Zylberberg, Maxine (ORCID: 0000-0002-2223-4620) Van Hemert, Caroline R. (ORCID: 0000-0002-6858-7165) Handel, Colleen M. (ORCID: 0000-0002-0267-7408) Liu, Rachel M. DeRisi, Joseph L. (ORCID: 0000-0002-4611-9205) 20200908 tabular digital data Anchorage, Alaska U.S. Geological Survey, Alaska Science Center Suggested Citation: Zylberberg, M., Van Hemert, C.R., Handel, C.M., Liu, R.M., DeRisi, J.L., 2020, Data associated with poecivirus testing of individual birds with beak deformities: U.S. Geological Survey data release, https://doi.org/10.5066/P9YQCHSR https://doi.org/10.5066/P9YQCHSR This data set is comprised of two tables, one with results of poecivirus screening of tissues from six North American avian species using PCR followed by Sanger sequencing in addition to unbiased metagenomic sequencing, the second lists the names and sequences of primers used. These data were collected to examine the potential connection between poecivirus and beak deformities in multiple avian species collected from 1999 - 2016 in Alaska and Maine. 19990329 20161108 observed Complete None planned Southcentral and Southeastern Alaska and Southeastern Maine. -149.91 -70.61 61.41 43.17 USGS Metadata Identifier USGS:ASC310 ISO 19115 Topic Category Biota Environment Health NASA GCMD Earth Science Keyword Thesaurus Animals/vertebrates Birds Waders/gulls/auks and allies Perching birds USGS CSA Biocomplexity Thesaurus Songbirds Migratory birds USGS Thesaurus Wildlife Terrestrial ecosystems Wildlife disease Genetics Polymerase chain reaction DNA sequencing NIH MeSH Thesaurus Viruses DNA primers None Emerging disease Avian keratin disorder Poecivirus Short-billed Gull Hairy Woodpecker Black-billed Magpie American Crow Red-breasted Nuthatch Blackpoll Warbler USGS Geographic Names Information System (GNIS) Alaska Maine None Sitta canadensis Corvus brachyrhynchos Dryobates villosus Pica hudsonia Larus brachyrhynchus Setophaga striata ITIS Integrated Taxonomic Information System Unknown database online ITIS-North America Taxonomic details were retrieved April 7, 2025 from the Integrated Taxonomic Information System on-line database https://www.itis.gov https://doi.org/10.5066/F7KH0KBK Avian species were identified by skilled observers in the field based on general appearance of feathers and plumage, behavior, and vocalization. Poecivirus was identified by the successful PCR amplification of a sequence with high pairwise nucleotide identity to Poecivirus (GenBank KU977108). Poecivirus was detected by reverse transcription followed by targeted PCR and Sanger sequencing and by unbiased metagenomic sequenceing. Taxonomy is complete for all samples. No voucher specimens were collected. Kingdom Animalia Subkingdom Bilateria Infrakingdom Deuterostomia Phylum Chordata Subphylum Vertebrata Infraphylum Gnathostomata Superclass Tetrapoda Class Aves Order Passeriformes Family Sittidae Genus Sitta Species Sitta canadensis TSN: 178784 Family Corvidae Genus Corvus Species Corvus brachyrhynchos TSN: 179731 Genus Pica Species Pica hudsonia TSN: 726117 Family Parulidae Genus Setophaga Species Setophaga striata TSN: 950041 Order Piciformes Family Picidae Subfamily Picinae Genus Leuconotopicus Species Leuconotopicus villosus Order Charadriiformes Family Laridae Genus Larus Species Larus brachyrhynchus TSN: 1192602 No access constraints. No use constraints. These data are marked with a Creative Common CC0 1.0 Universal License and are in the public domain. It is requested that this USGS data release be cited for any subsequent publications that reference or utilize these data. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. U.S. Geological Survey, Alaska Science Center Mailing and Physical

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Anchorage Alaska 99508 USA 907-786-7000 gs-ak_asc_datamanagers@usgs.gov Laboratory work was conducted at the University of California Department of Biochemistry and Biophysics San Francisco, CA. FGDC metadata was prepared by Danielle Gerik of the U.S. Geological Survey, Alaska Science Center. Zylberberg, M. Van Hemert, C.R. Handel, C.M. Liu, R.M. DeRisi, J.L. 2021 journal article Journal of Wildlife Diseases 57(2):273-281 online Wildlife Disease Association Zylberberg, M., Van Hemert, C.R., Handel, C.M., Liu, R.M., DeRisi, J.L., 2021. Poecivirus is present in individuals with beak deformities in seven species of North American birds. Journal of Wildlife Diseases 57(2):273-281. https://doi.org/10.7589/JWD-D-20-00017 https://doi.org/10.7589/JWD-D-20-00017 Individual specimen ID's, taxonomic identification, collection locations, collection dates, and primer sets were cross-checked and verified to match lab data. We observed sterile techniques in the handling of all samples. Positive and negative controls were included in all RT and PCR assays. When testing of beak and cloaca tissue samples from the same individual resulted in contradictory results, PCR tests were confirmed in triplicate; in each case, the results for each individual tissue were consistent across replicates. Attribute values fall within expected ranges. Data were proofed for the presence of duplication and omission. Avian tissues that tested negative for Poecivirus were designated "nd" (not detected). Avian tissues that tested positive are indicated by specifying the tissue type (See Attribute Definitions for details). No data were omitted and there are no missing data. FIELD: We opportunistically obtained specimens with grossly deformed beaks from 1999-2016. Birds were either euthanized after capture, shot, or collected after dying in the wild. Specimens were stored frozen at -20°C until processed. Unknown LAB: Total RNA was extracted from beak and cloacal tissues. A total of 200 ng of RNA was reverse transcribed in 10 μl reactions containing 100 pmol random hexamer, 1x reaction buffer, 5 mM dithiothreitol, 1.25 mM (each) deoxynucleoside triphosphates (dNTPs), and 100 U Superscript III (Life Technologies, Carlsbad, CA, USA); mixtures were incubated at 25°C for 5 min, 42°C for 60 min, and 70°C for 15 min. cDNA was screened via polymerase chain reaction (PCR) amplification using Poecivirus-specific primers. PCR mixtures contained 1x iProof master mix (Bio-Rad Laboratories, Hercules, CA, USA), 0.5 M primer, and 5µl cDNA. Thermocycler conditions were set at 98°C for 30s, then 40 cycles of 98°C for 10 s, 58-62°C for 10 s, and 72°C for 30 s, then a 5-min elongation step of 72°C. Annealing temperature was optimized for each set of primers using a gradient cycler. Amplicons were visualized on 1.5% agarose gels; those in the correct size range were extracted and purified using a Zymoclean gel DNA recovery kit (Zymo Research, Irvine, CA, USA) and Sanger sequenced (Quintara Biosciences, South San Francisco, CA, USA). Samples were prepped for high-throughput sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s protocol. Sequencing was conducted on the Illumina HiSeq 4000 using a single sequencing lane and resulted in 135-nucleotide-long paired-end reads. Additional methodological details are available in Zylberberg et al. 2021 (cross-referenced publication). Unknown Point 0.001 0.001 Decimal degrees World Geodetic System of 1984 World Geodetic System of 1984 6378137 298.257223563 poecivirus_geneticsAvianHosts_sampleData_zylberberg_1999_2016.csv Table with specimen information and results of unbiased metagenomic sequencing and PCR screening for poecivirus using 12 different primers. Presented in a Comma Separated Value (CSV) formatted table. Author Defined Specimen_ID Lab-assigned unique numeric identification code for each individual bird. Author Defined Unique Identifier: numeric value Common_name Common name of bird species. Details provided in the Taxonomy section of this metadata record. Author Defined Common name of bird species. Scientific_name Scientific name of bird species. Details provided in the Taxonomy section of this metadata record. Author Defined Scientific name of bird species. Latitude Latitude of sampling location in the field. Author Defined 43.17 61.41 Decimal degrees (WGS84) Longitude Longitude of sampling location in the field. Author Defined -149.91 -70.61 Decimal degrees (WGS84) Collection_date Date of sampling event in the field. Author Defined 1999-03-29 2016-11-08 Date (YYYY-MM-DD) BCCHpic_2 through Poeci_14 These 12 columns represent poecivirus detection by 12 different pairs of DNA primers. Attribute values indicate the tissue type in which the virus was detected. Forward and reverse sequences of each primer are provided in the other table included with this data package "poecivirus_primerDefinitions_zylberberg_1999_2016.csv" Author Defined beak Poecivirus detected from sample of beak tissue Author defined cloaca Poecivirus detected from sample of cloacal tissue Author defined nd Poecivirus not detected Author defined GenBank_accession_numbers GenBank Accession Number. A unique identifier (assigned by the National Center for Biotechnology Information; NCBI) for the genome sequences from either Sanger or unbiased metagenomic sequencing. This number may be used to retrieve sequence information from the NCBI GenBank database https://www.ncbi.nlm.nih.gov/genbank NCBI GenBank Unique Identifier: an alphanumeric accession number available in the NCBI GenBank database Genomic_coverage Coverage of the genome represented. Either partial or complete. Author defined partial The sequence is a partial genomic sequence. Author defined complete The sequence is a complete genomic sequence. Author defined poecivirus_geneticsAvianHosts_primers_zylberberg_1999_2016.csv Table with primer sequences used to screen for poecivirus. Presented in a Comma Separated Value (CSV) formatted table. Author Defined Primer_name Name of the primer. Primer names that are identical except for the final characters (F = forward, or R = reverse) indicate these primers were used as a pair for the amplification and identification of poecivirus cDNA. Author defined Unique Identifier: alphanumeric identifier for each primer sequence. Sequence DNA sequence of the primer. Author defined DNA sequence of the primer. U.S. Geological Survey USGS ScienceBase Team Mailing and Physical

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Denver Colorado 80225 USA 1-888-275-8747 sciencebase@usgs.gov The U.S. Geological Survey, Alaska Science Center is the authoritative source of these data, distributed by ScienceBase (a USGS Trusted Digital Repository). 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, no warranty expressed or implied is made regarding the display or utility of the data for other purposes or on all computer systems, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. CSV Tabular data in CSV format; FGDC metadata in XML and HTML formats. https://doi.org/10.5066/P9YQCHSR None 20250411 U.S. Geological Survey, Alaska Science Center Mailing and Physical

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Anchorage Alaska 99508 USA 907-786-7000 gs-ak_asc_datamanagers@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (CSDGM) FGDC-STD-001.1-1999