Detection of rare hepatitis C viruses of subtype 4r in Southeastern France  L. Dubourg  Clinical Microbiology and Infection  Volume 23, Issue 7, Pages 493-495 (July 2017) DOI: 10.1016/j.cmi.2017.01.021 Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

FIG. 1 Hepatitis C virus phylogenetic tree based on NS5b encoding region (a) and amino acid substitutions described as associated with reduced susceptibility to DAA (b). (a) NS5b encoding region was 1204-nucleotide long and corresponded to nucleotides 7915-9118 of the HCV genome GenBank accession no. M62321. The HCV sequence obtained from the index case are indicated by a white bold font and a black background, and a triangle. The 10 sequences with the highest BLAST scores recovered from the NBCI GenBank (http://www.ncbi.nlm.nih.gov/nucleotide/) and IHU Mediterranee Infection nucleotide sequence databases, labelled with 10BBH (BBH being for Best BLAST Hit) and Gbk or IHU, respectively, were incorporated into the phylogeny reconstruction, in addition to reference sequences for HCV genotypes (http://talk.ictvonline.org/links/hcv/hcv-classification.htm). Other HCV-4r sequences than those obtained from the index case are indicated by a white bold font with a grey background for those retrieved from the NBCI GenBank nucleotide sequence database and labelled as 4r, and by a white bold font and a black background for those retrieved from the IHU Méditerranée Infection nucleotide sequence database. Nucleotide alignments were performed using MUSCLE software (http://www.ebi.ac.uk/Tools/msa/muscle/). The evolutionary history was inferred using MEGA6 software (http://www.megasoftware.net/) using the Neighbor-Joining method and the Kimura 2-parameter method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree; the scale bars indicate the number of nucleotide substitutions per site. Bootstrap values >50% are labelled on the tree. (b) Amino acids described as associated with reduced susceptibility to DAA were taken from http://hcv.geno2pheno.org/. Amino acids in boldface are those associated with reduced susceptibility to DAA in HCV genotype 4; the other amino acids are described in HCV genotypes other than 4. N.a., not available. * Up to amino acid 505. Clinical Microbiology and Infection 2017 23, 493-495DOI: (10.1016/j.cmi.2017.01.021) Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions