Sample pooling on the Cepheid Xpert® Xpress SARS-CoV-2 assay.

The COVID-19 pandemic has placed unprecedented global demand on laboratory supplies required for testing. Sample pooling has been investigated by laboratories as a strategy to preserve testing capacity. We evaluate the performance of Cepheid Xpert® Xpress SARS-CoV-2 RT-PCR assay for testing samples in pools of 4 and 6. Clinical samples containing SARS-CoV-2, and confirmed negative clinical samples were used to create sample pools. Clinical samples had 'neat' Xpert® E gene cycle threshold values ranging between 20 and 28 and all were detected qualitatively when contained in pools of 4 or 6 samples. For these samples, pooling had a median change in cycle threshold value of 2.0 in pools of 4, and of 2.9 in pools of 6. With the use of Cepheid Xpert® Xpress SARS-CoV-2 RT-PCR assay, pooling of 4 or 6 samples may be an effective strategy to increase testing capacity.

Mass gathering enhanced syndromic surveillance for the 8th Micronesian Games in 2014, Pohnpei State, Federated States of Micronesia.

Pohnpei State's Division of Primary Health Care implemented enhanced surveillance for early warning and detection of disease to support the 8th Micronesian Games (the Games) in July 2014. The surveillance comprised 11 point-of-care sentinel sites around Pohnpei, Federated States of Micronesia, collecting data daily for eight syndromes using standard case definitions. Each sentinel site reported total acute care encounters, total syndrome cases and the total for each syndrome. A public health response, including epidemiological investigation and laboratory testing, followed when syndrome counts reached predetermined threshold levels. The surveillance was implemented using the web-based Suite for Automated Global Electronic bioSurveillance Open-ESSENCE (SAGES-OE) application that was customized for the Games. Data were summarized in daily situation reports (SitReps) issued to key stakeholders and posted on PacNet, a Pacific public health e-mail network. Influenza-like illness (ILI) was the most common syndrome reported (55%, n = 225). Most syndrome cases (75%) were among people from Pohnpei. Only 30 cases out of a total of 408 syndrome cases (7%) presented with acute fever and rash, despite the large and ongoing measles outbreak at the time. No new infectious disease outbreak was recorded during the Games. Peaks in diarrhoeal and ILI cases were followed up and did not result in widespread transmission. The technology was a key feature of the enhanced surveillance. The introduction of the web-based tool greatly improved the timeliness of data entry, analysis and SitRep dissemination, providing assurance to the Games organizers that communicable diseases would not adversely impact the Games.

Prevalence of HIV and sexually transmitted infections among young women engaged in sex work aboard foreign fishing vessels in Kiribati.

OBJECTIVE: To assess the prevalence of HIV and sexually transmitted infections (STIs) among women who board foreign fishing vessels for sex work in Kiribati. METHODS: A cross-sectional study was designed to collect data on behavioural risk factors for STIs and knowledge of and attitudes towards HIV and STIs during 2007. Urine and blood samples were collected to test for HIV and select STIs. Descriptive statistics were performed for sociodemographic and behavioural characteristics, and χ2 tests were used to assess associations between potential key determinants and the presence of genital Chlamydia infection. RESULTS: Women who boarded foreign fishing vessels for transactional sex were younger, had less education, were less likely to live with a partner and were less likely to be otherwise employed. Although no HIV infections were detected, more than half (57.5%) of the women were diagnosed with an STI. One quarter of the women tested positive for chlamydia, and 40% tested positive for mycoplasma. The presence of chlamydia was strongly associated with age at first sexual intercourse (P = 0.02) and number of sexual partners during the prior seven days (P = 0.02). CONCLUSION: The high rate of STIs in this population of sex workers is concerning given the potential of severe pregnancy-related and chronic health problems and the increased risk of transmission within the general population of Kiribati. We identified a specific sex worker population as a priority group for targeted public health efforts to prevent and control the spread of STIs in Kiribati.

Response to a large rotavirus outbreak on South Tarawa, Kiribati, 2013.

INTRODUCTION: In July 2013, during annual independence celebrations in Kiribati, staff at Tungaru Central Hospital on South Tarawa reported an increase in children presenting with severe diarrhoea. This report describes the outbreak investigation, findings and response. METHOD: After notification of the outbreak, all health facilities on South Tarawa began reporting cases of acute diarrhoea and/or vomiting through the early warning syndromic surveillance system on a daily basis. Community awareness was raised and the public was encouraged to present to a health facility if ill with acute gastroenteritis. Specimens were collected and sent for laboratory testing. RESULTS: Between 10 and 24 July 2013, 1118 cases of gastroenteritis were reported; 103 were hospitalized and six died. The median age of cases was one year (range: 0-68 years); 93.4% were aged less than five years. Rotavirus was identified in 81% of specimens tested. The outbreak response included enhanced surveillance, community education, clinical training and changes to in-hospital patient management for infection control. DISCUSSION: This outbreak was the largest diarrhoea outbreak in Kiribati in five years. Factors that may have contributed to the magnitude and severity of the outbreak included high household density, inadequate sanitation infrastructure and a mass gathering--all increasing the chance of transmission--as well as limited clinical response capacity. The current outbreak highlights the importance of clinical management to minimize severe dehydration and death. Rotavirus vaccination should be considered as an adjunct to other comprehensive enteric disease control measures as recommended by the World Health Organization.

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 Organisation's 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.

Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation.

Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements.

Sexual behaviour of Kiribati seafarers: second generation surveillance in 2005 and 2008.

High-risk sexual activity, including engaging in transactional sex, concurrent sexual partnerships, and inconsistent condom use, increases the risk of infection with HIV and other sexually transmitted infections (STI). The demands of seafaring, such as long periods spent away from home, and the availability of commercial sex around seaports, can contribute to a culture of high-risk activity such as multiple casual sexual encounters and poor condom use. In 2005 and 2008, the Kiribati Ministry of Health conducted HIV and STI prevalence and behaviour surveys among seafarers. The results suggest that, while knowledge of HIV prevention and transmission improved from 2005 to 2008, this did not correlate with reduced levels of risky sexual activity in the same period. These findings suggest that HIV and STI prevention programs must extend beyond providing information, and testing and treatment facilities, towards implementing strategies that encourage and support safer sexual behaviours amongst seafarers and their partners, in particular transactional sex partners.