A novel B/C inter-genotype recombinant of hepatitis B virus identified in north-west China

Abstract

The characteristics of life-long persistent infection of hepatitis B virus (HBV) and the prevalence of different genotypes of HBV in China may cause new recombinants. In north-west China, HBV inter-genotype recombinants have been reported frequently over the last decade. Here, we report a B/C inter-genotype recombinant HBV with a novel genome mosaic structure from Lanzhou, a city in north-west China.

Epidemiology of Hepatitis B Virus Infection in China: Current Status and Challenges

“…In the southern region, including Tibet and Xinjiang provinces, the proportion of mixed infection of genotype C and D was higher, and recombinations of C and D, B and C were often detected, 47 , 53 , 54 The heterogeneity of C/D recombinants was more than 8% compared with genotypes A, B, D, E, or F but was 3.8%–8.0% compared with genotype C based on phylogenetic analysis. 53 The site of recombination with genotype D was located in the preS2/S region, spanning nt 10–799 in some isolates and nt 10–1499 in the other isolates.…”

Characterization of small genomic regions of the hepatitis B virus should be performed with more caution

“…The genotype references adopted in the current work originated from 2 resources. One is a previous publication by Chen et al [ 6 ]. The other is the HBV database [ 12 ].…”

“…The usual performance of recombination detection on circular viruses is that the circular genomes are first manually linearized and then a linear model is used [ 6 , 23 , 32 , 38 , 41 ]. A major defect of this strategy is that dependencies between nucleotides at the 5′ and 3′ end of a sequence cannot be modeled [ 32 ].…”

“…The clear and unified definition of genotype representatives is important to both recombination analysis by RDP4 and subsequent confirmation by phylogenetic analysis. All reference sequences are selected based on previous works and HBVdb [ 6 , 12 ]. These sequences were all further verified via jpHMM to ensure the consistency.…”

“…Many are inter-genotype recombinant forms due to co-circulation of multiple genotypes in a region. With the development of sequencing and recombination detection techniques, increasing numbers of inter-genotype recombinants have been revealed [ 1 , 2 , 6 , 7 , 19 , 44 ]. Even though the details of genetic recombination of HBV are not fully clear, they may benefit from the proposed intertwinement model for HIV-1 recombination during reverse transcription [ 15 ].…”