scholarly journals Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever

2012 ◽  
Vol 367 (1590) ◽  
pp. 868-877 ◽  
Author(s):  
Kristian G. Andersen ◽  
Ilya Shylakhter ◽  
Shervin Tabrizi ◽  
Sharon R. Grossman ◽  
Christian T. Happi ◽  
...  
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Lassa Fever ◽  
West African ◽  
Lassa Virus ◽  
Genome Wide ◽  
African Populations ◽  
Genome Wide Data ◽  
Differential Gene ◽  
Selection Of

Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural selection in West African populations where Lassa haemorrhagic fever is endemic. In this study, we provide further evidence for this notion. By applying tests for selection to genome-wide data from the International Haplotype Map Consortium and the 1000 Genomes Consortium, we demonstrate evidence for positive selection in LARGE and interleukin 21 ( IL21 ), two genes implicated in LASV infectivity and immunity. We further localized the signals of selection, using the recently developed composite of multiple signals method, to introns and putative regulatory regions of those genes. Our results suggest that natural selection may have targeted variants giving rise to alternative splicing or differential gene expression of LARGE and IL21 . Overall, our study supports the hypothesis that selective pressures imposed by LASV may have led to the emergence of particular alleles conferring resistance to Lassa fever, and opens up new avenues of research pursuit.

scholarly journals Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Tian-Qi Shi ◽  
Hai-Mo Shen ◽  
Shen-Bo Chen ◽  
Kokouvi Kassegne ◽  
Yan-Bing Cui ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Positive Selection ◽  
Plasmodium Vivax ◽  
Yunnan Province ◽  
Duffy Binding Protein ◽  
Synonymous Mutations ◽  
Selection Of

Malaria incidence has declined dramatically over the past decade and China was certified malaria-free in 2021. However, the presence of malaria in border areas and the importation of cases of malaria parasites are major challenges for the consolidation of the achievements made by China. Plasmodium vivax Duffy binding protein (PvDBP) performs a significant role in erythrocyte invasion, and is considered a promising P. vivax vaccine. However, the highly polymorphic region of PvDBP (PvDBP-II) impedes the development of blood-stage vaccine against P. vivax. In this study, we investigated the genetic diversity and natural selection of PvDBP-II among 124 P. vivax isolates collected from the China-Myanmar border (CMB) in Yunnan Province, China, during 2009–2011. To compare genetic diversity, natural selection, and population structure with CMB isolates, 85 pvdbp-II sequences of eastern Myanmar isolates were obtained from GenBank. In addition, global sequences of pvdbp-II were retrieved from GenBank to establish genetic differentiation relationships and networks with the CMB isolates. In total, 22 single nucleotide polymorphisms reflected in 20 non-synonymous and two synonymous mutations were identified. The overall nucleotide diversity of PvDBP-II from the 124 CMB isolates was 0.0059 with 21 haplotypes identified (Hd = 0.91). The high ratio of non-synonymous to synonymous mutations suggests that PvDBP-II had evolved under positive selection. Population structure analysis of the CMB and eastern Myanmar isolates were optimally grouped into five sub-populations (K = 5). Polymorphisms of PvDBP-II display that CMB isolates were genetically diverse. Mutation, recombination, and positive selection promote polymorphism of PvDBP-II of P. vivax population. Although low-level genetic differentiation in eastern Myanmar was identified along with the more effective malaria control measures, the complexity of population structure in malaria parasites has maintained. In conclusion, findings from this study advance knowledge of the understanding of the dynamic of P. vivax population, which will contribute to guiding the rational design of a PvDBP-II based vaccine.

scholarly journals Recovering signals of ghost archaic introgression in African populations

2020 ◽  
Vol 6 (7) ◽  
pp. eaax5097 ◽  
Author(s):  
Arun Durvasula ◽  
Sriram Sankararaman
Keyword(s):  
High Frequency ◽  
West African ◽  
Substantial Contribution ◽  
Modern Humans ◽  
Frequency Spectra ◽  
Adaptive Introgression ◽  
Genome Wide ◽  
African Populations ◽  
Archaic Introgression ◽  
Lines Of Evidence

While introgression from Neanderthals and Denisovans has been documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations.

scholarly journals Towards a new history and geography of human genes informed by ancient DNA

2014 ◽  
Author(s):  
Joseph Pickrell ◽  
David Reich
Keyword(s):  
Natural Selection ◽  
Ancient Dna ◽  
Population Replacement ◽  
Local Conditions ◽  
Geographic Locations ◽  
Technological Advances ◽  
Genome Wide ◽  
Human Genes ◽  
Genome Wide Data ◽  
History Of

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement have been the rule rather than the exception in human history. In light of this, we argue that it is time to critically re-evaluate current views of the peopling of the globe and the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.

scholarly journals Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension

2020 ◽  
Vol 12 (3) ◽  
pp. 77-87 ◽  
Author(s):  
Muthukrishnan Eaaswarkhanth ◽  
Andre Luiz Campelo dos Santos ◽  
Omer Gokcumen ◽  
Fahd Al-Mulla ◽  
Thangavel Alphonse Thanaraj
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Arabian Peninsula ◽  
Integrative Approach ◽  
Human Populations ◽  
Extended Haplotype ◽  
Major Health ◽  
Fitness Advantage ◽  
Genome Wide ◽  
Kuwaiti Population

Abstract Despite the extreme and varying environmental conditions prevalent in the Arabian Peninsula, it has experienced several waves of human migrations following the out-of-Africa diaspora. Eventually, the inhabitants of the peninsula region adapted to the hot and dry environment. The adaptation and natural selection that shaped the extant human populations of the Arabian Peninsula region have been scarcely studied. In an attempt to explore natural selection in the region, we analyzed 662,750 variants in 583 Kuwaiti individuals. We searched for regions in the genome that display signatures of positive selection in the Kuwaiti population using an integrative approach in a conservative manner. We highlight a haplotype overlapping TNKS that showed strong signals of positive selection based on the results of the multiple selection tests conducted (integrated Haplotype Score, Cross Population Extended Haplotype Homozygosity, Population Branch Statistics, and log-likelihood ratio scores). Notably, the TNKS haplotype under selection potentially conferred a fitness advantage to the Kuwaiti ancestors for surviving in the harsh environment while posing a major health risk to present-day Kuwaitis.

scholarly journals The niche of One Health approaches in Lassa fever surveillance and control

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Liã Bárbara Arruda ◽  
Najmul Haider ◽  
Ayodeji Olayemi ◽  
David Simons ◽  
Deborah Ehichioya ◽  
...  
Keyword(s):  
Public Health ◽  
One Health ◽  
Population Expansion ◽  
Lassa Fever ◽  
West African ◽  
Lassa Virus ◽  
African Countries ◽  
Rodent Host ◽  
Public Health Burden ◽  
And Control

AbstractLassa fever (LF), a zoonotic illness, represents a public health burden in West African countries where the Lassa virus (LASV) circulates among rodents. Human exposure hinges significantly on LASV ecology, which is in turn shaped by various parameters such as weather seasonality and even virus and rodent-host genetics. Furthermore, human behaviour, despite playing a key role in the zoonotic nature of the disease, critically affects either the spread or control of human-to-human transmission. Previous estimations on LF burden date from the 80s and it is unclear how the population expansion and the improvement on diagnostics and surveillance methods have affected such predictions. Although recent data have contributed to the awareness of epidemics, the real impact of LF in West African communities will only be possible with the intensification of interdisciplinary efforts in research and public health approaches. This review discusses the causes and consequences of LF from a One Health perspective, and how the application of this concept can improve the surveillance and control of this disease in West Africa.

scholarly journals Genome-wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS haplotype Linked to Metabolic Traits and Hypertension

2019 ◽  
Author(s):  
Muthukrishnan Eaaswarkhanth ◽  
Andre Luiz Campelo dos Santos ◽  
Omer Gokcumen ◽  
Fahd Al-Mulla ◽  
Thangavel Alphonse Thanaraj
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Arabian Peninsula ◽  
Integrative Approach ◽  
Human Populations ◽  
Extended Haplotype ◽  
Major Health ◽  
Fitness Advantage ◽  
Genome Wide ◽  
Kuwaiti Population

AbstractDespite the extreme and varying environmental conditions prevalent in the Arabian Peninsula, it has experienced several waves of human migrations following the out-of-Africa diaspora. Eventually, the inhabitants of the peninsula region adapted to the hot and dry environment. The adaptation and natural selection that shaped the extant human populations of the Arabian Peninsula region have been scarcely studied. In an attempt to explore natural selection in the region, we analyzed 662,750 variants in 583 Kuwaiti individuals. We searched for regions in the genome that display signatures of positive selection in the Kuwaiti population using an integrative approach in a conservative manner. We highlight a haplotype overlapping TNKS that showed strong signals of positive selection based on the results of the multiple selection tests conducted (integrated Haplotype Score, Cross Population Extended Haplotype Homozygosity, Population Branch Statistics, and log-likelihood ratio scores). Notably, the TNKS haplotype under selection potentially conferred a fitness advantage to the Kuwaiti ancestors for surviving in the harsh environment while posing a major health risk to present-day Kuwaitis.

scholarly journals The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1605
Author(s):  
Yolanda Botti-Lodovico ◽  
Parvathy Nair ◽  
Dolo Nosamiefan ◽  
Matthew Stremlau ◽  
Stephen Schaffner ◽  
...  
Keyword(s):  
Large Scale ◽  
Critical Role ◽  
Warning System ◽  
Field Work ◽  
Lassa Fever ◽  
Lassa Virus ◽  
Virus Binding ◽  
The Public ◽  
Health Community ◽  
African Populations

While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work to test our hypothesis that natural selection acting on LARGE—detected in the Yoruba population of Nigeria—conferred resistance to Lassa Fever in some West African populations. As we delved further, we conjectured that the “emerging” nature of recently discovered diseases like Lassa fever is related to a newfound capacity for detection, rather than a novel viral presence, and that humans have in fact been exposed to the viruses that cause such diseases for much longer than previously suspected. Dr. Stefan Kunz’s critical efforts not only laid the groundwork for this discovery, but also inspired and catalyzed a series of events that birthed Sentinel, an ambitious and large-scale pandemic prevention effort in West Africa. Sentinel aims to detect and characterize deadly pathogens before they spread across the globe, through implementation of its three fundamental pillars: Detect, Connect, and Empower. More specifically, Sentinel is designed to detect known and novel infections rapidly, connect and share information in real time to identify emerging threats, and empower the public health community to improve pandemic preparedness and response anywhere in the world. We are proud to dedicate this work to Stefan Kunz, and eagerly invite new collaborators, experts, and others to join us in our efforts.

scholarly journals Dynamical System Analysis of a Lassa Fever Model with Varying Socioeconomic Classes

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Ifeanyi Sunday Onah ◽  
Obiora Cornelius Collins
Keyword(s):  
Disease Transmission ◽  
System Analysis ◽  
Lassa Fever ◽  
West African ◽  
Sensitivity Analyses ◽  
Model Parameters ◽  
Lassa Virus ◽  
African Countries ◽  
Patch Model ◽  
Viral Illness

Lassa fever is an animal-borne acute viral illness caused by Lassa virus. It poses a serious health challenge around the world today, especially in West African countries like Ghana, Benin, Guinea, Liberia, Mali, Sierra Leone, and Nigeria. In this work, we formulate a multiple-patch Lassa fever model, where each patch denotes a socioeconomic class (SEC). Some of the important epidemiological features such as basic reproduction number of the model were determined and analysed accordingly. We further investigated how varying SECs affect the transmission dynamics of Lassa fever. We analysed the required state at which each SEC is responsible in driving the Lassa fever disease outbreak. Sensitivity analyses were carried out to determine the importance of model parameters to the disease transmission and prevalence. We carried out numerical simulation to support our analytical results. Finally, we extend some of the results of the 2-patch model to the general n -patch model.

scholarly journals Beta-globin gene haplotypes and selected Malaria-associated variants among black Southern African populations

2017 ◽  
Vol 2 ◽  
Author(s):  
G. D. Pule ◽  
E. R. Chimusa ◽  
K. Mnika ◽  
K. Mhandire ◽  
E. Kampira ◽  
...  
Keyword(s):  
Positive Selection ◽  
Sickle Cell ◽  
Evolutionary Dynamics ◽  
Globin Gene ◽  
Sub Saharan Africa ◽  
Migration Route ◽  
Beta Globin ◽  
African Populations ◽  
Sub Saharan ◽  
Selection Of

Partial carrier-resistance toPlasmodium falciparummalaria conferred by the sickle cell (HbS) mutation has resulted in the local amplification and positive selection of sickle cell disease (SCD) in malaria-endemic regions and particularly in sub-Saharan Africa (SSA). The present study investigated theβ-globin gene haplotypes, and selected malaria-associated variants among three cohorts of Bantu-speaking individuals from Malawi, Zimbabwe and South Africa compared with reports with data from others SSA populations. The data suggest a south-ward frequency decrease of malaria-associated variants in SSA linked to the evolutionary dynamics of various African populations’ genomes through selective pressure of malaria. These selected genomics differences, positive selection of SCD in malaria-endemic regions among ‘Bantus’ from various part of Africa emphasise the evidence of the dissociation between genetics, anthropology and culture. The present study also showed a relatively prevalent Benin haplotype, which is mostly found in West Africa, among Southern African Blacks and very low Bantu haplotype, which could suggest a major migration route, of Southern Africa Bantu, along the African west coast, post-occurrence of the Sickle cell mutation, which date remain to be fully elucidated.

Sign in / Sign up

Export Citation Format

Share Document