Daniel Grear Jeffrey M Lorch 20250328 spreadsheet https://doi.org/10.5066/P903JHON Sabrina S. Greening Julie C. Ellis Nicole L. Lewis David B. Needle Cristina M. Tato Susan Knowles Valerie Shearn-Bochsler Jaimie L. Miller Daniel A Grear Jeffrey M. Lorch David S. Blehert Caitlin Burrell Lisa A. Murphy Erica A. Miller C. Brandon Ogbunugafor Andrea J. Ayala W. Kelley Thomas Joseph L. Sevigny Lawrence M. Gordon Tessa Baillargeon Lusajo Mwakibete Megan Kirchgessner Christine L. Casey Ethan Barton Michael J. Yabsley Eman Anis Roderick B. Gagne Patrice Klein Cindy Driscoll Chelsea A. Sykes Robert H. Poppenga Nicole M. Nemeth 20250111 publication Veterinary Sciences vol. 12, issue 1 n/a MDPI AG ppg. 48 https://doi.org/10.3390/vetsci12010048 This data set describes post-mortem examination of avian species from a rapid response to a wildlife health event. We reported on the response to a 2021 mortality event in wild passerines in the eastern US. Early ground efforts by wildlife rehabilitators and veterinarians, with public participation, fueled rapid responses by government agencies including sample submission and evaluation, information sharing, and coordinated messaging. Extensive diagnostic evaluations failed to reveal a common cause, in part, because thorough epidemiologic investigations were lacking. These data were collected to investigate the cause of death and morbidity in wild passerines throughout the eastern US on summer 2021 20210520 20210822 ground condition Complete None planned United States -103.9746 -74.5313 47.2196 24.5271 ISO 19115 Topic Category biota None Songbird Mass mortality Outbreak response Passerine Conjunctivitis Diagnostic evaluation USGS Thesaurus wildlife wildlife disease USGS Metadata Identifier USGS:64552b9fd34eefd5da84e1b6 None USGS National Wildlife Health Center Common geographic areas Maryland District of Columbia Florida Wisconsin Ohio Nebraska None. Please see 'Distribution Info' for details. None. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. Daniel A Grear U.S. Geological Survey mailing address

6006 Schroeder Road

Madison WI 53711 US 608-270-2478 608-270-2415 dgrear@usgs.gov None. All values within expected ranges. All data included. We performed a standard post-mortem investigation of carcasses that were submitted either chilled or frozen to the U.S. Geological Survey National Wildlife Health Center. Gross and microscopic evaluations were performed by board certified veterinary pathologists. Gross examinations included descriptions of all abnormal observations of external structures and internal tissues; evaluation of body condition based on presence and amount of subcutaneous, visceral, and epicardial fat stores; and examination of gastro-intestinal tract contents. Tissue samples that included heart, lung, liver, kidney, spleen, gastrointestinal tract, and brain were collected, fixed in 10% neutral buffered formalin, dehydrated, embedded in paraffin, sectioned at 5 µm, and stained with H&E for histopathological examination (Luna, 1968). Microorganism identification included avian influenza virus and avian paramyxovirus from tracheal and cloacal swabs using real-time quantitative polymerase chain reaction (NVSL-SOP-0068 rev 04, USDA); West Nile virus from spleen and kidney tissue using real-time quantitative polymerase chain reaction (Lanciotti et al., 2000); Salmonella bacteria from culture of gastro-intestinal tissue (Fu et al., 2022); Chlamydia bacteria from PCR of multiple organ tissue (Sachse and Hotzel, 2003); and Mycoplasma bacteria identification from PCR of eye tissue, conjunctiva, and other tissue (Rebelo et al., 2011). Fu, Y., M’ikanatha, N.M., Whitehouse, C.A., Tate, H., Ottesen, A., Lorch, J.M., Blehert, D.S., Berlowski-Zier, B., Dudley, E.G., 2022. Low occurrence of multi-antimicrobial and heavy metal resistance in Salmonella enterica from wild birds in the United States. Environ. Microbiol. 24, 1380–1394. doi:10.1111/1462-2920.15865 Lanciotti, R.S., Kerst, A.J., Nasci, R.S., Godsey, M.S., Mitchell, C.J., Savage, H.M., Komar, N., Panella, N.A., Allen, B.C., Volpe, K.., Davis, B.S., Roehrig, J.T., 2000. Rapid detection of West Nile virus from human clinical specimens, field-collected mosquitoes, and avian samples by a TaqMan reverse transcriptase-PCR assay. J. Clin. Microbiol. 38, 4066–4071. doi:10.1128/jcm.38.11.4066-4071.2000 Luna, L.G., 1968. Manual of histologic staining methods of the Armed Forces Institute of Pathology, 3rd Editio. ed. Blakiston Division, McGraw-Hill, New York, New York. Rebelo, A.R., Parker, L., Cai, H.Y., 2011. Use of high-resolution melting curve analysis to identify mycoplasma species commonly isolated from ruminant, avian, and canine samples. J. Vet. Diagnostic Investig. 23, 932–936. doi:10.1177/1040638711416846 Sachse, K., Hotzel, H., 2003. Detection and differentiation of Chlamydiae by nested PCR, in: Methods in Molectular Biology. Humana Press, Clifton, N.J., pp. 123–136. doi:10.1385/1-59259-344-5:123 USDA, National Laboratory Animal Health Network. 2022. Real-time RT-PCR detection of influenza type A and avian paramyxovirus type-1. NVSL-SOP-0068-04. 20210520 GrearLorch2023_data.csv Comma Separated Value (CSV) file containing data. Producer Defined Identifier unique identifier for the carcass Producer Defined unique identifier for the carcass Species Common name of the species, according to: Chesser, R. T., S. M. Billerman, K. J. Burns, C. Cicero, J. L. Dunn, B. E. Hernández-Baños, R. A. Jiménez, A. W. Kratter, N. A. Mason, P. C. Rasmussen, J. V. Remsen, Jr., D. F. Stotz, and K. Winker. 2022. Check-list of North American Birds (online). American Ornithological Society. https://checklist.americanornithology.org/taxa/ Producer Defined << empty cell >> No Data Producer defined Blue Jay Blue Jay Producer defined Common Grackle Common Grackle Producer defined European Starling European Starling Producer defined American Robin American Robin Producer defined State State where the carcass was collected. 2 letter abbreviation for U.S. states or full name Producer Defined << empty cell >> No Data Producer defined MD Maryland Producer defined DC District of Columbia Producer defined FL Florida Producer defined OH Ohio Producer defined WI Wisconsin Producer defined NE Nebraska Producer defined County County where the caracass was collected Producer Defined Montgomery Montgomery County Producer defined Frederick Frederick County Producer defined District of Columbia District of Columbia Producer defined Lee Lee County Producer defined Delaware Delaware County Producer defined Franklin Franklin County Producer defined Hamilton Hamilton County Producer defined Prince Georges Prince Georges County Producer defined Pierce Pierce County Producer defined Lancaster Lancaster County Producer defined Date Collected date the carcass was collected, MM/DD/YYYY Producer Defined 5/20/2021 8/22/2021 Age Age of the carcass Values = Adult, Immature (juvenile), Subadult (adolescent), Nestling or suckling, not recorded Producer Defined juvenile juvenile Producer defined Sex Sex of the carcass. Values = M, F, U, NE. NE = not examined Producer Defined M Male Producer defined F Female Producer defined U Unknown Producer defined Nutritional condition Nutritional condition determined by amount of subcutaneous, visceral, and epicardial fat stores Producer Defined good good Producer defined fair fair Producer defined poor poor Producer defined emaciated emaciated Producer defined Euthanized Indicator if the cause of death was euthanasia. Values = Yes, No Producer Defined No No Producer defined Yes Yes Producer defined Periocular swelling Indicator if there was observation of periocular swelling on gross exam. Values = Yes, No, NE. NE = not examined Producer Defined No No Producer defined Yes Yes Producer defined NE Not examined Producer defined Gross signs of conjunctivitis or blepharitis Indicator if there was observation of conjuctivitis or blepharitis on gross exam. Values = Yes, No, NE. NE = not examined Producer Defined Yes Yes Producer defined No No Producer defined Mycoplasma detected Detection and speciation of Mycoplasma organisms. Species name, 0 = none detected, NT = not tested Producer Defined M. sturni M. sturni detected Producer defined 0 none detected Producer defined NT not tested Producer defined Chlamydia detected Indicator if Chlamydia organism was detected. Values = Yes, No, NT. NT = not tested Producer Defined No No Producer defined NT Not tested Producer defined Salmonella spp. detected Indicator if Salmonella organism was detected. Values = Yes, No, NT. NT = not tested Producer Defined NT Not tested Producer defined No No Producer defined Trichomonas detected Indicator if Trichomonas organism was detected. Values = Yes, No, NT. NT = not tested Producer Defined NT Not tested Producer defined Avian influenza detected Indicator if Avian Influenza virus was detected. Values = Yes, No, NT. NT = not tested Producer Defined No No Producer defined APMV detected Indicator if Avian Paraomyxovirus type 1 was detected. Values = Yes, No, NT. NT = not tested Producer Defined No No Producer defined NT Not tested Producer defined West Nile virus detected Indicator if West Nile virus was detected. Values = Yes, No, NT. NT = not tested Producer Defined No No Producer defined NT Not tested Producer defined GCMS Note of any known toxic substances or pesticide subtances detected with Gas Chromatography and Mass Spectrometry (GCMS). Values are names of compounds, wnl = sample tested and all compounds detected within normal linits; NT = not tested Producer Defined << empty cell >> No Data Producer defined Note of any known toxic substances or pesticide subtances detected with Gas Chromatography and Mass Spectrometry (GCMS). Values are names of compounds, wnl = sample tested and all compounds detected within normal linits; NT = not tested ICP-MS Note of any known toxic substances or pesticide subtances detected with Induced Coupled Plasma Mass spectrometry (ICPMS). Values are names of compounds, wnl = sample tested and all compounds detected within normal linits; NT = not tested Producer Defined NT Not tested Producer defined conjunctivitis Indicator if Inflamation of the conjunctiva was observed histopathologically. Values = Yes, No, NE. NE = not examined Producer Defined << empty cell >> No Data Producer defined Yes Yes Producer defined No No Producer defined NE Not examined Producer defined blepharitis Indicator if Inflamation of the eyelid was observed histopathologically. Values = Yes, No, NE. NE = not examined Producer Defined Yes Yes Producer defined NE Not examined Producer defined No No Producer defined edema of eyelid Indicator if edema in the eyelid was observed histopathologically. Values = Yes, No, NE. NE = not examined Producer Defined Yes Yes Producer defined No No Producer defined NE Not examined Producer defined periocular swelling Indicator if periocular swelling was observed histopathologically. Values = Yes, No, NE. NE = not examined Producer Defined No No Producer defined Yes Yes Producer defined NE Not examined Producer defined inflammation of cornea Indicator if Inflamation of the cornea was observed histopathologically. Values = Yes, No, NE. NE = not examined Producer Defined No No Producer defined Yes Yes Producer defined NE Not examined Producer defined inflammation of internal ocular structures Indicator if Inflamation of iris, ciliary body, or uvea was observed histopathologically. Values = Yes, No, NE. NE = not examined Producer Defined Yes Yes Producer defined No No Producer defined NE Not examined Producer defined inflammation of brain Indicator if Inflamation of the brain was observed histopathologically. Values = Yes, No, NE. NE = not examined Producer Defined No No Producer defined Yes Yes Producer defined skull fracture Indicator if skull fracture was observed histopathologically. Values = Yes, No, NE. NE = not examined Producer Defined No No Producer defined Yes Yes Producer defined hemmorhage around eye Indicator if hemmorhage around the eye was observed histopathologically. Values = Yes, No, NE. NE = not examined Producer Defined No No Producer defined Yes Yes Producer defined cicadas Indicator if cicada insects were observed in gastrointestinal tract. Values = Yes, No, NE. NE = not examined Producer Defined No No Producer defined trauma Indicator if evidence of trauma was observed on gross examination. Values = Yes, No, NE. NE = not examined Producer Defined No No Producer defined Yes Yes Producer defined U.S. Geological Survey GS ScienceBase mailing address

Denver Federal Center, Building 810, Mail Stop 302

Denver CO 80225 United States 1-888-275-8747 sciencebase@usgs.gov Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty. Digital Data https://doi.org/10.5066/P903JHON None 20250328 Daniel A Grear U.S. Geological Survey mailing address

6006 Schroeder Road

Madison WI 53711 US 608-270-2478 608-270-2415 dgrear@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata FGDC-STD-001.1-1999