Genetic Characterization of Seoul Virus in the Seaport of Cotonou, Benin.
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ABSTRACT:
SUBMITTER: Castel G
PROVIDER: S-EPMC8462318 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Seoul virus (SEOV), which causes hemorrhagic fever with renal syndrome (HFRS) in humans, has spread all over the world, especially in mainland China. Understanding basic mechanisms of SEOV evolution is essential to better combat and prevent viral diseases. Here, we examined SEOV prevalence and evolution in the residential area of four districts in Guangzhou city, China. The carriage of SEOV was observed in 33.33% of the sampled rodents, with 35.96% of the sampled Rattus norvegicus and 13.33% of R. tanezumi. Based on the comprehensive analyses of large (L), medium (M), and small (S) segments, our study first demonstrated that the genetic characterization of urban SEOV was shaped by high nucleotide substitution rates, purifying selection, and recombination. Additionally, we detected mutational saturation in the S segment of SEOV, which may lead to the biases of genetic divergence and substitution rates in our study. Importantly, we have filled the gap of SEOV evolution in the urban area. The genetic variation of SEOV may highlight the risk of HFRS, which merits further investigation.
| S-EPMC6950471 | biostudies-literature
Project description:BACKGROUND:Hantaviruses are single-stranded RNA viruses, which are transmitted to humans primarily via inhalation of aerosolised virus in contaminated rodent urine and faeces. Whilst infected reservoir hosts are asymptomatic, human infections can lead to two clinical manifestations, haemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), with varying degrees of clinical severity. The incidence of rodent and human cases of Seoul virus (SEOV) in Europe has been considered to be low, and speculated to be driven by the sporadic introduction of infected brown rats (Rattus norvegicus) via ports. METHODS:Between October 2010 and March 2012, 128 brown rats were caught at sites across the Lyon region in France. RESULTS:SEOV RNA was detected in the lungs of 14% (95% CI 8.01-20.11) of brown rats tested using a nested pan-hantavirus RT-PCR (polymerase gene). Phylogenetic analysis supports the inclusion of the Lyon SEOV within Lineage 7 with SEOV strains originating from SE Asia and the previously reported French & Belgian SEOV strains. Sequence data obtained from the recent human SEOV case (Replonges) was most similar to that obtained from one brown rat trapped in a public park in Lyon city centre. We obtained significantly improved recovery of virus genome sequence directly from SEOV infected lung material using a simple viral enrichment approach and NGS technology. CONCLUSIONS:The detection of SEOV in two wild caught brown rats in the UK and the multiple detection of SEOV infected brown rats in the Lyon region of France, suggests that SEOV is circulating in European brown rats. Under-reporting and difficulties in identifying the hantaviruses associated with HFRS may mask the public health impact of SEOV in Europe.
| S-EPMC3944734 | biostudies-literature
Project description:BACKGROUND:The literature on migration-fertility relationship uses various measures of fertility, such as fertility rates, actual fertility and family size preferences. This study introduces a different measure-interbirth intervals over women's reproductive years-to examine how internal migration is associated with short interbirth intervals (less than 24 months) and long interbirth intervals (greater than 60 months) in Cotonou, the largest city of Benin Republic. METHODS:The paper uses primary data on 2852 live births to 1659 women aged 15-49 years from the 2018 Fertility and Migration Survey in Cotonou. Competing-risks models were fitted for the analysis. RESULTS:Nineteen percent of live births were of short interbirth intervals and 16% were of long interbirth intervals. The prevalence of short interbirth intervals was higher among migrants who spent less than 5 years in Cotonou (29%) than among non-migrants (19%) and earlier migrants (18%). Non-migrants had the highest proportion of long interbirth intervals (19%). Within the first 5 years following the migration to Cotonou, migrants had higher subhazard ratio (SHR) of short interbirth intervals (SHR: 1.71, 95% CI: 1.33-2.21) and lower SHR of long interbirth intervals (SHR: 0.64, 95% CI: 0.47-0.87) than non-migrants. This association holds after controlling for socioeconomic characteristics-but with a slightly reduced gap between migrants who spent less than 5 years in Cotonou and non-migrants. Afterwards and irrespective of women's socioeconomic backgrounds, migrants who spent 5 or more years in Cotonou and non-migrants had similar risks of short and long interbirth intervals. Finally, from 5 years of stay in Cotonou, migrants for reasons other than school or job were less likely to experience short interbirth intervals (SHR: 0.65, 95% CI: 0.46-0.98 for migrants who spent 5-10 years in Cotonou, and SHR: 0.74, 95% CI: 0.54-1.02 for migrants who spent more than 10 years in Cotonou) than non-migrants. CONCLUSION:Family planning programmes should mainly target migrants in the early years after their arrival in Cotonou. Moreover, non-migrants need to be sensitised on the adverse health outcomes of long interbirth intervals.
| S-EPMC6813098 | biostudies-literature
Project description:Female sex workers (FSWs) continue to carry a heavy burden of sexually transmitted infections (STI). For prevention purposes, there is a need to identify most-at-risk subgroups among them. The objective of this longitudinal cohort study conducted at Dispensaire IST, Cotonou, Benin, was to assess Neisseria gonorrhoeae (NG) / Chlamydia trachomatis (CT) incidence and determinants; and HIV incidence among FSWs in presence of STI/HIV risk reduction activities. Overall, 319 adult FSWs were followed quarterly from September 2008 to March 2012. NG/CT were detected from endocervical swabs by Amplified DNA Assays employing Strand displacement amplification technology. HIV testing was done on capillary blood using two consecutive rapid diagnostic tests. Anderson-Gill proportional hazard models (HR) were used to determine factors independently associated with NG/CT incidence. The majority of FSWs were HIV-negative (188, 58.9%). There were 6 HIV seroconversions among these 188 HIV-negative women. HIV incidence (95% Confidence interval, CI) was 1.41 (0.28-2.54) seroconversions per 100 person-years at risk (PYAR): 6 events / 425.1 PYAR. Sixty-two out of 319 women experienced 83 new episodes of NG/CT for an overall incidence rate (95% CI) of 10.8 (8.17-13.88) events / 100 PYAR. From month-24 onwards, HIV-positive women (treated: HR (95%CI): 4.2 (1.60-10.77); untreated: HR (95%CI): 4.2 (1.59-11.49) were more likely to acquire NG/CT compared to HIV-negative FSWs. Longer duration in sex work (>2 years: HR; 95%CI: 0.4 (0.22-0.72)) was protective against NG/CT. Refusal by clients (55.8%) was the main reason for non-condom use. Enrolling women from one clinic (Dispensaire IST) may have impaired generalizability of the findings. New NG/CT/HIV infections were observed among FSWs notwithstanding ongoing prevention interventions. To eliminate HIV transmission among FSWs, STI/HIV control programs need to promote women's empowerment and address vulnerability to infection of HIV-positive FSWs.
| S-EPMC5945000 | biostudies-literature
Project description:BackgroundType 2 diabetes (T2D) is becoming an epidemic with significant disability and premature death in Sub-Saharan Africa, including Benin. However, little is known about the level of knowledge, attitude, and practice (KAP) necessary for diabetic patients to enhance therapeutic outcomes and prevent diabetes complications. The study aimed to assess patients' KAP levels and identify the factors associated in Cotonou, southern Benin.MethodsA cross-sectional study was conducted from July to August 2019 among 300 diabetic patients from four health centers. Data was collected using validated questionnaires. KAP levels were determined by calculating the scores, and multivariate logistic regression was used to explore factors influencing KAP scores.ResultsAbout 53, 52, and 47% of all patients had good knowledge, attitude, and practice towards diabetes. In logistic regression, factors such as being female, married, educated, government/non-government employee, and longer duration of diabetes were significantly associated with good knowledge. Being married, having a longer duration of diabetes, and good knowledge were significantly associated with a good attitude while being educated, having a longer duration of diabetes, and good knowledge with good practice.ConclusionsLack of knowledge, poor attitude, and inadequate practice were found in this surveyed community, suggesting a need for structured educational programs to assist diabetic patients. However, education should be considered a priority for male, newly diagnosed, and uneducated patients.
| S-EPMC7881446 | biostudies-literature
Project description:OBJECTIVES:Female sex workers (FSWs) play a key role in HIV transmission in West Africa, while they have limited access to antiretroviral therapy (ART). In line with UNAIDS recommendations extending ART to all HIV-infected individuals, we conducted this demonstration project on immediate treatment as prevention (TasP) among FSWs in Cotonou, Benin. We report data on treatment response and its relation to adherence, as well as on ART-resistant genotypes. METHODS:Complete follow-up varied between 12 and 24 months. At each three-monthly visit, a questionnaire was administered, clinical examinations were carried out and blood samples collected. Adherence to treatment was estimated by self-report. Viral RNA was genotyped at baseline and final visits for drug resistance. Generalized estimating equations for repeated measures with a log-binomial link were used to analyze time trends and the association between adherence and virological response to treatment. RESULTS:One-hundred-seven HIV-positive and ART-naive FSWs were enrolled; 59.8% remained in the cohort till study completion and 62.6% had a final visit. Viral load<1000 (below quantification limit [<50]) was attained in 73.1% (64.6%) of participants at month-6, 84.8% (71.2%) at month-12, and 80.9% (65.1%) at the final visit. The proportion of women with suppressed (below quantification limit) viral load increased with increasing self-reported adherence (p = 0.06 (0.003), tests for trend). The proportion of participants with CD4≤500 also decreased drastically throughout follow-up (p < .0001). Twelve participants exhibited ART-resistant genotypes at baseline, but only two at their final visit. CONCLUSION:Our findings indicate that TasP is widely accepted among FSWs in Cotonou and could be implemented with relative success. However, due to mobility in this population, follow-up was sub-optimal, suggesting that large geographical coverage of FSW-friendly clinics is needed for sustained treatment implementation. We also fell short of the UNAIDS objective of 90% viral suppression among treated patients, underlining the need for better adherence support programs.
| S-EPMC6977752 | biostudies-literature
Project description:BACKGROUND:Malaria is the main cause of hospital admissions in Benin and a leading cause of death in childhood. Beside consultations, various studies have underlined the management of the disease through home treatment. The medicines used can be purchased in informal market of pharmaceutical drugs (IMPD) without prescription or any involvement of healthcare professional. Pharmaceutical drugs are sold by informal private vendors, who operate at any time in the immediate environment of the patients. The present study was conducted in Cotonou to study the health-seeking behaviour of caregivers to treat malaria in children under 12 years old. Factors associated with malaria home treatment and drugs purchase in IMPD were studied. METHODS:A cross-sectional study was carried out among 340 children's caregivers who were interviewed about their socio-demographic characteristics and their care-seeking behaviour during the most recent episode of malaria in their children under 12. Medicines used and purchase place were also collected. Multivariate logistic regression model was used to determine factors associated with malaria home treatment and drug purchase in IMPD. RESULTS:Beyond all the 340 caregivers, 116 (34%) consulted healthcare professional, 224 (66%) home treat the children, among whom 207 (61%) gave pharmaceutical drugs and 17 (5%) gave traditional remedies to children. Malaria home treatment was associated with family size, health insurance (OR?=?0.396, 95% CI 0.169-0.928), and wealth quintiles where home treatment was less used by the richest (OR?=?0.199, 95% CI 0.0676-0.522) compared to those in the poorest quintile. The caregivers age group 30-39 years was associated to the use of IMPD (OR?=?0.383, 95% CI 0.152-0.964), the most economically wealthy people were less likely to use IMPD (wealth quintile richest: OR?=?0.239, 95% CI 0.064-0.887; wealth quintile fourth OR?=?0.271, 95% CI 0.100-0.735) compared to those in the poorest quintile. All caregivers who benefited from health insurance did not use IMPD. CONCLUSION:This study highlights the link between worse economic conditions and accessibility to medical care as one of the main factors of malaria home treatment and drug purchase in IMPD, even if those two phenomena need to be understood apart.
| S-EPMC6180418 | biostudies-literature
Project description:BackgroundThe diagnosis of tuberculosis (TB) using smear microscopy has been based on testing two specimens: one spot and one early morning sputa. Recently, the World Health Organization (WHO) has recommended to replace, whenever possible, microscopy with GeneXpert® MTB/RIF performed on a single specimen. However, as the bacterial load is higher in early morning specimens than in spot specimens, one could expect lower sensitivity of GeneXpert® MTB/RIF performed only on spot specimens. In this study, we compared results of GeneXpert® MTB/RIF on spot specimens versus early morning specimens, under programmatic conditions in Cotonou, Benin.MethodsFrom June to September 2018, all sputa received from presumptive TB patients at the Supranational Reference Laboratory for Tuberculosis of Cotonou were included in the study. From each patient, two specimens were collected (one spot and one early morning) and GeneXpert® MTB/RIF was performed on both specimens.ResultsIn total, 886 participants were included in the study, of whom 737 provided both sputa and 149 (16.8%) gave only the spot specimen. For the 737 participants who provided both sputa, GeneXpert® MTB/RIF was positive for both specimens in 152 participants; for three participants GeneXpert® MTB/RIF was positive on spot specimen but negative on morning specimen while for another three, the test was positive on morning specimen but negative on spot specimen. The overall percentage of agreement was excellent (99.2%) with a positive and negative percent agreement greater than 98%.ConclusionFor TB diagnosis under programmatic conditions in Cotonou, GeneXpert® MTB/RIF in spot specimens gave similar results with the test in morning specimens. Performing GeneXpert® MTB/RIF in both specimens did not significantly increase the number of cases detected. To avoid losing patients from the diagnostic cascade, it is preferable to test sputa produced at the time of the first visit at the health center.
| S-EPMC8454072 | biostudies-literature
Project description:We report two outbreaks of Lassa fever that occurred in Benin in 2014 and 2016 with 20 confirmed cases and 50% (10/20) mortality. Benin was not previously considered to be an endemic country for Lassa fever, resulting in a delay to diagnose the disease and its human transmission. Molecular investigations showed the viral genomes to be similar to that of the Togo strain, which is genetically very different from other known strains and confirms the existence of a new lineage. Endemic circulation of Lassa virus in a new territory and the genetic diversity thus confirm that this virus represents a growing threat for West African people. Given the divergence of the Benin strain from the prototypic Josiah Sierra Leone strain frequently used to generate vaccine candidates, the efficacy of vaccine candidates should also be demonstrated with this strain.
| S-EPMC7473144 | biostudies-literature
Project description:Rodent-borne pathogens pose a critical public health threat in urban areas. An epidemiological survey of urban rodents was conducted from 2006 to 2010 at the U.S. Army Garrison (USAG), Seoul, Republic of Korea (ROK), to determine the prevalence of Seoul virus (SEOV), a rodent-borne hantavirus. A total of 1,950 rodents were captured at USAG, Yongsan, near/in 19.4% (234/1,206) of the numbered buildings. Annual mean rodent infestation rates were the highest for food service facilities, e.g., the Dragon Hill Lodge complex (38.0 rodents) and the Hartell House (18.8 rodents). The brown rat, Rattus norvegicus, accounted for 99.4% (1,939/1,950) of all the rodents captured in the urban area, whereas only 0.6% (11/1,950) of the rodents was house mice (Mus musculus). In November 2006, higher numbers of rats captured were likely associated with climatic factors, e.g., rainfall and temperatures as rats sought harborage in and around buildings. Only 4.7% (34/718) of the rodents assayed for hantaviruses was serologically positive for SEOV. A total of 8.8% (3/34) R. norvegicus were positive for SEOV RNA by reverse transcription polymerase chain reaction, of which two SEOV strains were completely sequenced and characterized. The 3' and 5' terminal sequences revealed incomplete complementary genomic configuration. Seoul virus strains Rn10-134 and Rn10-145 formed a monophyletic lineage with the prototype SEOV strain 80-39. Seoul virus Medium segment showed the highest evolutionary rates compared with the Large and Small segments. In conclusion, this report provides significant insights into continued rodent-borne disease surveillance programs that identify hantaviruses for analysis of disease risk assessments and development of mitigation strategies.
| S-EPMC6090319 | biostudies-literature