Tag: Influenza

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” →

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 influenza virus names in NCBI Taxonomy

In order 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 introduce new binomial influenza species names like ‘Alphainfluenzavirus influenzae.’ Changes are expected to be in place near summer 2023.

We recognize that the traditional influenza virus names like ‘Influenza A virus’ and ‘Influenza B virus’ are broadly used in public health, educational institutions, and research. To minimize the impact of this change to those who use NCBI resources, the taxonomy schema will keep the former names in the lineages for each species; however, they will be moved below the (new) species taxa in the hierarchy. See example below.

Continue reading “Upcoming changes to influenza virus names in NCBI Taxonomy” →

Introducing the new Virus Sequence Search Interface

BLAST is a powerful search tool, but often a search is just the beginning of the journey. We put ourselves in the shoes of a researcher who has just sequenced a handful of samples from the latest viral outbreak and tried to understand what information would be most useful. We also reached out to researchers in the field and asked: a) what questions do they really want to answer? and b) how can NCBI best provide the answers? Based on insights from those questions and answers, we developed the new Virus Sequence Search Interface (Fig. 1). The Search Interface is an NCBI Labs project, which means it is an experimental project, and we may modify the resource based on your feedback and experiences.

Figure 1. The Virus Sequence Selection Interface. — **Figure 1.** The Virus Sequence Selection Interface. The Virus Sequence Selection Interface accepts as input nucleotide and protein accessions, as well as FASTA and plain-text formatted sequences. The user selects either “Nucleotide” or “Protein,” depending on the sequence type, and selects the virus type from the pull-down menu below the text entry field.

Continue reading “Introducing the new Virus Sequence Search Interface” →

New Influenza Virus Submission Wizard Makes Flu Sequence Submissions Easier

NCBI now offers a flu sequence submission wizard that makes submissions easier and will provide you with accession numbers sooner. To get started, sign in to NCBI, go to the Submission Portal and choose the link for “Ribosomal RNA (rRNA), rRNA-ITS or Influenza sequences” from the GenBank section.

Continue reading “New Influenza Virus Submission Wizard Makes Flu Sequence Submissions Easier” →

NCBI’s Virus Variation Resource Enhancements Include Standardized Search Criteria

NCBI’s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses – no more stumbling through multiple synonyms to find what you need. Now you can search using standardized biological criteria and intuitive pull-down menus.

Continue reading “NCBI’s Virus Variation Resource Enhancements Include Standardized Search Criteria” →