Challenges to implementation and strengthening of initial COVID-19 surveillance in Vanuatu: January-April 2020.

The Pacific island nation of Vanuatu is vulnerable to emerging infectious diseases, including epidemics and pandemics; chronic food and water insecurity; and natural hazards, including cyclones, earthquakes, tsunamis, landslides and flooding. In March 2020, the World Health Organization characterized the outbreak of novel coronavirus disease 2019 (COVID-19) as a global pandemic. By the end of April 2020, Vanuatu had reported no confirmed cases of COVID-19. Data from several sources are collected in Vanuatu's COVID-19 surveillance system to provide an overview of the situation, including data from case investigations and management, syndromic surveillance for influenza-like illness, hospital surveillance and laboratory surveillance. Review of data collected from January to the end of April 2020 suggests that there was no sustained increase in influenza-like illness in the community and no confirmed cases were identified. Lessons learnt from the early implementation of surveillance activities, the changing landscape of laboratory testing and pharmaceutical interventions, as well as the global experience, particularly in other Pacific island countries, will inform the refinement of COVID-19 surveillance activities in Vanuatu.

Molecular Characterization of Dengue Type 2 Outbreak in Pacific Islands Countries and Territories, 2017-2020.

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.

Validation of the easyscreen flavivirus dengue alphavirus detection kit based on 3base amplification technology and its application to the 2016/17 Vanuatu dengue outbreak.

BACKGROUND: The family flaviviridae and alphaviridae contain a diverse group of pathogens that cause significant morbidity and mortality worldwide. Diagnosis of the virus responsible for disease is essential to ensure patients receive appropriate clinical management. Very few real-time RT-PCR based assays are able to detect the presence of all members of these families using a single primer and probe set. We have developed a novel chemistry, 3base, which simplifies the viral nucleic acids allowing the design of RT-PCR assays capable of pan-family identification. METHODOLOGY/PRINCIPAL FINDING: Synthetic constructs, viral nucleic acids, intact viral particles and characterised reference materials were used to determine the specificity and sensitivity of the assays. Synthetic constructs demonstrated the sensitivities of the pan-flavivirus detection component were in the range of 13 copies per PCR. The pan-alphavirus assay had a sensitivity range of 10-25 copies per reaction depending on the viral strain. Lower limit of detection studies using whole virus particles demonstrated that sensitivity for assays was in the range of 1-2 copies per reaction. No cross reactivity was observed with a number of commonly encountered viral strains. Proficiency panels showed 100% concordance with the expected results and the assays performed as well as, if not better than, other assays used in laboratories worldwide. After initial assay validation the pan-viral assays were then tested during the 2016-2017 Vanuatu dengue-2 outbreak. Positive results were detected in 116 positives from a total of 187 suspected dengue samples. CONCLUSIONS/SIGNIFICANCE: The pan-viral screening assays described here utilise a novel 3base technology and are shown to provide a sensitive and specific method to screen and thereafter speciate flavi- and/or alpha- viruses in clinical samples. The assays performed well in an outbreak situation and can be used to detect positive clinical samples containing any flavivirus or alphavirus in approximately 3 hours 30 minutes.