Campbell Biology 11th Edition by Lisa Urry,Michael Cain,Steven Wasserman,Peter Minorsky,Jane Reece

Exercise 9

How Can DNA Sequence Data Be Used to Track Flu Virus Evolution During Pandemic Waves
In 2009, an influenza A H1N1virus caused a pandemic, and the virus has continued to resurface in outbreaks across the world. Researchers in Taiwan were curious about why the virus kept appearing despite widespread flu vaccine initiatives. They hypothesized that newly evolved variants of the H1N1 virus were able to evade human immune system defenses. To test this hypothesis, they needed to determine if each wave of the flu infection was caused by a different H1N1 variant strain.
How the Experiment Was Done Scientists obtained the genome sequences for 4,703 virus isolates collected from patients with H1N1 flu in Taiwan. They compared the sequences in different strains for the viral hemagglutinin (HA) gene, and based on mutations that had occurred, arranged the isolates into a phylogenetic tree (see Figure 20.5 for information on how to read phylogenetic trees).
Data from the Experiment In the phylogenetic tree; each branch tip is one variant strain of the H1N1 virus with a unique HA gene sequence. The tree is a way to visualize a working hypothesis about the evolutionary relationships between H1N1 variants.
The graph shows the number of isolates collected (each from an ill patient) on the y -axis and the month and year that the isolates were collected on the x -axis. Each group of variants is plotted separately with a line color that matches the tree diagram. (a) Which group of variants was the earliest to cause the first wave of H1N1 flu in over 100 patients in Taiwan (b) After a group of variants had a peak number of infections, did members of that same group cause another (later) wave of infection (c) One variant in Group 1 (green, uppermost branch) was used to make a vaccine that was distributed very early in the pandemic. Based on the graphed data, does it look like the vaccine was effective