Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia.
Plasmodium vivax has become the predominant malaria parasite and a major challenge for malaria elimination in the Greater Mekong Subregion (GMS). Yet, our knowledge about the evolution of P. vivax populations in the GMS is fragmental. We performed whole genome sequencing on 23 P. vivax samples from...
Published in: | PLOS Neglected Tropical Diseases |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science (PLoS)
2020
|
Subjects: | |
Online Access: | https://doi.org/10.1371/journal.pntd.0008506 https://doaj.org/article/7e83b85177da4241958fe8d891dae15c |
id |
ftdoajarticles:oai:doaj.org/article:7e83b85177da4241958fe8d891dae15c |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:7e83b85177da4241958fe8d891dae15c 2023-05-15T15:12:32+02:00 Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia. Awtum M Brashear Qi Fan Yubing Hu Yuling Li Yan Zhao Zenglei Wang Yaming Cao Jun Miao Alyssa Barry Liwang Cui 2020-08-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0008506 https://doaj.org/article/7e83b85177da4241958fe8d891dae15c EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pntd.0008506 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0008506 https://doaj.org/article/7e83b85177da4241958fe8d891dae15c PLoS Neglected Tropical Diseases, Vol 14, Iss 8, p e0008506 (2020) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2020 ftdoajarticles https://doi.org/10.1371/journal.pntd.0008506 2022-12-31T13:48:05Z Plasmodium vivax has become the predominant malaria parasite and a major challenge for malaria elimination in the Greater Mekong Subregion (GMS). Yet, our knowledge about the evolution of P. vivax populations in the GMS is fragmental. We performed whole genome sequencing on 23 P. vivax samples from the China-Myanmar border (CMB) and used 21 high-coverage samples to compare to over 200 samples from the rest of the GMS. Using genome-wide single nucleotide polymorphisms (SNPs), we analyzed population differentiation, genetic structure, migration and potential selection using an array of methods. The CMB parasites displayed a higher proportion of monoclonal infections, and 52% shared over 90% of their genomes in identity-by-descent segments with at least one other sample from the CMB, suggesting preferential expansion of certain parasite strains in this region, likely resulting from the P. vivax outbreaks occurring during this study period. Principal component, admixture, fixation index and phylogenetic analyses all identified that parasites from the CMB were genetically distinct from parasites from eastern parts of the GMS (Cambodia, Laos, Vietnam, and Thailand), whereas the eastern GMS parasite populations were largely undifferentiated. Such a genetic differentiation pattern of the P. vivax populations from the GMS parasite was largely explainable through geographic distance. Using the genome-wide SNPs, we narrowed down to a set of 36 SNPs for differentiating parasites from different areas of the GMS. Genome-wide scans to determine selection in the genome with two statistical methods identified genes potentially under drug selection, including genes associated with antifolate resistance and genes linked to chloroquine resistance in Plasmodium falciparum. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 14 8 e0008506 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Awtum M Brashear Qi Fan Yubing Hu Yuling Li Yan Zhao Zenglei Wang Yaming Cao Jun Miao Alyssa Barry Liwang Cui Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
Plasmodium vivax has become the predominant malaria parasite and a major challenge for malaria elimination in the Greater Mekong Subregion (GMS). Yet, our knowledge about the evolution of P. vivax populations in the GMS is fragmental. We performed whole genome sequencing on 23 P. vivax samples from the China-Myanmar border (CMB) and used 21 high-coverage samples to compare to over 200 samples from the rest of the GMS. Using genome-wide single nucleotide polymorphisms (SNPs), we analyzed population differentiation, genetic structure, migration and potential selection using an array of methods. The CMB parasites displayed a higher proportion of monoclonal infections, and 52% shared over 90% of their genomes in identity-by-descent segments with at least one other sample from the CMB, suggesting preferential expansion of certain parasite strains in this region, likely resulting from the P. vivax outbreaks occurring during this study period. Principal component, admixture, fixation index and phylogenetic analyses all identified that parasites from the CMB were genetically distinct from parasites from eastern parts of the GMS (Cambodia, Laos, Vietnam, and Thailand), whereas the eastern GMS parasite populations were largely undifferentiated. Such a genetic differentiation pattern of the P. vivax populations from the GMS parasite was largely explainable through geographic distance. Using the genome-wide SNPs, we narrowed down to a set of 36 SNPs for differentiating parasites from different areas of the GMS. Genome-wide scans to determine selection in the genome with two statistical methods identified genes potentially under drug selection, including genes associated with antifolate resistance and genes linked to chloroquine resistance in Plasmodium falciparum. |
format |
Article in Journal/Newspaper |
author |
Awtum M Brashear Qi Fan Yubing Hu Yuling Li Yan Zhao Zenglei Wang Yaming Cao Jun Miao Alyssa Barry Liwang Cui |
author_facet |
Awtum M Brashear Qi Fan Yubing Hu Yuling Li Yan Zhao Zenglei Wang Yaming Cao Jun Miao Alyssa Barry Liwang Cui |
author_sort |
Awtum M Brashear |
title |
Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia. |
title_short |
Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia. |
title_full |
Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia. |
title_fullStr |
Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia. |
title_full_unstemmed |
Population genomics identifies a distinct Plasmodium vivax population on the China-Myanmar border of Southeast Asia. |
title_sort |
population genomics identifies a distinct plasmodium vivax population on the china-myanmar border of southeast asia. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2020 |
url |
https://doi.org/10.1371/journal.pntd.0008506 https://doaj.org/article/7e83b85177da4241958fe8d891dae15c |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 14, Iss 8, p e0008506 (2020) |
op_relation |
https://doi.org/10.1371/journal.pntd.0008506 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0008506 https://doaj.org/article/7e83b85177da4241958fe8d891dae15c |
op_doi |
https://doi.org/10.1371/journal.pntd.0008506 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
14 |
container_issue |
8 |
container_start_page |
e0008506 |
_version_ |
1766343210240573440 |