G. L. Abby Harrison

Changing epidemiology of human parvovirus 4 infection in sub-Saharan Africa

Human parvovirus 4 infections are primarily associated with parenteral exposure in western countries. By ELISA, we demonstrate frequent seropositivity for antibody to parvovirus 4 viral protein 2 among adult populations throughout sub-Saharan Africa (Burkina Faso, 37%; Cameroon, 25%; Democratic Republic of the Congo, 35%; South Africa, 20%), which implies existence of alternative transmission routes.

Phylogeography and epidemic history of hepatitis C virus genotype 4 in Africa

HCV genotype 4 is prevalent in many African countries, yet little is known about the genotype׳s epidemic history on the continent. We present a comprehensive study of the molecular epidemiology of genotype 4. To address the deficit of data from the Democratic Republic of the Congo (DRC) we PCR amplified 60 new HCV isolates from the DRC, resulting in 33 core- and 48 NS5B-region sequences. Our data, together with genotype 4 database sequences, were analysed using Bayesian phylogenetic approaches. We find three well-supported intra-genotypic lineages and estimate that the genotype 4 common ancestor existed around 1733 (1650–1805). We show that genotype 4 originated in central Africa and that multiple lineages have been exported to north Africa since ~1850, including subtype 4a which dominates the epidemic in Egypt. We speculate on the causes of the historical intra-continental spread of genotype 4, including population movements during World War 2.

Merozoite Antigens of Plasmodium falciparum Elicit Strain-Transcending Opsonizing Immunity

ABSTRACT It is unclear whether naturally acquired immunity to Plasmodium falciparum results from the acquisition of antibodies to multiple, diverse antigens or to fewer, highly conserved antigens. Moreover, the specific antibody functions required for malaria immunity are unknown, and hence informative immunological assays are urgently needed to address these knowledge gaps and guide vaccine development. In this study, we investigated whether merozoite-opsonizing antibodies are associated with protection from malaria in a strain-specific or strain-transcending manner by using a novel field isolate and an immune plasma-matched cohort from Papua New Guinea with our validated assay of merozoite phagocytosis. Highly correlated opsonization responses were observed across the 15 parasite strains tested, as were strong associations with protection (composite phagocytosis score across all strains in children uninfected at baseline: hazard ratio of 0.15, 95% confidence interval of 0.04 to 0.63). Opsonizing antibodies had a strong strain-transcending component, and the opsonization of transgenic parasites deficient for MSP3, MSP6, MSPDBL1, or P. falciparum MSP1-19 (PfMSP1-19) was similar to that of wild-type parasites. We have provided the first evidence that merozoite opsonization is predominantly strain transcending, and the highly consistent associations with protection against diverse parasite strains strongly supports the use of merozoite opsonization as a correlate of immunity for field studies and vaccine trials. These results demonstrate that conserved domains within merozoite antigens targeted by opsonization generate strain-transcending immune responses and represent promising vaccine candidates.

Hepatitis E virus infection, Papua New Guinea, Fiji, and Kiribati, 2003-2005.

To the Editor: We report hepatitis E virus (HEV) infection rates in 3 South Pacific island countries—Papua New Guinea (PNG), Fiji, and Kiribati—determined from results of HEV IgG testing. During 2003–2005, specimens were collected from volunteers as part of a study of the epidemiology of viral hepatitis (1,2). Participants recruited were apparently healthy adults in the community and mother–infant pairs (specifically infants who were receiving, or had recently completed, their vaccinations). No specific inclusion/exclusion criteria were applied. Samples were collected from outpatient clinics and hospitals in PNG from Port Moresby, Goroka, Mt Hagen, Madang, and Daru. Samples from Fiji were collected in Suva from outpatient clinics and hospital wards. A proportion of samples from children were taken from nonjaundiced inpatients in PNG and Fiji. In Kiribati, samples were collected from participants at village preschools, vaccination clinics, and outpatient clinics on North Tarawa and North Tabiteuea (2). These were convenience samples and therefore might not be nationally representative cohorts. We obtained ethics permission for the study from appropriate national agencies. Signed informed consent was obtained from each participant or, for children, from a parent or guardian. From this sample pool, in a time sequential manner, the first serum samples were assayed: 545 from PNG (48 Goroka, 99 Mt Hagen, 87 Daru, 47 Madang, 156 Port Moresby), 265 from Fiji, and 238 from Kiribati. We evaluated samples using the Wantai (PE2) HEV IgG ELISA kit (Wantai Pharmaceutical Enterprise, Beijing, China), which detects IgG for all 4 known strains of human HEV. The assays were used according to the manufacturer’s instructions, and repeat equivocal results were defined as negative (3,4). HEV IgG positivity was highest in PNG (15.2%), followed by Kiribati (8.8%) and Fiji (2.2%) (Table). IgG positivity did not differ significantly between adults and children (<16 years of age) (PNG: 16.1% vs. 11.4%, p = 0.23; Kiribati: 6.0% vs. 13.3%, p = 0.06; and Fiji: 1.7% vs. 3.3%, p = 0.42 [Fisher exact test]). Table Seroprevalence of HEV, Papua New Guinea, Fiji, and Kiribati, 2003–2005* To investigate potential parent–child transmission, we tested mother/child (MC); father/child (FC); and when possible, mother/father/child (MFC) sets. We found no transmission association: In PNG, we tested 88 sets (67 MC, 2 MFC, and 19 FC); in Fiji, 29 sets (20 MC and 9 MFC); and in Kiribati, 65 sets (59 MC and 6 MFC); of the 11 PNG, 1 Fijian, and 8 Kiribati HEV IgG–positive children, none had IgG-positive parents. Because these samples were tested retrospectively, ascertaining the HEV IgG status of other family members was not possible. The high percentage of HEV-seropositive children <5 years of age in PNG and Kiribati implies active viral circulation in these countries. This is an unusual finding, compared with findings from seroprevalence studies in developing countries where IgG prevalence increases with age (3). The reason for this difference remains to be determined. It is unlikely to relate to acute HEV infection in hospitalized children sampled because the Wantai assay measures IgG, not IgM. The finding that these young seropositive children commonly have seronegative parents suggests that parent–child transmission is not the primary mechanism of infection in the population studied, which is in accord with published data (4). To investigate whether HEV seropositivity was higher in certain areas, we partitioned the data into regions defined by participant’s place of birth and tribal ethnicity. In Fiji and Kiribati, no significant region association was detected. However, in PNG, the proportion of HEV antibody–positive specimens was greater among participants from highland communities (altitude >1,500 m) than from lowland communities (20.4% vs. 9.7%, p = 0.01). (Port Moresby has a mixed immigrant population and was excluded from this analysis). The reason for the higher proportion of HEV IgG–positive specimens among participants in highland than lowland communities is unclear but might be explained by increased zoonotic transmission. In highland regions, pigs are more frequently kept, and the animals are kept closer to home (5). HEV genotypes 1 and 2 are hyperendemic to many developing countries and typically cause waterborne outbreaks of acute hepatitis in humans (6). Genotypes 3 and 4 are endemic to industrialized countries and are known to be a porcine zoonosis (7). Genotype 3 has been found in pigs in New Caledonia (8). In our investigation of 3 developing nations in Oceania, we found that HEV IgG positivity varies substantially between, and within, countries; it is high in PNG (15.2%) and low in Fiji (2.2%). By using the same sensitive, diagnostic assay, the seroprevalence of HEV in blood donors in New Zealand was reportedly 4% (9). In New Caledonia, 1.7% of 351 military recruits tested positive (10). In our study, the sampling method limits the applicability of the data to the general population. Nevertheless, our findings suggest HEV infection should be considered in cases of unexplained hepatitis.

Higher Complexity of Infection and Genetic Diversity of Plasmodium vivax Than Plasmodium falciparum Across All Malaria Transmission Zones of Papua New Guinea

Plasmodium falciparum and Plasmodium vivax have varying transmission dynamics that are informed by molecular epidemiology. This study aimed to determine the complexity of infection and genetic diversity of P. vivax and P. falciparum throughout Papua New Guinea (PNG) to evaluate transmission dynamics across the country. In 2008-2009, a nationwide malaria indicator survey collected 8,936 samples from all 16 endemic provinces of PNG. Of these, 892 positive P. vivax samples were genotyped at PvMS16 and PvmspF3, and 758 positive P. falciparum samples were genotyped at Pfmsp2. The data were analyzed for multiplicity of infection (MOI) and genetic diversity. Overall, P. vivax had higher polyclonality (71%) and mean MOI (2.32) than P. falciparum (20%, 1.39). These measures were significantly associated with prevalence for P. falciparum but not for P. vivax. The genetic diversity of P. vivax (PvMS16: expected heterozygosity = 0.95, 0.85-0.98; PvMsp1F3: 0.78, 0.66-0.89) was higher and less variable than that of P. falciparum (Pfmsp2: 0.89, 0.65-0.97). Significant associations of MOI with allelic richness (rho = 0.69, P = 0.009) and expected heterozygosity (rho = 0.87, P < 0.001) were observed for P. falciparum. Conversely, genetic diversity was not correlated with polyclonality nor mean MOI for P. vivax. The results demonstrate higher complexity of infection and genetic diversity of P. vivax across the country. Although P. falciparum shows a strong association of these parameters with prevalence, a lack of association was observed for P. vivax and is consistent with higher potential for outcrossing of this species.

Infection frequency of hepatitis C virus and IL28B haplotypes in Papua New Guinea, Fiji, and Kiribati.

It has been estimated that there are more than 60 million Hepatitis C virus (HCV) carriers in the World Health Organisations Western Pacific region (WHO-WPR), where liver cancer is among the top three causes of cancer death. WHO and the US Centres for Disease Control and Prevention report the prevalence of HCV in the South Pacific islands (countries within the WHO-WPR) to be high (5–10% and >2% respectively). However, since HCV is not tested for in many of these countries, there is sparse data available to support this assertion. We screened ∼2000 apparently healthy individuals from Papua New Guinea, Fiji and Kiribati and found a sero-prevalence of 2.0%, 0.1% and 0%, respectively. All sero-positive samples tested negative for HCV RNA. Curious as to why all the sero-positive individuals were negative for HCV-RNA, we also screened them for the HCV protective IL28B SNP markers rs12979860 and rs8099917. All antibody-positive participants bar one had HCV protective haplotypes. Our results suggest that HCV is present in these Pacific island countries, albeit at a prevalence lower than previous estimates. As none of our participants had undergone antiviral treatment, and therefore must have cleared infection naturally, we hypothesise that genotypes 1 and/or 4 are circulating in South Pacific Island people and that these peoples are genetically predisposed to be more likely to spontaneous resolve HCV infection than to become chronic carriers.

Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific

The human malaria parasite Plasmodium vivax is more resistant to malaria control strategies than Plasmodium falciparum, and maintains high genetic diversity even when transmission is low. To investigate whether declining P. vivax transmission leads to increasing population structure that would facilitate elimination, we genotyped samples from across the Southwest Pacific region, which experiences an eastward decline in malaria transmission, as well as samples from two time points at one site (Tetere, Solomon Islands) during intensified malaria control. Analysis of 887 P. vivax microsatellite haplotypes from hyperendemic Papua New Guinea (PNG, n = 443), meso-hyperendemic Solomon Islands (n = 420), and hypoendemic Vanuatu (n = 24) revealed increasing population structure and multilocus linkage disequilibrium yet a modest decline in diversity as transmission decreases over space and time. In Solomon Islands, which has had sustained control efforts for 20 years, and Vanuatu, which has experienced sustained low transmission for many years, significant population structure was observed at different spatial scales. We conclude that control efforts will eventually impact P. vivax population structure and with sustained pressure, populations may eventually fragment into a limited number of clustered foci that could be targeted for elimination.

Nationwide genetic surveillance of Plasmodium vivax in Papua New Guinea reveals heterogeneous transmission dynamics and routes of migration amongst subdivided populations

The Asia Pacific Leaders in Malaria Alliance (APLMA) have committed to eliminate malaria from the region by 2030. Papua New Guinea (PNG) has the highest malaria burden in the Asia-Pacific region but with the intensification of control efforts since 2005, transmission has been dramatically reduced and Plasmodium vivax is now the dominant malaria infection in some parts of the country. To gain a better understanding of the transmission dynamics and migration patterns of P. vivax in PNG, here we investigate population structure in eight geographically and ecologically distinct regions of the country. A total of 219 P. vivax isolates (16-30 per population) were successfully haplotyped using 10 microsatellite markers. A wide range of genetic diversity (He=0.37-0.87, Rs=3.60-7.58) and significant multilocus linkage disequilibrium (LD) was observed in six of the eight populations (IAS=0.08-0.15 p-value<0.05) reflecting a spectrum of transmission intensities across the country. Genetic differentiation between regions was evident (Josts D=0.07-0.72), with increasing divergence of populations with geographic distance. Overall, P. vivax isolates clustered into three major genetic populations subdividing the Mainland lowland and coastal regions, the Islands and the Highlands. P. vivax gene flow follows major human migration routes, and there was higher gene flow amongst Mainland parasite populations than among Island populations. The Central Province (samples collected in villages close to the capital city, Port Moresby), acts as a sink for imported infections from the three major endemic areas. These insights into P. vivax transmission dynamics and population networks will inform targeted strategies to contain malaria infections and to prevent the spread of drug resistance in PNG.

Long-term sustained malaria control leads to inbreeding and fragmentation of Plasmodium vivax populations

Plasmodium vivax populations are more resistant to malaria control strategies than Plasmodium falciparum, maintaining high genetic diversity and gene flow even at low transmission. To quantify the impact of declining transmission on P. vivax populations, we investigated population genetic structure over time during intensified control efforts and over a wide range of transmission intensities and spatial scales in the Southwest Pacific. Analysis of 887 P. vivax microsatellite haplotypes (Papua New Guinea, PNG = 443, Solomon Islands = 420, Vanuatu =24) revealed substantial population structure among countries and modestly declining diversity as transmission decreases over space and time. In the Solomon Islands, which has had sustained control efforts for 20 years, significant population structure was observed on different spatial scales down to the sub-village level. Up to 37% of alleles were partitioned between populations and significant multilocus linkage disequilibrium was observed indicating substantial inbreeding. High levels of haplotype relatedness around households and within a range of 300m are consistent with a focal and clustered infections suggesting that restricted local transmission occurs within the range of vector movement and that subsequent focal inbreeding may be a key factor contributing to the observed population structure. We conclude that unique transmission strategies, including relapse allows P. vivax populations to withstand pressure from control efforts for longer than P. falciparum. However sustained control efforts do eventually impact parasite population structure and with further control pressure, populations may eventually fragment into clustered foci that could be targeted for elimination.The human malaria parasite Plasmodium vivax is resistant to malaria control strategies maintaining high genetic diversity even when transmission is low. To investigate whether declining P. vivax transmission leads to increasing P. vivax population structure that would facilitate elimination, we genotyped samples from a wide range of transmission intensities and spatial scales in the Southwest Pacific, including two time points at one site (Tetere, Solomon Islands) during intensified control. Analysis of 887 P. vivax microsatellite haplotypes from hyperendemic Papua New Guinea (PNG, n = 443), meso-hyperendemic Solomon Islands (n= 420), and hypoendemic Vanuatu (n=24) revealed increasing population structure and multilocus linkage disequilibrium and a modest decline in diversity as transmission decreases over space and time. In Solomon Islands, which has had sustained control efforts for 20 years, and Vanuatu, which has experienced sustained low transmission for many years, significant population structure was observed at different spatial scales. We conclude that control efforts will eventually impact P. vivax population structure and with sustained pressure, populations may eventually fragment into a limited number of clustered foci that could be targeted for elimination.

The Q2 Mitochondrial Haplogroup in Oceania

Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the ‘Melanesian’ contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.