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Fig. 7 in New molecular data help clarify the taxonomy of Central European avian Dicrocoeliidae Looss, 1899 (Trematoda: Plagiorchiida)

Fig. 7. Representative photographs of slides with Lyperosomum tenori sp. n. (upper part of the figure) and Lyperosomum hirundinis sp. n. (lower part of the figure). Host species, sampling dates and host identification numbers are indicated. All specimens originated from the Czech Republic. Photographs of L. hirundinis sp. n. are composite photographs merged from multiple images. Note that the seeming differences in forebody shape of L. tenori sp. n. individuals is caused by differences in handling with host birds prior the fixation of the trematodes - L. tenori sp. n. from hosts that were frozen prior the examination are highly susceptible to forebody prolongation.

Fig. 11 in New molecular data help clarify the taxonomy of Central European avian Dicrocoeliidae Looss, 1899 (Trematoda: Plagiorchiida)

Fig. 11. Representative photographs of slides with Stromitrema acrocephali sp. n. and Lutztrema atricapillae. Host species, sampling dates and host identification numbers are indicated. All specimens originated from the Czech Republic.

Fig. 6 in New molecular data help clarify the taxonomy of Central European avian Dicrocoeliidae Looss, 1899 (Trematoda: Plagiorchiida)

Fig. 6. Drawings of holotype specimens of Lyperosomum tenori sp. n. (A), Lyperosomum atricapillae sp. n. (B), Stromitrema acrocephali sp. n. (C), Lutztrema atricapillae sp. n. (D), and Lyperosomum hirundinis sp. n. (E–F).

Fig. 8 in New molecular data help clarify the taxonomy of Central European avian Dicrocoeliidae Looss, 1899 (Trematoda: Plagiorchiida)

Fig. 8. Representative photographs of slides with Lyperosomum atricapillae sp. n. Host species, sampling dates and host identification numbers are indicated. All specimens originated from the Czech Republic.

Fig. 6 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 6. Analysis of the sensitivity and specificity of the P. relictum MSP-1 capture antigen-based ELISA. Serial dilutions of normal chicken serum and three sera samples from P. relictum-infected penguins (8776, 8783 and 8784) were used for coating the assay wells. Each dilution was performed in triplicate, and the data shown represent means of three independent experiments with standard error bars and levels of statistical significance (****: P <0.0001).

Fig. 4 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 4. Validation of ELISA. The ELISA developed using P. relictum MSP-1 protein was tested with known P. relictum positive penguin serum collected from penguin # 8790 at week 26. Black column represents positive penguin serum. Hatched and white columns represent negative controls containing normal chicken serum and PBS, respectively. Grey column represents the positive reaction containing streptavidin alkaline-phosphatase and its substrate pnitrophenyl phosphate. Each reaction was performed in triplicate, and the data shown represent means of three independent experiments with standard error bars and levels of statistical significance (****: P <0.0001).

Fig. 2 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 2. Verification of the biotinylation of recombinant P. relictum MSP-1. Purified recombinant P. relictum MSP-1 protein was labeled with biotin. Biotinylation of MSP-1 was confirmed using an enzyme (streptavidin alkaline phosphatase)-linking assay and absorbance read at 405 nm indicated the presence of biotinylated MSP-1. Black column represents biotinylated MSP-1 protein. Hatched column and white column represent negative controls containing non-biotinylated MSP-1 and PBS, respectively. Grey column represents the positive control containing streptavidin alkaline-phosphatase (SAP) and its substrate p-nitrophenyl phosphate (PNPP). Each reaction was performed in triplicate, and the data shown represent means of three independent experiments with standard error bars and levels of statistical significance (****: P <0.0001).

Fig. 3 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 3. Biotin-labeled MSP-1 protein titration curve. Serially diluted (300 ng/ μL to 0.003 ng/μL) biotinylated MSP-1 was used for coating the surfaces of the reaction wells overnight at 4 ◦C. The amount of biotinylated MSP-1 immobilized on the surface of the well was proportional to the intensity of the colored product generated which in turn was proportional to the absorbance value measured at 405 nm wavelength. Reactions were performed in triplicate, and the data shown represent means of three independent experiments with standard error bars.

Fig. 7. MSP-1 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 7. MSP-1 capture antigen-based ELISA analysis of 370 sera samples collected from 11 penguins during three consecutive seasons of Spring (March to May), Summer (June to August) and Fall (September to November). (A) ELISA absorbance readings for the 370 sera samples collected from Spring to Fall are arranged in ascending order. Time of collection is indicated by color. Light grey represents Spring, dark grey represents Summer, and black represents Fall. Black dashed line indicates the single cut-off point (0.488) determined by change-point analysis. (B) Left: percentage of positive (A405 ≥ 0.488) and negative (A405 <0.488) sera samples; Right: distribution of positive samples in Spring (March to May), Summer (June to August), and Fall (September to November). (C) Percentage of penguin sera samples that tested positive (A405> = 0.488) in each month from March to November.

Fig. 5. P. relictum MSP-1 in Plasmodium relictum MSP-1 capture antigen-based ELISA for detection of avian malaria antibodies in African penguins (Spheniscus demersus)

Fig. 5. P. relictum MSP-1 capture antigen-based ELISA analysis of test sera from penguins. Sera samples (370 total) from eleven penguins collected from Spring through Fall season were used as test samples in the assay to determine anti-P. relictum antibodies level. Light grey, dark grey, and black columns represent penguin sera samples collected in Spring, Summer, and Fall, respectively. Panel A–K represents ELISA results for individual penguins' sera collected at different time points from Spring to Fall. Panel L represents average ELISA absorbances for all 11 penguins at different sampling points. Each sample was assayed in triplicate, and the data shown represent means of three independent experiments with standard error bars.

Fig. 5 in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification

Fig. 5 Percentage of template sequences coverage of the primer subsets analyzed on the second evaluation round. The red dashed line represents the complete coverage of the analyzed template sequences

Fig. 4 Primers binding position distributed along the 1,500 in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification

Fig. 4 Primers binding position distributed along the 1,500 bp of the avian COI gene. A Binding position of forward primers. B Binding position of reverse primers

Fig. 3 in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification

Fig. 3 Effect of the number of allowed primer-template mismatches on primer binding. Y-axis = number of primers with at least one binding event on every scenario of allowed mismatches (X-axis)

Fig. 1 Retrieved data distribution. A in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification

Fig. 1 Retrieved data distribution. A Distribution of published primers for the barcode region of the avian COI gene throughout the years. B Number of complete COI sequences available for each bird order

Fig. 2 in Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification

Fig. 2 Variation on the number of primers bound to the template sequences of each bird order. The dots represent data outliers

opencc-by-4.0May 2024View details →

Extra tables and fastq files for "Virome Sequencing Identifies H5N1 Avian Influenza in Wastewater from Nine Cities."

Tables: "mutation_analysis.xlsx" = detailed notes on variant analysis of H5N1 reads. "TEPHI_samples_H5N1_status1.xlsx" = Table of samples with metadata and H5N1 status "BioSampleObjects.txt" = Table from SRA mapping BioSample IDs to library (sample) IDs   H5N1_reads_thru_p1858: Paired-end Illumina read files (.fastq) from all samples. Includes automated H5N1 called reads from iav_serotype tool from samples that were manually validated to have H5N1 specific reads.

opencc-by-4.0Oct 2020View details →

Fig. 4 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease

Fig. 4 Replication of yellow-legged seagull-derived WNV in Vero and C6/36 cells. Cytopathic effect (left) was observed after one passage in both cell lines. The control cells (right) were grown under the same conditions. Scale-bars: 100 µM

opencc-by-4.0Oct 2020View details →

Fig. 5 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease

Fig. 5 Phylogenetic analysis of West Nile viruses (WNVs) from avian and equine hosts studied in Israel during 2016 and 2018. The analysis was conducted on a nucleotide sequence of the genes encoding the capsid, pre-membrane protein, and membrane protein, using the neighbor-joining method implemented in MEGA X software. The robustness of branching pattern was tested by 1000 bootstrap replications. The rates among sites algorithm used was gamma distribution with invariant sites (G+I). The bar denotes 0.02 nucleotide substitutions per site. Lineage 1 and 2 reference strains are present with country and year of isolation. The GenBank annotated sequences are underlined and the sequences obtained in this study (during 2016 and 2018) are marked with rectangles

opencc-by-4.0Oct 2024View details →

Data complementing the Avian influenza overview June - September 2024

Data complementing the Avian influenza overview June - September 2024   Annex A – Data on birds The annex contains figures and tables on HPAI virus detections in birds in Europe as well as a description of the vaccination campaign implemented in France in 2023–2024. Annex B – Characteristics of the HPAI-affected poultry establishments The annex contains a table with the characteristics of the HPAI-affected poultry establishments by affected European country submitted to ADIS between 15 June and 20 September 2024. Annex C – Data on virus sequences The annex contains information on authors, originating and submitting laboratories of the sequences from GISAID's EpiFlu™ Database on which this research is based. All data submitters may be contacted directly via <a title="https://eur03.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.gisaid.org%2f&data=05%7c02%7c%7cbccd5bb40f5e4a4ccee508dbfbeb3823%7c406a174be31548bdaa0acdaddc44250b%7c1%7c0%7c638380763212264062%7cunknown%7ctwfpbgzsb3d8eyjwijoimc4wljawmdailcjqijoiv2lumziilcjbtii6ik1hawwilcjxvci6mn0%3d%7c3000%7c%7c%7c&sdata=yxkh9bn0bh3m4pak8dja4mkdj1ptc6%2fyqioei05qg1m%3d&reserved=0" href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gisaid.org%2F&data=05%7C02%7C%7Cbccd5bb40f5e4a4ccee508dbfbeb3823%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C638380763212264062%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Yxkh9bN0bH3m4Pak8DJa4Mkdj1PTc6%2FYqIoei05qg1M%3D&reserved=0" target="_blank" rel="noreferrer noopener">www.gisaid.org</a>.