A novel HBV recombinant (genotype I) similar to Vietnam/Laos in a primitive tribe in eastern India

Abstract

Genotyping of 20 strains of Hepatitis B virus (HBV) from the Idu Mishmi primitive tribe of northeast India identified multiple genotypes and the presence of a unique cluster grouping with strains from Vietnam and Laos identified as novel recombinants/genotype I. Sequence analysis (similarity and bootscan plots) of three complete HBV genomes from the tribe provided evidence of recombination. Phylogenetic analyses supported recombination between genotypes A, G and C. The Pre-S gene between nt 2943 and 397 was clearly of genotype A origin, whereas nt 397-1397 represented genotype G and nt 1397-2943 represented genotype C. Percentage divergence from genotypes B, D, E, F, G and H varied from 9.2 +/- 0.45% to 13.8 +/- 0.53%, whereas genotype A and C differed by 7.9 +/- 0.42% and 7.4 +/- 0.39% respectively. The identification of similar recombinant viruses in three countries, especially in a primitive tribe with no contact with the outside world suggests that these viruses do not represent recent recombination events, but circulation of closely related viruses highly divergent from known HBV genotypes and should be classified as members of genotype 'I'.

Genotypes and Genetic Variability of Hepatitis B Virus

“…This proposal was not accepted because the mean genetic divergence of these 4 strains from genotype C was 7% and the recombination analysis was not robust [40]. Subsequently, sequences derived from Laos [41], the Idu Mishmi tribe in northeast India [42], a Canadian of Vietnamese descent [43], and China [10] have expanded the number of sequences. The nucleotide divergence of most of these sequences relative to genotype C was at least 7.5%, with good bootstrap support for the group, thus meeting the criteria for genotype assignment [14].…”

“…Two subgenotypes, I1 and I2, with serological subtypes adw 2 and ayw 2, respectively, were described [41]. This separation into subgenotypes was questioned when additional strains from India clustering within subgenotype I2 were sequenced and the intersubgenotype divergence was calculated to be <4% [42]. By analyzing all 19 complete genotype I genomes, without indels, available in the GenBank, the intergroup divergence between subgenotype I1 and I2 was found to be 3.40 ± 0.30% (mean ± SD), below the 4% cutoff.…”

“…The wide geographical distribution suggests this genotype has been endemic in a wide area of Asia for a long time [10]. Genotype I is a recombinant of genotypes A/C/G and an indeterminate genotype [10,41,42,43], which clusters close to genotype C when the complete genome is analyzed, and with genotype A in the polymerase [10]. The genotype A and C regions are closely related to subgenotypes A3 and C3, respectively [10,41,42,43].…”

Genotypes of the hepatitis B virus within the area of Terni, Italy: our experience

“…The HBV genotype was assessed through sequencing. Each specimen was subjected to a manual extraction of the virus (QIAamp DNA Blood Mini Kit, QIAGEN, Venlo, Netherlands) followed by polymerase chain reaction amplification (TRUGENE HBV Genotyping kit; Siemens Medical Solutions Diagnostics, NY, USA), of the central region of the surface antigen gene (s101-s237) and overlapped region encoding the viral reverse transcriptase gene (rt99-rt280) (1,3).…”

“…Genotype E is found in Africa, in the sub-Saharan region, genotype F in Central and South America, genotype G in Eastern and Western Europe and genotype H, a variant of genotype F, from which it has probably broken up within the New World, in Central and South America (2,12,18,21). Genotype I has recently been reported in Vietnam and Laos and genotype J has been identified in the Ryukyu Islands in Japan, from an old Japanese patient with hepatocellular carcinoma (1,21,23,24). The various genotypes are associated with a different evolution of the disease and with distinct responses to treatment (18,22).…”