Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico.
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ABSTRACT:
SUBMITTER: Garces-Ayala F
PROVIDER: S-EPMC4498119 | biostudies-literature | 2015 Jul
REPOSITORIES: biostudies-literature
Publications
Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico.
Garcés-Ayala Fabiola F Rodríguez-Castillo Araceli A Ortiz-Alcántara Joanna María JM Gonzalez-Durán Elizabeth E Segura-Candelas José Miguel JM Pérez-Agüeros Sandra Ivette SI Escobar-Escamilla Noé N Méndez-Tenorio Alfonso A Diaz-Quiñonez José Alberto JA Ramirez-González José Ernesto JE
Genome announcements 20150709 4
Varicella-zoster virus (VZV) is a member of the Herpesviridae family, which causes varicella (chicken pox) and herpes zoster (shingles) in humans. Here, we report the complete genome sequence of varicella-zoster virus, isolated from a vesicular fluid sample, revealing the circulation of VZV clade VIII in Mexico. ...[more]
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Project description:BackgroundThe multi-country mpox outbreak across the globe has led to the systematic surveillance of mpox cases in India. During the surveillance of mpox, we encountered cases of Varicella Zoster Virus (VZV) in suspected mpox cases amongst children & adults. This study focused on the genomic characterization of VZV in India.MethodsA total of 331 mpox suspected cases were tested for VZV through real-time PCR, and the positive samples were subjected to next-generation sequencing to retrieve the whole genome of VZV using CLC genomics software. Phylogenetic analysis has been done in MEGA 11.0 software to identify circulating clades.ResultOf the 331 suspected cases, 28 cases with vesicular rashes were found to be positive for VZV. The maximum genome could be retrieved from the clinical specimens of 16 cases with coverage greater than 98% when mapped with reference strain Dumas (NC 001348). The phylogenetic analyses of these sequences determined the circulation of clades 1, 5, and 9 in India. Further, the sequence analysis demonstrated non-synonymous single nucleotide polymorphism (SNPs) among specific ORF of VZV including ORF 14, ORF 22, ORF 36, ORF 37 and ORF 51. Although clade 1 and 5 has been reported earlier, the circulation of clade 9 of VZV has been determined for the first time in India.ConclusionAlthough the circulation of different clades of VZV was reported from India, the presence of clade 9 was detected for the first time during the mpox surveillance.
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Project description:BackgroundVaricella Zoster Virus (VZV) is consistently in circulation and shows an increase in disease burden during the spring season. Due to a wide range of clinical presentation from a vesicular rash to bleeding or neurological complications, it makes the clinical diagnosis difficult. The present study aims to understand whether the same strain of virus is responsible for the increase in the seasonal outbreaks occurring in different parts of the country with reference to the samples from Maharashtra, Rajasthan and Gujarat states of India.Materials and methodsThis study reports the clinico-epidemiological and laboratory findings of suspected Varicella cases. To understand the circulating clade few representative real-time Polymerase Chain Reaction (PCR) positive were analyzed by conventional PCR and partial Open Reading Frame (ORF) 22, partial ORF 38 and partial ORF 54 were sequenced to identify single nucleotide polymorphisms responsible for clade determination. Further partial glycoprotein B gene was sequenced, and a phylogenetic tree was generated.ResultsA total of 50 cases from Maharashtra (Mumbai district) and referred clinical samples of Rajasthan (Barmer district; n = 12) and Gujarat States (Gandhi Nagar, Surat districts; n = 17) were tested for the presence of VZV. Vesicular rash with fever was a common clinical presentation with 82% cases having contact history with VZV positive cases, suggesting higher secondary attack rate. The vesicular fluid of all 50 cases from Mumbai revealed the presence of VZV by real-time PCR. Urine, serum and throat swab samples showed positivity by real-time PCR. Healthcare provider's samples from Rajasthan showed 36.4% [4/11] positivity. Clinical samples from Gujarat had positivity of 41.2% [7/17].ConclusionsThis study analyses the clade based circulation of VZV in three states in India and suggests different clades circulating in Maharashtra state. Health education amongst the general population is suggested to reduce the secondary cases by early diagnosis, effective isolation policies and vaccination to reduce the burden of disease.
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