
Eastern Europe327 (3.0)
Latin America225 (2.7)
Oceania623 (2.5)
Sub-Saharan Africa820 (2.2)
North America216 (1.8)
Central Europe214 (1.5)
Caribbean211 (1.2)
Southeast Asia210 (1.1)
Total52916 (100)
  1. * HBV, hepatitis B virus.

Table 2
HBV* genotype D percentages of clustering based on the geographic region of sampling.
https://doi.org/10.7554/eLife.36709.008
Region of samplingMonophyletic clusters (N)Clustered sequences (N, %)
Australasia136 (90)
Oceania119 (83)
Asia-Pacific130 (83)
Southeast Asia18 (80)
East Asia224 (69)
Caribbean17 (64)
Latin America114 (56)
Sub-Saharan Africa211 (55)
North America18 (50)
Western Europe321 (30)
South Asia334 (23)
Eastern Europe15 (19)
North Africa/Middle East663 (16)
Central Asia00 (0)
Central Europe00 (0)
Total24279 (31)
  1. * HBV, hepatitis B virus.

Table 3
Sampling of HBV* genotype A sequences from different geographic regions.
https://doi.org/10.7554/eLife.36709.012
Region of samplingCountries (N)Sequences (N, %)
Sub-Saharan Africa14112 (22.7)
Western Europe8108 (21.9)
Latin America562 (12.6)
Asia-Pacific153 (10.8)
Caribbean252 (10.5)
Central Europe237 (7.5)
South Asia326 (5.3)
Eastern Europe417 (3.5)
North America211 (2.2)
Southeast Asia28 (1.6)
East Asia24 (0.8)
North Africa/Middle East22 (0.4)
Central Asia11 (0.2)
Total48493 (100)
  1. * HBV, hepatitis B virus.

Table 4
HBV* genotype A percentages of clustering based on the geographic region of sampling.
https://doi.org/10.7554/eLife.36709.013
Region of samplingMonophyletic clusters (N)Clustered sequences (N, %)
South Asia123 (88)
Caribbean344 (85)
Latin America444 (71)
Sub-Saharan Africa670 (63)
Western Europe133 (31)
Asia-Pacific211 (21)
Central Europe00 (0)
Eastern Europe00 (0)
Southeast Asia00 (0)
East Asia00 (0)
North America00 (0)
North Africa/Middle East00 (0)
Central Asia00 (0)
Total17255 (52)
  1. * HBV, hepatitis B virus.

Additional files

Supplementary file 1

Sampling and percentages of clustering of HBV genotype D sequences from different countries and geographic regions.

https://doi.org/10.7554/eLife.36709.009
Supplementary file 2

Sampling and percentages of clustering of HBV genotype A sequences from different countries and geographic regions.

https://doi.org/10.7554/eLife.36709.017
Supplementary file 3

List of papers for HBV genotype D sequences included in the analysis.

https://doi.org/10.7554/eLife.36709.018
Supplementary file 4

List of papers for HBV genotype A sequences included in the analysis.

https://doi.org/10.7554/eLife.36709.019
Supplementary file 5

List of countries within each geographic region (as defined by the Global Burden of Disease classification system), in which HBV genotype D sequences were included in the analysis.

https://doi.org/10.7554/eLife.36709.020
Supplementary file 6

List of countries within each geographic region (as defined by the Global Burden of Disease classification system), in which HBV genotype A sequences were included in the analysis.

https://doi.org/10.7554/eLife.36709.021
Transparent reporting form
https://doi.org/10.7554/eLife.36709.022

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