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. 2020 Jan 31;8(2):196.
doi: 10.3390/microorganisms8020196.

Evaluation of A Phylogenetic Pipeline to Examine Transmission Networks in A Canadian HIV Cohort

Lauren Mak  1 , Deshan Perera  1 , Raynell Lang  2 , Pathum Kossinna  1 , Jingni He  1 , M John Gill  2 , Quan Long  1   3   4 , Guido van Marle  5
Affiliations

Evaluation of A Phylogenetic Pipeline to Examine Transmission Networks in A Canadian HIV Cohort

Lauren Mak et al. Microorganisms. .

Abstract

Keywords: HIV; Canada; molecular phylogenetics; viral evolution; person-to-person transmission inference; transmission network; summary statistics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Workflow of data analysis procedures. (a) Graphic representation of the data input/output. (b) Pipeline tools and how they were used. (c) Parameters tested for each tool.
Figure 2
Figure 2
The Southern Alberta HIV Clinic (SAC) patient sequence and transmission data. Patient (A) has HIV, and their estimated infection date is the red star on their branch. They have a positive (First Positive—FP) HIV test result after their infection. At some time-point, represented by a red star and the red arrow, (a) infects (b). Previously, (b) had a negative HIV test. Afterwards, (a) has a positive HIV test result. The HIV sequences of samples from (a) and (b) are phylogenetically related, as represented by the tree. (b) is in transmission category 1 and infection category 1. (a) is in transmission category 2 and infection category 2. Samples for (a) and (b) were collected at the end of their respective branches.
Figure 3
Figure 3
The transmission tree generated by MUSCLE, adjusted BEAST2 parameters, and adjusted TransPhylo parameters. Sampled patients are represented by black branches, and unsampled patients by light grey branches. The symbols represent person-to-person transmission events. Green and red triangles represent correctly and incorrectly inferred relationships respectively. Grey squares represent novel inferences of transmission relationships that have no precedence in the SAC dataset. The branches involved in Figure 4 clusters are highlighted in the correspondingly coloured boxes.
Figure 4
Figure 4
Novel transmission clusters (A, B, C and D) identified from the transmission tree in Figure 3. Each node represents a sampled patient from the SAC database, and each arrow a directed transmission relationship. Coloured nodes represent sampled patients and indicate the corresponding coloured boxes in Figure 3. White nodes represent predicted unsampled patients. Solid arrows represent transmission relationships already known to the SAC, whereas dashed arrows represent novel inferences of transmission.
See this image and copyright information in PMC

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