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Metagenomic analysis of a throat swab sample collected in China on a patient infected with Varicella Zoster Virus.

ABSTRACT: Varicella Zoster Virus (VZV) is endemic worldwide, causing varicella in children and zoster upon reactivation in adults. This study concerned a metagenomic analysis of a throat swab sample collected in China, on a young patient suffering from Systemic Lupus Erythematosus (SLE) and diagnosed with varicella. The complete genome sequence of a VZV strain of clade 2 has been generated. Clade 2 strains are the most prevalent in Asian countries. A comparison of 223 VZV genomes identified 77 clade specific markers, 20 of them specific to clade 2. The metagenomic analysis also identified sequences covering most of the genome of the bacteria Schaalia odontolytica also known as Actinomyces odontolyticus. VZV infection and bacterial infection in the context of SLE is further discussed. Even though the patient presented only mild symptoms, this study is a reminder that vaccination against VZV is critical to avoid severe complications like bacterial superinfection or even death in the case of immunodeficiency.

SUBMITTER: Guo H

PROVIDER: S-EPMC8260771 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:In 2010, a universal nomenclature for varicella-zoster virus (VZV) clades was established, which is very useful in the monitoring of viral evolution, recombination, spread and genetic diversity. Currently, information about VZV clades has been disclosed worldwide, however, there are limited data regarding the characterization of circulating VZV clades in China, even where varicella remains widely epidemic.From 2008 to 2012, clinical samples with varicella or zoster were collected in General Hospital in eight provinces and analyzed by PCR, restriction endonuclease digestion and sequencing. The viral clades were determined by analysis of five single nucleotide polymorphisms (SNPs) within the 447-bp fragment of open reading frame (ORF) 22, and the restriction fragment length polymorphisms (RFLPs) of ORF 38 (PstI), ORF 54 (BglI) and ORF 62 (SmaI) were evaluated to understand genetic diversity of VZV and determinate varicella vaccine adverse event (VVAE).Seventy-seven varicella and 11 zoster samples were identified as being positive for VZV. The five SNPs profile showed that the majority of VZV strains belonged to clade 2, but clade 5 and clade 4 strains were also found in Guangdong. The RFLPs analysis of the DNA fragments of ORF 38, 54 and 62 showed that 85 of these samples were characterized as PstI?+?BglI?+?SamI-, and the remaining three VZV strains from varicella patients were characterized as PstI-BglI?+?SamI+ which is the genetic profile of VVAEs.The study suggested that the predominant clade 2 VZVs had been continually circulating since at least the 1950s in China. Nearly all VZV strains except VVAEs possessed the genetic profile of PstI?+?BglI?+?Sam-. However, the other clades were also found to be co-circulating with clade 2, especially in the border regions. These results highlighted the need for the constant and broad use of virologic surveillance to provide an important genetic baseline for varicella control and vaccination programs in China.

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Metagenomic analysis of a throat swab sample collected in China on a patient infected with Varicella Zoster Virus.

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