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Detection of a new variant of herpes simplex virus type 2 among HIV-1-infected individuals

2013; Elsevier BV; Volume: 57; Issue: 3 Linguagem: Inglês

10.1016/j.jcv.2013.03.008

1873-5967

Sonia Burrel, Emiliana Pereira Abrão, Nathalie Désiré, Sophie Seang, Éric Caumes, Henri Agut, David Boutolleau,

Cytomegalovirus and herpesvirus research

Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines.Genital lesion swabs containing ≥ 107 log10 copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (UL_US) regions were identified. Phylogenetic trees were created using maximum likelihood reconstruction.Among 46 samples from 38 persons, 1468 intragenic base-pair substitutions were identified. The maximum nucleotide distance between strains for concatenated UL_US segments was 0.4%. Phylogeny did not reveal geographic clustering. The most variable proteins had non-synonymous mutations in < 3% of amino acids.Unenriched HSV-2 DNA can undergo next-generation sequencing to identify intragenic variability. The use of clinical swabs for sequencing expands the information that can be gathered directly from these specimens.