A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity
Abstract Background Humans living in regions with high falciparum malaria transmission intensity harbour multi-strain infections comprised of several genetically distinct malaria haplotypes. The number of distinct malaria parasite haplotypes identified from an infected human host at a given time is...
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ftdoajarticles:oai:doaj.org/article:0a9e2e374da14c94bd681a063b6bc210 2023-05-15T15:15:18+02:00 A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity Robin H. Miller Nicholas J. Hathaway Oksana Kharabora Kashamuka Mwandagalirwa Antoinette Tshefu Steven R. Meshnick Steve M. Taylor Jonathan J. Juliano V. Ann Stewart Jeffrey A. Bailey 2017-12-01T00:00:00Z https://doi.org/10.1186/s12936-017-2137-9 https://doaj.org/article/0a9e2e374da14c94bd681a063b6bc210 EN eng BMC http://link.springer.com/article/10.1186/s12936-017-2137-9 https://doaj.org/toc/1475-2875 doi:10.1186/s12936-017-2137-9 1475-2875 https://doaj.org/article/0a9e2e374da14c94bd681a063b6bc210 Malaria Journal, Vol 16, Iss 1, Pp 1-15 (2017) Plasmodium falciparum Complexity of infection Amplicon-based deep sequencing Apical membrane antigen 1 Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2017 ftdoajarticles https://doi.org/10.1186/s12936-017-2137-9 2022-12-31T05:30:02Z Abstract Background Humans living in regions with high falciparum malaria transmission intensity harbour multi-strain infections comprised of several genetically distinct malaria haplotypes. The number of distinct malaria parasite haplotypes identified from an infected human host at a given time is referred to as the complexity of infection (COI). In this study, an amplicon-based deep sequencing method targeting the Plasmodium falciparum apical membrane antigen 1 (pfama1) was utilized to (1) investigate the relationship between P. falciparum prevalence and COI, (2) to explore the population genetic structure of P. falciparum parasites from malaria asymptomatic individuals participating in the 2007 Demographic and Health Survey (DHS) in the Democratic Republic of Congo (DRC), and (3) to explore selection pressures on geospatially divergent parasite populations by comparing AMA1 amino acid frequencies in the DRC and Mali. Results A total of 900 P. falciparum infections across 11 DRC provinces were examined. Deep sequencing of both individuals, for COI analysis, and pools of individuals, to examine population structure, identified 77 unique pfama1 haplotypes. The majority of individual infections (64.5%) contained polyclonal (COI > 1) malaria infections based on the presence of genetically distinct pfama1 haplotypes. A minimal correlation between COI and malaria prevalence as determined by sensitive real-time PCR was identified. Population genetic analyses revealed extensive haplotype diversity, the vast majority of which was shared across the sites. AMA1 amino acid frequencies were similar between parasite populations in the DRC and Mali. Conclusions Amplicon-based deep sequencing is a useful tool for the detection of multi-strain infections that can aid in the understanding of antigen heterogeneity of potential malaria vaccine candidates, population genetics of malaria parasites, and factors that influence complex, polyclonal malaria infections. While AMA1 and other diverse markers under balancing selection ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Malaria Journal 16 1 |
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topic |
Plasmodium falciparum Complexity of infection Amplicon-based deep sequencing Apical membrane antigen 1 Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
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Plasmodium falciparum Complexity of infection Amplicon-based deep sequencing Apical membrane antigen 1 Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Robin H. Miller Nicholas J. Hathaway Oksana Kharabora Kashamuka Mwandagalirwa Antoinette Tshefu Steven R. Meshnick Steve M. Taylor Jonathan J. Juliano V. Ann Stewart Jeffrey A. Bailey A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity |
topic_facet |
Plasmodium falciparum Complexity of infection Amplicon-based deep sequencing Apical membrane antigen 1 Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
Abstract Background Humans living in regions with high falciparum malaria transmission intensity harbour multi-strain infections comprised of several genetically distinct malaria haplotypes. The number of distinct malaria parasite haplotypes identified from an infected human host at a given time is referred to as the complexity of infection (COI). In this study, an amplicon-based deep sequencing method targeting the Plasmodium falciparum apical membrane antigen 1 (pfama1) was utilized to (1) investigate the relationship between P. falciparum prevalence and COI, (2) to explore the population genetic structure of P. falciparum parasites from malaria asymptomatic individuals participating in the 2007 Demographic and Health Survey (DHS) in the Democratic Republic of Congo (DRC), and (3) to explore selection pressures on geospatially divergent parasite populations by comparing AMA1 amino acid frequencies in the DRC and Mali. Results A total of 900 P. falciparum infections across 11 DRC provinces were examined. Deep sequencing of both individuals, for COI analysis, and pools of individuals, to examine population structure, identified 77 unique pfama1 haplotypes. The majority of individual infections (64.5%) contained polyclonal (COI > 1) malaria infections based on the presence of genetically distinct pfama1 haplotypes. A minimal correlation between COI and malaria prevalence as determined by sensitive real-time PCR was identified. Population genetic analyses revealed extensive haplotype diversity, the vast majority of which was shared across the sites. AMA1 amino acid frequencies were similar between parasite populations in the DRC and Mali. Conclusions Amplicon-based deep sequencing is a useful tool for the detection of multi-strain infections that can aid in the understanding of antigen heterogeneity of potential malaria vaccine candidates, population genetics of malaria parasites, and factors that influence complex, polyclonal malaria infections. While AMA1 and other diverse markers under balancing selection ... |
format |
Article in Journal/Newspaper |
author |
Robin H. Miller Nicholas J. Hathaway Oksana Kharabora Kashamuka Mwandagalirwa Antoinette Tshefu Steven R. Meshnick Steve M. Taylor Jonathan J. Juliano V. Ann Stewart Jeffrey A. Bailey |
author_facet |
Robin H. Miller Nicholas J. Hathaway Oksana Kharabora Kashamuka Mwandagalirwa Antoinette Tshefu Steven R. Meshnick Steve M. Taylor Jonathan J. Juliano V. Ann Stewart Jeffrey A. Bailey |
author_sort |
Robin H. Miller |
title |
A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity |
title_short |
A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity |
title_full |
A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity |
title_fullStr |
A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity |
title_full_unstemmed |
A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity |
title_sort |
deep sequencing approach to estimate plasmodium falciparum complexity of infection (coi) and explore apical membrane antigen 1 diversity |
publisher |
BMC |
publishDate |
2017 |
url |
https://doi.org/10.1186/s12936-017-2137-9 https://doaj.org/article/0a9e2e374da14c94bd681a063b6bc210 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Malaria Journal, Vol 16, Iss 1, Pp 1-15 (2017) |
op_relation |
http://link.springer.com/article/10.1186/s12936-017-2137-9 https://doaj.org/toc/1475-2875 doi:10.1186/s12936-017-2137-9 1475-2875 https://doaj.org/article/0a9e2e374da14c94bd681a063b6bc210 |
op_doi |
https://doi.org/10.1186/s12936-017-2137-9 |
container_title |
Malaria Journal |
container_volume |
16 |
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1 |
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1766345665439334400 |