Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania.
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ABSTRACT:
SUBMITTER: Malaria Genomic Epidemiology Network
PROVIDER: S-EPMC6914791 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Recent genome-wide association studies (GWASs) of severe malaria have identified several association variants. However, much about the underlying biological functions are yet to be discovered. Here, we systematically predicted plausible candidate genes and pathways from functional analysis of severe malaria resistance GWAS summary statistics (N = 17,000) meta-analysed across 11 populations in malaria endemic regions. We applied positional mapping, expression quantitative trait locus (eQTL), chromatin interaction mapping, and gene-based association analyses to identify candidate severe malaria resistance genes. We further applied rare variant analysis to raw GWAS datasets (N = 11,000) of three malaria endemic populations including Kenya, Malawi, and Gambia and performed various population genetic structures of the identified genes in the three populations and global populations. We performed network and pathway analyses to investigate their shared biological functions. Our functional mapping analysis identified 57 genes located in the known malaria genomic loci, while our gene-based GWAS analysis identified additional 125 genes across the genome. The identified genes were significantly enriched in malaria pathogenic pathways including multiple overlapping pathways in erythrocyte-related functions, blood coagulations, ion channels, adhesion molecules, membrane signalling elements, and neuronal systems. Our population genetic analysis revealed that the minor allele frequencies (MAF) of the single nucleotide polymorphisms (SNPs) residing in the identified genes are generally higher in the three malaria endemic populations compared to global populations. Overall, our results suggest that severe malaria resistance trait is attributed to multiple genes, highlighting the possibility of harnessing new malaria therapeutics that can simultaneously target multiple malaria protective host molecular pathways.
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Project description:A widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration circa 50,000 years ago (ya), and the more recent Austronesian expansion, which reached the Bismarck Archipelago by 3,450 ya. Whereas earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic, and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide data set of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal single nucleotide polymorphisms (SNPs). We show that the initial dispersal of people from the Bismarck Archipelago into Remote Oceania occurred in a "leapfrog" fashion, completely by-passing the main chain of the Solomon Islands, and that the colonization of the Solomon Islands proceeded in a bidirectional manner. Our results also support a divergence between western and eastern Solomons, in agreement with the sharp linguistic divide known as the Tryon-Hackman line. We also report substantial post-Austronesian gene flow across the Solomons. In particular, Santa Cruz (in Remote Oceania) exhibits extraordinarily high levels of Papuan ancestry that cannot be explained by a simple bottleneck/founder event scenario. Finally, we use simulations to show that discrepancies between different methods for dating admixture likely reflect different sensitivities of the methods to multiple admixture events from the same (or similar) sources. Overall, this study points to the importance of fine-scale sampling to understand the complexities of human population history.
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Project description:The Asia-Oceania Human Proteome Organization (AOHUPO; www.aohupo.org) was officially founded on June 7, 2001, by Richard J. Simpson (Australia), Akira Tsugita (Japan), and Young-Ki Paik (Korea) and launched on October 1-4, 2001, at the second scientific meeting of the International Proteomics Conference held in Canberra, Australia. Inaugural council members of the AOHUPO elected were Richard J. Simpson (Australia, president), Qi-Chang Xia (China), Kazuyuki Nakamura (Japan), Akira Tsugita (Japan, VIce President), Young-Ki Paik (Korea, secretary general), Mike Hubbard (New Zealand), Max C. M. Chung (Singapore), Shui-Tien Chen (Taiwan), and John Bennett (Philippines). The first AOHUPO conference was held on March 26-27, 2002, at the Seoul National University, Seoul, Korea, conjointly with the second Annual Meeting of KHUPO. Since then, biennial AOHUPO conferences have been held in Taipei (2004), Singapore (2006), Cairns (2008), Hyderabad (2010), Beijing (2012), Bangkok (2014), Sun Moon Lake (2016), and Osaka (2018). The 10th AOHUPO conference is scheduled to be held in Busan on June 30 to July 2, 2021, to celebrate our 20th anniversary.
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Project description:Variations in the functional response of legume pod borer (Maruca vitrata) populations to sex pheromone blends were observed in Asia and Africa. Hence, this study was carried out to understand the differences in pheromone-binding proteins (PBPs) among Maruca populations in Asia, Africa, Oceania, and South America. A de novo transcriptome assembly was adopted to sequence the entire transcribed mRNAs in M. vitrata from Taiwan. The raw-sequence data were assembled using homologous genes from related organisms in GenBank to detect M. vitrata PBPs (MvitPBPs). Sections of the cDNA of MvitPBP of different length were used to design primers to amplify the full-length cDNA of PBPs. All three PBP sequences comprised three exons interspersed by two introns. In total, 92 MvitPBP1 haplotypes, 77 MvitPBP2 haplotypes, and 64 MvitPBP3 haplotypes were identified in 105, 98, and 68 Maruca individuals, respectively. High pairwise F ST values (0.41-0.73) and phylogenetic analyses distinguished the putative Maruca species in South America from those occurring in rest of the world, and possibly two putative subspecies in Asia and Africa. The haplotype networks and Automatic Barcode Gap Discovery analyses also confirmed these results. The negative Tajima's D and Fu's F S values showed the recent demographic expansion of Maruca populations. Thus, this study confirmed the presence of different Maruca species and/or subspecies in different continents based on the diversity within PBP genes. Additional sampling and studies are suggested for Oceania and South America. The genetic differences among Maruca populations should be carefully considered while using sex pheromone lures and bio-control agents.
| S-EPMC6706176 | biostudies-literature
Project description:Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called "wild" pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region.
| S-EPMC1829225 | biostudies-literature
Project description:This paper presents results from the first survey of training and education undertaken by the Europe-Middle East-Africa (EMEAC), the Latin America (LAC) and the Asia-Oceania (AOC) Chapters of the International Federation of Clinical Neurophysiology (IFCN). The survey was conducted initially by the EMEAC in 2012 and updated in 2016, 2019, and 2020. It had the following categories: status of specialty and training in member country (21 questions), competency and accreditation (12 questions), practice and concerns (23 questions). An abbreviated version of the survey was conducted by the LAC and AOC in 2018-2019. Clinical neurophysiology (CN) was a single specialty in a minority of member societies' countries: 8/33 EMEAC, 2/12 AOC and 2/10 LAC. In others it was usually a subspecialty of neurology. Training periods in CN were split fairly evenly between 1, 2, 3, 4 and 5 years in EMEAC, while neurology takes 4 to 5 years. In the AOC, neurology training was for 3 to 4 years and CN for up to 2 years. In LAC a majority of countries trained for 2 to 3 years in both neurology and CN. An exit exam was performed in 16/30 EMEAC respondents, 8/12 in the AOC and 3/10 in the LAC. Competence was considered to require a wide range of numbers of tests performed under supervision, from <250 to >750 in EMEAC and AOC, with the EMEAC tending to require more. The main concerns were in recruitment and workload in EMEAC, training in AOC and the need for more recognition of the specialty in some countries within the LAC. This survey, the first across the three chapters, revealed considerable differences in training durations and numbers of tests performed for competence between national societies.
| S-EPMC9065461 | biostudies-literature
Project description:BackgroundMalaria and visceral leishmaniasis (VL) co-infection can occur due to the overlapping geographical distributions of these diseases; however, only limited data of this co-infection have been reported and reviewed. This study aimed to explore the pooled prevalence and characteristics of this co-infection using a systematic review approach.MethodsThe PubMed, Web of Science and Scopus databases were searched for relevant studies. The quality of these studies was assessed in accordance with strengthening the reporting of observational studies in epidemiology (STROBE) guidelines. The numbers of individuals co-infected with Plasmodium and VL and the total numbers of individuals with VL were used to estimate the pooled prevalence using random-effects models. Differences in age, sex and the presence of anemia and malnutrition on admission were compared between co-infected individuals and individuals with VL using a random-effects model; the results are presented as odds ratios (ORs) and 95% confidence intervals (CIs). Heterogeneity among the included studies was assessed and quantified using Cochrane Q and I2 statistics.ResultsOf the 3075 studies identified, 12 met the eligibility criteria and were included in this systematic review. The pooled prevalence of Plasmodium infection among the 6453 individuals with VL was 13%, with substantial heterogeneity of the data (95% CI 7-18%, I2 97.9%). Subgroup analysis demonstrated that the highest prevalence of co-infection occurred in African countries, whereas the lowest prevalence occurred in Asian countries. Patients aged < 5 years had higher odds of having co-infection than having VL (co-infection, n = 202; VL, n = 410) (OR 1.66, 95% CI 1.37-2.01, I2 0%; P < 0.0001), whereas patients aged 20-29 years had lower odds of having co-infection than having VL (co-infection, n = 170; VL, n = 699) (OR 0.75, 95% CI 0.60-0.93, I2 18%; P = 0.01). Male patients had equivalent odds of having co-infection and having VL (co-infection, n = 525; VL, n = 2232) (OR 0.92, 95% CI 0.078-1.08, I2 0%; P = 0.29). Patients with co-infection had lower odds of having anemia at admission than those with VL (co-infection, n = 902; VL, n = 2939) (OR 0.64, 95% CI 0.44-0.93, I2 0%; P = 0.02). No difference in malnutrition at admission was found in the meta-analysis.ConclusionsThe prevalence of malaria co-infection among individuals with VL was heterogeneous and ranged from 7 to 18%, depending on geographical area. Age and anemia at admission were associated with co-infection status. Further longitudinal studies are needed to determine if co-infection with malaria has an impact on the severity of VL.
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Project description:Thailand and Laos, located in the center of Mainland Southeast Asia (MSEA), harbor diverse ethnolinguistic groups encompassing all five language families of MSEA: Tai-Kadai (TK), Austroasiatic (AA), Sino-Tibetan (ST), Hmong-Mien (HM), and Austronesian (AN). Previous genetic studies of Thai/Lao populations have focused almost exclusively on uniparental markers and there is a paucity of genome-wide studies. We therefore generated genome-wide SNP data for 33 ethnolinguistic groups, belonging to the five MSEA language families from Thailand and Laos, and analyzed these together with data from modern Asian populations and SEA ancient samples. Overall, we find genetic structure according to language family, albeit with heterogeneity in the AA-, HM-, and ST-speaking groups, and in the hill tribes, that reflects both population interactions and genetic drift. For the TK speaking groups, we find localized genetic structure that is driven by different levels of interaction with other groups in the same geographic region. Several Thai groups exhibit admixture from South Asia, which we date to ∼600-1000 years ago, corresponding to a time of intensive international trade networks that had a major cultural impact on Thailand. An AN group from Southern Thailand shows both South Asian admixture as well as overall affinities with AA-speaking groups in the region, suggesting an impact of cultural diffusion. Overall, we provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies.
| S-EPMC8321548 | biostudies-literature
Project description:It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.
| S-EPMC3188841 | biostudies-literature
Project description:IntroductionThe transmission dynamics of the recent mpox outbreak highlights the lack of infrastructure available to rapidly respond to novel STI outbreaks, of which Asia and Oceania remains particularly susceptible. Here, we simulate outbreaks in this setting and propose the use of pre-emptive vaccination within the men who have sex with men (MSM) community before the arrival and establishment of the virus.Materials and methodsUsing data driven heterogeneous sexual contact networks, we simulated outbreaks of mpox in Singapore, Hong Kong, and Sydney. An individual based SEIR compartmental model was used to simulate epidemic trajectories and the impact of different vaccination uptakes was assessed in their ability to avert or suppress outbreaks upon the arrival of mpox within the MSM populations.ResultsThe highly dense sexual networks of Singapore and Sydney experience rapid outbreaks, with infection peaks occurring at day 41 and 23 respectively, compared to Hong Kong which occurs at day 77. Across the simulations with no vaccination, 68.2%-89.7% of the MSM community will become infected with mpox across the different cities, over a simulation period of 1 year. By implementing vaccination strategies, the infection rate across the cities can be reduced to as low as 3.1% of the population (range: 3.1%-82.2%) depending on the implementation and uptake of the vaccine. Vaccination is also extremely effective in slowing the start of the epidemic, delaying the epidemic peak by 36-50 days in Hong Kong, or even preventing the outbreak of mpox.DiscussionWith extremely dense and well-connected sexual contact networks, where 65.2%-83.2% of the population are connected to a super-spreader in the different contact networks, pre-emptive or immediate vaccination upon identification of the first case is strongly recommended to help better manage the outbreak of mpox and prevent potential straining of healthcare systems.
| S-EPMC10825486 | biostudies-literature