Sequence of Genomes
Is it possible for you to find unique nucleic acid sequences for the different H and N variants using information available at a public database?
Khadeeja & Sara write: Is it possible for you to find unique nucleic acid sequences for the different H and N variants using information available at a public database? How is influenza different from many other viruses with respect to the composition of the genome?
There are three main nucleotide sequence databases which collect publicly available sequences in the world.
Genbank is maintained by the National Center for Biotechnology Information (NCBI) in the US
EMBL (European Molecular Biology Laboratory) maintained by the European Bioinformatics Institute (EBI) in the UK
DDBJ (DNA Database of Japan) is based in Japan.
There are also other databases that can provide information such as the protein databases.
Rob Schintzius writes: It is certainly possible to find unique nucleic acid sequences for the different H and N variants. H and N stand for Hemagglutinin and Neuraminidase, which are both proteins. There are different structures to both, meaning they have different nucleic acid sequences. An article that I was able to easily find on PubMed compared the complete sequence of a cDNA clone of the hemagglutinin gene from an H5N1 virus from Scotland with a contemporary North American strain. Sequencing was done by the Sanger dideoxy method. The end result showed that there is a homology of 81% at the nucleotide level and 87% at the amino acid level.
How is influenza different from many other viruses with respect to the composition of the genome?
Khadeeja & Sara write: All organisms whose cells contain a nucleus in their cells, together with many bacteria and viruses, base their reproduction on a DNA (deoxyribonucleic acid) genome, but the influenza virus is among a minority of organisms that base their replication on RNA. The properties of RNA help to explain the epidemiology of influenza and the difficulty of achieving successful prophylactic treatment by using vaccines. Both DNA and RNA genomes use polymerase enzymes for replication, but under suitable conditions, RNA molecules can replicate spontaneously and maintain continuous synthesis, and between the two viruses, RNA viruses have the ability to evolve a million times more rapidly than their DNA based host. Then again, a given human influenza virus can evolve rapidly by one of two mechanisms: antigenic shift or a genetic re-assortment between a human and a non-human virus in a non-human host, and an antigenic drift or an accumulation of mutations that facilitate evasion of the host immune response. Regardless, influenza is also caused by an orthomyxovirus which consists of ribonucleoproteins surrounded by a lipid envelope that contains two types of glycoproteins, haemagglutinin (H) and neuraminidase (N).