Sadayuki Ohkura

All Three Variable Regions of the TRIM5α B30.2 Domain Can Contribute to the Specificity of Retrovirus Restriction

ABSTRACT Recent studies have revealed the contribution of TRIM5α to retrovirus restriction in cells from a variety of primate species. TRIM5α consists of a tripartite motif (the RBCC domain) followed by a B30.2 domain. The B30.2 domain is thought to be involved in determination of restriction specificity and contains three variable regions. To investigate the relationship between the phylogeny of primate TRIM5α and retrovirus restriction specificity, a series of chimeric TRIM5α consisting of the human RBCC domain followed by the B30.2 domain from various primates was constructed. These constructs showed restriction profiles largely consistent with the origin of the B30.2 domain. Restriction specificity was further investigated with a variety of TRIM5αs containing mixed or mutated B30.2 domains. This study revealed the importance of all three variable regions for determining restriction specificity. Based on the molecular structures of other PRYSPRY domains solved recently, a model for the molecular structure of the B30.2 domain of TRIM5α was developed. The model revealed that the variable regions of the B30.2 domain are present as loops located on one side of the B30.2 core structure. It is hypothesized that these three loops form a binding surface for virus and that evolutionary changes in any one of the loops can alter restriction specificity.

High Prevalence of Simian T-Lymphotropic Virus Type L in Wild Ethiopian Baboons

ABSTRACT Simian T-cell leukemia viruses (STLVs) are the simian counterparts of human T-cell leukemia viruses (HTLVs). A novel, divergent type of STLV (STLV-L) from captive baboons was reported in 1994, but its natural prevalence remained unclear. We investigated the prevalence of STLV-L in 519 blood samples from wild-living nonhuman primates in Ethiopia. Seropositive monkeys having cross-reactive antibodies against HTLV were found among 22 out of 40 hamadryas baboons, 8 of 96 anubis baboons, 24 of 50 baboons that are hybrids between hamadryas and anubis baboons, and 41 of 177 grivet monkeys, but not in 156 gelada baboons. A Western blotting assay showed that sera obtained from seropositive hamadryas and hybrid baboons exhibited STLV-L-like reactivity. A PCR assay successfully amplified STLV sequences, which were subsequently sequenced and confirmed as being closely related to STLV-L. Surprisingly, further PCR showed that nearly half of the hamadryas (20 out of 40) and hybrid (19 out of 50) baboons had STLV-L DNA sequences. In contrast, most of the seropositive anubis baboons and grivet monkeys carried typical STLV-1 but not STLV-L. These observations demonstrate that STLV-L naturally prevails among hamadryas and hybrid baboons at significantly high rates. STLV-1 and -2, the close relative of STLV-L, are believed to have jumped across simian-human barriers, which resulted in widespread infection of HTLV-1 and -2. Further studies are required to know if STLV-L is spreading into human populations.

HTLV-Is in Argentina are phylogenetically similar to those of other South American countries, but different from HTLV-Is in Africa

To understand the origin and past dissemination of human T‐cell leukemia/lymphotropic virus type I (HTLV‐I) in Latin America, we conducted a phylogenetic study of five new HTLV‐I isolates from Argentina. We sequenced partial fragments of long terminal repeats (LTR) of the new HTLV‐Is, and then the sequences were subjected to a phylogenetic analysis for comparison with other HTLV‐Is of various geographical origins. Our results indicated that all the isolates were members of the Cosmopolitan group. Furthermore, most (four out of five isolates) of the new HTLV‐Is belonged to the Transcontinental (A) subgroup, the most widespread subgroup of the four subgroups in the Cosmopolitan group. In this subgroup, they were closely related to HTLV‐Is found in other South American countries including those of Amerindians, and were different from those found in Africa. In contrast, the remaining one HTLV‐I (ARGMF) did not show any clear similarity to known HTLV‐I isolates belonging to the Cosmopolitan group. The close similarity of South American HTLV‐Is strongly suggests a common origin of the virus in this continent. Our results do not support the proposed idea of recent introduction of HTLV‐I into South America as a consequence of the slave trade from Africa, where phylogenetically different HTLV‐Is predominate. J. Med. Virol. 55:152–160, 1998.

Prevalence and Phylogenetic Analysis of HTLV–I Isolates in Cameroon, Including Those of the Baka Pygmy

Our previous analysis of an HTLV–I isolate (CMR229) from a Cameroonian Pygmy demonstrated that the isolate is distinct from typical HTLV–ls of the “Central African group,” which has a close similarity to HTLV–I–related simian viruses (STLV–I) in Africa. In this study, we analyzed six new HTLV–ls from Cameroon consisting of three isolates from the Pygmy and three from the Bantu to examine further the genetic features of HTLV–I in Cameroon, especially in the Pygmy. A phylogenetic tree based on the long terminal repeats (LTR) region showed that all the new HTLV–ls belong to the Central African group. On the other hand, an env–based analysis of CMR229 confirmed the previous finding derived from LTR–based analysis that CMR229 has a similarity to African STLV–Is, but is distinct from the typical Central African group of HTLV–I. This suggests that multiple interspecies transmissions from non–human primates to humans have occurred in Central Africa, resulting in the presence of two distinct HTLV–I strains in this area. In addition, it seems likely that the Pygmy harbors the heterogeneous HTLV–I strains from which the main HTLV–I population spread into the Bantu.

Phylogenetic Characterization of a New HTLV Type 1 from the Ainu in Japan

Human T cell leukemia virus type 1 (HTLV-1) is endemic among three ethnically distinguishable populations in Japan (the Ainu, Ryukyuans, and Wajin), which, together, account for most of the population in Japan. While much is known about the phylogeny of the Ryukyuan and Wajin strains of HTLV-1, only one Ainu strain has been phylogenetically analyzed. We report here a new HTLV-1 strain from the Ainu. The new isolate (U8306), as well as the previously reported isolate, are members of the Cosmopolitan group and further belong to the Transcontinental subgroup. This subgroup also predominates among the Ryukyuans, whereas the Japanese subgroup is the major subgroup among the Wajin. The predominance of subgroup A in the Ainu and Ryukyuans suggests that they share a common origin of HTLV-1.

Linkage of Amino Acid Variation and Evolution of Human Immunodeficiency Virus Type 1 gp120 Envelope Glycoprotein (Subtype B) with Usage of the Second Receptor

To clarify the relationship between the amino acid variations of the gp120 of human immunodeficiency virus type 1 (HIV-1) and the chemokine receptors that are used as the second receptor for HIV, we evaluated amino acid site variation of gp120 between the X4 strains (use CXCR4) and the R5 strains (use CCR5) from 21 sequences of subtype B. Our analysis showed that residues 306 and 322 in the V3 loop and residue 440 in the C4 region were associated with usage of the second receptor. The polymorphism at residue 440 is clearly associated with the usage of the second receptor: The amino acid at position 440 was a basic amino acid in the R5 strains, and a nonbasic and smaller amino acid in the X4 strains, while the V3 loop of the X4 strains was more basic than that of the R5 strains. This suggests that residue 440 in the C4 region, which is close to the V3 loop in the three-dimensional structure, is critical in determining which second receptor is used. Analysis of codon frequency suggests that, in almost all cases, the difference at residue 440 between basic amino acids in the R5 strains and nonbasic amino acids in the X4 strains could be due to a single nucleotide change. These findings predict that the evolutionary changes in amino acid residue 440 may be correlated with evolutionary changes in the V3 loop. One possibility is that a change in electric charge at residue 440 compensates for a change in electric charge in the V3 loop. The amino acid polymorphism at position 440 can be useful to predict the cell tropism of a strain of HIV-1 subtype B.

Identification and phylogenetic characterization of a human T-cell leukaemia virus type I isolate from a native inhabitant (Rapa Nui) of Easter Island.

Human T-cell leukaemia virus type I (HTLV-I) is endemic in Melanesia, one of the three ethnogeographic regions of the Pacific; in the other two regions, Polynesia and Micronesia, the incidence of the virus is relatively low. In an effort to gain new insights into the prevalence of HTLV-I in the Pacific region, we did a seroepidemiological survey on Easter Island, which is located on the eastern edge of Polynesia. Of 138 subjects surveyed, including 108 Rapa Nui (the native inhabitants of this island), we identified one HTLV-I-seropositive Rapa Nui. The new HTLV-I isolate derived from this carrier (E-12) was phylogenetically analysed to ascertain the origin and past dissemination of HTLV-I in the island. The analysis demonstrated that isolate E-12 belongs to subgroup A of the Cosmopolitan group, and that it differs from HTLV-Is found in Melanesia, which are highly divergent variants. In subgroup A, E-12 grouped with South American HTLV-Is including those from Amerindians. This result suggests that this isolate originated in South America rather than in Melanesia.

Protective Efficacy of Nonpathogenic Nef-Deleted SHIV Vaccination Combined with Recombinant IFN-γ Administration against a Pathogenic SHIV Challenge in Rhesus Monkeys

We previously reported that a nef‐deleted SHIV (SHIV‐NI) is nonpathogenic and gave macaques protection from challenge infection with pathogenic SHIV‐C2/1. To investigate whether IFN‐γ augments the immune response induced by this vaccination, we examined the antiviral and adjuvant effect of recombinant human IFN‐γ (rIFN‐γ) in vaccinated and unvaccinated monkeys. Nine monkeys were vaccinated with nef‐deleted nonpathogenic SHIV‐NI. Four of them were administered with rIFN‐γ and the other five monkeys were administered with placebo. After the challenge with pathogenic SHIV‐C2/1, CD4+ T‐cell counts were maintained similarly in monkeys of both groups, while those of the unvaccinated monkeys decreased dramatically at 2 weeks after challenge. However, the peaks of plasma viral load were reduced to 100‐fold in SHIV‐NI vaccinated monkeys combined with rIFN‐γ compared with those in SHIV‐NI vaccinated monkeys without rIFN‐γ. The peaks of plasma viral load were inversely correlated with the number of SIV Gag‐specific IFN‐γ‐producing cells. In SHIV‐NI‐vaccinated monkeys with rIFN‐γ, the number of SIV Gag‐specific IFN‐γ‐producing cells of PBMCs increased 2‐fold compared with those in SHIV‐NI‐vaccinated monkeys without rIFN‐γ, and the NK activity and MIP‐1α production of PBMCs were also enhanced. Thus, vaccination of SHIV‐NI in combination with rIFN‐γ was more effective in modulating the antiviral immune system into a Th1 type response than SHIV‐NI vaccination alone. These results suggest that IFN‐γ augmented the anti‐viral effect by enhancing innate immunity and shifting the immune response to Th1.

Phylogenetic relatedness of HTLV type I from Bellona, a Polynesian outlier within the Solomon Islands, to HTLV type I from Japan and far eastern Asia

1041 HUM AN T LY M PHO TR OPIC VIR US TY PE I (HTLV-I) is endemic in southwestern Japan, the Caribbean basin, South America, the Middle East, Africa, and Melanesia. 1,2 While the majority of HTLV-I isolates from throughout the world are genetically quite homogeneous (Cosmopolitan group), 3 HTLV-I variants, collectively called the Central African group, exist in Africa.4 HTLV-I from Melanesians of Papua New Guinea and the Solomon Islands comprise a surprisingly different phylogenetic group (Melanesian group), which is more divergent than the other two groups. 5 That HTLV-I in aboriginals of Australia also belongs to the Melanesian group6 supports a founder effect, namely, that HTLV-I was introduced by the early settlers who immigrated from the Southeast Asian land mass (Sunda) to colonize the great continent of New Guinea, Australia, and Tasmania (Sahul). Epidemiologic al surveys in the Pacific have uncovered other HTLV-I-endemic foci in Rennell, Bellona, and Ontong Java, Polynesian outliers within the Solomon archipelago.7 Partial env gene sequence analysis of two HTLV-I strains from native inhabitants of Bellona Island (BEL1 and BEL2) indicate that they belong to the Cosmopolitan group.8 Since these strains represent the first examples of Cosmopolitan HTLV-I in the Pacific region, except for the well-known HTLV-I of Japanese immigrants in Hawaii, it has been of considerable interest to ascertain the origin of HTLV-I in Bellona and to verify whether these isolates are indeed phylogenetically distinct from HTLV-I in Melanesia. To this end, we analyzed the long terminal repeat (LTR) of BEL1, since this region is somewhat more informative than the partial env gene region previously analyzed. Moreover, analysis of the LTR permits finer separation of taxa within the Cosmopolitan group into four subgroups. By using nested PCR, proviral HTLV-I was amplified from DNA extracted from an HTLV-I-infected cell line derived from an asymptomatic native woman (a 60-year-old) from Bellona Island. Details of this individual have been provided previously.9 To sequence the entire LTR, we performed three independent nested PCRs. First, we amplified an approximately 590-bp region of the LTR, which corresponded to positions 99 to 685 of ATK (the prototype Japanese HTLV-I strain), to obtain sequences of a 507-bp region (positions 122 to 628), as described previously. 2 Then, for sequencing the remaining parts of the LTR, fragments adjacent to the 507-bp region were amplified by nested PCR (see Fig. 12,4 ,7,10 for oligonucleotide primer sequences). Amplified fragments were subcloned using the TA cloning method, and the full-length LTR sequence was determined by combining the nucleotide sequences of the three fragm ents, each of which was sequenced in both directions. The GenBank accession number for the BEL1 LTR is AF124043. As shown in Fig. 1A and B, phylogenet ic trees, based on the entire LTR and on a 507-bp region of the LTR, indicated that BEL1 was a member of the Cosmopolitan group. Moreover, in both trees, BEL1 belonged to subgroup A of the four subgroups in the Cosmopolita n group. Because of the geographic proxim ity of Bellona to Guadalcana l (which is inhabited by Melanesians), we compared the LTR sequence of BEL1 with that of HTLV-I MEL5, the prototypic Melanesian strain from the Solomon Islands. As mentioned above, BEL1 did not exhibit close similarities to MEL5 (Fig. 1). In fact, the entire LTR sequence of BEL1 differed from MEL5 by 9.3%, whereas it differed by only 2.4% from ATK. This finding was confirmed by the restriction fragm ent length polym orphism (RFLP) profile, according to the classificati on system proposed by Ureta Vidal and colleagues. 11 The deduced RFLP pattern of BEL1 was consistent with that of subgroup A and differed markedly from that of the Melanesian group (data not shown). Collective ly, these results indicate that HTLV-I in Bellona is closely related to Cosmopolitan HTLV-I isolates of subgroup A, and differs considerabl y from the HTLV-I found in Melanesia.