HerpesDRG: a comprehensive resource for human herpesvirus antiviral drug resistance genotyping

et al. 2022

Preprint

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Human cytomegalovirus (HCMV) is the most common and most serious opportunistic infection after solid organ (SOT) and haematopoietic stem cell transplantation (HSCT). There is considerable interest in using virus sequence data to investigate and monitor viral factors associated with the clinical outcome, including failure to respond to available antiviral therapies.To assess this, we used target-enrichment to deep-sequence 16 paediatric patients with HSCT, SOT or primary immunodeficiency of whom 9 died with HCMV and 35 infected SOT adult recipients of whom one died with HCMV.We first showed that samples from both groups have fixed drug-resistance mutations and mixed infections. Deep sequencing also revealed non-fixed resistance mutations in most of the patients who died (6/9). A machine learning approach identified 10 genes with high within-host variability in these patients. These genes formed a viral signature which discriminated patients with HCMV who died from those that survived with high accuracy (AUC=0.96). Lymphocyte numbers for a subset of 17 patients showed no recovery post-transplant of counts in the five who died.We hypothesise that the viral signature identified in this study may be a useful biomarker for poor response of HCMV to antiviral drug treatment and indirectly for poor T cell function, potentially identifying early, those patients requiring non-pharmacological interventions.

Section: Resultsmentioning

confidence: 99%

Section: Sample Collection and Ethicsmentioning

confidence: 99%

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Persistent low-level variants in a subset of HCMV genes are highly predictive of poor outcome in immunocompromised patients with cytomegalovirus infection

Venturini

Colston

et al. 2022

Preprint

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“…Single nucleotide polymorphisms (SNPs) were called using VarScan 2 ( 66 ) with a minimum average quality of 20, minimum variant frequency of 2%, and in at least 100 reads. These were then annotated by gene, codon, and amino acid alterations using an in-house script ( 67 ) modified to utilize HIV genomes.…”

Section: Methodsmentioning

confidence: 99%

HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy

Kemp

Derache

et al. 2022

mBio

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“…Single nucleotides polymorphisms (SNPs) were called using VarScan2 66 with a minimum average quality of 20, minimum variant frequency of 2% and in at least 100 reads. These were then annotated by gene, codon and amino acid alterations using an in-house script 67 modified to utilise HIV genomes.…”

Section: Methodsmentioning

confidence: 99%

HIV-1 evolutionary dynamics under non-suppressive antiretroviral therapy

Kemp

Derache

et al. 2021

Preprint

Background: Viral population dynamics in long term viraemic antiretroviral therapy (ART) treated individuals have not been well characterised. Prolonged virologic failure on 2nd-line protease inhibitor (PI) based ART without emergence of major protease mutations is well recognised, providing an opportunity to study within-host evolution. Methods: Using next-generation Illumina short read sequencing and in silico haplotype reconstruction we analysed whole genome sequences from longitudinal plasma samples of eight chronically infected HIV-1 individuals failing 2nd-line regimens from the ANRS 12249 TasP trial, in the absence of high frequency major PI resistance mutations. Plasma drug levels were measured by HPLC. Three participants were selective for in-depth variant and haplotype analyses, each with five or more timepoints spanning at least 16 months. Results: During PI failure synonymous mutations were around twice as frequent as non-synonymous mutations across participants. Prior to or during exposure to PI, we observed several polymorphic amino acids in gag (e.g. T81A, T375N) which are have also been previously associated with exposure to protease inhibitor exposure. Although overall SNP frequency at abundance above 2% appeared stable across time in each individual, divergence from the consensus baseline sequence did increase over time. Non-synonymous changes were enriched in known polymorphic regions such as env whereas synonymous changes were more often observed to fluctuate in the conserved pol gene. Phylogenetic analyses of whole genome viral haplotypes demonstrated two common features: Firstly, evidence for selective sweeps following therapy switches or large changes in plasma drug concentrations, with hitchhiking of synonymous and non-synonymous mutations. Secondly, we observed competition between multiple viral haplotypes that intermingled phylogenetically alongside soft selective sweeps. The diversity of viral populations was maintained between successive timepoints with ongoing viremia, particularly in env. Changes in haplotype dominance were often distinct from the dynamics of drug resistance mutations in reverse transcriptase (RT), indicating the presence of softer selective sweeps and/or recombination. Conclusions: Large fluctuations in variant frequencies with diversification occur during apparently "stable" viremia on non-suppressive ART. Reconstructed haplotypes provided further evidence for sweeps during periods of partial adherence, and competition between haplotypes during periods of low drug exposure. Drug resistance mutations in RT can be used as markers of viral populations in the reservoir and we found evidence for loss of linkage disequilibrium for drug resistance mutations, indicative of recombination. These data imply that even years of exposure to PIs, within the context of large stable populations displaying ongoing selective competition, may not precipitate emergence of major PI resistance mutations, indicating significant fitness costs for such mutations. Ongoing viral diversification within reservoirs may compromise the goal of sustained viral suppression.