Phylogenetics for those who never had time to ask

VOL 62: AUGUST • AOÛT 2016

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Case scenario

Your spouse (also an FP) is ensconced in the living room doing some journal reading when you hear her say,

“Wow. I have always wondered what that meant.” You ask her what she is talking about. “Phylogenetics. It is high-tech detective work. It is the analysis of the small genetic changes that viruses and bacteria undergo in order to map out where they come from.”

“Really?” you say, not quite understanding how that would work. “What is it used for?”

“Well this article describes how it was used to identify the source of measles cases in Canada last year. It is like paternity testing—if you suspect where the measles cases might be coming from, you can do genetic testing to either confirm or exclude that possibility.” You sit down with her to have a look.

CCDR Highlights

Evidence

Phylo refers to a race, tribe, or related group. A phyloge- netic figure is a lot like a family tree.¹ The root of the tree represents the ancestral lineage, and the branches repre- sent the descendants of that ancestor. As you move from root to tip, you move forward in time. Figure 1 shows the phylogenetic tree for measles in Canada in 2015.²

The yellow area represents a group (measles B3 gen- otype) endemic to Africa that developed new lineages (or branches) in the United States. The green represents a genotype linked to China, and the blue represents a genotype linked to India. This was established by the National Microbiology Laboratory, which examined the specific nucleotide sequencing of virus samples sent for testing. They send this information on to the World Health Organization, which maintains a measles nucleotide

database.³ The turquoise area represents a new lineage in the D4 genotype. There were 17 cases in Canada from this “new branch on the family tree.” Phylogenetics pro- vided genetic evidence that these cases were linked—even though links could not be established with public health investigation and the actual source was never found.⁴

Measles remains one of the most contagious infec- tions on the planet and it is endemic in many countries, such as India and China.⁵ Maintaining Canada’s measles elimination status requires phylogenetic reporting to doc- ument that the few cases we have each year are repeated travel-related cases rather than sustained local transmis- sion. Every FP can help maintain Canada’s elimination status by early diagnosis: ask for a travel history from anyone with fever and a rash and check for the “4 Cs”:

cough, coryza, conjunctivitis, and Koplik spots.

Bottom line

Phylogenetics is fascinating in that it documents evolu- tion—the tiny genetic changes in viruses and bacteria—

in close to real time. It is increasingly being applied to advancing our understanding of all infectious diseases.

References

1. Understanding phylogenies. In: Understanding Evolution Team. Evolution 101.

Berkeley, CA: University of California Museum of Paleontology; 2016. http://

evolution.berkeley.edu/evolibrary/article/evo_05. Accessed 2016 Jul 6.

2. Sherrard L, Hiebert J, Cunliffe J, Mendoza L, Cutler J. Measles surveillance in Canada:

2015. Can Comm Dis Rep 2016;42(7):139-45.

3. Hiebert J, Severini A. Measles molecular epidemiology: what does it tell us and why is it important? Can Comm Dis Rep 2014;40(12):257-60.

4. Gournis E, Shane A, Shane E, Arthur A, Berger L. Exploring gaps in surveillance of a small measles outbreak in Toronto. Can Comm Dis Rep 2016;42(7):146-8.

5. World Health Organization [website]. Number of reported of measles cases with onset date from Nov 2015 to Apr 2016 (6M period). Geneva, Switz: World Health Organization; 2016. Available from: www.who.int/immunization/monitoring_

surveillance/burden/vpd/surveillance_type/active/big_measles_reportedcases- 6months.jpg. Accessed 2016 Jul 6.

CCDR Highlights summarize the latest evidence on infectious diseases from recent articles in the Canada Communicable Disease Report, a peer-reviewed online journal published by the Public Health Agency of Canada.

This highlight was prepared by Dr Patricia Huston, a family physician, public health physician, and Editor-in-Chief of the Canada Communicable Disease Report.

La traduction en français de cet article se trouve à www.cfp.ca dans la table des matières du numéro d’août 2016 à la page e439.

Phylogenetics for those who never had time to ask

Figure 1. Phylogenetic tree for measles in Canada, 2015

Adapted from Sherrard et al.²