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. 2021 Dec 24;11(1):20.
doi: 10.3390/pathogens11010020.

Comparison of Two Diagnostic Methods for the Detection of Hepatitis B Virus Genotypes in the Slovak Republic

Mariia Logoida  1 , Pavol Kristian  2 , Andrea Schreiberova  3 , Patrícia Denisa Lenártová  2 , Veronika Bednárová  1 , Elena Hatalová  1 , Ivana Hockicková  2 , Sylvia Dražilová  4 , Peter Jarčuška  4 , Martin Janičko  4 , Štefan Porhinčák  5 , Monika Halánová  1
Affiliations

Comparison of Two Diagnostic Methods for the Detection of Hepatitis B Virus Genotypes in the Slovak Republic

Mariia Logoida et al. Pathogens. .

Abstract

The hepatitis B virus (HBV), belonging to the Hepadnaviridae family, is responsible for a global health concern still in the 21st century. The virus is divided into 10 genotypes, which differ in geographical distribution and in their effect on disease progression and transmission, susceptibility to mutations, and response to treatment. There are many methods for diagnostics of HBV and differentiating its genotypes. Various commercial kits based on real-time polymerase chain reaction (RT PCR) and hybridization available, as well as whole genome sequencing or the sequencing of only individual parts of the genomes. We compared a commercial kit AmpliSens HBV-genotype-FRT, based on RT PCR, with an adapted method of amplification of the surface genomic region combined with Sanger sequencing. In the examined samples we identified the A, B, C, D, and E genotypes. By PCR with Sanger sequencing, the genotypes were determined in all 103 samples, while by using the commercial kit we successfully genotyped only 95 samples, including combined genotypes, which we could not detect by sequencing.

Keywords: HBV genotype; genotyping methods; hepatitis B virus; sequencing.

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Conflict of interest statement

The authors declare that they have no competing interest.

Figures

Figure 1
Figure 1
(a) Genotyping by RT PCR; (b) genotyping by NCBI annotation; (c) genotyping by the Geno2pheno[hbv] tool; (d) genotyping by the MEGA X software Phylogenetic tree.
Figure 2
Figure 2
Phylogenetic analysis of the HBV S-gene region sequences. The 103 specimens were aligned with 21 representative sequences of 5 genotype (including the relevant subgenotypes) available from GenBank. Reference sequences were marked by filled square labels. The final length was 337 bp. The alignment was analyzed using the Maximum Likelihood method and Kimura 2-parameter model with 1000 bootstrap replicates in the MEGA X software. Branch nodes with bootstrap values >50 are included next to the corresponding node.
Figure 3
Figure 3
Occurrence of resistance and escape mutation divided per genotype (genotypes are marked by MEGA X phylogenetic analysis).
Figure 4
Figure 4
Prevalence of the HBV genotypes among patients in the Slovak Republic.
See this image and copyright information in PMC

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