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Single Nucleotide Polymorphisms in the U86 Gene of Human betaherpesvirus 6B

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Abstract

There are single publications dedicated to identifying and typing the Human Herpesvirus type 6 (HHV-6) in the domestic scientific literature. Meanwhile, the determination of the genetic polymorphism of HHV-6A and HHV-6B will allow studying the geographic distribution and circulation patterns in human populations of various genotypes of the virus. The study aimed to analyze single nucleotide polymorphisms in the U86 gene to characterize the population of HHV-6B in Russia. The Sanger sequencing of HHV-6 DNA from 49 blood samples of children with acute HHV-6 infection in St. Petersburg was carried out. The nucleotide sequences of the 317 bp-fragment of the U86 gene of clinical isolates were aligned to the reference genome HHV-6B NC_000898 (strain Z29). The majority (63%) of HHV-6B isolates for this gene region were identical to the reference strain; 18 isolates showed four variants of single nucleotide substitutions, including three non-synonymous polymorphisms. Of the 18 isolates, 11 (6%) differed from the reference in two SNPs and six (3%) in all four SNPs, while one (0.5%) had three single nucleotide substitutions. All four profiles of single nucleotide substitutions (sequence types) of the U86 gene fragment of Russian isolates had analogs among HHV-6B isolates of various geographic origins presented in the NCBI GenBank. Sequencing of the U86 gene fragment confirmed the species affiliation to HHV-6B of 49 studied isolates, making it possible to estimate the prevalence and establish phylogenetic relationships of four sequence types in Russian and foreign populations of the virus.

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Authors and Affiliations

  1. St. Petersburg Pasteur Institute, 197101, St. Petersburg, Russia

    A. A. Vyazovaya & O. V. Narvskaya

  2. St. Petersburg Research Institute of Phthisiopulmonology, 191036, St. Petersburg, Russia

    O. V. Narvskaya

  3. Alkor Bio Group of Companies, 192148, St. Petersburg, Russia

    V. E. Vedernikov

  4. Pavlov First St. Petersburg State Medical University, 197022, St. Petersburg, Russia

    M. A. Nikolskiy

Authors
  1. A. A. Vyazovaya
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  2. O. V. Narvskaya
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  3. V. E. Vedernikov
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  4. M. A. Nikolskiy
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Corresponding author

Correspondence to A. A. Vyazovaya.

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COMPLIANCE WITH ETHICAL STANDARDS

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. Informed consent was obtained from all participants involved in the study.

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The authors declare that they have no conflicts of interest.

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Translated by M. Novikova

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Vyazovaya, A.A., Narvskaya, O.V., Vedernikov, V.E. et al. Single Nucleotide Polymorphisms in the U86 Gene of Human betaherpesvirus 6B. Mol. Genet. Microbiol. Virol. 37, 127–130 (2022). https://doi.org/10.3103/S0891416822030090

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  • DOI: https://doi.org/10.3103/S0891416822030090

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