Phylogenetic analysis and interpretation can be challenging for many students, but
emerging infections can provide a rich tapestry for addressing these topics while
maintaining student interest. Ranaviruses are a group of emerging infections in
amphibians that have been associated with morbidity and mortality events
around the globe. They have also been implicated in population declines and
local extirpations of some amphibian species. Many ranaviruses have been
subject to intense study by scientists as they seek to understand the impacts of
these viruses on a variety of ectothermic animals. A large amount of sequence
data is available on GenBank and is easily accessible for students to use to study
phylogenetic relationships between different viral species, strains, and isolates.
This article examines the general process of obtaining sequence data, sequence
alignments, and tree building by using databases, servers, and computer
programs that are freely available to all high school and undergraduate students
and their instructors. Providing students with a guided framework for exploring
their own questions with respect to the evolutionary relationships of ranaviruses
can produce some very unique and thought-provoking results.
Keywords: Emerging infection; amphibian; Ranavirus; phylogenetic reconstruction;
Students are typically aware that amphibians are in decline globally
(Stuart et al., 2004) and that a disease called chytridiomycosis,
caused by the pathogenic fungus Batrachochytrium dendrobatidis,
has been associated with many of the declines and extinction events.
However, they are surprised to learn that other infectious agents,
such as the ranaviruses (Ranavirus spp.), have also been implicated.
For over a decade, I have been working with ranaviruses, a globally
distributed group of emerging pathogens that infect ectothermic vertebrates, including several endangered species (Duffus et al., 2015).
Ranaviruses are a great model system for studying phylogenetics
because they can yield some interesting and unique results. The
emergence of Ranavirus infections and the resultant disease has not
only caused population declines in some areas (Teacher et al.,
2010), but has resulted in the entire collapse of some amphibian
communities (Price et al., 2014).
Studying phylogenetics can be challenging for many students as
they struggle to comprehend how sequence data are transformed into
a tree and how the results are then interpreted. Emerging infectious
diseases like Ebola virus disease, Middle East respiratory syndrome
(MERS), and ranaviral diseases are a great way to get students interested in a variety of evolutionary questions, including how to reconstruct phylogenetic relationships. One of the most important roles
that phylogenetic reconstruction may play in the context of emerging
diseases is predicting whether a species, strain, or isolate is going to be
virulent. If a new strain or isolate groups closely with known highly
virulent strains, there is a good chance that it too might be virulent,
and if it appears in a new area, it may be possible to take steps to limit
or mitigate pathogen emergence.
For ranaviruses, there are a large number of partial and complete
gene sequences and completely sequenced genomes available on
GenBank ( http://www.ncbi.nlm.nih.gov; Benson et al., 2013). Currently, 26 core genes have been identified in the Ranavirus genome
(Eaton et al., 2007) and almost all of these genes can provide some
fascinating and quickly generated results for students studying the
evolutionary relationships between different Ranavirus species, and
sometimes even between different Ranavirus strains or isolates. Frog
virus 3 (FV3), the type virus of the ranaviruses (Tan et al., 2004), is
a great place to start when looking for open reading frames (ORFs).
Eaton et al. (2007: tables 6 and 7) describe all 26 core genes and their
corresponding ORFs in more than 10 ranaviruses. In GenBank, there
are a plethora of gene sequences for the Ambystoma tigrinum virus
(ATV), the common midwife toad virus (CMTV), FV3, and nonamphibian ranaviruses (e.g., European sheatfish iridovirus). The most
commonly used gene to reconstruct Ranavirus phylogenetic relationships is the major capsid protein (MCP; ORF 90R in FV3). The
MCP is a great place to start; however, it is not the only notable
ORF. The students can potentially explore a huge variety of interesting
phylogenetic questions, some examples of which can be found below:
The American Biology Teacher, Vol. 81, No. 1, pp. 32–39, ISSN 0002-7685, electronic ISSN 1938-4211. © 2019 National Association of Biology Teachers. All rights
reserved. Please direct all requests for permission to photocopy or reproduce article content through the University of California Press’s Reprints and Permissions web page,
www.ucpress.edu/journals.php?p=reprints. DOI: https://doi.org/10.1525/abt.2019.81.1.32.
An Emerging Amphibian Infection
as a Model for Teaching
• AMANDA L. J. DUFFUS