Retrospective Study of an Adenovirus Pneumonia Outbreak in Shenzhen in 2017.
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ABSTRACT:
SUBMITTER: Lu Z
PROVIDER: S-EPMC8158460 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We used the Virochip microarray to detect and discover a novel adenovirus, TMAdV (titi monkey adenovirus). We used custom-commercial microarrays from Agilent Technologies. The microarray platform GPL11662 consists of 62,976 probes, of which 19,058 probes are 70-mer viral oligonucleotides (the union of the V3 and V4 platforms -- please see Wang, et al., PNAS, 2002; Chiu, et al., Clin Infect Dis, 2006; Chiu, et al., PNAS, 2008).
2011-02-05 | GSE26898 | GEO
Project description:BACKGROUND:Preterm birth is the leading cause of child mortality under 5 years of age. Temporal trends in preterm birth rates are highly heterogeneous among countries and little information exists for China. To address this data gap, we investigated annual changes in preterm birth incidence rate and explored potential determinants of these changes in Shenzhen, China. METHODS:A total of 1.4 million live births, during 2003-2012, were included from the Shenzhen birth registry. Negative-binominal regression models were used to estimate the annual percent changes in incidence. To identify the potential determinants behind temporal trends, we estimated the contribution of each changing risk factor to changes in rate by calculating the difference in population-attributable risk fraction. RESULTS:Annual preterm birth incidence rates increased by 0.94% (95% CI 0.30%, 1.58%) overall, 3.60% (95% CI 2.73%, 4.48%) for medically induced, and 3.13% (95% CI 1.01%, 5.31%) for preterm premature rupture of membranes, but decreased by 2.34% (95% CI 1.62%, 3.06%) for spontaneous preterm labor. Higher maternal educational attainment (0.20 rate increase), lower proportion of inadequate prenatal care (0.15 rate reduction), more multipara (0.08 rate reduction), decreased proportion of preeclampsia or eclampsia (0.05 rate reduction), and larger proportion of young and older pregnant women (0.04 rate increase) were significant contributors to the overall change over time. Contributions of changing risk factors were different between preterm birth subtypes. CONCLUSIONS:Preterm birth rate in Shenzhen, China increased overall during 2003-2012, although trends varied across three preterm birth subtypes. The rising rates were associated with changes in maternal education and age.
| S-EPMC5851155 | biostudies-literature
Project description:BackgroundNorovirus (NoV) is the main cause of non-bacterial acute gastroenteritis (AGE) outbreaks worldwide. From September 2015 through August 2018, 203 NoV outbreaks involving 2500 cases were reported to the Shenzhen Center for Disease Control and Prevention.MethodsFaecal specimens for 203 outbreaks were collected and epidemiological data were obtained through the AGE outbreak surveillance system in Shenzhen. Genotypes were determined by sequencing analysis. To gain a better understanding of the evolutionary characteristics of NoV in Shenzhen, molecular evolution and mutations were evaluated based on time-scale evolutionary phylogeny and amino acid mutations.ResultsA total of nine districts reported NoV outbreaks and the reported NoV outbreaks peaked from November to March. Among the 203 NoV outbreaks, 150 were sequenced successfully. Most of these outbreaks were associated with the NoV GII.2[P16] strain (45.3%, 92/203) and occurred in school settings (91.6%, 186/203). The evolutionary rates of the RdRp region and the VP1 sequence were 2.1 × 10-3 (95% HPD interval, 1.7 × 10-3-2.5 × 10-3) substitutions/site/year and 2.7 × 10-3 (95% HPD interval, 2.4 × 10-3-3.1 × 10-3) substitutions/site/year, respectively. The common ancestors of the GII.2[P16] strain from Shenzhen and GII.4 Sydney 2012[P16] diverged from 2011 to 2012. The common ancestors of the GII.2[P16] strain from Shenzhen and previous GII.2[P16] (2010-2012) diverged from 2003 to 2004. The results of amino acid mutations showed 6 amino acid substitutions (*77E, R750K, P845Q, H1310Y, K1546Q, T1549A) were found only in GII.4 Sydney 2012[P16] and the GII.2[P16] recombinant strain.ConclusionsThis study illustrates the molecular epidemiological patterns in Shenzhen, China, from September 2015 to August 2018 and provides evidence that the epidemic trend of GII.2[P16] recombinant strain had weakened and the non-structural proteins of the recombinant strain might have played a more significant role than VP1.
| S-EPMC8556823 | biostudies-literature
Project description:We used the Virochip microarray to detect and discover a novel adenovirus, TMAdV (titi monkey adenovirus). We used custom-commercial microarrays from Agilent Technologies. The microarray platform GPL11662 consists of 62,976 probes, of which 19,058 probes are 70-mer viral oligonucleotides (the union of the V3 and V4 platforms -- please see Wang, et al., PNAS, 2002; Chiu, et al., Clin Infect Dis, 2006; Chiu, et al., PNAS, 2008). For this study, 4 experimental Virochip microarrays derived from tissue and swabs from affected titi monkeys were analyzed. We also used 18 Virochip microarrays derived from sera from healthy random human blood donors as a negative background set for Z-score analysis (see Chiu, et al., Clin Infect Dis, 2006). Raw Agilent microarray .txt files are background normalized and the 19,058 70-mer viral probes are then selected and displayed as columns in the processed data table.
2011-02-05 | E-GEOD-26898 | biostudies-arrayexpress
Project description:IntroductionDengue fever is a re-emerging pathology in Burkina Faso. It affects everyone and pregnant women are not left out. The objective of this study was to estimate the burden of dengue fever and to assess its effects on pregnancy outcomes in hospitalized pregnant women during the 2017 outbreak in Ouagadougou, Burkina Faso.MethodThis was a retrospective cohort study including febrile pregnant women from five health facilities in Ouagadougou. The study was carried out from July 1st to December 31st, 2017. A logistic stepwise regression was performed to identify the pregnancy adverse outcomes risk factors.ResultsOur study included 424 pregnant women at a mean age of 27.1 years old (Standard deviation: 6.23 years). Overall 28.54% (121/424) were infected with dengue virus. During follow-up, 29.01% (123/424) presented an adverse pregnancy outcome. Adjusted for gestational age and clinical symptoms, the risk of adverse pregnancy outcome was twice as high among dengue infected women as compared to uninfected women with an adjusted Odds Ratio (aOR) = 2.09 (1.08-4.05). The risk of the adverse pregnancy outcome was higher in the third trimester of pregnancy with aOR = 1.66 (1.02-2.72) in dengue fever infected women.ConclusionDengue fever is a risk factor for adverse pregnancy outcomes, especially in the third trimester in Burkina Faso. The implementation of effective anti-vectorial control interventions and better management of dengue fever during pregnancy are needed to improve pregnancy outcomes.
| S-EPMC7473539 | biostudies-literature
Project description:Community-acquired pneumonia (CAP) is a common disease responsible for significant morbidity and mortality. However, the definite etiology of CAP often remains unresolved, suggesting that unknown agents of pneumonia remain to be identified. The recently discovered members of the order Chlamydiales, Chlamydia-related bacteria (CRB), are considered as possible emerging agents of CAP. Parachlamydia acanthamoebae is the most studied candidate. It survives and replicates inside free-living amoeba, which it might potentially use as a vehicle to infect animals and humans. A Mycoplasma pneumoniae outbreak was observed in Kymenlaakso region in Southeastern Finland during August 2017-January 2018. We determined the occurrence of Chlamydiales bacteria and their natural host, free-living amoeba in respiratory specimens collected during this outbreak with molecular methods. Altogether, 22/278 (7.9%) of the samples contained Chlamydiales DNA. By sequence analysis, majority of the CRBs detected were members of the Parachlamydiaceae family. Amoebal DNA was not detected within the sample material. Our study further proposes that Parachlamydiaceae could be a potential agent causing atypical CAP in children and adolescents.
| S-EPMC6560421 | biostudies-literature
Project description:BackgroundThe number of pneumonia patients increased suddenly in Korean military hospitals in late December 2014, indicating the urgent need for an epidemic outbreak investigation.MethodsWe conducted a prospective study of pneumonia etiology among immunocompetent young adults admitted to Daejeon Armed Forces hospital. Patient blood and sputum samples were subjected to conventional culture, serology, and polymerase chain reaction tests for respiratory viruses and atypical pathogens.ResultsFrom January to May 2015, we enrolled 191 (189 male) adults with pneumonia; the mean age was 20.1 ± 1.3 years. Five patients had severe pneumonia, and one died. Pathogenic human adenoviruses were most common (HAdV, 153/191 [80.1%]), indicating a HAdV pneumonia outbreak. Genotyping of 35 isolates indicated that 34 matched HAdV-55 and one matched HAdV-2. HAdV pneumonia infected recruit trainees most frequently. High and prolonged fever, nasal congestion, sore throat, and pharyngeal inflammation were significantly more common in the HAdV pneumonia group, compared to patients with other or unknown causes of pneumonia. Only 12% of HAdV pneumonia patients displayed leukocytosis, whereas febrile leukopenia (62.7%) and thrombocytopenia (41%) were commonly observed. HAdV pneumonia patient chest CT scans displayed ground glass opacity (with or without septal thickness) with consolidation in 50.0% of patients.ConclusionsAn outbreak of HAdV respiratory infection occurred at the Korean military training center. HAdV pneumonia exhibited specific laboratory and clinical features, and although most patients were cured without complication, some progressed to respiratory failure and fatality. Therefore, HAdV vaccine should be provided to military trainees in Korea.
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Project description:These samples are part of the ENCODE consortium’s proposed time-limited Pilot Study for confirmation of the utility of RNA abundance measurements as a standard reference phenotyping tool. Keywords: cell type comparison For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2008-09-16 | GSE12760 | GEO
Project description:On June 22, 2017, the Los Angeles County Department of Public Health (LAC DPH) was notified of seven patients who were seen at an eye care clinic on June 8, 2017, and later developed symptoms of epidemic keratoconjunctivitis (EKC). EKC is a contagious, severe form of viral conjunctivitis that can cause pain and blurred vision for up to 4 weeks (1). LAC DPH conducted an investigation, which identified 17 patients with EKC, including 15 who had visited the optometry clinic and two who were household contacts of clinic patients. Observations in the clinic found deficiencies in disinfection of tonometers (an instrument connected to a slit lamp and used to test for glaucoma by measuring intraocular pressure) and multiuse eye drop administration. Staff member education and revision of disinfection practices interrupted further transmission. Patient specimens tested positive for human adenovirus (HAdV) type D53 (HAdV-53). As the first documented EKC outbreak associated with HAdV-D53 in the United States, this outbreak highlights the need for rigorous implementation of recommended infection prevention practices in eye care settings.
| S-EPMC6329482 | biostudies-literature
Project description:ObjectiveTo compare outcomes of early and delayed treatment with cidofovir for human adenovirus (HAdV) pneumonia.MethodsA retrospective cohort study in Korean military hospitals was conducted between January 2012 and December 2018. Patients with potentially severe HAdV pneumonia with risk factors for respiratory failure were included and divided into early (within 7 days from symptom onset) and delayed (after 7 days from symptom onset) treatment groups. The primary outcome was respiratory failure development within 21 days after symptom onset.ResultsA total of 89 patients with potentially severe HAdV pneumonia were enrolled in the cohort; they included 62 early and 27 delayed treatment patients. All patients were males in their early 20s. Significantly fewer patients in the early treatment group progressed to respiratory failure (8/62, 12.9%), compared to the delayed group (18/27, 66.7%, p < 0.001). Early treatment was associated with a lower 21-day probability of respiratory failure by the Kaplan-Meier method (p < 0.001). On multivariate analysis, monocyte count, hypoxaemia, confusion, whole lung involvement, and early cidofovir treatment within 7 days from symptom onset were included, and monocyte count (HR 0.995, 95%CI 0.991-1.000, p 0.042), confusion (HR 4.964, 95%CI 1.189-20.721, p = 0.028), and early cidofovir treatment (HR 0.319, 95%CI 0.115-0.883, p = 0.028) were significantly associated with respiratory failure.ConclusionsEarly administration of cidofovir was associated with a lower hazard for respiratory failure development. It is suggested that cidofovir be administered within 7 days from symptom onset to prevent respiratory failure in patients with potentially severe HAdV pneumonia.
| S-EPMC7129699 | biostudies-literature