Phylogenomics of Dengue Virus Isolates Causing Dengue Outbreak, Sao Tome and Principe, 2022.
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ABSTRACT:
SUBMITTER: Lazaro L
PROVIDER: S-EPMC10826765 | biostudies-literature | 2024 Feb
REPOSITORIES: biostudies-literature
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Phylogenomics of Dengue Virus Isolates Causing Dengue Outbreak, São Tomé and Príncipe, 2022.
Lázaro Lazismino L Winter Doris D Toancha Katia K Borges Adjaia A Gonçalves Anabela A Santos Asmiralda A do Nascimento Marcos M Teixeira Nilton N Sequeira Yardlene Sacramento YS Lima Anery Katia AK da Costa Pina Bakissy B de Sousa Andreza Batista AB May Jürgen J Neto Rosa Maria Afonso RMA Schuldt Kathrin K
Emerging infectious diseases 20240102 2
We determined that the dengue outbreak in São Tomé and Príncipe during 2022 was caused by dengue virus serotype 3 genotype III. Phylogenomic analyses showed that the outbreak strain was closely related to the newly identified GIII-American-II lineage and that the virus probably was introduced from the Americas. ...[more]
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Project description:BackgroundDengue has emerged as a significant public health concern in Sao Tome and Principe, with the first documented outbreak occurring between 2022 and 2024. This study examined the epidemiological patterns, environmental determinants, and demographic characteristics of dengue transmission during this period.MethodsWe conducted a comprehensive retrospective analysis of laboratory-confirmed dengue cases using national surveillance data, clinical records, and environmental monitoring data. Statistical analyses included demographic profiling, temporal trend assessment, and environmental correlation studies using multiple regression modeling.ResultsAmong 1264 laboratory-confirmed cases, we observed distinct age-specific vulnerability patterns, with the highest incidence rate in the 70-79 age group (829.6 per 100,000) despite most cases occurring in younger adults. Rainfall emerged as the strongest predictor of dengue transmission (r = 0.96, p < 0.001), explaining 92% of case variance in the regression model. Case distribution showed marked temporal variation, with 91.9% of cases reported in 2022, coinciding with exceptional rainfall (3205 mm). The overall case fatality rate was 0.71% (95% CI: 0.33-1.35), with significant quarterly variations. Geographical analysis revealed concentration in the Água Grande district (68.2% of cases).ConclusionsThis first comprehensive analysis of dengue in Sao Tome and Principe demonstrates the crucial role of rainfall in disease transmission and reveals important age-specific vulnerability patterns. These findings provide an evidence base for developing targeted interventions, particularly during high-rainfall periods, and suggest the need for age-stratified clinical protocols in similar island settings.
| S-EPMC11860262 | biostudies-literature
Project description:Understanding species distribution across habitats and environmental variables is important to inform area-based management. However, observational data are often lacking, particularly from developing countries, hindering effective conservation design. One such data-poor area is the Gulf of Guinea, an understudied and biodiverse region where coastal waters play a critical role in coastal livelihoods. Here, we describe the results of the largest national-scale Baited Remote Underwater Video Systems (BRUVS) survey in the region, aiming to understand the effects of several environmental variables on fish community composition and diversity. From 2018 to 2020, we successfully deployed 417 benthic BRUVS in the coastal waters of the São Tomé and Príncipe (STP) archipelago. Species richness and relative abundance were higher in deeper waters, on steeper slopes, and in rocky reef habitats. Nevertheless, maerl and sand habitats also hosted unique, and economically important species. Our results potentially indicate historical impacts of fishing in the archipelago, especially in São Tomé Island, where observed fishing effort is higher. Indeed, abundance of large predatory fish was low in both islands and abundance of species targeted by artisanal fisheries was lower in São Tomé than in Príncipe. Our results provide crucial information supporting the designation and future monitoring of marine protected areas in STP.
| S-EPMC11530061 | biostudies-literature
Project description:BackgroundNeonatal mortality reduction is a global goal, but its factors are seldom studied in most resource-constrained settings. This is the first study conducted to identify the factors affecting perinatal and neonatal deaths in Sao Tome & Principe (STP), the smallest Central Africa country.MethodsInstitution-based prospective cohort study conducted at Hospital Dr. Ayres Menezes. Maternal-neonate dyads enrolled were followed up after the 28th day of life (n = 194) for identification of neonatal death-outcome (n = 22) and alive-outcome groups (n = 172). Data were collected from pregnancy cards, hospital records and face-to-face interviews. After the 28th day of birth, a phone call was made to evaluate the newborn's health status. Crude odds ratios and corresponding 95% confidence intervals were obtained. A p value <0.05 was considered statistically significant.ResultsThe mean gestational age of the death-outcome and alive-outcome groups was 36 (SD = 4.8) and 39 (SD = 1.4) weeks, respectively. Death-outcome group (n = 22) included sixteen stillbirths, four early and two late neonatal deaths. High-risk pregnancy score [cOR 2.91, 95% CI: 1.18-7.22], meconium-stained fluid [cOR 4.38, 95% CI: 1.74-10.98], prolonged rupture of membranes [cOR 4.84, 95% CI: 1.47-15.93], transfer from another unit [cOR 6.08, 95% CI:1.95-18.90], and instrumental vaginal delivery [cOR 8.90, 95% CI: 1.68-47.21], were factors significantly associated with deaths. The odds of experiencing death were higher for newborns with infectious risk, IUGR, resuscitation maneuvers, fetal distress at birth, birth asphyxia, and unit care admission. Female newborn [cOR 0.37, 95% CI: 0.14-1.00] and birth weight of more than 2,500 g [cOR 0.017, 95% CI: 0.002-0.162] were found to be protective factors.ConclusionFactors such as having a high-risk pregnancy score, meconium-stained amniotic fluid, prolonged rupture of membranes, being transferred from another unit, and an instrumental-assisted vaginal delivery increased 4- to 9-fold the risk of stillbirth and neonatal deaths. Thus, avoiding delays in prompt intrapartum care is a key strategy to implement in Sao Tome & Principe.
| S-EPMC10904650 | biostudies-literature
Project description:The mosquito Aedes albopictus (Diptera: Culicidae) is a vector species of the causal agents of Dengue, yellow fever, and Zika among other diseases pathogens. The species originated in Southeast Asia and has spread widely and rapidly in the last century. The species has been reported in localities from the Gulf of Guinea since the early 2000s, but systematic sampling has been scant. We sampled Ae. albopictus twice, in 2013 and 2023 across the altitudinal gradient in São Tomé and found that the species was present in all sampled years at altitudes up to 680 m. We also found some evidence of increases in proportional representation compared to Ae. aegypti over time. We report the presence of the species in Príncipe for the first time, suggesting that the range of Ae. albopictus is larger than previously thought. Finally, we use bioclimatic niche modeling to infer the potential range of Ae. albopictus and infer that the species has the potential to spread across a large portion of São Tomé and Príncipe. Our results suggest that Ae. albopictus has established itself as a resident species of the islands of the Gulf of Guinea and should be incorporated into the list of potential vectors that need to be surveyed and controlled.
| S-EPMC11559242 | biostudies-literature
Project description:Despite efforts to eliminate malaria in Sao Tome and Principe (STP), cases have recently increased. Understanding residual transmission structure is crucial for developing effective elimination strategies. This study collected surveillance data and generated amplicon sequencing data from 980 samples between 2010 and 2016 to examine the genetic structure of the parasite population. The mean multiplicity of infection (MOI) was 1.3, with 11% polyclonal infections, indicating low transmission intensity. Temporal trends of these genetic metrics did not align with incidence rates, suggesting that changes in genetic metrics may not straightforwardly reflect changes in transmission intensity, particularly in low transmission settings where genetic drift and importation have a substantial impact. While 88% of samples were genetically linked, continuous turnover in genetic clusters and changes in drug-resistance haplotypes were observed. Principal component analysis revealed some STP samples were genetically similar to those from Central and West Africa, indicating possible importation. These findings highlight the need to prioritize several interventions such as targeted interventions against transmission hotspots, reactive case detection, and strategies to reduce the introduction of new parasites into this island nation as it approaches elimination. This study also serves as a case study for implementing genetic surveillance in a low transmission setting.
| S-EPMC11275696 | biostudies-literature
Project description:The outbreak-causing monkeypox virus of 2022 (2022 MPXV) is classified as a clade IIb strain and phylogenetically distinct from prior endemic MPXV strains (clades I or IIa), suggesting that its virological properties may also differ. Here, we used human keratinocytes and induced pluripotent stem cell-derived colon organoids to examine the efficiency of viral growth in these cells and the MPXV infection-mediated host responses. MPXV replication was much more productive in keratinocytes than in colon organoids. We observed that MPXV infections, regardless of strain, caused cellular dysfunction and mitochondrial damage in keratinocytes. Notably, a significant increase in the expression of hypoxia-related genes was observed specifically in 2022 MPXV-infected keratinocytes. Our comparison of virological features between 2022 MPXV and prior endemic MPXV strains revealed signaling pathways potentially involved with the cellular damages caused by MPXV infections and highlights host vulnerabilities that could be utilized as protective therapeutic strategies against human mpox in the future.
2023-06-06 | GSE219036 | GEO
Project description:BackgroundNewborns with one-or-more adverse birth outcomes (ABOs) are at greater risk of mortality or long-term morbidity with health impacts into adulthood. Hence, identifying ABO-associated factors is crucial for devising relevant interventions. For this study, ABOs were defined as prematurity (PTB) for gestational age <37 weeks, low birth weight (LBW) <2.5 kg, macrosomia >4 kg, asphyxia for a 5-minute Apgar score <7, congenital anomalies, and neonatal sepsis. This study aimed to assess factors associated with ABOs among babies delivered at the only hospital of Sao Tome & Principe (STP), a resource-constrained sub-Saharan-Central African country.MethodsA hospital-based unmatched case‒control study was conducted among newborns from randomly selected mothers. Newborns with one-or-more ABO were the cases (ABO group), while healthy newborns were the controls (no-ABO group). Data were collected by a face-to-face interview and abstracted from antenatal care (ANC) pregnancy cards and medical records. Multivariable logistic regression analysis was performed to identify ABO-associated factors considering a level of significance of α = 0.05.ResultsA total of 519 newborns (176 with ABO and 343 no-ABO) were enrolled. The mean gestational age and birthweight of cases and controls were 36 (SD = 3.7) weeks with 2659 (SD = 881.44) g and 39.6 (SD = 1.0) weeks with 3256 (SD = 345.83) g, respectively. In the multivariable analysis, twin pregnancy [aOR 4.92, 95% CI 2.25-10.74], prolonged rupture of membranes [aOR 3.43, 95% CI 1.69-6.95], and meconium- fluid [aOR 1.59, 95% CI 0.97-2.62] were significantly associated with ABOs. Eight or more ANC contacts were found to be protective [aOR 0.33, 95% CI 0.18-0.60, p<0.001].ConclusionModifiable factors were associated with ABOs in this study and should be considered in cost-effective interventions. The provision of high-quality ANC should be a priority. Twin pregnancies and intrapartum factors such as prolonged rupture of membranes and meconium-stained amniotic fluid are red flags for ABOs that should receive prompt intervention and follow-up.
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Project description:BackgroundPlasmodium falciparum is the major cause of malaria infection in the island of São Tomé, in the Republic of São Tomé and Príncipe (STP), with an incidence of 40 - 50% before 2004. Since 2004, through the coordination of the Ministry of Health of STP and their Centro Nacional de Endemias (CNE), an integrated malaria control programme has been intensively deployed on the island of São Tomé. Malaria morbidity and mortality decreased by 95% after three years of effective intervention. In the low transmission settings, however, malaria seasonal fluctuation can be a potential problem directly related to epidemics if ongoing control measures are interrupted. Studies on a number of associated factors with malaria epidemics and the measures taken to respond to outbreaks are presented.MethodsThe integrated malaria control programme included indoor residual spraying (IRS), long-lasting insecticidal nets (LLINs), intermittent preventive therapy for pregnant women, as well as early diagnosis and prompt treatment with artemisinin-based combination therapy (ACT). Regular implementation of an island-wide IRS programme was carried out yearly in 2004-2007, and enhanced throughout the island in 2009. Malaria incidence and prevalence were estimated based on passive case detection and mass screening, respectively. Slide positivity rates were used for monitoring the beginning of a malaria epidemic or a seasonal peak.ResultsA steep decline of ca. 95% of malaria morbidity and mortality was observed between 2004 and 2008 with use of the combined control methods. Malaria incidence was 2.0%, 1.5%, and 3.0% for 2007, 2008, and 2009, respectively. In April 2008, a cross-sectional country-wide surveillance showed malaria prevalence of 3.5%, of which 95% cases were asymptomatic carriers. Only 50% of asymptomatic carriers were cured with ACT treatment, while 90% of the symptomatic patients were cured by ACT treatment as confirmed with a follow up study. Malaria morbidity increased by three-fold during the first half of 2009 as compared to the same period in 2008. Over this period of six months, severe malaria was also noted in all age groups and malaria mortality increased by two-fold in children less than five years old. After an emergency IRS was deployed, with increased use of LLINs, and an active search of asymptomatic carriers was followed and given complete ACT treatment, malaria incidence decreased to less than 1% in the second half of 2009.ConclusionAt the initial stage of the integrated malaria control programme, IRS contributed to the visible effect on the rapid reduction of malaria morbidity and mortality, while this programme highlights an urgent demand for the improvement of other measures, particularly promotion of LLINs usage, with close monitoring of asymptomatic carriers and with ACT treatment in malaria transmission hotspots. In addition, both daily reports and a regular active surveillance to prevent malaria outbreaks should be established permanently, so that a fast response to epidemics can be effectively made when necessary.
| S-EPMC2955676 | biostudies-literature
Project description:São Tomé and Príncipe (STP) uses a selective hepatitis B birth-dose vaccination (HepB-BD) strategy targeting infants born to mothers who test positive for hepatitis B virus (HBV) surface antigen. We conducted a field assessment and economic analysis of the HepB-BD strategy to provide evidence to guide development of cost-effective policies to prevent perinatal HBV transmission in STP. We interviewed national stakeholders and key informants to understand policies, knowledge, and practices related to HepB-BD, vaccine management, and data recording/reporting. Cost-effectiveness of the existing strategy was compared with an alternate approach of universal HepB-BD to all newborns using a decision analytic model. Incremental cost-effectiveness ratios (ICERs) were calculated in 2015 USD per HBV-associated death and per chronic HBV case prevented, from the STP health-care system perspective. We found that STP lacked national or facility-specific written policies and procedures related to HepB-BD. Timely HepB-BD to eligible newborns was considered a high priority, although timeliness of HepB-BD was not monitored. Compared with the existing selective vaccination strategy, universal HepB-BD would result in a 19% decrease in chronic HBV infections per year at overall cost savings of approximately 44% (savings of USD 5,441 each year). We estimate an ICER of USD 5,012 saved per HBV-associated death averted. The existing selective HepB-BD strategy in STP could be improved through documentation of policies, procedures, and timeliness of HepB-BD. Expansion to universal newborn HepB-BD without maternal screening is feasible and could result in cost savings if actual implementation costs and effectiveness fall within the ranges modeled.
| S-EPMC6779202 | biostudies-literature
Project description:BackgroundSickle Cell Disorder is Africa's most prevalent genetic disease. Yet, it remains a neglected condition, with high mortality under-five, and a lack of population-based studies in the region. This is the first of its kind in São Tomé e Príncipe, aiming to estimate the prevalence of sickle cell trait and other haemoglobin variants in women of reproductive age and its associated factors.MethodsWe conducted a cluster survey in 35 neighbourhoods. Haemoglobin was assessed through point-of-care capillary electrophoresis or high-performance liquid chromatography, and sociodemographic data through questionnaires. The weighted prevalence of sickle cell trait (HbAS) and HbC carriers was estimated with a 95% confidence interval (95% CI). We calculated weighted prevalence ratios (95% CI) through robust Poisson regression for its association with age and individual and collective genetic heritage.FindingsThe prevalence of sickle cell trait in women of reproductive age in São Tomé e Príncipe (n = 376) was 13.45% (95% CI: 9.05-19.00). The prevalence of HbC carriers was 8.00% (95% CI: 4.71-12.00). Older age and speaking Forro or Angolar were positively associated with having sickle cell trait.InterpretationThe prevalence of sickle cell trait in São Tomé e Príncipe ranks high in the West African region. The country should follow international guidelines, implementing newborn screening and comprehensive healthcare management.
| S-EPMC10949760 | biostudies-literature