Tag: NCBI Virus

Access Avian Influenza A (H5N1) Virus Sequences from the Current Outbreak at NCBI

The U.S. Centers for Disease Control and Prevention (CDC) has been monitoring the ongoing outbreak of the avian influenza A (H5N1) virus. This is widespread globally in wild birds, and has led to sporadic outbreaks in poultry, cows, several species of wild animals, and has been detected in exposed humans. The CDC recently sequenced the H5N1 virus in two respiratory specimens collected from a U.S. patient who was severely ill and has now died (PQ809549-PQ809564).

As previously announced, the GenBank sequences, annotations, and metadata including from this patient are available through NLM’s NCBI resources. Continue reading “Access Avian Influenza A (H5N1) Virus Sequences from the Current Outbreak at NCBI” →

NCBI Taxonomy: Upcoming Changes to Viruses

To reflect changes to the International Code of Virus Classification and Nomenclature (ICVCN) made by the International Committee on Taxonomy of Viruses (ICTV), NCBI will add binomial species names to about 3000 viruses. These updates to NCBI Taxonomy are planned for spring 2025, but you can view the changes now in the ICTV’s Virus Metadata Resource.

We recognize that the former species names like Human immunodeficiency virus 1 (HIV-1) are broadly used in public health, educational institutions, and research. To minimize the impact of this change on those who use NCBI resources, we will add the new binomial species names (e.g. Lentivirus humimdef1) while keeping the former names available in the lineage for each species. The former names will move below the new binomial species name in the taxonomy hierarchy, ensuring continuity. Examples are provided below.  Continue reading “NCBI Taxonomy: Upcoming Changes to Viruses” →

Quick & Easy Access to Mpox Data Through NCBI Virus

The World Health Organization (WHO) declared the recent upsurge of the mpox virus to be a public health emergency of international concern. Having timely viral genome data freely and widely available enables researchers to explore how this virus differs from viruses isolated and sequenced in the past. Therefore, NCBI’s GenBank is expediting the release of mpox data by annotating gene and coding region features as part of the submission process. Continue reading “Quick & Easy Access to Mpox Data Through NCBI Virus” →

Coming Soon! Rapid Access to Influenza Data

Improved Influenza GenBank submission process

Do you submit flu sequences to GenBank? Thanks to community feedback, NCBI is excited to announce that we are improving the influenza GenBank submission process. We continue to play a key role in providing the biomedical community free and easy access to genome sequences from viruses. To further advance public health research, in the coming weeks we will begin to expedite the release of influenza data. This means you will see the rapid assignment of accession numbers and data becoming publicly accessible within hours. In addition, we will automatically process all Influenza genomes to produce standardized, consistent annotation which saves you time and benefits the researchers who find your data valuable. Continue reading “Coming Soon! Rapid Access to Influenza Data” →

Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus

NCBI Virus now offers genomes for viruses such as Influenza A by using an automated process to group segments from the same samples. We group these segments into genomes based on metadata for the sample including species, isolate name, host organism, collection date, and location. Newly released GenBank records are added daily.

Access these genome assemblies through NCBI Virus using the new “NCBI Virus Assembly” tab above the Results Table as shown below. Continue reading “Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus” →

New Data Available! Access Avian Influenza A (H5N1) Virus Sequences at NCBI

Sequence data from the ongoing avian influenza A (H5N1) virus outbreak in cattle are now available through NLM’s NCBI resources NCBI Virus and NCBI Datasets.

These data were submitted by the U.S. Department of Agriculture (USDA), U.S. Centers for Disease Control and Prevention (CDC), the World Health Organization (WHO), Iowa State University, and St. Jude Children’s Research Hospital. Continue reading “New Data Available! Access Avian Influenza A (H5N1) Virus Sequences at NCBI” →

Upcoming Changes to Virus Data Resources at NCBI

Effective June 2024, NCBI Virus will replace legacy virus web resources

Coming soon! As part of our ongoing effort to enhance your experience and modernize our services, several of our legacy virus-related web resources will be replaced by NCBI Virus – our community portal for viral sequence data. NCBI Virus is more comprehensive, modernized, and has more powerful features and analysis tools than our legacy resources.

What will change?

Below is a list of the legacy virus resources that will be replaced by NCBI Virus. The list includes a description of features that will continue to be supported through NCBI Virus: Continue reading “Upcoming Changes to Virus Data Resources at NCBI” →

NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data

Millions of SARS-CoV-2 samples from around the world have been made publicly available as assembled and unassembled sequence data in GenBank and the Sequence Read Archive (SRA). Now you can find sequences with a particular mutation by searching with the protein and the amino acid change (e.g. S:F486V). Visit our SARS-CoV-2 Variant Overview on NCBI Virus and click on the ‘Mutation’ tab to get started (Figure 1).

Figure 1: SARS-CoV-2 Variants Overview. Arrows indicate important features on the page, including the “Lineages” and “Mutations” tabs to switch between views, the search box, and the information box describing the mutation format. The results are also indicated, including a summary of the total records found that contain the searched term as well as the results table. Continue reading “NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data” →

NCBI SARS-CoV-2 Resources Page Will Redirect Soon

End of the COVID-19 Public Health Emergency

During the COVID-19 pandemic, we provided the NCBI SARS-CoV-2 Resources Page as a central location to help you quickly and easily find our SARS-CoV-2 related content and tools. Since the federal public health emergency is now over, this page will be redirected to the SARS-CoV-2 Data Hub in NCBI Virus effective August 1, 2023.

Don’t worry! All this information will remain available. Check out the NLM Knowledge Base to access a list of NCBI SARS-CoV-2 data and tools.

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Questions?

If you have questions or would like to provide feedback, please reach out to us at info@ncbi.nlm.nih.gov.

Download Randomized Data Subset from NCBI Virus

Do you need a smaller dataset for your analyses of virus data? In response to your feedback, NCBI Virus now allows you to download a randomized subset of your results for nucleotide, protein, or RefSeq genome sequences from any supported virus (Figure 1). This option is useful for viruses such as SARS-CoV-2 or Influenza A that have very large numbers of records, where the entire dataset may present a challenge. In such cases, a smaller representative sample is easier to work with to support your analysis. You can also reduce the bias in a dataset by getting a representative number of records for each country or host (Figure 2). Continue reading “Download Randomized Data Subset from NCBI Virus” →

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