HIV-1 strains in the pandemic are genetically diverse. Nine subtypes (A, B, C, D, F, G, H, J, and K) and 15 circulating recombinant forms (CRFs) have been identified to date (Kuiken et al., 2002). Figure 1 shows a phylogenetic tree of representative full-genome sequences of all of these forms, illustrating the genetic complexity of this important pathogen.

Molecular Epidemiology of HIV in Asia and the Pacific

Identification and phylogenetic analysis of hepatitis C virus in forensic blood samples obtained from injecting drug users.

To determine the incidence of human immunodeficiency virus type-1 (HIV-1) subtypes in Fukuoka, Japan, viruses from 41 HIV-1 infected individuals were subtyped. Subtyping by V3-loop enzyme-linked immunosorbent assay (ELISA) showed 31 of the 41 subjects as subtype B (MN type), one as subtype A, one as subtype C, and eight untypable. The subject infected with subtype C was identified as a foreigner; the subtype A subject was Japanese. A phylogenetic analysis of nucleic acid sequences from the env C2-V3 region was also conducted. Genetic subtyping was successful for 25 samples: 23 samples were determined as subtype B, one subtype A and one subtype E. One of the individuals infected with subtype B, as well as the subtype A and subtype E subjects, were not Japanese. This study indicated that subtype B (USA and European type) is still dominant among HIV-1 infections in Fukuoka. Further, no Japanese were subtype E positive, which is increasing in the Kanto region. It is notable, however, that subtype A and subtype C infections, which are rare in Japan, were found in Fukuoka, located far from the metropolitan area of Tokyo.

The distribution of HIV-1 subtypes in Fukuoka, Japan.

Differentiation of subtypes B and E of human immunodeficiency virus type 1 by polymerase chain reaction using novel env gene primers

In Japan, the number of human immunodeficiency virus (HIV)-1 infections remains relatively low; nevertheless, the annual incidence of HIV-1 infection has not decreased. New infections remain a great concern, and an improved understanding of epidemiological trends is critical for public health. The env C2V3 and pol sequences of HIV-1 RNA from 240 early (1996-2001) and 223 more recent (2010-2012) blood donations were used to compare the distribution of virus subtypes and to generate phylogenetic trees. Subtype B was clearly predominant in both early and more recent donations (both were 88.3%), and CRF01_AE was the second most common subtype. Phylogenetic analysis revealed a peculiar epidemiological transition. Compared to early subtype B isolates from 2 major endemic areas (Tokyo and Osaka), the more recent subtype B isolates formed fewer tight clusters in phylogenetic trees (from 8 to 2 clusters in Tokyo and 5 to zero clusters in Osaka). Furthermore, mixing of HIV-1 infections between these 2 endemic areas appear to increase. Analysis of phylogenetic trees suggested that local outbreaks have become smaller in Japan; however, intermixing of viral types between these 2 areas was more evident in the more recent samples.

Genetic Analysis of HIV-1 in Japan: a Comprehensive Analysis of Donated Blood.

We analyzed the clade distribution of B and E in HIV-1 isolates in Japan by a nested PCR method using 5'-CCCACAAGATTTAAATATG-3' of the gag gene as clade B primer and 5'-CCCACAAGATTTAAACTCC-3' of the gag gene as clade E primer. Seventy-two anti-HIV-1 confirmatory positive serum samples were collected during a period of 1991-1996 in two hospitals in Yokohama City. Peripheral blood mononuclear cells were obtained from the buffy coat of these samples and extracted DNA were used for nested PCR. The 72 cases comprised of 11 Japanese hemophiliacs, 14 Japanese male homosexuals, 19 Japanese male heterosexuals, 5 Japanese female heterosexuals and 23 Thai female heterosexuals. Of these 36 were clade B and 35 were clade E and one case showed positive PCR results for both B and E primers. Almost all male Japanese hemophiliacs and homosexuals in our sample have clade B, while the female Thai heterosexuals have clade E, irrespective of the year of isolation. As for Japanese male heterosexuals, through 1993, clade B was predominant but since 1994, the predominate clade switched to clade E. Although the number of Japanese female heterosexuals in our sample is small, clade B was isolated in 2 cases even after 1994.

[Simple method for typing human immunodeficiency virus type I (B, E) by PCR and chronological change of distribution of subtype (B to E) in Japan].

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[Simple method for typing human immunodeficiency virus type I (B, E) by PCR and chronological change of distribution of subtype (B to E) in Japan].