# Virus Isolation Course

The Virus Isolation Course is a phage isolation course and the first semester of the two-semester [Phage Discovery Program](/teaching/phage-discovery), Tarleton State University's part of SEA-PHAGES. It is taught as Special Topics (BIOL 4090). Undergraduates find a new bacteriophage in an environmental sample, purify it, image it and extract its DNA. The second semester is the [Phage Bioinformatics course](/teaching/phage-bioinformatics).

## What students do

1. Collect soil or water samples and bring them back to the lab.
2. Look for bacteriophages in them by direct and enriched isolation.
3. Purify a phage.
4. Amplify the purified phage to a high titer.
5. Image the phage by transmission electron microscopy and analyze the images to determine its morphology and type.
6. Extract the viral DNA and run a genetic analysis.

The bench protocols are the ones in the [SEA-PHAGES Phage Discovery Guide](https://discoveryguide.seaphages.org/), which students follow at the bench. The lab's own notes on isolation and DNA extraction are the [phage isolation](/research/protocols/phage-isolation) and [phage DNA extraction](/research/protocols/phage-dna-extraction) pages, and the dilutions, titers and other lab math, with the lab's own numbers, are worked through in [Lab Calculations and Common Questions](/teaching/virus-isolation/faq). The [phage lab calculators](/research/tools) do the titer, dilution, webbed plate, lysate volume, MOI and efficiency of plating arithmetic on your own numbers and show each step.

## What students finish with

By the end of the semester each student has an isolated, purified phage amplified to a high titer, electron micrographs showing its morphology, and extracted phage DNA. If the DNA is unique and of high quality and quantity, it is sent to the Pittsburgh Bacteriophage Institute for next-generation whole genome sequencing, and that genome is what students annotate in the [Phage Bioinformatics course](/teaching/phage-bioinformatics). The phages found so far are listed in the [phage table](/research/phages).

## Safety training

The course begins with the lab safety section of the [SEA-PHAGES Phage Discovery Guide](https://discoveryguide.seaphages.org/).

Before the first class session, students complete Texas A&M University System [TrainTraq](https://traintraq.tamus.edu/) course 2111743, Lab Safety.

An additional on-site safety training covers lab-specific hazards, the location of safety equipment and evacuation routes, and students sign an acknowledgement that they have completed all safety training by the first class session. Lab safety is a component of the final course grade, and negligence can result in a student being dropped from the course.

## Host bacteria

- *Mycobacterium smegmatis* mc²155 (ATCC 700084)
- *Microbacterium foliorum* NRRL B-24224

## Lab equipment

Each student research group has a dedicated laptop for the Phage Discovery Guide and the online electronic lab notebook, and the lab has dedicated digital cameras and ink markers for labeling and imaging tube contents, plaques and gels.