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18) and quality trimmed by using Trimmomatic version 0.36 (
19). Viral contigs were generated by using default settings with Vicuna version 1.1 (
20), and a de novo consensus assembly was generated by using Viral Finishing and Annotation Toolkit (V-FAT) version 1.1 (https://www.broadinstitute.org/viral-genomics/v-fat). Read data are available from the National Center for Biotechnology Information Read Archive (https://www.ncbi.nlm.nih.gov) under BioProject accession no. PRJNA661611.
Phylogenetic Reconstruction
21) and IQ-TREE version 1.6 (
22). We then constructed a maximum-likelihood phylogenetic tree with 1,000 ultrafast bootstrap replicates (
HCV Transmission Network Analyses
We uploaded Illumina paired-end reads to GHOST and subjected them to automatic quality control criteria. In brief, read pairs were filtered out if a read had 3 Ns (N indicates that software was not able to make a basecall for this base) or a length 185 bp. Each identifier on forward and reverse reads
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