Development and validation for intra-species classification of HHV6A and HHV6B molecular genetic diversity

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Abstract

Human herpesvirus 6A (HHV6A) and human herpesvirus 6B (HHV6B) are ubiquitous viruses that infect more than 95% of the population. Clinical manifestations of HHV6 infection and associated diseases are diverse, which may depend on virus molecular genetic characteristics (genovariants). Estimating the significance of the molecular genetic diversity is complicated due to the lack of proper classification. The aim of the study was to develop an intraspecies HHV6A and HHV6B classification. Using 50 and 207 HHV6A and HHV6B full-genome sequences retrieved from the NCBI Nucleotide database, various fragments of virus genome were analyzed. Multiple sequence alignment was performed using MAFFT L-INS-i algorithm; F81 nucleotide substitution model and maximum likelihood method were used to construct dendrograms. Nucleotide substitutions were determined relative to reference sequences X83413 (HHV6A) and AF157706 (HHV6B). Genovariants were defined based on the nucleotide substitutions in variable positions of the genomic fragment. The results were confirmed by constructing dendrograms. An opportunity of using fragments of HHV6A and HHV6B genomes to construct an intraspecies classification was assessed. Fragments U90(part206) and U90В(part431) were selected as optimal. Based on the nucleotide sequences of the fragments, the intraspecies classification for HHV6A and HHV6B was constructed, including seven genovariants of each virus. The genovariants were characterized by unique nucleotide composition in the signature positions. A minimum (0.001 or less for both viruses) nucleotide diversity within the isolated genovariants was established. The classification reflects the phylogenetic relationships of circulating and inherited chromosomally integrated forms of HHV6A and HHV6B: divergence of HHV6A genovariants depending on its persistence form and integration site and coevolution of two HHV6B forms within several genovariants. Further studies on virus molecular genetic diversity in different regions of Russia and abroad may supplement the classification. The method of HHV6A and HHV6B classification is characterized by simplicity, technological accessibility and can be implemented in laboratories of different levels of technical equipment. The classification can be used to analyze an effect of virus molecular genetic diversity on the clinical characteristics of associated diseases, optimize the epidemiological surveillance system and develop new approaches for diagnostics, prevention, and treatment of HHV6 infection.

About the authors

Elena N. Filatova

Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology

Author for correspondence.
Email: el.filatova83@mail.ru

PhD (Biology), Leading Researcher, Laboratory of Molecular Biology and Biotechnology

Russian Federation, Nizhny Novgorod

Oleg V. Utkin

Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology

Email: el.filatova83@mail.ru

PhD (Biology), Head of the Laboratory of Molecular Biology and Biotechnology

Russian Federation, Nizhny Novgorod

A. E. Khrulev

Privolzhskiy Research Medical University

Email: el.filatova83@mail.ru

DSc (Medicine), Associate Professor, Professor of the Department of Nervous Diseases

Russian Federation, Nizhny Novgorod

N. N. Zaitseva

Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology

Email: el.filatova83@mail.ru

DSc (Medicine), Director

Russian Federation, Nizhny Novgorod

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