Molecular Characterization of Dengue Type 2 Outbreak in Pacific Islands Countries and Territories, 2017-2020.
ABSTRACT: Dengue virus (DENV) serotype-2 was detected in the South Pacific region in 2014 for the first time in 15 years. In 2016-2020, DENV-2 re-emerged in French Polynesia, Vanuatu, Wallis and Futuna, and New Caledonia, co-circulating with and later replacing DENV-1. In this context, epidemiological and molecular evolution data are paramount to decipher the diffusion route of this DENV-2 in the South Pacific region. In the current work, the E gene from 23 DENV-2 serum samples collected in Vanuatu, Fiji, Wallis and Futuna, and New Caledonia was sequenced. Both maximum likelihood and Bayesian phylogenetic analyses were performed. While all DENV-2 strains sequenced belong to the Cosmopolitan genotype, phylogenetic analysis suggests at least three different DENV-2 introductions in the South Pacific between 2017 and 2020. Strains retrieved in these Pacific Islands Countries and Territories (PICTs) in 2017-2020 are phylogenetically related, with strong phylogenetic links between strains retrieved from French PICTs. These phylogenetic data substantiate epidemiological data of the DENV-2 diffusion pattern between these countries.
Project description:Deep-sea fisheries provide an important source of protein to Pacific Island countries and territories that are highly dependent on fish for food security. However, spatial management of these deep-sea habitats is hindered by insufficient data. We developed species distribution models using spatially limited presence data for the main harvested species in the Western Central Pacific Ocean. We used bathymetric and water temperature data to develop presence-only species distribution models for the commercially exploited deep-sea snappers Etelis Cuvier 1828, Pristipomoides Valenciennes 1830, and Aphareus Cuvier 1830. We evaluated the performance of four different algorithms (CTA, GLM, MARS, and MAXENT) within the BIOMOD framework to obtain an ensemble of predicted distributions. We projected these predictions across the Western Central Pacific Ocean to produce maps of potential deep-sea snapper distributions in 32 countries and territories. Depth was consistently the best predictor of presence for all species groups across all models. Bathymetric slope was consistently the poorest predictor. Temperature at depth was a good predictor of presence for GLM only. Model precision was highest for MAXENT and CTA. There were strong regional patterns in predicted distribution of suitable habitat, with the largest areas of suitable habitat (> 35% of the Exclusive Economic Zone) predicted in seven South Pacific countries and territories (Fiji, Matthew & Hunter, Nauru, New Caledonia, Tonga, Vanuatu and Wallis & Futuna). Predicted habitat also varied among species, with the proportion of predicted habitat highest for Aphareus and lowest for Etelis. Despite data paucity, the relationship between deep-sea snapper presence and their environments was sufficiently strong to predict their distribution across a large area of the Pacific Ocean. Our results therefore provide a strong baseline for designing monitoring programs that balance resource exploitation and conservation planning, and for predicting future distributions of deep-sea snappers.
Project description:Dengue virus (DENV) is the arbovirus with the highest incidence in New Caledonia and in the South Pacific region. In 2012-2014, a major DENV-1 outbreak occurred in New Caledonia. The only known vector of DENV in New Caledonia is Aedes aegypti but no study has yet evaluated the competence of New Caledonia Ae. aegypti populations to transmit DENV. This study compared the ability of field-collected Ae. aegypti from different locations in New Caledonia to transmit the DENV-1 responsible for the 2012-2014 outbreak. This study also aimed to compare the New Caledonia results with the vector competence of Ae. aegypti from French Polynesia as these two French countries have close links, including arbovirus circulation.Three wild Ae. aegypti populations were collected in New Caledonia and one in French Polynesia. Female mosquitoes were orally exposed to DENV-1 (106 FFU/ml). Mosquito bodies (thorax and abdomen), heads and saliva were analyzed to measure infection, dissemination, transmission rates and transmission efficiency, at 7, 14 and 21 days post-infection (dpi), respectively.DENV-1 infection rates were heterogeneous, but dissemination rates were high and homogenous among the three Ae. aegypti populations from New Caledonia. Despite this high DENV-1 dissemination rate, the transmission rate, and therefore the transmission efficiency, observed were low. Aedes aegypti population from New Caledonia was less susceptible to infection and had lower ability to transmit DENV-1 than Ae. aegypti populations from French Polynesia.This study suggests that even if susceptible to infection, the New Caledonian Ae. aegypti populations were moderately competent vectors for DENV-1 strain from the 2012-2014 outbreak. These results strongly suggest that other factors might have contributed to the spread of this DENV-1 strain in New Caledonia and in the Pacific region.
Project description:The epidemiology of dengue in the South Pacific has been characterized by transmission of a single dominant serotype for 3-5 years, with subsequent replacement by another serotype. From 2001 to 2008 only DENV-1 was reported in the Pacific. In 2008, DENV-4 emerged and quickly displaced DENV-1 in the Pacific, except in New Caledonia (NC) where DENV-1 and DENV-4 co-circulated in 2008-2009. During 2012-2013, another DENV-1 outbreak occurred in NC, the third DENV-1 outbreak in a decade. Given that dengue is a serotype-specific immunizing infection, the recurrent outbreaks of a single serotype within a 10-year period was unexpected.This study aimed to inform this phenomenon by examining the phylogenetic characteristics of the DENV-1 viruses in NC and other Pacific islands between 2001 and 2013. As a result, we have demonstrated that NC experienced introductions of viruses from both the Pacific (genotype IV) and South-east Asia (genotype I). Moreover, whereas genotype IV and I were co-circulating at the beginning of 2012, we observed that from the second half of 2012, i.e. during the major DENV-1 outbreak, all analyzed viruses were genotype I suggesting that a genotype switch occurred.Repeated outbreaks of the same dengue serotype, as observed in NC, is uncommon in the Pacific islands. Why the earlier DENV-1 outbreaks did not induce sufficient herd immunity is unclear, and likely multifactorial, but the robust vector control program may have played a role by limiting transmission and thus maintaining a large susceptible pool in the population.
Project description:When dealing with the taxonomy of Pacific coastal species within the region of New Caledonia and Vanuatu, one should examine all names published in Australasia and other Pacific islands. When the putative new species is also closely related to a highly praised ornamental species with many cultigens and with many old horticultural names, the task becomes more arduous. This is the case for the new species we describe as Pseuderanthemum melanesicum Gâteblé, Ramon & Butaud, which is closely related to the now pantropical cultivated species P. carruthersii (Seem.) Guillaumin s.l. Compared to P. carruthersii, P. melanesicum has carnose and shiny leaves, pedicels and sepals covered with glandular hairs, a short and enlarged corolla tube and can produce fertile capsules. The new species is a coastal taxon occurring naturally in the Melanesian archipelagos of New Caledonia and Vanuatu. This species seems uncommon in the Loyalty Islands but more common in the archipelago of Vanuatu and we propose it as Critically Endangered in New Caledonia, Vulnerable in Vanuatu and Least Concern when the IUCN evaluation is done globally.
Project description:Several studies have investigated antimicrobial resistance in low- and middle-income countries, but to date little attention has been paid to the Pacific Islands Countries and Territories (PICTs). This study aims to review the literature on antibiotic resistance (ABR) in healthcare settings in PICTs to inform further research and future policy development for the region. Following the PRISMA-ScR checklist health databases and grey literature sources were searched. Three reviewers independently screened the literature for inclusion, data was extracted using a charting tool and the results were described and synthesised. Sixty-five studies about ABR in PICTs were identified and these are primarily about New Caledonia, Fiji and Papua New Guinea. Ten PICTs contributed the remaining 21 studies and nine PICTs were not represented. The predominant gram-positive pathogen reported was community-acquired methicillin resistant S. aureus and the rates of resistance ranged widely (>50% to <20%). Resistance reported in gram-negative pathogens was mainly associated with healthcare-associated infections (HCAIs). Extended spectrum beta-lactamase (ESBL) producing K. pneumoniae isolates were reported in New Caledonia (3.4%) and Fiji (22%) and carbapenem resistant A. baumannii (CR-ab) isolates in the French Territories (24.8%). ABR is a problem in the PICTs, but the epidemiology requires further characterisation. Action on strengthening surveillance in PICTs needs to be prioritised so strategies to contain ABR can be fully realised.
Project description:A new species of fiddler crab, <i>Austruca citrus</i> n. sp. from Fiji, Wallis & Futuna, and Samoa, in the South Pacific is described based on morphological and molecular evidence. This species is closely related to <i>Austruca perplexa</i> (H. Milne Edwards, 1852), but can be distinguished by a suite of characters, including adult size, carapace morphology, shape and coloration of the major chela, the ratio of major pollex length as a function of carapace width, and male first gonopod form. The molecular evidence of the mitochondrial 16S rDNA and cytochrome oxidase subunit I (<i>COI</i>) supports these morphological differences.
Project description:<h4>Background</h4>Human T-Lymphotropic Virus type 1 (HTLV-1) is endemic among people of Melanesian descent in Papua New Guinea, Solomon Islands and Vanuatu, and in Indigenous populations from Central Australia. Molecular studies revealed that these Australo-Melanesian strains constitute the highly divergent HTLV-1c subtype. New Caledonia is a French overseas territory located in the Southwest Pacific Ocean. HTLV-1 situation is poorly documented in New Caledonia and the molecular epidemiology of HTLV-1 infection remains unknown.<h4>Objectives</h4>Studying 500 older adults Melanesian natives from New Caledonia, we aim to evaluate the HTLV-1 seroprevalence and to molecularly characterize HTLV-1 proviral strains.<h4>Study design</h4>Plasma from 262 men and 238 females (age range: 60-96 years old, mean age: 70.5) were screened for anti-HTLV-1 antibodies by particle agglutination (PA) and indirect immunofluorescence assay (IFA). Serological confirmation was obtained using Western blot assay. DNAs were extracted from peripheral blood buffy coat of HTLV-1 seropositive individuals, and subjected to four series of PCR (LTR-gag; pro-pol; pol-env and tax-LTR). Primers were designed from highly common conserved regions of the major HTLV-1 subtypes to characterize the entire HTLV-1 proviral genome.<h4>Results</h4>Among 500 samples, 3 were PA and IFA positive. The overall seroprevalence was 0.6%. The DNA sample from 1 New Caledonian woman (NCP201) was found positive by PCR and the complete HTLV-1 proviral genome (9,033-bp) was obtained. The full-length HTLV-1 genomic sequence from a native woman from Vanuatu (EM5), obtained in the frame of our previous studies, was also characterized. Both sequences belonged to the HTLV-1c Australo-Melanesian subtype. The NCP201 strain exhibited 0.3% nucleotide divergence with the EM5 strain from Vanuatu. Furthermore, divergence reached 1.1% to 2.9% with the Solomon and Australian sequences respectively. Phylogenetic analyses on a 522-bp-long fragment of the gp21-env gene showed the existence of two major clades. The first is composed of strains from Papua New Guinea; the second includes strains from all neighboring archipelagos (Solomon, Vanuatu, New Caledonia), and Australia. Interestingly, this second clade itself is divided into two sub-clades: strains from Australia on one hand, and strains from Solomon Islands, Vanuatu and New Caledonia on the other hand.<h4>Conclusions</h4>The HTLV-1 seroprevalence (0.6%) in the studied adult population from New Caledonia appears to be low. This seroprevalence is quite similar to the situation observed in Vanuatu and Solomon Islands. However it is very different to the one encountered in Central Australia. Taken together, these results demonstrated that Australo-Melanesia is endemic for HTLV-1 infection with a high diversity of HTLV-1c strains and a clear geographic clustering according to the island of origin of HTLV-1 infected persons.
Project description:Dengue is an expanding arboviral disease of variable severity characterized by the emergence of virus strains with greater fitness, epidemic potential and possibly virulence. To investigate the role of dengue virus (DENV) strain variation on epidemic activity we studied DENV-2 viruses from a series of South Pacific islands experiencing outbreaks of varying intensity and clinical severity. Initially appearing in 1971 in Tahiti and Fiji, the virus was responsible for subsequent epidemics in American Samoa, New Caledonia and Niue Island in 1972, reaching Tonga in 1973 where there was near-silent transmission for over a year. Based on whole-genome sequencing and phylogenetic analysis on 20 virus isolates, Tonga viruses were genetically unique, clustering in a single clade. Substitutions in the pre-membrane (prM) and nonstructural genes NS2A and NS4A correlated with the attenuation of the Tongan viruses and suggest that genetic change may play a significant role in dengue epidemic severity.
Project description:BACKGROUND: Mitochondrial DNA (mtDNA) hypervariable region (HVR) sequences of prehistoric Polynesian chicken samples reflect dispersal of two haplogroups--D and E--by the settlers of the Pacific. The distribution of these chicken haplogroups has been used as an indicator of human movement. Recent analyses suggested similarities between prehistoric Pacific and South American chicken samples, perhaps reflecting prehistoric Polynesian introduction of the chicken into South America. These analyses have been heavily debated. The current distribution of the D and E lineages among contemporary chicken populations in the Western Pacific is unclear, but might ultimately help to inform debates about the movements of humans that carried them. OBJECTIVES: We sought to characterize contemporary mtDNA diversity among chickens in two of the earliest settled archipelagos of Remote Oceania, the Marianas and Vanuatu. METHODS: We generated HVR sequences for 43 chickens from four islands in Vanuatu, and for 5 chickens from Guam in the Marianas. RESULTS: Forty samples from Vanuatu and three from Guam were assigned to haplogroup D, supporting this as a Pacific chicken haplogroup that persists in the Western Pacific. Two haplogroup E lineages were observed in Guam and two in Vanuatu. Of the E lineages in Vanuatu, one was identical to prehistoric Vanuatu and Polynesian samples and the other differed by one polymorphism. Contrary to our expectations, we observed few globally distributed domesticate lineages not associated with Pacific chicken dispersal. This might suggest less European introgression of chickens into Vanuatu than expected. If so, the E lineages might represent lineages maintained from ancient Pacific chicken introductions. The Vanuatu sample might thus provide an opportunity to distinguish between maintained ancestral Pacific chicken lineages and replacement by global domesticates through genomic analyses, which could resolve questions of contemporary haplogroup E chicken relationships and inform interpretations of debated sequences from archaeological samples.
Project description:In French Polynesia, the four serotypes of dengue virus (DENV-1 to -4) have caused 14 epidemics since the mid-1940s. From the end of 2016, an increasing number of Pacific Island Countries and Territories have reported DENV-2 outbreaks and in February 2017, DENV-2 infection was detected in French Polynesia in three travellers from Vanuatu. As DENV-2 has not been circulating in French Polynesia since December 2000, there is high risk for an outbreak to occur.