Population structure and migration in the Eastern Highlands of Papua New Guinea, a region impacted by the kuru epidemic

Populations of the Eastern Highlands of Papua New Guinea (EHPNG, area 11,157 km2) lived in relative isolation from the rest of the world until the mid-20th century, and the region contains a wealth of linguistic and cultural diversity. Notably, several populations of EHPNG were devastated by an epidemic prion disease, kuru, which at its peak in the mid-twentieth century led to some villages being almost depleted of adult women. Until now, population genetic analyses to learn about genetic diversity, migration, admixture, and the impact of the kuru epidemic have been restricted to a small number of variants or samples. Here, we present a population genetic analysis of the region based on genome-wide genotype data of 943 individuals from 21 linguistic groups and 68 villages in EHPNG, including 34 villages in the South Fore linguistic group, the group most affected by kuru. We find a striking degree of genetic population structure in the relatively small region (average FST between linguistic groups 0.024). The genetic population structure correlates well with linguistic grouping, with some noticeable exceptions that reflect the clan system of community organization that has historically existed in EHPNG. We also detect the presence of migrant individuals within the EHPNG region and observe a significant excess of females among migrants compared to among non-migrants in areas of high kuru exposure (p = 0.0145, chi-squared test). This likely reflects the continued practice of patrilocality despite documented fears and strains placed on communities as a result of kuru and its associated skew in female incidence.

[Epidemiological and clinical profile of age-related macular degeneration in Cameroon]

PURPOSE

To determine the epidemiological and clinical characteristics of age-related macular degeneration in patients in Yaoundé.

METHODOLOGY

A multicenter, analytical and cross-sectional study was carried out from March 2017 to June 2018 in four hospitals in the city of Yaoundé. Included were all consenting patients aged at least 40 years with an established diagnosis of AMD both clinically and by imaging. The data were analyzed with CSPro software version 7.0. Chi² and Student's "t" tests in univariate mode and logistic regression in multivariate mode were used with a significance of P≤5%.

RESULTS

Of the 9,989 patients who were seen during the 16-month study period, 38 met our inclusion criteria - a frequency of 0.4%. The sex ratio was 0.3, and the mean age was 68±11 years. As a function of geographic origin, AMD is more common in patients from the forest and mountain areas. The systemic comorbidities associated recorded were hypertension (47.4%) and diabetes (21.1%). After optical correction, 60 of 76 eyes (78.9%) had useful visual acuity according to WHO criteria, and the rate of blindness was 9.2%. Fundus examination revealed fewer lesions than optical coherence tomography, which demonstrated miliary drusen in 57 (75%) eyes, serous drusen in 27 (35.5%), retinal atrophy in 19 (25%) and neovascularization in 3 (3.9%). The clinical forms were dominated by age-related maculopathy, found in 45 eyes (69.2%), followed by atrophic AMD in 17 (26.2%) and finally by exudative AMD in 3 (4.6%), for a total of 65 out of 76 eyes. Age was related to the risk of MLA and atrophic AMD (P≤0.05).

CONCLUSION

AMD is an uncommon pathology in our setting, predominant in women over the age of 60 years.

[Retinal manifestations of neuro-malaria or "malarial retinopathy" in Yaoundé]

AIM

Contribute to the improvement of diagnostic and prognostic approaches to treating children with neuro-malaria in Yaoundé.

PATIENTS AND METHOD

A prospective and analytical study carried out in 2 hospitals of Yaoundé from October 2015 to March 2016. All patients aged 3 months to 15 years hospitalized for neuro-malaria in one of the 2 hospitals benefited from a fundus examination. The variables studied were: age, sex, Glasgow or Blantyre score, fundus examination and parasitaemia. For statistical analysis, we used the software R 3.3.0, Chi², exact of Fisher or Kolmogorov-Smirnov tests with a significance P<5%.

RESULTS

Out of the 178 children hospitalized during the study period, 44 had neuro-malaria (24.71%) and 26 (46 diseased eyes) among them presented retinal lesions at a frequency of 14.60%. The mean age was 5.54±3.49 years with a sex ratio of 1.09. The under 5-years-old were the most affected with 31 (70.45%) cases. The fundus lesions of 26 (59.09%) were retinal hemorrhages in 24 (54.54%), retinal whitening and vessel discoloration in 8 (18.18%) respectively. Papillary edema was associated in 4 (9.09%). Macular involvement was noted in 9 cases. These lesions were correlated with age, depth of coma, duration, and clinical course. The rate of parasitaemia did not affect their occurrence.

CONCLUSION

Retinal lesions are frequent and serious during neuro-malaria in our environment, especially in children under five. They must therefore be an emphasis in the systematic exam to rule it out for a better prognostic evaluation and a fast and adequate multidisciplinary management.

[Characteristics of post-traumatic blindness at the Yaoundé Army Training, Application and Referral Hospital]

PURPOSE

To study the characteristics of blindness after ocular trauma.

METHODOLOGY

In this retrospective descriptive study, we considered the files of patients who had consulted the service for ocular trauma between January 2008 and December 2014. Included were patients of both sexes and all ages whose monocular or binocular vision with best optical correction was strictly below 1/20. Statistical analysis was performed with EPI Info version 3.5.4 software, and the Chi² test was used with statistically significant values of P≤0.05.

RESULTS

Over the period from 2008 to 2014, we found 100 cases of blindness (101 eyes) resulting from 591 cases of ocular trauma, for a frequency of 16.92 %. Among them, 75 men with a median age of 35.5±19.8 years. Children younger than 15 years accounted for 11 % of the series. The blindness was monocular in 99 % and binocular in 1 %, distributed as follows: 55 cases (55 %) category V, 27 (27 %) category IV and 18 (18 %) category III according to the CIM-10. In the anterior segment, cataract was responsible for category III and IV blindness, while in the posterior segment, retinal detachment was found in all categories. In all age ranges irrespective of sex, category V blindness was most frequent.

CONCLUSION

Blindness following ocular trauma is frequent in our context. It can be avoided. Consequently, it is essential to put in place strategies for prevention of ocular trauma via education of the population through public awareness campaigns.

Sickle cell retinopathy and other chronic complications of sickle cell anemia: A clinical study of 84 Sub-Saharan African cases (Cameroon)

OBJECTIVE

Sickle retinopathy is a severe complication of sickle cell disease than can lead to blindness. We aim to describe the epidemiology of sickle retinopathy in homozygous sickle cell (SS) African patients and to analyze its association with non-ophthalmologic disease complications of sickle cell anemia.

METHODS

We conducted a nested study within the CADRE cohort in Cameroon. Eighty-four consecutive SS outpatients, aged 10 years and older, with no visual symptoms, underwent an ophthalmologic examination. Mean age was 23±10 years. Clinical and biological features were compared between patients with and without sickle retinopathy. We compared the prevalence of the clinical complications and main biological characteristics in patients with and without sickle retinopathy using a univariate logistic regression. The same analysis was used to compare the patients with non-proliferative sickle retinopathy to those with proliferative sickle retinopathy. Statistical analyses were done using the R software (version 3.1.2).

RESULTS

Fifty-two patients (62%) displayed sickle retinopathy, among them 23 (27%) had a non-proliferative sickle retinopathy, and 29 (35%) had proliferative sickle retinopathy. Patients with proliferative sickle cell retinopathy had a mean age of 28±11 years. Sickle retinopathy was associated with higher hemoglobin level (P=0.047) and fewer leg ulcers (P=0.018). Proliferative SR was associated with increasing age (P=0.008) and male sex (P=0.025) independently of the hemoglobin level.

CONCLUSIONS

Sickle retinopathy is particularly frequent in sub-Saharan sickle cell SS patients, which advocates for early systematic screening.

A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea

New Guinea shows human occupation since ~50 thousand years ago (ka), independent adoption of plant cultivation ~10 ka, and great cultural and linguistic diversity today. We performed genome-wide single-nucleotide polymorphism genotyping on 381 individuals from 85 language groups in Papua New Guinea and find a sharp divide originating 10 to 20 ka between lowland and highland groups and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 thousand years, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in Papua New Guinea is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies.

[Epidemiological and clinical aspects of tropical endemic limbo-conjunctivitis in students in Yaoundé]

INTRODUCTION

TELC, tropical endemic limbo-conjunctivitis, is a keratoconjunctivitis seen more frequently in dry intertropical settings than humid ones. We aim to determine the epidemiologic and clinical profile of this condition in a city with a humid equatorial climate.

PATIENTS AND METHODS

During first third of 2014, we conducted a cross-sectional descriptive study in schools. Included were children aged 3-15 years who received parental consent. The selection was conducted in two steps. After an initial examination of children within the schools, the diagnosis was then confirmed by a complete ophthalmologic examination carried out in the hospital. For ethical clearance, the study received all necessary authorizations. The data were analyzed using the CSPro version 4.0 software in French and the comparison test used was χ² with a confidence limit of 95 %.

RESULTS

Out of 353 students examined, 129 were referred to the Yaoundé central hospital, among which 82 (23.2 %) were confirmed with TELC. The median age of the children diagnosed with TELC was 8.24+0.6 years. Boys (57.3 %) were affected more than girls. The age range of 6-12 years (64.6 %) was the most represented. A recrudescence of the attacks was observed during the dry season (93 %) of cases. Dust (49 %) and sun exposure (43 %) were aggravating factors.

CONCLUSION

The prevalence of TELC observed in school in this study is significant.

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.

Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario.

Distribution of an allele associated with blond hair color across Northern Island Melanesia

Pigmentation of the skin, hair, and eyes is a complex trait controlled by multiple genetic loci. Recently a non-synonymous mutation in the pigmentation candidate gene TYRP1 was shown to be significantly associated with a blond-hair phenotype in populations from the Solomon Islands. The distribution of this mutation in the islands of Northern Island Melanesia, where the blondism phenotype is also prevalent, was unknown. Here, we present data describing the distribution of this allele in 550 individuals sampled from across this region, and test for associations between genotype at this locus and quantitatively measured skin and hair pigmentation phenotype. We report that the frequency of the 93C allele is notably lower than observed in the Solomons (0.12 vs. 0.26). The allele exhibits significant geographic heterogeneity across the islands sampled (χ(2)  = 108.4, P < 0.0001). It is observed at its highest frequencies on the islands of New Ireland and New Hanover, while being almost completely absent from the large island of New Britain. Using linear regression with age, sex, and island as covariates we report that, as in the Solomons, the 93C allele is significantly associated with a decrease in hair pigmentation but not skin pigmentation. We discuss the distribution of the 93C allele across the Southwest Pacific in light of its possible place of origin and dispersal.

[Tropical endemic limboconjunctivitis (vernal conjunctivitis) in northern Cameroon]

INTRODUCTION

A retrospective study was conducted in the ophthalmology unit of the Garoua regional hospital on children examined from January 2001 to December 2007. We aimed to determine the epidemiological aspects of tropical endemic limboconjunctivitis in northern Cameroon. Included were all the files of patients aged 0-15 years seen with a positive diagnosis of tropical endemic limboconjunctivitis. The data analyzed were obtained through inspection, interview, and a comprehensive ocular exam done for every case, assessing far visual acuity, slit lamp biomicroscopy, and funduscopy when possible. The variables analyzed were age, sex, signs and symptoms, residential area, associated pathologies, and the month and the year of the diagnosis. The data were analyzed with Epi-Info, version 6.04d (French) and the results compared with the Chi(2) test with a 95% confidence interval.

RESULTS

A total of 6453 children were included: 2036 had a positive diagnosis of tropical endemic limboconjunctivitis, with a frequency of 31.55%. The mean age was 6.5 years. The 1- to 4-year-old age group had the highest number of patients, with a frequency of 33.25%. There were 1120 males (55%). Itching was the most frequent complaint encountered in 60.90% of the patients. Ocular involvement was always bilateral. Tropical endemic limboconjunctivitis is an allergic conjunctivitis present throughout the year with two peaks in March and July.

DISCUSSION

Tropical endemic limboconjunctivitis can be considered an allergic conjunctivitis affecting boys more frequently than girls in warm and dry environments. It is frequent in children less than 5 years old and regresses with age.

CONCLUSION

Tropical endemic limboconjunctivitis is a tropical disease with an intertropical aspect.

Characterization of population structure from the mitochondrial DNA vis-à-vis language and geography in Papua New Guinea

Situated along a corridor linking the Asian continent with the outer islands of the Pacific, Papua New Guinea has long played a key role in understanding the initial peopling of Oceania. The vast diversity in languages and unique geographical environments in the region have been central to the debates on human migration and the degree of interaction between the Pleistocene settlers and newer migrants. To better understand the role of Papua New Guinea in shaping the region's prehistory, we sequenced the mitochondrial DNA (mtDNA) control region of three populations, a total of 94 individuals, located in the East Sepik Province of Papua New Guinea. We analyzed these samples with a large data set of Oceania populations to examine the role of geography and language in shaping population structure within New Guinea and between the region and Island Melanesia. Our results from median-joining networks, star-cluster age estimates, and population genetic analyses show that while highland New Guinea populations seem to be the oldest settlers, there has been significant gene flow within New Guinea with little influence from geography or language. The highest genetic division is between Papuan speakers of New Guinea versus East Papuan speakers located outside of mainland New Guinea. Our study supports the weak language barriers to genetic structuring among populations in close contact and highlights the complexity of understanding the genetic histories of Papua New Guinea in association with language and geography.

[Exophthalmia in children at the African Institute of Tropical Ophthalmology (AITO)]

INTRODUCTION

Exophthalmia is a rare entity. The purpose of this study was to ascertain epidemiological features, clinical aspects, and potential treatment modalities for exophthalmia in children at the University Teaching Hospital- African Institute of Tropical Ophthalmology (UTH-AITO).

PATIENTS AND METHOD

This prospective and descriptive study was carried out from July 2006 to June 2007 at the IOTA-UTH in collaboration with the pediatric hematology and oncology unit of the Gabriel Toure UTH. All patients between the ages of 0 to 15 years who presented unilateral or bilateral exophthalmia whether measurable or not were included. In all cases thorough clinical workup was performed and any appropriate additional examinations were ordered. All data were consigned to a questionnaire.

RESULTS

A total of 46 eyes in 38 children were included, i.e., unilateral right in 15 cases, unilateral left in 15 and bilateral in 8. Mean age was 9.6 years (range, 2 days to 15 years). The male-to-female sex ratio was 1.9:1. The incidence of exophthalmia was 0.3%. Exophthalmia was the reason for seeking medical advice in 68.4% of cases (26 children). Classification according to underlying pathology divided patients into four groups, i.e., inflammatory and/or infectious pathologies in 36.9% (14 cases), tumor pathologies in 31.6% (12 cases), trauma in 13.1% (5 cases) and undetermined in 18.4% (7 cases). A Hertel millimetric regression of exophthalmia was observed in 23.9% of cases (11 eyes) and a gain in visual lines of acuity was observed in 8.7% (4 eyes).

DISCUSSION

Given the normally low frequency of exophthalmia, observation of a 0.3% incidence at a third level reference center warrants alerting of health authorities. Etiological classification was comparable to Crawford's as described by Desjardins. Cellulites (50%) and retinoblastoma (33.3%) were the main causes of exophthalmia.

CONCLUSION

Since exophthalmia can cause loss of vision and even be life-threatening, early diagnosis and treatment is important particularly in children.

Genetic and linguistic coevolution in Northern Island Melanesia

Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may emphasize more ancient demographic events, including population splits associated with the early colonization of major world regions.

The coevolution of genes and languages has been a subject of enduring interest among geneticists and linguists. Progress has been limited by the available data and by the methods employed to compare patterns of genetic and linguistic variation. Here, we use high-quality data and novel methods to test two models of genetic and linguistic coevolution in Northern Island Melanesia, a region known for its complex history and remarkable biological and linguistic diversity. The first model predicts that congruent genetic and linguistic trees formed following serial population splits and isolation that occurred early in the settlement history of the region. The second model emphasizes the role of post-settlement exchange among neighboring groups in determining genetic and linguistic affinities. We rejected both models for the larger region, but found strong evidence for the post-settlement exchange model in the rugged interior of its largest island, where people have maintained close ties to their ancestral lands. The exchange (particularly genetic exchange) has obscured but not completely erased signals of early migrations into Island Melanesia, and such exchange has probably obscured early prehistory within other regions. In contrast, local exchange is less likely to have obscured evidence of population history at larger geographic scales.

Melanesian mtDNA complexity

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at ∼30–50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval ∼3,500–8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved.

Unexpected NRY chromosome variation in Northern Island Melanesia

To investigate the paternal population history of populations in Northern Island Melanesia, 685 paternally unrelated males from 36 populations in this region and New Guinea were analyzed at 14 regionally informative binary markers and 7 short tandem repeat (STR) loci from the nonrecombining portion of the Y chromosome. Three newly defined binary markers (K6-P79, K7-P117, and M2-P87) aided in identifying considerable heterozygosity that would have otherwise gone undetected. Judging from their geographic distributions and network analyses of their associated STR profiles, 4 lineages appear to have developed in this region and to be of considerable age: K6-P79, K7-P117, M2-P87, and M2a-P22. The origins of K5-M230 and M-M4 are also confirmed as being located further west, probably in New Guinea. In the 25 adequately sampled populations, the number of different haplogroups ranged from 2 in the single most isolated group (the Aita of Bougainville), to 9, and measures of molecular diversity were generally not particularly low. The resulting pattern contradicts earlier findings that suggested far lower male-mediated diversity and gene exchange rates in the region. However, these earlier studies had not included the newly defined haplogroups. We could only identify a very weak signal of recent male Southeast Asian genetic influence (<10%), which was almost entirely restricted to Austronesian (Oceanic)-speaking groups. This contradicts earlier assumptions on the ancestral composition of these groups and requires a revision of hypotheses concerning the settlement of the islands of the central Pacific, which commenced from this region.

Skin and hair pigmentation variation in Island Melanesia

Skin and hair pigmentation are two of the most easily visible examples of human phenotypic variation. Selection-based explanations for pigmentation variation in humans have focused on the relationship between melanin and ultraviolet radiation, which is largely dependent on latitude. In this study, skin and hair pigmentation were measured as the melanin (M) index, using narrow-band reflectance spectroscopy for 1,135 individuals from Island Melanesia. Overall, the results show remarkable pigmentation variation, given the small geographic region surveyed. This variation is discussed in terms of differences between males and females, among islands, and among neighborhoods within those islands. The relationship of pigmentation to age, latitude, and longitude is also examined. We found that male skin pigmentation was significantly darker than females in 5 of 6 islands examined. Hair pigmentation showed a negative, but weak, correlation with age, while skin pigmentation showed a positive, but also weak, correlation with age. Skin and hair pigmentation varied significantly between islands as well as between neighborhoods within those islands. Bougainvilleans showed significantly darker skin than individuals from any other island considered, and are darker than a previously described African-American population. These findings are discussed in relation to prevailing hypotheses about the role of natural selection in shaping pigmentation variation in the human species, as well as the role of demographic processes such as admixture and drift in Island Melanesia.

Ancient mitochondrial M haplogroups identified in the Southwest Pacific

Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize three formerly unresolved branches of macrohaplogroup M that we call haplogroups M27, M28, and M29. Our 1,399 mtDNA control region sequences and a literature search indicate these haplogroups have extremely limited geographical distributions. Their coding region variation suggests diversification times older than the estimated date for the initial settlement of Northern Island Melanesia. This finding indicates that they were among the earliest mtDNA variants to appear in these islands or in the ancient continent of Sahul. These haplogroups from Northern Island Melanesia extend the existing schema for macrohaplogroup M, with many independent branches distributed across Asia, East Africa, Australia, and Near Oceania.

Expanding Southwest Pacific Mitochondrial Haplogroups P and Q

Modern humans have occupied New Guinea and the nearby Bismarck and Solomon archipelagos of Island Melanesia for at least 40,000 years. Previous mitochondrial DNA (mtDNA) studies indicated that two common lineages in this region, haplogroups P and Q, were particularly diverse, with the coalescence for P considered significantly older than that for Q. In this study, we expand the definition of haplogroup Q so that it includes three major branches, each separated by multiple mutational distinctions (Q1, equivalent to the earlier definition of Q, plus Q2 and Q3). We report three whole-mtDNA genomes that establish Q2 as a major Q branch. In addition, we describe 314 control region sequences that belong to the expanded haplogroups P and Q from our Southwest Pacific collection. The coalescence dates for the largest P and Q branches (P1 and Q1) are similar to each other (approximately 50,000 years old) and considerably older than prior estimates. Newly identified Q2, which was found in Island Melanesian samples just to the east, is somewhat younger by more than 10,000 years. Our coalescence estimates should be more reliable than prior ones because they were based on significantly larger samples as well as complete mtDNA-coding region sequencing. Our estimates are roughly in accord with the current suggested dates for the first settlement of New Guinea-Sahul. The phylogeography of P and Q indicates almost total (female) isolation of ancient New Guinea-Island Melanesia from Australia that may have existed from the time of the first settlement. While Q subsequently diversified extensively in New Guinea-Island Melanesia, it has not been found in Australia. The only shared mtDNA haplogroup between Australia and New Guinea identified to date remains one minor branch of P.

New JC virus (JCV) genotypes from papua new guinea and micronesia (type 8 and type 2E) and evolutionary analysis of 32 complete JCV genomes

The JC virus (JCV) is a ubiquitous human polyomavirus that frequently resides in the kidneys of healthy individuals and is excreted in the urine of a large percentage of the population. Geographic-specific JCV variants, isolated from urine and from brain of progressive multifocal leukoencephalopathy (PML) patients, have been grouped into seven distinct genotypes based on whole genome analysis and by individual polymorphic nucleotides (typing sites) in the VP1 coding region. Mutations in the archetypal regulatory region, sometimes consisting of deletions and/or duplications, are also useful taxonomic characters for further characterizing and subdividing genotypes. Investigation of JCV variation in Papua New Guinea (PNG) revealed three distinct variants called PNG- 1, PNG-2, and PNG-3. These variants exhibited consistent coding region and regulatory region mutations. Evolutionary analysis of 32 complete JCV genomes including six new viral genomes from the western Pacific suggests that the new PNG JCV variants are closely associated with the broad group of Type 2 strains of JCV found throughout Asia, forming a monophyletic group with the Northeast Asian strains (Type 2A). Within the Type 2 clade, however, the PNG JCV variants cluster as two distinct groups and are therefore described here as new JCV genotypes designated Type 2E and Type 8.

Human polyomavirus JC variants in Papua New Guinea and Guam reflect ancient population settlement and viral evolution

The peopling of the Pacific was a complex sequence of events that is best reconstructed by reconciling insights from various disciplines. Here we analyze the human polyomavirus JC (JCV) in Highlanders of Papua New Guinea (PNG), in Austronesian-speaking Tolai people on the island of New Britain, and in nearby non-Austronesian-speaking Baining people. We also characterize JCV from the Chamorro of Guam, a Micronesian population. All JCV strains from PNG and Guam fall within the broad Asian group previously defined in the VP1 gene as Type 2 or Type 7, but the PNG strains were distinct from both genotypes. Among the Chamorro JCV samples, 8 strains (Guam-1) were like the Type 7 strains found in Southeast Asia, while nine strains (Guam-2) were distinct from both the mainland strains and most PNG strains. We identified three JCV variants within Papua New Guinea (PNG-1, PNG-2 and PNG-3), but none of the Southeast Asian (Type 7) strains. PNG-1 strains were present in all three populations (Highlanders and the Baining and Tolai of New Britain), but PNG-2 strains were restricted to the Highlanders. Their relative lack of DNA sequence variation suggests that they arose comparatively recently. The single PNG-3 strain, identified in an Austronesian-speaking Tolai individual, was closely related to the Chamorro variants (Guam-2), consistent with a common Austronesian ancestor. In PNG-2 variants a complex regulatory region mutation inserts a duplication into a nearby deletion, a change reminiscent of those seen in the brains of progressive multifocal leukoencephalopathy patients. This is the first instance of a complex JCV rearrangement circulating in a human population.

A novel JC virus variant found in the Highlands of Papua New Guinea has a 21-base pair deletion in the agnoprotein gene

OBJECTIVES

This paper describes a unique JC virus (JCV) variant recovered from the Highlands of Papua New Guinea that contains an inframe 21-bp deletion in the agnoprotein gene. We characterize the mutation and suggest possible roles for the deletion in JCV evolution.

STUDY DESIGN/METHODS

JCV DNA was extracted from urine and polymerase chain reaction (PCR) amplified using whole genome primers. PCR products were cloned, and multiple clones were sequenced. The JCV agnogene was PCR amplified to verify the presence of the agnogene deletion.

RESULTS

This mutation creates a 21-bp deletion near the 3' end, which alters the predicted secondary structure of the messenger RNA and changes local codon usage at the 3' end of the agnogene. Protein secondary structure predictions suggest the deleted portion of the agnoprotein may be a flexible surface feature.

CONCLUSIONS

We describe the first stable coding region deletion in JCV that presumably signifies a single evolutionary event that led to the split from other Highlands viral groups and occurred well after the human expansions that led to the peopling of the Southwest Pacific.

Occurrence of the erythrocyte band 3 (AE1) gene deletion in relation to malaria endemicity in Papua New Guinea

South-east Asian ovalocytosis status was determined in 1629 individuals originating from 12 different geographical areas of Papua New Guinea, representing different ethnic groups and degrees of malaria endemicity. This was achieved by using polymerase chain reaction amplification to demonstrate a 27 base pair deletion in the erythrocyte band 3 (AE1) gene. By using this method, the prevalence of erythrocyte band 3 gene deletion was determined to range from zero in both the lowland inland area of Wosera, East Sepik Province and the highland region of Goroka, Eastern Highlands Province to 35% on the north coast of Madang Province. In general, the prevalence correlated well with altitude, being highest on the coast where malaria transmission is high, intermediate in the lowlands, and lowest in the non-malarious highlands. However, Wosera, a lowland area in the Sepik River Plains, which is hyperendemic for malaria, was an exception in that no ovalocytosis was detected. These results largely confirm the prevalence rates that have been reported in the past using microscopy. In keeping with the autosomal dominant mode of inheritance, the male:female ratio was 1.02 and no homozygote was detected, indicating that homozygosity for the ovalocytosis band 3 gene deletion is lethal.

Modernity and obesity in coastal and Highland Papua New Guinea

OBJECTIVE

To investigate the association between individual degree of modernization and obesity in Papua New Guineans using a score of relative 'modernity'.

DESIGN

Cross-sectional survey in six populations with varying degrees of modernity. Independent effects of modernity score, components of modernity score, age and physical activity were assessed in relation to general obesity (body mass index (BMI)) and body fat distribution (waist-hip ratio (WHR)). A sub-study of the relationship between diet and modernity was also performed.

SETTING

Population-based samples of subjects in three Highland and three coastal locations in the developing country of Papua New Guinea (PNG).

SUBJECTS

1877 subjects > or = 25 years of age attended the survey.

MEASUREMENTS

Age, physical activity, BMI, WHR, 2-h oral glucose tolerance test, and modernity score, based on area of origin, father's employment, type and duration of individual's employment, education, years in an urban centre, housing type and spouse score.

RESULTS

More modern subjects had higher mean BMI and lower levels of physical activity, and mean WHR also varied with modernity in men but not women. In linear regression analysis, total modernity score was significantly associated with both BMI and WHR in men and women, independently of age and physical activity. When components of the modernity score were examined, younger age, more sophisticated housing and increasing number of years in an urban centre were independently associated with BMI in men and women, while education level and reduced physical activity were also significant predictors in men. Associations with WHR were weaker. Results of the dietary sub-study suggested that the lowest energy and nutrient intakes occurred in the least modern men and women.

CONCLUSION

Aspects of modernity, such as more sophisticated housing and greater number of years spent in an urban centre, may be markers of higher income and increasing adoption of Western ways, which in turn are associated with physical inactivity and increased availability of energy-dense Western food, thus promoting obesity in this rapidly developing Pacific nation.

Altitude, language, and class I HLA allele frequencies in Papua New Guinea

Class I HLA gene frequencies show considerable variation over short geographical distances in Papua New Guinea. Hypothesis to account for this invoke natural selection, population structure, the pattern of population movement, or past demographic changes. To determine the role of the various factors in shaping this distribution, we have studied correlations between HLA-based genetic distances, geographical distances, altitude, and linguistic differences in Papua New Guinea. Linguistic differences at the family or stock level within the Trans-New Guinea Phylum generally correspond to genetic differences. However, on the basis of their HLA gene frequencies, speakers of Austronesian (AN) languages do not form a distinct group of populations. Linguistic variation and spatial autocorrelation do not fully account for the altitudinal cline differences noted in gene frequencies, particularly at the HLA-A locus. We propose that the distribution of HLA gene frequencies in Papua New Guinea is partially under the control of selection operating differentially along the altitude gradient.

Extraordinary prevalence of non-insulin-dependent diabetes mellitus and bimodal plasma glucose distribution in the Wanigela people of Papua New Guinea

OBJECTIVE

To determine the current prevalence of impaired glucose tolerance (IGT) and non-insulin-dependent diabetes mellitus (NIDDM) in Melanesians of three coastal Papua New Guinean communities, to relate this to previous studies, and to investigate plasma glucose distributions in these populations.

DESIGN

Cross-sectional survey, using 75 g oral glucose tolerance tests and World Health Organization criteria.

SETTING

Rural Papuan villages of Wanigela and Kalo, and Wanigela people of the urban squatter settlement of Koki, Port Moresby.

SUBJECTS

All adults aged 25 years or more living in the three communities were eligible, with response rates of 77.2% (Koki), 88.1% (Wanigela) and 72.5% (Kalo).

MAIN OUTCOME MEASURES

Prevalence of abnormal glucose tolerance, risk factor levels, fasting and two-hour plasma glucose concentration.

RESULTS

Age-standardised prevalence of NIDDM in Koki Wanigelas was 27.5% in men and 33.0% in women; an additional 20.5% of men and 22.0% of women had IGT. Even in the youngest age group (25-34 years), 36.5% of subjects had abnormal glucose tolerance. The overall prevalences of NIDDM and IGT in rural Wanigelas were 11.7% and 17.0% respectively. In Kalo both were uncommon. The prevalences of IGT and NIDDM in Koki had doubled over a 14-year period. The age-standardised prevalence of abnormal glucose tolerance in the Koki Wanigelas is the second highest in the world after the Arizona Pima Indians, and higher than in Micronesian Nauruans, even though the latter are more obese. Both fasting and two-hour glucose concentrations in all age groups in Koki were clearly bimodal, a mixture of two log-normal distributions.

CONCLUSIONS

The Wanigela people of Papua New Guinea have an extra-ordinary susceptibility to glucose intolerance which is exposed after adoption of modern lifestyle habits. A "founder effect" may explain the high frequency of a diabetogenic genotype in this population.

Glucose tolerance in Papua New Guinea: comparison of Austronesian and non-Austronesian communities of Karkar Island

Epidemiological studies in Pacific populations have suggested a relationship between glucose tolerance and proportional Austronesian genetic admixture, with non-Austronesian Melanesians relatively free of glucose intolerance. However, a survey conducted in 1985 demonstrated the apparent emergence of glucose intolerance in a peri-urban non-Austronesian community, casting doubt on this hypothesis. In 1986 glucose tolerance was studied in three village communities on Karkar Island, Papua New Guinea. Two were of Austronesian and one was of non-Austronesian genetic ancestry. Prevalence of diabetes was low in all communities. However, prevalence of impaired glucose tolerance (IGT) was 7% in the more developed Austronesian community, as compared with 2% in the equivalent non-Austronesian group (p less than 0.05). Multiple regression analysis demonstrated not only a highly significant association between 2-h plasma glucose and insulin concentrations (p less than 0.001), but also that for a given value of plasma insulin, 2-h plasma glucose values were lower for non-Austronesian than for Austronesian subjects (males, p less than 0.05, females, p less than 0.01). However, average plasma insulin concentrations were relatively high in the non-Austronesian community, despite lower average plasma glucose concentrations.

HLA-B27, arthritis and spondylitis in an isolated community in Papua New Guinea

Rheumatic complaints in a sample of 109 individuals from an isolated community in Papua New Guinea were documented and 92/109 were tissue typed for HLA-B27. Eleven (10.1%) subjects had active peripheral arthritis, but 38 (34.9%) had previously suffered an episode of arthritis. In those with current peripheral arthritis, 6/10 (60%) were HLA-B27 positive compared to 15/58 (25.9%) with no history of arthritis (P less than 0.05). In total, 16/34 (47.1%) with either current or a previous history of peripheral arthritis were HLA-B27 positive compared to the 15/58 (25.9%) with no history of arthritis (P less than 0.05). Back pain was common. In 84/109 individuals the cause was mechanical injury; 24/72 (33.3%) of these were HLA-B27 positive. Ankylosing spondylitis was identified in one HLA-B27-negative woman.

Multiple colonization of the upper respiratory tract of Papua New Guinea children with Haemophilus influenzae and Streptococcus pneumoniae

Nasal secretions from Papua New Guinea children were cultured using selective agents, to determine the prevalence of multiple colonization for both S. pneumoniae and H. influenzae. 29.5% of 156 and 53% of 93 carriage positive subjects harbored more than one type of S. pneumoniae and H. influenzae respectively. Of 95 strains of pneumococci isolated from multiply colonized children, 40% were relatively resistant to benzylpenicillin. In more than one half of the children in this group both penicillin sensitive and resistant serotypes coexisted. Significantly more penicillin resistant pneumococci were isolated from children with ready access to primary and regional health care services. Among H. influenzae the prevalence of multiple isolations due to nonencapsulated variants only, and encapsulated plus nonencapsulated organisms was similar. The commonest biotypes were types I, II, III and V, and each was similarly associated with multiple carriage.

Glucose tolerance in Papua New Guinea: ethnic differences, association with environmental and behavioural factors and the possible emergence of glucose intolerance in a highland community

That Melanesians of non-Austronesian genetic ancestry may be relatively resistant to glucose intolerance was supported by the results of a study of two semitraditional non-Austronesian villages in the Papua New Guinean highlands in 1983, in which an absence of diabetes and a high degree of glucose tolerance and insulin sensitivity were observed. The second of this series of surveys was conducted in 1985 in three non-traditional communities: a periurban, non-Austronesian village in the highlands, and rural and periurban Austronesian villages in coastal locations. Although an absence of diabetes was demonstrated once again in the highlanders, these periurban subjects showed an unexpectedly high insulin response which may be a precursor of glucose intolerance. The notion that highland communities that are living in non-traditional circumstances in Papua New Guinea presently are in "metabolic transition" towards diabetes and other non-communicable diseases, if correct, is of importance to the public health of the nation. In the periurban, coastal-dwelling Austronesians, diabetes with severe hyperglycaemia was demonstrated, and there was some evidence of a secular trend towards increasing glucose intolerance. The two-hour plasma glucose concentrations were shown to be associated with obesity, modernity and Seventh-Day Adventist religious persuasion. However, important and unexplained differences in glucose tolerance remained between rural and periurban coastal dwellers after taking these factors into account.

Immunogenetic studies of two recently contacted populations from Papua New Guinea

We have examined the HLA profiles of the Hagahai and the Haruai people, two linguistic groups in the remote western Schrader mountains who have only recently had administrative contact, and compared them with those of other populations in Papua New Guinea. None of the antigens detected in the two groups was found missing in other populations although significant differences in allele frequencies exist. Recent contact history does not appear to have played any significant role in shaping these differences. Similarly, no evidence of differential selection pressures contributing to HLA heterogeneity was found. The genetic profiles of the Hagahai and the Haruai appear to be a result of recent admixture between unrelated, genetically disparate groups.

Family resemblance for glucose tolerance in a Melanesian population, the Tolai

Path analysis of family resemblance for plasma glucose concentration, 2 h after an oral glucose challenge, failed to detect significant genetic heritability. There were no intergenerational differences and marital resemblance was moderate. Over one-third of sibling environmental similarity was due to non-inherited factors. Cultural inheritance was very strong, tending to mimic genetic inheritance, and cultural heritability was considerable. Measures of obesity were included in the environmental index, an estimate of familial environment, in this analysis, for comparability with previous studies. Since obesity appears, in part, to be a heritable trait, in future studies a bivariate approach to family resemblance for both glucose tolerance and obesity could yield important additional insight.

Antigen and haplotype frequencies at three human leucocyte antigen loci (HLA-A, -B, -C) in the Pawaia of Papua New Guinea

The genetic profile of the Pawaia, a seminomadic, linguistic isolate from the highlands fringe of Papua New Guinea, is described in terms of antigen and haplotype frequencies at three class I human leucocyte antigen loci (HLA-A, -B, and -C). The Pawaia, like other Papua New Guinea populations, exhibit restricted polymorphisms at all three loci studied, both in the number of alleles segregating and in the level of average heterozygosity. An extremely high frequency (52.9%) of HLA-B27, the antigen implicated in the pathogenesis of seronegative arthropathies, was found. A novel HLA-C locus specificity, CNG, resulting probably from a gene duplication event, was also observed in significant numbers. Although the gene frequency comparisons suggest their strong affinities with the highlanders, the Pawaia haplotypes reveal significant admixture from other neighbouring groups as well. The usefulness of HLA haplotypes in tracing the movements of human populations in the New Guinea area is discussed.

High prevalence of the haplotype HLA-A11, B27 in arthritis patients from the highlands of Papua New Guinea

The haplotype HLA-A11, B27 is present in significantly increased numbers in arthritis patients, over and above the numbers expected from its relative proportion in B27-positive healthy controls, from the highlands of Papua New Guinea.

Colonisation of Haemophilus influenzae and Streptococcus pneumoniae in the upper respiratory tract of neonates in Papua New Guinea: primary acquisition, duration of carriage, and relationship to carriage in mothers

In order to determine the age of acquisition and duration of carriage of the first strains of Haemophilus influenzae and Streptococcus pneumoniae in the upper respiratory tract of Papua New Guinea children, 25 babies were recruited at, or shortly after birth. Nasal secretions from mothers and children were cultured at 1- to 2-weekly intervals. H. influenzae and S. pneumoniae were acquired within the neonatal period by 60% of the infants, and all were colonised by both organisms within the first 3 months of life. Carriage periods for H. influenzae ranged from 6 to 221 days (mean, 74 days), and for S. pneumoniae from 5 to 290 days (mean, 96 days). Penicillin resistance was detected in 36% of the first acquired strains of pneumococci. Mothers, generally either did not carry H. influenzae or S. pneumoniae, or harboured types different to those first acquired by their infants. However, one-third of mothers subsequently became colonised with H. influenzae and S. pneumoniae types similar to those carried by their babies.

Respiratory impairment in coffee factory workers in the Asaro Valley of Papua New Guinea

In a coffee growing area of Papua New Guinea, a developing country in the western Pacific region, coffee factory workers were found to have more chronic symptomatic respiratory impairment than a carefully matched group of neighbouring villagers. This impairment was not related to their duration of employment. Coffee factory workers were found also to have a greater prevalence of reversible but asymptomatic airways obstruction on entering their factories after two days off duty than a group of soft drink factory workers. These findings are thought to be related to exposure to the dust produced in large quantities during coffee processing.

HLA-A,B,C and DR antigens in Asaro speakers of Papua New Guinea

The HLA profile of the Asaro speakers of Papua New Guinea exhibits restricted polymorphisms. Antigens like AW24, MT1, and MB1 were present in almost every individual assayed. A CW6-related antigen and a DR locus antigen FT19 (a split of DRW6), not previously found in Pacific populations, were observed in a significant number of individuals. Ancestral HLA-B,C haplotypic combinations, such as B13, CW4 and BW60,CW3, were frequently found. Preliminary evidence is provided for an association between BW62 and CW65 in this population. The observed distributions of multiple-locus heterozygosities are similar to those expected under the null hypothesis of linkage equilibrium. The results indicate that the Asaro, among other highland populations, have been isolated long enough for pre-existing linkage disequilibria at recombinational distances of 0.8% or more (such as occur with HLA-A,B and HLA-B,DR haplotypes) to have broken down.