Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions

Abstract

The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term "recombino-subgenotype". Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term "immigro-subgenotype" to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.

Serological and molecular epidemiological outcomes after two decades of universal infant hepatitis B virus (HBV) vaccination in Nunavut, Canada

“…Subgenotyping designation usually requires full genome sequence analysis [110]. All HBV/B study sequences clustered together within the same clade as reference genotype B5 sequences, which was expected as genotype B5 is the majority genotype in Nunavut.…”

Genotypes of hepatitis B virus identified in patients tested prior to endoscopy from a Teaching Hospital in the Central Province of Sri Lanka

“…Sequence analysis of both PCR products gave a homology of almost 98% to HBV genotype A instead of the expected 100%, this 2 to 4% heterogeneity may be attributed to different recombinants, quasi-sub-genotypes or differences in the A1 and A2 sub-genotypes. It is also worthy to note that the HepSEQ tool used here utilizes only the polymerase or surface genes for genotype identification that allows the identification of any escape mutants, but is less accurate for detecting any recombinants if they are present in the sample sequences [7].…”

Molecular Epidemiology of Hepatitis B Virus

“…Subgenotip D1, İran ve komşu Ortadoğu ülkeleri için de dominanttır. Subgenotip D2, Doğu Avrupa ve Rusya'da yaygın iken; subgenotip D3, Sırbistan, Güney Afrika ve Alaska'dan; subgenotip D4, Melanezya, Okyanusya, Avustralya, Yeni Zelanda, Mikronezya ve Polinezya dahil olmak üzere Orta ve Güney Pasifik adalarından; subgenotip D5-D9, Japonya, Hindistan, Endonezya, Tunus ve Nijerya'dan bildirilmiştir (19,24).…”

“…Genotip A, kronik aktif hepatitlerde baskın olarak saptanırken; akut hepatitlerde sıklıkla genotip D saptanmıştır. Bazı çalışmalarda genotip A'nın antiviral direnç varyantlarının genotip D'ye göre daha erken oluştuğu bildirilmektedir (3,19,28). ABD'de genotip A, B, C ve D'li hastalarla yapılan bir çalışmada, pre-kor varyantlar sırasıyla %3, %46, %24 ve %73 oranında bildirilmiştir (29).…”

“…HBV genotip ve subgenotipleri çeşitli moleküler yöntemlerle belirlenebilmektedir. Bu yöntemler, altın standard olan direkt dizilemenin yanı sıra restriksiyon fragman uzunluk polimorfizmi (RFLP), restriksiyon fragman kitle polimorfizmi (RFMP), oligonükleotid mikroçip (DNA çip), kütle spektrometrisi, ters noktasal grafik analizi, INNO-LiPA ® ve gerçek zamanlı polimeraz zincir reaksiyonudur (6,19).…”