This tool helps identify the genotype of a viral sequence.

국내에서 발생하는 고병원성 조류인플루엔자 바이러스를 분리하여 해당 바이러스의 HA 유전자의 염기서열이다. 해당 유전자 정보를 이용하여 다양한 연구에 활용이 가능할 것으로 판단한다.

These data describe the results of virus isolation from oropharyngeal/cloacal swabs and testing of sera by a commercial blocking enzyme-linked immunosorbent assay (bELISA) and hemagglutinin (HA) specific testing by microneutralization (MN) and hemagglutination inhibition (HI) for Lesser Scaup in both the Atlantic and Pacific Flyways and Greater Scaup in the Pacific Flyway. These data support a USGS published manuscript.

Raw sequencing data as generated by the five different methods used are provided for each of the three samples used in the comparison. The files are in FASTQ format as exported from the Oxford Nanopore’s MK1C using MinION flowcells. Files are labeled according to the method (as described in the paper) and the Sample ID). The MK1C exports data in blocks of 6000 reads per FASTQ file and all the FASTQ files from each method and sample are grouped in a common folder.

,Influenza A virus in swine hemagglutinin (HA) gene sequence data for 9 virus strains.,,

Background Freshwater planarians are widely used as models for investigation of pattern formation and studies on genetic variation in populations. Despite extensive information on the biology and genetics of planaria, the occurrence and distribution of viruses in these animals remains an unexplored area of research. Results Using a combination of Suppression Subtractive Hybridization (SSH) and Mirror Orientation Selection (MOS), we compared the genomes of two strains of freshwater planarian, Girardia tigrina. The novel extrachromosomal DNA-containing virus-like element denoted PEVE (Planarian Extrachromosomal Virus-like Element) was identified in one planarian strain. The PEVE genome (about 7.5 kb) consists of two unique regions (Ul and Us) flanked by inverted repeats. Sequence analyses reveal that PEVE comprises two helicase-like sequences in the genome, of which the first is a homolog of a circoviral replication initiator protein (Rep), and the second is similar to the papillomavirus E1 helicase domain. PEVE genome exists in at least two variant forms with different arrangements of single-stranded and double-stranded DNA stretches that correspond to the Us and Ul regions. Using PCR analysis and whole-mount in situ hybridization, we characterized PEVE distribution and expression in the planarian body. Conclusions PEVE is the first viral element identified in free-living flatworms. This element differs from all known viruses and viral elements, and comprises two potential helicases that are homologous to proteins from distant viral phyla. PEVE is unevenly distributed in the worm body, and is detected in specific parenchyma cells.

,This repository contains scripts and data to replicate the experiments from Markin, A., Macken, C.A., Baker, A.L., and Anderson, T.K., 2024. Revealing reassortment in influenza A viruses with TreeSort. bioRxiv 2024.11.15.623781; doi: https://doi.org/10.1101/2024.11.15.623781,,,For the TreeSort tool and tutorial, see https://github.com/flu-crew/TreeSort.,Unzip TreeSort-experiments.zip and see the nested directories and README files for instructions to replicate the study.,- See 'simulations' directory for code and instructions to replicate the simulation study. - See 'IAV-reasortment-analysis' directory for data and code to replicate the analysis of reassortment rates and patterns among avian, swine, and human IAV lineages.,,Contact alexey.markn@usda.gov for questions.,,

Intraspecific variation in pathogen shedding impacts disease transmission dynamics; therefore, understanding the host factors associated with individual variation in pathogen shedding is key to controlling and preventing outbreaks. In this study, ileum and bursa of Fabricius tissues of wild-bred mallards (Anas platyrhynchos) infected with low-pathogenic avian influenza (LPAIV) were evaluated at various post-infection time points to determine genetic host factors associated with intraspecific variation in viral shedding. By analysing transcriptome sequencing data (RNA-seq), we found that LPAIV-infected wild-bred mallards do not exhibit differential gene expression compared to uninfected birds, but that gene expression was associated with cloacal viral shedding quantity early in the infection. In both tissues, immune gene expression was higher in high/moderate shedding birds compared to low shedding birds, and significant positive relationships with viral shedding were observed. In the ileum, expression for host genes involved in viral cell entry was lower in low shedders compared to moderate shedders at 1 day post-infection (DPI), and expression for host genes promoting viral replication was higher in high shedders compared to low shedders at 2 DPI. Our findings indicate that viral shedding is a key factor for gene expression differences in LPAIV-infected wild-bred mallards, and the genes identified in this study could be important for understanding the molecular mechanisms driving intraspecific variation in pathogen shedding. Citation information for this dataset can be found in Data.gov's References section.

,The dataset includes clinical data from an experimental swine and ferret challenge and transmission study with 3 strains of swine H1 influenza A virus. Data are presented in two spreadsheets, one for pigs and one for ferrets.,,

Data set containing avian influenza sampling information for late summer and early autumn waterfowl and gulls within and around the Izembek National Wildlife Refuge (NWR), Alaska, 2011-2016. Data contains species, age, sex, collection data and location of sampled migratory birds. Laboratory specific data used to identify presence and absence of influenza A viruses (IAVs) from collected samples are included.