Viral Genome Sequencing Proves Nosocomial Transmission of Fatal Varicella

Coverage rates against vaccine-preventable diseases among healthcare workers in Sicily (Italy)

BACKGROUND

Vaccination of healthcare workers (HCWs) reduces the risk of occupational vaccine-preventable diseases (VPDs), prevents their nosocomial transmission and preserves healthcare delivery during outbreaks. Extensive implementation of vaccination programmes for HCWs allowed the elimination or control of several VPDs within healthcare facilities; despite these, the vaccine adherence rates among HCWs are persistently suboptimal.

METHODS

A questionnaire was self-administered by HCWs to assess their vaccination rates against several VPDs and self-reported immunity in two university hospitals of Southern Italy (Catania and Palermo).

RESULTS

A total of 2586 questionnaires were analysed. More than 50% of HCWs did not know their own immunization status against diphtheria, tetanus and pertussis. More than half of the HCWs interviewed at University Hospital (UH) of Catania (UHC) was immune against measles (72.1%), in contrast with data reported at the UH of Palermo (UHP) (45.9%). Immunization status against mumps (67.5% UHC vs. 40.6% UHP), rubella (69.9% UHC vs. 46.6% UHP) and varicella (70.4% UHC vs. 50.7% UHP). Overall, about 30% of HCWs did not know their own immunization status against these VPDs. Moreover, 84.2% at UHC and 66.7% at UHP stated that was previously vaccinated against hepatitis B.

CONCLUSION

Vaccination coverage rates reported from the HCWs against influenza during the last three seasons were considerably low. In conclusion, totally inadequate vaccination rates against several VPDs were found in two university hospitals in Sicily, in terms of preventing not only disease transmission by susceptible HCWs, but also nosocomial outbreaks, confirming data from previous national and international studies.

Serologic screening and infectious diseases consultation in renal transplant candidates for measles, mumps, rubella and varicella

Background. Renal transplant recipients are at increased risk for developing complications of vaccine-preventable diseases. They benefit from a comprehensive pre-transplant evaluation when they might safely receive live vaccines. The primary aim of our study was to investigate the number of renal transplant recipients who were evaluated for serologic status against measles, mumps, rubella (MMR), and varicella. Secondarily, we investigated if pre-transplant Infectious Diseases consultation (IDC) improved vaccination rates.Methods. We retrospectively analyzed 282 kidney-alone and kidney-plus adult transplant recipients who were born in or after 1957. Patients were evaluated at Mayo Clinic, Florida Transplant Center between January 2015 and December 2017. Serologic status evaluation and vaccination rates were compared in two groups created based on IDC and no ID consultation (NIDC).Results. 235 (83%) of a total 282 patients received an IDC pre-transplantation. Varicella IgG levels were screened in all 235 IDC candidates. Among the IDC patients, mumps, measles and rubella IgG serologies were performed in 7 (3%), 143 (61%) and 144 (61%), respectively. Among 44 patients seronegative for any of MMR, 24 (55%) were vaccinated. Ten (66%) of 15 varicella seronegative patients were vaccinated. Zostavax was not given to 18% of IDC patients. Zostavax and MMR were administered more frequently in the IDC group compared to NIDC (p < .001 and p = 0.0016, respectively).Conclusion. Although the majority of patients had IDC, the screening rate for MMR serologies was lower than varicella. A protocol-driven serologic screening similar to the one for VZV is required for MMR. Pre-transplant IDC increases vaccination rates.

Pneumonia and central nervous system infection caused by reactivation of varicella-zoster virus in a living-donor kidney transplantation patient: case report and review of the literature

Varicella-zoster virus (VZV) typically causes herpes zoster in the elderly due to reactivation, but immunocompromised individuals may develop organ damage such as pneumonia with a poor prognosis. We herein report a case of pneumonia and central nervous system (CNS) infection caused by reactivation of VZV in a 50-year-old man who had received a living-donor kidney transplant. We also conducted a literature review of adult cases with pneumonia or CNS infection caused by VZV after kidney transplantation. It showed that there are cases in which eruptions appeared upto 21 days after the onset of the disease and others in which eruptions did not appear at any time during the clinical course. Furthermore, there may be a wide variety of intervals from kidney transplantation to VZV infection (including both primary infection and reactivation of VZV), ranging from 2 weeks to 11 years. Therefore, it should be kept in mind that kidney transplant patients are always at high risk of VZV infection, as early recognition and treatment of the disease improves its prognosis. Although the diagnosis of varicella pneumonia is generally made by PCR test of bronchoalveolar lavage fluid, our case experience suggests that the less invasive PCR test of sputum may be useful for rapid and accurate diagnosis. The efficacy of inactivated recombinant zoster vaccine in immunocompromised individuals at high risk of reactivation of VZV also needs to be examined in the future.

Alphaherpesvirus Genomics: Past, Present and Future

Alphaherpesviruses, as large double-stranded DNA viruses, were long considered to be genetically stable and to exist in a homogeneous state. Recently, the proliferation of high-throughput sequencing (HTS) and bioinformatics analysis has expanded our understanding of herpesvirus genomes and the variations found therein. Recent data indicate that herpesviruses exist as diverse populations, both in culture and in vivo, in a manner reminiscent of RNA viruses. In this review, we discuss the past, present, and potential future of alphaherpesvirus genomics, including the technical challenges that face the field. We also review how recent data has enabled genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures, including those introduced by cell culture. While we focus on the human alphaherpesviruses, we draw key insights from related veterinary species and from the beta- and gamma-subfamilies of herpesviruses. Promising technologies and potential future directions for herpesvirus genomics are highlighted as well, including the potential to link viral genetic differences to phenotypic and disease outcomes.

Personalized viral genomic investigation of herpes simplex virus 1 perinatal viremic transmission with dual fatality

Here we present a personalized viral genomics approach to investigating a rare case of perinatal herpes simplex virus 1 (HSV-1) transmission that ended in death of both mother and neonate. We sought to determine whether the virus involved in this rare case had any unusual features that may have contributed to the dire patient outcome. A pregnant woman with negative HerpeSelect antibody test underwent cesarean section at 30 wk gestation and died the same day. The premature newborn died 5 d later. Both individuals were found postmortem to have positive blood HSV-1 PCR tests. Using oligonucleotide enrichment and deep sequencing, we determined that viral transmission from mother to infant was nearly perfect at the consensus genome level. At the virus population level, 77% of minor variants (MVs) in the mother's blood also appeared on the neonate's skin, of which more than half were disseminated into the neonate's blood. We also detected nonmaternal MVs that arose de novo in the neonate's viral populations. Of note, one de novo MV in the neonate's skin virus induced a nonsynonymous mutation in the UL6 protein, which is a component of the portal that allows DNA entry into new progeny capsids. This case suggests that perinatal viremic HSV-1 transmission includes the majority of genetic diversity from the maternal virus population and that new, nonsynonymous mutations can occur after relatively few rounds of replication. This report expands our understanding of viral transmission in humans and may lead to improved diagnostic strategies for neonatal HSV-1 acquisition.

High Viral Diversity and Mixed Infections in Cerebral Spinal Fluid From Cases of Varicella Zoster Virus Encephalitis

Background

Varicella zoster virus (VZV) may cause encephalitis, both with and without rash. Here we investigate whether viruses recovered from the central nervous system (CNS; encephalitis or meningitis) differ genetically from those recovered from non-CNS samples.

Methods

Enrichment-based deep sequencing of 45 VZV genomes from cerebral spinal fluid (CSF), plasma, bronchoalveolar lavage (BAL), and vesicles was carried out with samples collected from 34 patients with and without VZV infection of the CNS.

Results

Viral sequences from multiple sites in the same patient were identical at the consensus level. Virus from vesicle fluid and CSF in cases of meningitis showed low-level diversity. By contrast, plasma, BAL, and encephalitis had higher numbers of variant alleles. Two CSF-encephalitis samples had high genetic diversity, with variant frequency patterns typical of mixed infections with different clades.

Conclusions

Low viral genetic diversity in vesicle fluid is compatible with previous observations that VZV skin lesions arise from single or low numbers of virions. A similar result was observed in VZV from cases of VZV meningitis, a generally self-limiting infection. CSF from cases of encephalitis had higher diversity with evidence for mixed clade infections in 2 cases. We hypothesize that reactivation from multiple neurons may contribute to the pathogenesis of VZV encephalitis.

Myths and Misconceptions: Varicella-Zoster Virus Exposure, Infection Risks, Complications, and Treatments

Varicella zoster and herpes zoster are infections caused by the highly contagious varicella-zoster virus (VZV). Despite widespread availability of vaccines against VZV, as well as varicella vaccination rates >95%, VZV remains a public health concern because of several common myths and misconceptions. Because of the success of routine varicella vaccination programs, some people mistakenly believe that varicella and herpes zoster are now no longer a threat to public health. Another common misconception is that shingles is less infectious than varicella; however, clinical evidence indicates otherwise. Several knowledge gaps exist around VZV transmission and the availability and use of varicella zoster immune globulin (human) for postexposure prophylaxis against VZV. To help reduce the incidence of severe disease in high-risk individuals (eg, elderly people, pregnant women, unvaccinated persons, infants, and immunocompromised children and adults), this article addresses misbeliefs and broadens awareness of VZV exposure, infection risks, complications, and treatments.

Risk of transmission of vaccine-preventable diseases in healthcare settings

The transmission of infectious agents within healthcare settings is a priority public health problem. Although the main burden of healthcare-associated infections is commonly caused by Gram-negative bacteria and fungi, vaccine-preventable diseases represent an additional infectious risk for patients attending healthcare facilities. Hepatitis B, rotavirus gastroenteritis, influenza, measles, pertussis and pneumococcal and meningococcal invasive bacterial infections still represent a threat, notwithstanding the presence of universal vaccination programs. For this reason, healthcare worker immunization is an important strategy to limit the risk of vaccine-preventable diseases in such a fragile population.

Vaccination of healthcare workers: is mandatory vaccination needed?

INTRODUCTION

Vaccinations of healthcare workers (HCWs) aim to directly protect them from occupational acquisition of vaccine-preventable diseases (VPDs) and to indirectly protect their patients and the essential healthcare infrastructure. However, outbreaks due to VPDs continue to challenge healthcare facilities and HCWs are frequently traced as sources of VPDs to vulnerable patients. In addition, HCWs were disproportionately affected during the current measles outbreak in Europe. Areas covered: We reviewed the recent published information about HCWs vaccinations with a focus on mandatory vaccination policies. Expert commentary: Although many countries have vaccination programs specifically for HCWs, their vaccination coverage remains suboptimal and a significant proportion of them remains susceptible to VPDs. The increasing vaccination hesitancy among HCWs is of concern, given their role as trusted sources of information about vaccines. Mandatory vaccinations for HCWs are implemented for specific VPDs in few countries. Mandatory influenza vaccination of HCWs was introduced in the United States a decade ago with excellent results. Mandatory vaccinations for VPDs that may cause significant morbidity and mortality should be considered. Issues of mistrust and misconceptions about vaccinations should also be addressed.

Varicella infections in patients with end stage renal disease: a systematic review

BACKGROUND

End stage renal disease (ESRD) is on the rise globally. Varicella infection among adult patients with ESRD has been reported to lead to multiple complications and even death. While varicella vaccination has been recommended in paediatric renal patients; recommendation on varicella vaccination among adult patients with ESRD remained sparse. This review is aimed at evaluating the impact of varicella infection among adult patients with ESRD and make a recommendation for vaccination.

METHODS

Three databases (PubMed, Embase and Cumulative Index to Nursing and Allied Health Literature (CINAHL)) were searched in April 2018 with keywords 'varicella, chronic kidney failure, chronic kidney disease, renal replacement therapy, kidney transplantation, end stage renal disease, end stage renal failure, chicken pox, vaccine, vaccination and complications'.

RESULTS

29 articles were selected for review. The studies were mainly case reports, and they included measured outcomes: prevalence of seronegativity, impact (morbidity, length of stay, and mortality) of varicella among patients with ESRD, seroconversion rates and safety of varicella vaccination. The prevalence of seronegativity among varicella-infected ESRD adults was found to be at 42 to 100%. Nineteen deaths were reported. At least 54 patients have had complications from varicella infection. Seroconversion rate post vaccination was found to be around 64-94%.

CONCLUSION

Varicella is associated with significant morbidity and mortality rates in adult patients with ESRD. Varicella vaccination should be considered for the vulnerable, seronegative patients.

Healthcare-Associated Viral Infections: Considerations for Nosocomial Transmission and Infection Control

Nosocomial and healthcare-associated viral infections are major contributors to patient morbidity and mortality, prolonged hospitalization, and increased healthcare costs in all pediatric age groups. Healthcare workers are also at risk of acquiring nosocomial viral infections, affecting their own health, as well as facilitating spread of the infection to other patients, their family, and the community. Healthcare-associated viral infections may occur in a variety of healthcare settings, including clinics, emergency centers, urgent care centers, procedure suites, operating rooms, hospital wards, nurseries, and intensive care units. In addition, non-patient care areas, such as the cafeteria, waiting areas, and playrooms may also be a source of viral infections that can spread in the healthcare setting. These infections may be device-related or transmitted via blood products or organ donation and respiratory droplets, through food including human milk, person to person, or via air ducts, fomites, and surfaces. They most commonly involve the respiratory and gastrointestinal tracts; however, all organ systems may potentially be involved. Both DNA and RNA viruses, either common or exotic, may contribute to healthcare-associated viral infections. Advances in molecular viral diagnostics have enabled rapid detection and routine surveillance for viral infections and now allow early identification of viruses. Prompt identification allows timely containment measures to minimize transmission to other patients or healthcare workers and avoids hospital, community, and global outbreaks.

Molecular Aspects of Varicella-Zoster Virus Latency

Primary varicella-zoster virus (VZV) infection causes varicella (chickenpox) and the establishment of a lifelong latent infection in ganglionic neurons. VZV reactivates in about one-third of infected individuals to cause herpes zoster, often accompanied by neurological complications. The restricted host range of VZV and, until recently, a lack of suitable in vitro models have seriously hampered molecular studies of VZV latency. Nevertheless, recent technological advances facilitated a series of exciting studies that resulted in the discovery of a VZV latency-associated transcript (VLT) and provide novel insights into our understanding of VZV latency and factors that may initiate reactivation. Deducing the function(s) of VLT and the molecular mechanisms involved should now be considered a priority to improve our understanding of factors that govern VZV latency and reactivation. In this review, we summarize the implications of recent discoveries in the VZV latency field from both a virus and host perspective and provide a roadmap for future studies.

Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture

Herpes simplex viruses (HSVs) are difficult to sequence due to their large DNA genome, high GC content, and the presence of repeats. To date, most HSV genomes have been recovered from culture isolates, raising concern that these genomes may not accurately represent circulating clinical strains. We report the development and validation of a DNA oligonucleotide hybridization panel to recover nearly complete HSV genomes at abundances up to 50,000-fold lower than previously reported. Using copy number information on herpesvirus and host DNA background via quantitative PCR, we developed a protocol for pooling for cost-effective recovery of more than 50 HSV-1 or HSV-2 genomes per MiSeq run. We demonstrate the ability to recover >99% of the HSV genome at >100× coverage in 72 h at viral loads that allow whole-genome recovery from latently infected ganglia. We also report a new computational pipeline for rapid HSV genome assembly and annotation. Using the above tools and a series of 17 HSV-1-positive clinical swabs sent to our laboratory for viral isolation, we show limited evolution of HSV-1 during viral isolation in human fibroblast cells compared to the original clinical samples. Our data indicate that previous studies using low-passage-number clinical isolates of herpes simplex viruses are reflective of the viral sequences present in the lesion and thus can be used in phylogenetic analyses. We also detect superinfection within a single sample with unrelated HSV-1 strains recovered from separate oral lesions in an immunosuppressed patient during a 2.5-week period, illustrating the power of direct-from-specimen sequencing of HSV.IMPORTANCE Herpes simplex viruses affect more than 4 billion people across the globe, constituting a large burden of disease. Understanding the global diversity of herpes simplex viruses is important for diagnostics and therapeutics as well as cure research and tracking transmission among humans. To date, most HSV genomics has been performed on culture isolates and DNA swabs with high quantities of virus. We describe the development of wet-lab and computational tools that enable the accurate sequencing of near-complete genomes of HSV-1 and HSV-2 directly from clinical specimens at abundances >50,000-fold lower than previously sequenced and at significantly reduced cost. We use these tools to profile circulating HSV-1 strains in the community and illustrate limited changes to the viral genome during the viral isolation process. These techniques enable cost-effective, rapid sequencing of HSV-1 and HSV-2 genomes that will help enable improved detection, surveillance, and control of this human pathogen.

Association of visitation policy and health care-acquired respiratory viral infections in hospitalized children

Visitor restriction policies are meant to prevent health care-acquired viral infections; however, data on their efficacy in hospitalized children are limited. We report a 37% reduction in health care-acquired respiratory viral infections in a children's hospital following standardization of the visitation policy that limited the number of visitors during a patient's hospitalization.

Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion

The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture.IMPORTANCE Viruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiple in vitro passages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture.

Differentiation between wild-type and vaccines strains of varicella zoster virus (VZV) based on four single nucleotide polymorphisms

Varicella-zoster virus (VZV) infection (chickenpox) results in latency and subsequent reactivation manifests as shingles. Effective attenuated vaccines (vOka) are available for prevention of both illnesses. In this study, an amplicon-based sequencing method capable of differentiating between VZV wild-type (wt) strains and vOka vaccine is described. A total of 44 vesicular fluid specimens collected from 43 patients (16 from China and 27 from the UK) with either chickenpox or shingles were investigated, of which 10 had received previous vaccination. Four sets of polymerase chain reactions were set up simultaneously with primers amplifying regions encompassing four single nucleotide polymorphisms (SNPs), '69349-106262-107252-108111'. Nucleotide sequences were generated by Sanger sequencing. All samples except one had a wt SNP profile of 'A-T-T-T'. The sample collected from a patient who received vaccine 7-10 days ago, along with VZV vaccine preparations, Zostavax and Baike-varicella gave a SNP profile 'G-C-C-C'. The results show that this method can distinguish vaccine-derived virus from wt viruses from main four clades, (clades 1-4) and should be of utility worldwide.