Revisiting the genotyping scheme for varicella-zoster viruses based on whole-genome comparisons

Jensen, Nancy J.; Rivailler, Pierre; Tseng, Hung Fu; Quinlivan, Mark; Radford, Kay; Folster, Jennifer; Harpaz, Rafael; LaRussa, Philip; Jacobsen, Steven J.; Schmid, Daniela

doi:10.1099/jgv.0.000772

Cited by 35 publications

(31 citation statements)

References 14 publications

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“…However, most studies of recombination in human herpesviruses have focused on naturally circulating variants and have inferred historical sites of recombination and phylogenetic relationships from the comparison of disparate strains. For example, increased genomic surveillance of VZV has expanded the number of known phylogenetic clades for this species in recent years; this has provided evidence for ancient, interclade recombination as well as for modern recombination between individual strains ( 28 – 32 ). For the beta-herpesvirus HCMV, multiple groups have confirmed the finding of rampant genome-wide recombination among different HCMV strains ( 19 , 33 , 34 ).…”

Section: Recombination As a Driving Force In Dna Virus Evolutionmentioning

confidence: 99%

“…The norm for HTS studies has now shifted to include either comparisons of a large number of viral strains at a time or a deeper investigation of viral setting or outbreak. This expansion of known diversity has driven the definition of new phylogenetic clades and facilitated the reconstruction of the evolutionary history of VZV ( 28 , 30 – 32 ), HSV-1 ( 23 , 36 , 70 – 72 ), HSV-2 ( 73 – 76 ), HCMV ( 20 , 33 , 34 , 77 ), HHV 6A/6B ( 119 ), EBV ( 78 , 79 ), and KSHV ( 80 ), as well as animal herpesviruses ( 41 ). While it is clear that increasing the number of fully sequenced genomes for each species widens our knowledge of viral diversity, the next challenge lies in dissecting the phenotypic impacts of the observed genetic differences in these viral populations.…”

Section: Capturing and Cataloging The Diversity Of Herpesvirusesmentioning

confidence: 99%

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Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution

Renner

Szpara

2018

J Virol

109

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Until fairly recently, genome-wide evolutionary dynamics and within-host diversity were more commonly examined in the context of small viruses than in the context of large double-stranded DNA viruses such as herpesviruses. The high mutation rates and more compact genomes of RNA viruses have inspired the investigation of population dynamics for these species, and recent data now suggest that herpesviruses might also be considered candidates for population modeling. High-throughput sequencing (HTS) and bioinformatics have expanded our understanding of herpesviruses through genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures. Here we discuss recent data on the mechanisms that generate herpesvirus genomic diversity and underlie the evolution of these virus families. We focus on human herpesviruses, with key insights drawn from veterinary herpesviruses and other large DNA virus families. We consider the impacts of cell culture on herpesvirus genomes and how to accurately describe the viral populations under study. The need for a strong foundation of high-quality genomes is also discussed, since it underlies all secondary genomic analyses such as RNA sequencing (RNA-Seq), chromatin immunoprecipitation, and ribosome profiling. Areas where we foresee future progress, such as the linking of viral genetic differences to phenotypic or clinical outcomes, are highlighted as well.

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Section: Recombination As a Driving Force In Dna Virus Evolutionmentioning

confidence: 99%

Section: Capturing and Cataloging The Diversity Of Herpesvirusesmentioning

confidence: 99%

Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution

Renner

Szpara

2018

J Virol

109

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“…For a small proportion of cases (3%), samples were tested for VZV only at CDC. For VZV PCR testing at CDC, four different PCR protocols were performed on every sample, each of which can detect <10 copies/reaction . VZV genotyping was also performed at CDC on a subset of VZV‐positive samples.…”

Section: Methodsmentioning

confidence: 99%

Varicella in Tshuapa Province, Democratic Republic of Congo, 2009–2014

Leung

McCollum

Radford

et al. 2019

Tropical Med Int Health

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Objective To describe varicella cases in Tshuapa Province of the Democratic Republic of the Congo identified during monkeypox surveillance. Methods Demographic, clinical and epidemiological data were collected from each suspected monkeypox case 2009–2014. Samples were tested by PCR for both Orthopoxviruses and varicella‐zoster virus (VZV); a subset of VZV‐positive samples was genotyped. We defined a varicella case as a rash illness with laboratory‐confirmed VZV. Results There were 366 varicella cases were identified; 66% were ≤19 years old. Most patients had non‐typical varicella rash with lesions reported as the same size and stage of evolution (86%), deep and profound (91%), on palms of hands and/or soles of feet (86%) and not itchy (49%). Many had non‐typical signs and symptoms, such as lymphadenopathy (70%) and sensitivity to light (23%). A higher proportion of persons aged ≥20 years than persons aged ≤19 years had ≥50 lesions (79% vs. 65%, P = 0.007) and were bedridden (15% vs. 9%, P = 0.056). All VZV isolates genotyped from 79 varicella cases were clade 5. During the surveillance period, one possible VZV‐related death occurred in a 7‐year‐old child. Conclusions A large proportion of patients presented with non‐typical varicella rash and clinical signs and symptoms, highlighting challenges identifying varicella in an area with endemic monkeypox. Continued surveillance and laboratory diagnosis will help in rapid identification and control of both monkeypox and varicella and improve our understanding of varicella epidemiology in Africa.

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“…The classifications of these samples are similar to those found in the US except that European clades (clades 1 and 3) predominate, followed by clade 5 (CDC, unpublished observation). VZV molecular epidemiology varies by geographical region, likely reflecting climatic conditions and the geographic isolation of populations, although this trend does not hold in countries with widespread immigration [6][7][8][9][10] . Clade 5 is the dominant genotype in Africa, and its dominance in Brazil may reflect large influxes of people from sub-Saharan Africa.…”

Section: /4mentioning

confidence: 99%

“…Seven isolates were determined to be clade 5 viruses (50%), 5 were clade 1 (36%), and 2 were clade 3 (14%) ( Table 1). Depletion of the samples precluded the use of the recently-published revisions to our SNPbased genotyping method 8 . The method used fails to distinguish clade 6 from clade VIII, but since no clade 6/VIII viruses were identified, it was not relevant to this study.…”

mentioning

confidence: 99%

Genotypes of clinical varicella-zoster virus isolates from Manaus, Brazil

Bastos

Folster

Alvarenga

et al. 2019

Rev. Soc. Bras. Med. Trop.

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Introduction: Vaccination against varicella-zoster virus (VZV) has been effective and safe in countries that routinely administer the vaccine. Brazil began universal VZV vaccination in 2013. This study aimed to identify VZV genotypes present in Manaus, Brazil prior to widespread immunization. Methods: Vesicular lesions or cerebral-spinal-fluid samples were collected from patients diagnosed with VZV, herpes zoster, or meningitis/encephalitis. DNA was extracted, amplified, and sequenced. Results: Half the isolates were clade-5 viruses and the remaining were divided between the European clades 1 and 3. Conclusions: This study provides insights into the circulating VZV genotypes in Manaus prior to widespread vaccination.

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Revisiting the genotyping scheme for varicella-zoster viruses based on whole-genome comparisons

Cited by 35 publications

References 14 publications

Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution

Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution

Varicella in Tshuapa Province, Democratic Republic of Congo, 2009–2014

Genotypes of clinical varicella-zoster virus isolates from Manaus, Brazil

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