Journal of Clinical Virology Phylogenetic analysis of an epidemic outbreak of acute hepatitis C in HIV-infected patients by ultra-deep pyrosequencing  Noelia Caro-Pérez, María Martínez-Rebollar, Josep Gregori, Josep Quer, Patricia González, Martina Gambato, Neris García-González, Fernando González-Candelas, Josep Costa, Juan Ignacio Esteban, Josep Mallolas, Xavier Forns, Montse Laguno, Sofía Pérez-del- Pulgar  Journal of Clinical Virology  Volume 92, Pages 42-47 (July 2017) DOI: 10.1016/j.jcv.2017.05.008 Copyright © 2017 Elsevier B.V. Terms and Conditions

Fig. 1 Maximum likelihood trees were constructed for each genotype separately: (a) gt1a, (b) gt1b and (c) gt4d. Only sequences with relative frequency >0.5% in the corresponding sample were included in the analyses. AHC HIV-coinfected patients are identified as pXX, where XX represents a number from 1 to 84, and control patients are identified as kXXXX, were XXXX represents a 4 digit number. Bootstrap support values >80% are indicated in the corresponding nodes. Triangle areas are proportional to the diversity and frequency of the different haplotypes (quasiespecies) in a sample. Capital letters indicate potential transmission clusters analyzed in more detail in Supplementary Table S4. Journal of Clinical Virology 2017 92, 42-47DOI: (10.1016/j.jcv.2017.05.008) Copyright © 2017 Elsevier B.V. Terms and Conditions

Fig. 1 Maximum likelihood trees were constructed for each genotype separately: (a) gt1a, (b) gt1b and (c) gt4d. Only sequences with relative frequency >0.5% in the corresponding sample were included in the analyses. AHC HIV-coinfected patients are identified as pXX, where XX represents a number from 1 to 84, and control patients are identified as kXXXX, were XXXX represents a 4 digit number. Bootstrap support values >80% are indicated in the corresponding nodes. Triangle areas are proportional to the diversity and frequency of the different haplotypes (quasiespecies) in a sample. Capital letters indicate potential transmission clusters analyzed in more detail in Supplementary Table S4. Journal of Clinical Virology 2017 92, 42-47DOI: (10.1016/j.jcv.2017.05.008) Copyright © 2017 Elsevier B.V. Terms and Conditions

Fig. 1 Maximum likelihood trees were constructed for each genotype separately: (a) gt1a, (b) gt1b and (c) gt4d. Only sequences with relative frequency >0.5% in the corresponding sample were included in the analyses. AHC HIV-coinfected patients are identified as pXX, where XX represents a number from 1 to 84, and control patients are identified as kXXXX, were XXXX represents a 4 digit number. Bootstrap support values >80% are indicated in the corresponding nodes. Triangle areas are proportional to the diversity and frequency of the different haplotypes (quasiespecies) in a sample. Capital letters indicate potential transmission clusters analyzed in more detail in Supplementary Table S4. Journal of Clinical Virology 2017 92, 42-47DOI: (10.1016/j.jcv.2017.05.008) Copyright © 2017 Elsevier B.V. Terms and Conditions

Fig. 2 Maximum likelihood tree constructed with HCV gt4d sequences derived from the international network reported by Van de Laar et al. (2009) and from our study cohort of AHC HIV-coinfected MSM. Patients in our study cohort are identified as pXX, for HAC (red), or kXXXX, for local controls (orange). Patients from the international network were denoted as reported: FP, France (blue); ELR, ELC and EB, United Kingdom (grey); S, NR, NA and PP, The Netherlands (purple); GB, Germany (green). Nodes with bootstrap >80% are indicated in the tree. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) Journal of Clinical Virology 2017 92, 42-47DOI: (10.1016/j.jcv.2017.05.008) Copyright © 2017 Elsevier B.V. Terms and Conditions