Chris Spencer, Eleanor Barnes and colleagues use human genotyping arrays and whole-genome viral sequencing to perform a systematic genome-to-genome study of 542 individuals chronically infected with hepatitis C virus (HCV). They show that both HLA alleles and genes encoding factors of the innate immune system drive viral genome polymorphism and that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific polymorphism encoded in the HCV polyprotein. Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. Here we use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals who were chronically infected with HCV, predominantly genotype 3. We show that both alleles of genes encoding human leukocyte antigen molecules and genes encoding components of the interferon lambda innate immune system drive viral polymorphism. Additionally, we show that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific amino acid residue in the HCV NS5A protein. These findings highlight the interplay between the innate immune system and the viral genome in HCV control.

Mosquitoes collected in northern Italy were screened for flavivirus RNA. Positive amplicons were sequenced and found most similar to insect flavivirus (ISF), Usutu virus (USUV) and surprisingly also to Japanese encephalitis virus (JEV). The sequence (167 bp), obtained from one pool of Culex pipiens, was found identical to JEV strains from bats in China. Unfortunately additional sequence data or virus isolations were not obtained in this study. Confirmation of potential introduction of JEV to Italy and other European countries is urgently needed.

KIR2DS2, an activating natural killer cell receptor, recognizes conserved peptides derived from the RNA helicases of pathogenic flaviviruses.

Background and aims: HCV genotype-3 (gt3) is highly prevalent globally, with non-gt3a subtypes common in Southeast Asia. Resistance-associated substitutions (RASs) have been shown to play a role in treatment failure. However, the role of RASs in gt3 is not well understood. We report the prevalence of RASs in a cohort of directly acting antivirals (DAA) treatment-naïve gt3 infected patients, including those with rarer subtypes and evaluate the effect of these RAS on DAAs in-vitro. Methods: Baseline samples from 496 gt3 patients enrolled in the BOSON clinical trial were analysed by next-generation sequencing after probe-based enrichment for HCV. Whole viral genomes were analysed for the presence of RASs to approved DAAs. The resistance phenotype of RASs in combination to daclatasvir, velpatasvir, pibrentasvir, elbasvir and sofosbuvir was measured using the S52 ΔN gt3a replicon model. Results: The NS5A A30K and Y93H substitutions were the most common at 8.8% (n=44) and 12.2% (n=61) respectively and showed a 10-fold and 11-fold increase in EC₅₀ for daclatasvir compared to the unmodified replicon. Paired RASs (A30K + L31M and A30K + Y93H) were identified in 18 patients (9 of each pair); these combinations were shown to be highly resistant to daclatasvir, velpatasvir, elbasvir and pibrentasvir. The A30K + L31M combination was found in all gt3b and gt3g samples. Conclusion: Our study reveals high frequencies of RASs to NS5A Inhibitors in gt3 HCV. The paired A30K + L31M substitutions occur in all patients with gt3b and gt3g virus. In vitro analysis suggests that these subtypes may be inherently resistant to all approved NS5A Inhibitors for gt3 HCV.