Contribution of next generation sequencing to early detection of cytomegalovirus UL97 emerging mutants and viral subpopulations analysis in kidney transplant recipients

Garrigue, Isabelle; Moulinas, Rémi; Recordon-Pinson, Patrícia; Delacour, Marie-Laure; Essig, Marie; Kaminski, Hannah; Merville, Pierre; Fleury, Hervé; Alain, Sophie

doi:10.1016/j.jcv.2016.04.017

Cited by 31 publications

(23 citation statements)

References 28 publications

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“…In summary we have demonstrated that deep sequencing of HCMV ORFs UL27, 54, and 97 could be achieved directly from whole blood with virus loads in the range 80,000–65,000,000 copies/ml without prior culture or PCR. We were able to detect resistance mutations occurring at 2% or more in patients with viraemia persisting at levels of ≥10 4 gc/ml for 2 weeks or more, comparable to other deep sequencing-based approaches (e.g., Görzer et al, 2010 ; Garrigue et al, 2016 ). Our data suggest that in contrast to amplicon and Sanger sequencing, our deep sequencing can exclude resistance in patients with persistently high levels of viraemia, thereby providing a measure of support prolonging current antiviral treatment or returning to them at a later date if further treatment is needed.…”

Section: Discussionsupporting

confidence: 57%

“…For patient B, UL27 consensus sequences clustered in different parts of the tree in a time dependent manner (Figure 3C ). The consensus sequences of genes UL54 and UL97 show change over time in patients B and I that is compatible with sequence evolution due to anti-viral drug pressure (Garrigue et al, 2016 ). In Patient B the changes in phylogenetic clustering for UL27 occurred after the start of MBV on day 133, and may reflect recombination or re-infection with a second strain of HCMV in this patient.…”

Section: Stop Codons Insertions and Deletionsmentioning

confidence: 83%

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Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus

et al. 2016

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Human cytomegalovirus (HCMV) is a significant pathogen in immunocompromised individuals, with the potential to cause fatal pneumonitis and colitis, as well as increasing the risk of organ rejection in transplant patients. With the advent of new anti-HCMV drugs there is therefore considerable interest in using virus sequence data to monitor emerging resistance to antiviral drugs in HCMV viraemia and disease, including the identification of putative new mutations. We used target-enrichment to deep sequence HCMV DNA from 11 immunosuppressed pediatric patients receiving single or combination anti-HCMV treatment, serially sampled over 1–27 weeks. Changes in consensus sequence and resistance mutations were analyzed for three ORFs targeted by anti-HCMV drugs and the frequencies of drug resistance mutations monitored. Targeted-enriched sequencing of clinical material detected mutations occurring at frequencies of 2%. Seven patients showed no evidence of drug resistance mutations. Four patients developed drug resistance mutations a mean of 16 weeks after starting treatment. In two patients, multiple resistance mutations accumulated at frequencies of 20% or less, including putative maribavir and ganciclovir resistance mutations P522Q (UL54) and C480F (UL97). In one patient, resistance was detected 14 days earlier than by PCR. Phylogenetic analysis suggested recombination or superinfection in one patient. Deep sequencing of HCMV enriched from clinical samples excluded resistance in 7 of 11 subjects and identified resistance mutations earlier than conventional PCR-based resistance testing in 2 patients. Detection of multiple low level resistance mutations was associated with poor outcome.

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Section: Discussionsupporting

confidence: 57%

Section: Stop Codons Insertions and Deletionsmentioning

confidence: 83%

Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus

et al. 2016

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“…Furthermore, Pokalyuk et al demonstrated that genetic sampling at individual loci can result in the misclassification of mixed infections as single infections, and Garrigue et al have also recently shown that even when looking at individual loci, traditional Sanger sequencing can miss even relatively high-frequency resistance mutations, highlighting the utility of high-throughput, genome-level characterization of HCMV infection. This is of particular importance given the emerging links between genetic diversity and patient outcome [ 28 , 58 ]. Yet, given the rapidly declining costs of high-throughput sequencing methods, genome-wide multi-compartment patient sequencing paired with newly developed virus-specific population genetic analyses may soon be accessible and affordable as part of routine medical care, and there is ample reason to be optimistic that improved treatment strategies may be on the near horizon.…”

Section: Discussionmentioning

confidence: 99%

On the Demographic and Selective Forces Shaping Patterns of Human Cytomegalovirus Variation within Hosts

et al. 2018

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Human cytomegalovirus (HCMV) is a member of the β-herpesvirus subfamily within Herpesviridae that is nearly ubiquitous in human populations, and infection generally results only in mild symptoms. However, symptoms can be severe in immunonaive individuals, and transplacental congenital infection of HCMV can result in serious neurological sequelae. Recent work has revealed much about the demographic and selective forces shaping the evolution of congenitally transmitted HCMV both on the level of hosts and within host compartments, providing insight into the dynamics of congenital infection, reinfection, and evolution of HCMV with important implications for the development of effective treatments and vaccines.

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“…292,294 Evolving deep sequencing technologies offer the potential of detecting far smaller mutant subpopulations. 292,[294][295][296] These early reports have not yet established properly calibrated, adequately sensitive, reproducible and stable technical platform to serve as a base for clinical validation, including comparison with existing technology. There are reports of discordant findings of resistance mutations at different body sites (eye, cerebrospinal fluid).…”

Section: How To Testmentioning

confidence: 99%

The Third International Consensus Guidelines on the Management of Cytomegalovirus in Solid-organ Transplantation

et al. 2018

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Despite recent advances, cytomegalovirus (CMV) infections remain one of the most common complications affecting solid organ transplant recipients, conveying higher risks of complications, graft loss, morbidity, and mortality. Research in the field and development of prior consensus guidelines supported by The Transplantation Society has allowed a more standardized approach to CMV management. An international multidisciplinary panel of experts was convened to expand and revise evidence and expert opinion-based consensus guidelines on CMV management including prevention, treatment, diagnostics, immunology, drug resistance, and pediatric issues. Highlights include advances in molecular and immunologic diagnostics, improved understanding of diagnostic thresholds, optimized methods of prevention, advances in the use of novel antiviral therapies and certain immunosuppressive agents, and more savvy approaches to treatment resistant/refractory disease. The following report summarizes the updated recommendations.

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Contribution of next generation sequencing to early detection of cytomegalovirus UL97 emerging mutants and viral subpopulations analysis in kidney transplant recipients

Cited by 31 publications

References 28 publications

Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus

Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus

On the Demographic and Selective Forces Shaping Patterns of Human Cytomegalovirus Variation within Hosts

The Third International Consensus Guidelines on the Management of Cytomegalovirus in Solid-organ Transplantation

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