Novel Genetic Rearrangements Termed “Structural Variation Polymorphisms“ Contribute to the Genetic Diversity of Orthohepadnaviruses

• Main Authors: Kei Fujiwara, Kentaro Matsuura, Kayoko Matsunami, Etsuko Iio, Yoshihito Nagura, Shunsuke Nojiri, Hiromi Kataoka
• Format: Article
• Language: English
• Published: MDPI AG 2019-09-01
• Series: Viruses
• Subjects: orthohepadnavirus; hepatitis B virus; genetic diversity; structural variation
• Online Access: https://www.mdpi.com/1999-4915/11/9/871

The genetic diversity of orthohepadnaviruses is not yet fully understood. This study was conducted to investigate the role of structural variations (SVs) in their diversity. Genetic sequences of orthohepadnaviruses were retrieved from databases. The positions of sequence gaps were investigated, since they were found to be related to SVs, and they were further used to search for SVs. Then, a combination of pair-wise and multiple alignment analyses was performed to analyze the genomic structure. Unique patterns of SVs were observed; genetic sequences at certain genomic positions could be separated into multiple patterns, such as no SV, SV pattern 1, SV pattern 2, and SV pattern 3, which were observed as polymorphic changes. We provisionally referred to these genetic changes as SV polymorphisms. Our data showed that higher frequency of sequence gaps and lower genetic identity were observed in the pre-S1-S2 region of various types of HBVs. Detailed examination of the genetic structure in the pre-S region by a combination of pair-wise and multiple alignment analyses showed that the genetic diversity of orthohepadnaviruses in the pre-S1 region could have been also induced by SV polymorphisms. Our data showed that novel genetic rearrangements provisionally termed SV polymorphisms were observed in various orthohepadnaviruses.