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Divergence and recombination of clinical herpes simplex virus type 2 isolates.

Review article
Authors Peter Norberg
Mabula J Kasubi
Lars Haarr
Tomas Bergström
Jan-Åke Liljeqvist
Published in Journal of virology
Volume 81
Issue 23
Pages 13158-67
ISSN 1098-5514
Publication year 2007
Published at Institute of Biomedicine, Department of Infectious Medicine
Pages 13158-67
Language en
Keywords Cluster Analysis, DNA, Viral, chemistry, genetics, Evolution, Molecular, Genotype, Geography, Herpes Genitalis, virology, Herpesvirus 2, Human, classification, genetics, isolation & purification, Humans, Molecular Sequence Data, Norway, Phylogeny, Polymorphism, Genetic, Recombination, Genetic, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Sweden, Tanzania, Viral Envelope Proteins, genetics
Subject categories Microbiology in the medical area


Herpes simplex virus type 2 (HSV-2) infects the genital mucosa and is one of the most common sexually transmitted viruses. Here we sequenced a segment comprising 3.5% of the HSV-2 genome, including genes coding for glycoproteins G, I, and E, from 27 clinical isolates from Tanzania, 10 isolates from Norway, and 10 isolates from Sweden. The sequence variation was low compared to that described for clinical HSV-1 isolates, with an overall similarity of 99.6% between the two most distant HSV-2 isolates. Phylogenetic analysis revealed a divergence into at least two genogroups arbitrarily designated A and B, supported by high bootstrap values and evolutionarily separated at the root. Genogroup A contained isolates collected in Tanzania, and genogroup B contained isolates collected in Tanzania and Scandinavia, implying that the genetic variability of HSV-2 is higher in Tanzania than in Scandinavia. Recombination network analysis and bootscan analysis revealed a complex pattern of phylogenetically conflicting informative sites in the sequence alignments. These signals were present in synonymous and nonsynonymous sites in all three genes and were not accumulated in specific regions, observations arguing against positive selection. Since the PHI test applied solely to synonymous sites revealed a high statistical probability of recombination, we suggest as a novel finding that homologous recombination is, as reported earlier for HSV-1 and varicella-zoster virus, a prominent feature in the evolution of HSV-2.

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