From:	Research Mentor
Subject:	Overview

Thanks for your work and attention to detail!

In this segment your team will be reading the seminal work on whole genome analysis published in 2006. One of the goals of this work was to investigate the relative contributions of antigenic drift (change through point mutations) and antigenic shift (change through reassortment of viral RNA segments) to influenza evolution. This paper also identifed an amino acid motif that may be related to both host specificity and pathogenicity.

In this activity, you will obtain a set of amino acid sequences from a diverse set of influenza viruses that were isolated from humans, with a couple of exceptions; one laboratory strain, and an H5N1 strain isolated from a goose.

Your goals are to learn how to recognize genetic changes that are due to antigenic drift, changes that are due to reassortment, and a specific amino acid motif associated with H5N1 strains of avian influenza. The presence of this motif can indicate the typical host for a given strain is most likely to be avian, swine, or human. This work will prepare you for looking at an influenza outbreak and determining if a virus has entered the human population with avian genes, i.e., were humans infected by a bird flu, instead of a strain that normally infects humans.

Deliverables:

1. Build a spreadsheet with outbreaks (year, location), serotypes, gene, accession number, and NS1 motif (4-6 amino acids), and preferred host.
2. A text file containing a data set with selected NS-1 sequences.
3. A phylogenetic tree dervied from the NS-1 data set.
4. A report summarizing your conclusions from analyzing the multiple sequence alignment and the phylogenetic tree.