WHONDRS-GUI: a web application for global survey of surface water metabolites.

BACKGROUND: The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. RESULTS: The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811, which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server (https://xmlin.shinyapps.io/whondrs/).

Circulation of human metapneumovirus among children with influenza-like illness in Wuhan, China.

Human metapneumovirus (HMPV) is a worldwide distributed pathogen of the respiratory tract. The objectives of this study were to identify HMPV infections among children with influenza-like illness (ILI) in Wuhan and to assess circulation patterns and molecular diversity of HMPV in this area. From July 2008 to December 2013, a total of 3,883 throat swab samples were collected from ILI outpatients under 16 years old. HMPV RNA was detected in 171 samples (4.40%). All the four subtypes of HMPV were identified, among which A2 was the most common subtype (61/145, 42.1%), followed by B1, B2, and A1. During the study period, HMPV circulation presented a biennial alternation between high and low incidence in Wuhan and the seasonal peak also shift between winter and spring in two continuous seasons. Subtype A2, B1, and B2 co-circulated during the study period, with genotype A prevailing in epidemic season 2008-2009 and 2012-2013, and genotype B prevailing during other periods. This large-scale analysis of HMPV prevalence in ILI outpatient children improves the understanding of local HMPV circulation patterns and provides molecular epidemic evidence for comparative analysis of HMPV infection.

[Epidemiological characteristics of influenza virus and respiratory syncytial virus among children in Wuhan area from 2008 to 2012].

OBJECTIVE: To investigate the infection status and epidemiological characteristics of influenza virus and respiratory syncytial virus (RSV) in influenza-like illness (ILI) of children ( ≤ 14 years) in Wuhan area from 2008 to 2012. METHODS: A total of 2854 cases of ILI patients ( ≤ 14 years) in a hospital of Wuhan were recruited in the study from July 2008 to June 2012. The sample of pharyngeal swab was collected from each patient, to extract the virus nucleic acids. Real-time fluorescent quantitation reverse transcription PCR (RT-PCR) method was applied to detect the subtypes of influenza virus and RSV, and then analyzed the time and age characteristics. RESULTS: Out of the 2854 cases, 758 (26.6%) were positive for influenza virus,including 547 (19.2%) influenza A virus positive samples and 211 (7.4%) influenza B virus positive samples. Usually, there were two peaks present in the annual curve of influenza virus, namely summer peak and winter/spring peak. The positive rate of influenza virus in 6-14 years old children (48.0%, 275/573) was significantly higher than that in 3-5 years old children (26.6%, 213/801) and that under 3 years old children (18.3%, 270/1480). The difference showed statistical significance (χ(2) = 187.432, P < 0.01). A total of 219 (7.7%) cases were positive for RSV,including 108 RSV-A positive samples and 112 RSV-B positive samples (1 co-infection). The epidemic of RSV showed an obvious seasonal pattern with peaks in autumn,winter and spring,which accounted for 96.8% (212/219) of all the cases; however, the annual incidence of RSV fluctuated greatly. The predominant subtype shifted every 2 years. RSV-B predominated during September 2008 and May 2009, December 2009 and March 2010, accounting for 76.6% (36/47) and 96.9% (62/64) respectively. RSV-A predominated during November 2010 and March 2011, September 2011 and April 2012, accounting for 92.5% (37/40) and 100.0% (48/48) respectively. With the increase of the age, the positive rate of RSV-A and RSV-B decreased gradually (RSV-A: χ(2) = 36.223, P < 0.01; RSV-B: χ(2) = 36.281, P < 0.01). The positive rates of RSV-A in children < 1,1,2,3,4,5-9 and 10-14 years old were 7.0% (26/373), 5.9% (39/662), 4.0% (18/445), 3.2% (13/406), 1.3% (3/236), 1.4% (7/517) and 0.9% (2/215) respectively; while, the positive rates of RSV-B in each age group were 6.4% (24/373), 6.0% (40/662), 4.5% (20/445), 4.4% (18/406), 1.3% (3/236), 1.0% (5/517) and 0.9% (2/215) respectively. The children aged 0-3 years old were more susceptible for RSV infection,accounting for 90.0% (197/219) of the total positive samples. During the outbreak of influenza A H1N1 in November 2009, the positive rate of RSW was 3.0% (3/100), lower than that in the same month of 2008, 2010 and 2011,which were separately 18.2% (6/33), 10.8% (10/93) and 10.0% (4/40). The difference showed statistical significance (χ(2) = 8.450, P < 0.05). During the outbreak of influenza A (H1N1) in January 2011,the positive rate of RSV was 5.7% (3/53), lower than those in the same month of 2009, 2010 and 2012, which was separately 21.7% (5/23), 28.6% (22/77) and 16.0% (8/50). The difference showed statistical significance (χ(2) = 11.233,P < 0.05). During the period of less influenza happened in September 2011, the RSV positive rate was 25.0% (10/40), higher than those in the same month of 2008, 2009 and 2010, which was separately 11.4% (4/35), 1.7% (2/118) and 0.0% (0/109). The difference showed statistical significance (χ(2) = 32.521, P < 0.01). CONCLUSION: Both influenza virus and RSV were important etiological agents of ILI of children in Wuhan. The characteristics of seasonal and age distributions of the two viruses were notably different; meanwhile, a certain inhibitional effect of influenza virus on RSV could be observed.

[Investigation on the distribution of avian influenza virus in external environment and the level of H5N1 antibody in poultry-exposed population in Wuhan].

OBJECTIVE: To survey the distribution of influenza A subtypes in external environment and investigate the infectious status of highly pathogenic avian influenza (H5N1) in poultry-exposed population in Wuhan. METHODS: Seventy-eight external environmental samples (water, cage surface and fecal samples) were collected from 3 habitats of wild migratory birds and 5 urban live-poultry markets in 2010. In 13 avian influenza monitoring points, 249 serum samples were collected from people living around habitats of wild migratory birds or working in live poultry markets. Real-time RT-PCR method was adopted to detect influenza A virus from external environmental samples; and multiple RT-PCR method and specific H3, H5, H7 and H9 primers were then applied to analyze the subtypes of the positive samples. The levels of H5N1 antibody in poultry-exposed population were tested by horse hemagglutination inhibition test and two avian influenza inactivated antigens: A/Hubei/1/10 and A/Anhui/1/05. RESULTS: Of the 50 external environmental samples collected from live poultry markets, 17 samples were determined to be influenza A virus positive (positive rate 34.0%), including specific subtypes as follows: 4 samples of H5 single-positive subtype, 3 samples of H9 single-positive subtype, 4 samples of H3 and H5 mixed-positive subtype, 2 samples of H3 and H9 mixed-positive subtype, 2 samples of H5 and H9 mixed-positive subtype, 2 samples of H3, H5 and H9 mixed-positive subtype, but no H7 positive subtype was found. The 28 external environmental samples collected from habitats of wild migratory birds were all influenza A virus negative. Considering different types of external environmental samples, the influenza A virus positive rates in water, cage surface and fecal samples were 37.5% (6/16), 16.7% (5/30) and 18.8% (6/32), respectively. There were total 100 samples of serum whose A/Hubei/1/10 antigen inhibiting titers ≥ 40, accounting for 40.2%; while 36 samples of serum (14.5%) whose A/Anhui/1/05 antigen inhibiting titers ≥ 40 were found. The difference had statistical significance (χ(2) = 41.433, P < 0.05). Among the 249 serum samples collected from poultry-exposed population, 5 samples were H5N1 antibody positive against A/Hubei/1/10 antigen (inhibition titer ≥ 160), which came from 4 different live poultry markets, however, no positive serum sample against A/Anhui/1/05 antigen was found. CONCLUSION: Multiple subtypes of avian influenza virus simultaneously prevailed in Wuhan urban poultry markets. Moreover, results from the distribution of avian influenza virus in external environment were consistent with the level of H5N1 antibody in poultry-exposed population.

[Phenols in seedling cortex of Magnolia officinalis from Enshi].

OBJECTIVE: To study the phenols in Cortex of Magnolia officinalis of biernial seedings produced in Enshi, Hubei. METHODS: The content of magnolol and honokiol in cortexes were determined by HPLC. The chromatograms of 10 samples seedling cortexes were recorded and compared. RESULTS: The content of magnolol and honokiol in Cortex of Magnolia officinalis of the seedlings from Enshi was higher than other samples. There were ten characteristic absorption bands in the HPLC chromatograms, which differed from the cortex of adult trees. CONCLUSION: The results can be used to identify the quality of the seedlings for the breeding.

[Influenza surveillance and antigenic and genetic characterization of predominant strains in Wuhan area in 2003].

OBJECTIVE: To study influenza epidemic and analyze antigenic and genetic characterization of the predominant strains in Wuhan area in 2003. METHODS: Epidemiological data and specimens from influenza patients were collected from surveillance sites weekly. Viruses were isolated from the specimens. Three H3 isolates were chosen to do antigenic analysis by hemagglutination inhibition (HI) test and their HA1 region was sequenced. RESULTS: Totally 58 influenza viruses were isolated from 418 specimens, 57 of them were identified as H3 subtype and 1 of them was B subtype; both monthly positive rate and numbers of influenza like illness had two peaks of winter and summer, the highest peak appeared in July. The 3 new H3 isolates were antigenically different from vaccine strain A/Panama/2007/99, 14 amino acid changes have been found in HA1 domain of these 3 strains compared with A/Panama/2007/99, phylogenetic analysis also confirmed the difference in HA1 domain. CONCLUSIONS: Influenza epidemic had two peaks in Wuhan area in 2003. The activity of H3 virus was strengthened remarkably. And they are antigenically and genetically different from the vaccine strain.