What the Pathogen Primer should look like
You are required to develop a Primer to inform an educated audience (e.g. other scientists,
healthcare professionals) on the biology of a pathogen and its interactions with the human
immune system. Your Primer will essentially be a short review article focusing on one
pathogen and covering its the epidemiology, genomics, pathogenesis and interactions with
host immunity. Ask yourself – what would another scientist want to know about this
pathogen? You can use a combination of text, tables and figures (or illustrations) to
produce the Primer.
The aim of this assessment piece is to increase your understanding of pathogen biology and
pathogenesis by integrating your knowledge of immunology and microbiology. You will be
required to perform a search of the scientific literature to find relevant papers on your
topic. This assessment piece will also develop your critical thinking, scientific writing and
analysis skills, as well as enhance your digital literacy in using scientific databases.
Structure of the Primer
Your primer must contain the following information about the pathogen, in this specific
1) Title: this should include the name of the pathogen
2) Introduction: this short section (2-3 sentences) should introduce the topic of the
3) Epidemiology: this section should describe global distribution of the pathogen,
transmission modes, estimated case numbers, which regions are primarily affected
and where it is found, who is primarily affected (e.g. children versus adults, pregnant
women) and any other demographic information, occurrence of any outbreaks (if
4) Genomics and evolution: this section should give details on the genome of the
pathogen such as the number of genes, type of nucleic acid, taxonomic classification,
any strain variation and history of emergence of the pathogen (if relevant).
5) Disease manifestations and pathogenesis: this section should summarize clinical
manifestations (signs and symptoms) of infection with the pathogen. You are also
required to pick one specific aspect of pathogenesis to detail more in depth. For
example, if you were to write a Primer on SARS-CoV-2, you could focus on
pathogenesis in the lung or pathogenesis in the nervous system.
6) Interactions with the human immune system: this section should detail one aspect
of the host immune interaction with the pathogen. This could include key host
receptors and TLRs involved, pathways in the innate immune response or adaptive
immune response that are specific to that pathogen, as well as key pathogen
proteins or molecules involved in mediating this interaction.
7) References: for more details see below
Display Items. Tables should have a short title at the top. Figures must have a figure legend
below the figure. The figure legend consists of a short title and all of the figure
components. You can include figures from papers, but you must reference them (in the
figure legend) to the original source.
You are free to choose from the pathogens below, but your primer must be on only one (1)
Hepatitis C virus
Human Papilloma virus
Herpes Simplex virus
Formatting and references
The length of the primer is up to 3 pages maximum, including figures and/or tables. One (1)
page extra allowed for references at the end. The Primer needs to be submitted as a Word
document, formatted in 12-point Times New Roman writing and with at least 2 cm page
margins. Please also include page numbers.
A primer of this nature and length would normally have ~ 10 references. At this stage in
your university studies, references should be primarily peer-reviewed scientific papers.
Chapters from books may also be used but the emphasis is on scientific papers. Websites
such as Wikipedia and MicrobesOnline are not appropriate! I will put together a short,
narrated video on how to use databases to search for scientific papers and place it on Bb.
References need to be cited in the text, either in numbered format or with the name of the
authors. Every time you mention a fact that was originally in a published paper, you must
cite that original paper as a reference. An example is: “Pathogen X was discovered to do Y
in the host (4).” Or “Pathogen X was discovered Y in the host (Smith et al. 2020).”
To organise references using Endnote, you can find more information at the following QUT
Ensure your file size is less than 40 MB total, as this is Turnitin’s maximum limit. Also be
aware that large files take some time to upload to Turnitin so allow yourself extra time
before the deadline.
Academic Dishonesty and/or Plagiarism
This is an individual assessment piece. All text should be in your own words. If images or
tables are used from elsewhere, these must be appropriately cited to the original source.
All work will be checked in Turnitin for content matching against numerous databases. Any
academic dishonesty and/or plagiarism will result in academic misconduct proceedings.
More information on academic integrity can be found here:
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