1
|
Cassar O, Charavay F, Touzain F, Jeannin P, Grangeon JP, Laumond S, Chungue E, Martin PMV, Gessain A. A Novel Human T-lymphotropic Virus Type 1c Molecular Variant in an Indigenous Individual from New Caledonia, Melanesia. PLoS Negl Trop Dis 2017; 11:e0005278. [PMID: 28060812 PMCID: PMC5245899 DOI: 10.1371/journal.pntd.0005278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/19/2017] [Accepted: 12/21/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Human T-Lymphotropic Virus type 1 (HTLV-1) is endemic among people of Melanesian descent in Papua New Guinea, Solomon Islands and Vanuatu, and in Indigenous populations from Central Australia. Molecular studies revealed that these Australo-Melanesian strains constitute the highly divergent HTLV-1c subtype. New Caledonia is a French overseas territory located in the Southwest Pacific Ocean. HTLV-1 situation is poorly documented in New Caledonia and the molecular epidemiology of HTLV-1 infection remains unknown. OBJECTIVES Studying 500 older adults Melanesian natives from New Caledonia, we aim to evaluate the HTLV-1 seroprevalence and to molecularly characterize HTLV-1 proviral strains. STUDY DESIGN Plasma from 262 men and 238 females (age range: 60-96 years old, mean age: 70.5) were screened for anti-HTLV-1 antibodies by particle agglutination (PA) and indirect immunofluorescence assay (IFA). Serological confirmation was obtained using Western blot assay. DNAs were extracted from peripheral blood buffy coat of HTLV-1 seropositive individuals, and subjected to four series of PCR (LTR-gag; pro-pol; pol-env and tax-LTR). Primers were designed from highly common conserved regions of the major HTLV-1 subtypes to characterize the entire HTLV-1 proviral genome. RESULTS Among 500 samples, 3 were PA and IFA positive. The overall seroprevalence was 0.6%. The DNA sample from 1 New Caledonian woman (NCP201) was found positive by PCR and the complete HTLV-1 proviral genome (9,033-bp) was obtained. The full-length HTLV-1 genomic sequence from a native woman from Vanuatu (EM5), obtained in the frame of our previous studies, was also characterized. Both sequences belonged to the HTLV-1c Australo-Melanesian subtype. The NCP201 strain exhibited 0.3% nucleotide divergence with the EM5 strain from Vanuatu. Furthermore, divergence reached 1.1% to 2.9% with the Solomon and Australian sequences respectively. Phylogenetic analyses on a 522-bp-long fragment of the gp21-env gene showed the existence of two major clades. The first is composed of strains from Papua New Guinea; the second includes strains from all neighboring archipelagos (Solomon, Vanuatu, New Caledonia), and Australia. Interestingly, this second clade itself is divided into two sub-clades: strains from Australia on one hand, and strains from Solomon Islands, Vanuatu and New Caledonia on the other hand. CONCLUSIONS The HTLV-1 seroprevalence (0.6%) in the studied adult population from New Caledonia appears to be low. This seroprevalence is quite similar to the situation observed in Vanuatu and Solomon Islands. However it is very different to the one encountered in Central Australia. Taken together, these results demonstrated that Australo-Melanesia is endemic for HTLV-1 infection with a high diversity of HTLV-1c strains and a clear geographic clustering according to the island of origin of HTLV-1 infected persons.
Collapse
Affiliation(s)
- Olivier Cassar
- Institut Pasteur, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France
- CNRS, UMR 3569, Paris, France
| | - Françoise Charavay
- Institut Pasteur de Nouvelle-Calédonie, Nouméa, Nouvelle-Calédonie, France
| | - Frédéric Touzain
- Centre Hospitalier Territorial de Nouvelle-Calédonie, Nouméa, Nouvelle-Calédonie, France
| | - Patricia Jeannin
- Institut Pasteur, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France
- CNRS, UMR 3569, Paris, France
| | - Jean-Paul Grangeon
- Direction des Affaires Sanitaires et Sociales, Service de Santé Publique, Nouméa, Nouvelle-Calédonie, France
| | - Sylvie Laumond
- Direction des Affaires Sanitaires et Sociales, Service de Santé Publique, Nouméa, Nouvelle-Calédonie, France
| | - Eliane Chungue
- Institut Pasteur de Nouvelle-Calédonie, Nouméa, Nouvelle-Calédonie, France
| | - Paul M. V. Martin
- Institut Pasteur de Nouvelle-Calédonie, Nouméa, Nouvelle-Calédonie, France
| | - Antoine Gessain
- Institut Pasteur, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France
- CNRS, UMR 3569, Paris, France
- * E-mail:
| |
Collapse
|
2
|
Cassar O, Einsiedel L, Afonso PV, Gessain A. Human T-cell lymphotropic virus type 1 subtype C molecular variants among indigenous australians: new insights into the molecular epidemiology of HTLV-1 in Australo-Melanesia. PLoS Negl Trop Dis 2013; 7:e2418. [PMID: 24086779 PMCID: PMC3784485 DOI: 10.1371/journal.pntd.0002418] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/29/2013] [Indexed: 11/18/2022] Open
Abstract
Background HTLV-1 infection is endemic among people of Melanesian descent in Papua New Guinea, the Solomon Islands and Vanuatu. Molecular studies reveal that these Melanesian strains belong to the highly divergent HTLV-1c subtype. In Australia, HTLV-1 is also endemic among the Indigenous people of central Australia; however, the molecular epidemiology of HTLV-1 infection in this population remains poorly documented. Findings Studying a series of 23 HTLV-1 strains from Indigenous residents of central Australia, we analyzed coding (gag, pol, env, tax) and non-coding (LTR) genomic proviral regions. Four complete HTLV-1 proviral sequences were also characterized. Phylogenetic analyses implemented with both Neighbor-Joining and Maximum Likelihood methods revealed that all proviral strains belong to the HTLV-1c subtype with a high genetic diversity, which varied with the geographic origin of the infected individuals. Two distinct Australians clades were found, the first including strains derived from most patients whose origins are in the North, and the second comprising a majority of those from the South of central Australia. Time divergence estimation suggests that the speciation of these two Australian clades probably occurred 9,120 years ago (38,000–4,500). Conclusions The HTLV-1c subtype is endemic to central Australia where the Indigenous population is infected with diverse subtype c variants. At least two Australian clades exist, which cluster according to the geographic origin of the human hosts. These molecular variants are probably of very ancient origin. Further studies could provide new insights into the evolution and modes of dissemination of these retrovirus variants and the associated ancient migration events through which early human settlement of Australia and Melanesia was achieved. The Human T-lymphotropic virus type 1 (HTLV-1) infects at least 5–10 million persons worldwide. In Oceania, previous studies have shown that HTLV-1 is present in a few ancient populations from remote areas of Papua New Guinea, the Solomon Islands, the Vanuatu archipelago and central Australia. The latter comprise one of the most socio-economically disadvantaged groups within any developed country. Characterization of the few available HTLV-1 viruses from Oceania indicates that these belong to a specific HTLV-1 genotype, the Australo-Melanesian c-subtype. In this study, we provide details for 23 HTLV-1 viruses derived from the Indigenous population of central Australia, a vast remote area of 1,000,000 km2. We reveal considerable genetic diversity of HTLV-1c subtype viruses and the existence of two HTLV-1c clades within which a high degree of genetic diversity was also apparent. These newly described HTLV-1c clades clustered according to the geographic origin of their human hosts. Indigenous Australians from the North of central Australia harbor HTLV-1c subtype viruses that are distinct from those of individuals from regions to the South. These data suggest that HTLV-1 was probably introduced to Australia during ancient migration events and was then confined to isolated Indigenous communities in central Australia.
Collapse
Affiliation(s)
- Olivier Cassar
- Institut Pasteur, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France
- CNRS, UMR 3569, Paris, France
| | - Lloyd Einsiedel
- Flinders University/Northern Territory Rural Clinical School, Alice Springs Hospital, Alice Springs, Northern Territory, Australia
| | - Philippe V. Afonso
- Institut Pasteur, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France
- CNRS, UMR 3569, Paris, France
| | - Antoine Gessain
- Institut Pasteur, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France
- CNRS, UMR 3569, Paris, France
- * E-mail:
| |
Collapse
|
3
|
Cassar O, Capuano C, Meertens L, Chungue E, Gessain A. Human T-cell leukemia virus type 1 molecular variants, Vanuatu, Melanesia. Emerg Infect Dis 2005; 11:706-10. [PMID: 15890124 PMCID: PMC3320372 DOI: 10.3201/eid1105.041015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Four of 391 Ni-Vanuatu women were infected with variants of human T-cell leukemia virus type 1 (HTLV-1) Melanesian subtype C. These strains had env nucleotide sequences ≈99% similar to each other and diverging from the main molecular subtypes of HTLV-1 by 6% to 9%. These strains were likely introduced during ancient human population movements in Melanesia.
Collapse
Affiliation(s)
- Olivier Cassar
- Institut Pasteur de Nouvelle-Calédonie, Nouméa, France
- Institut Pasteur, Paris, France
| | | | | | | | | |
Collapse
|
4
|
Ryschkewitsch CF, Friedlaender JS, Mgone CS, Jobes DV, Agostini HT, Chima SC, Alpers MP, Koki G, Yanagihara R, Stoner GL. Human polyomavirus JC variants in Papua New Guinea and Guam reflect ancient population settlement and viral evolution. Microbes Infect 2000; 2:987-96. [PMID: 10967279 DOI: 10.1016/s1286-4579(00)01252-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The peopling of the Pacific was a complex sequence of events that is best reconstructed by reconciling insights from various disciplines. Here we analyze the human polyomavirus JC (JCV) in Highlanders of Papua New Guinea (PNG), in Austronesian-speaking Tolai people on the island of New Britain, and in nearby non-Austronesian-speaking Baining people. We also characterize JCV from the Chamorro of Guam, a Micronesian population. All JCV strains from PNG and Guam fall within the broad Asian group previously defined in the VP1 gene as Type 2 or Type 7, but the PNG strains were distinct from both genotypes. Among the Chamorro JCV samples, 8 strains (Guam-1) were like the Type 7 strains found in Southeast Asia, while nine strains (Guam-2) were distinct from both the mainland strains and most PNG strains. We identified three JCV variants within Papua New Guinea (PNG-1, PNG-2 and PNG-3), but none of the Southeast Asian (Type 7) strains. PNG-1 strains were present in all three populations (Highlanders and the Baining and Tolai of New Britain), but PNG-2 strains were restricted to the Highlanders. Their relative lack of DNA sequence variation suggests that they arose comparatively recently. The single PNG-3 strain, identified in an Austronesian-speaking Tolai individual, was closely related to the Chamorro variants (Guam-2), consistent with a common Austronesian ancestor. In PNG-2 variants a complex regulatory region mutation inserts a duplication into a nearby deletion, a change reminiscent of those seen in the brains of progressive multifocal leukoencephalopathy patients. This is the first instance of a complex JCV rearrangement circulating in a human population.
Collapse
Affiliation(s)
- C F Ryschkewitsch
- Neurotoxicology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Yamashita M, Picchio G, Veronesi R, Ohkura S, Bare P, Hayami M. HTLV-Is in Argentina are phylogenetically similar to those of other South American countries, but different from HTLV-Is in Africa. J Med Virol 1998; 55:152-60. [PMID: 9598937 DOI: 10.1002/(sici)1096-9071(199806)55:2<152::aid-jmv12>3.0.co;2-k] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
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.
Collapse
Affiliation(s)
- M Yamashita
- Laboratory of Pathogenic Virus, Institute for Virus Research, Kyoto University, Japan
| | | | | | | | | | | |
Collapse
|
6
|
Song JW, Baek LJ, Nagle JW, Schlitter D, Yanagihara R. Genetic and phylogenetic analyses of hantaviral sequences amplified from archival tissues of deer mice (Peromyscus maniculatus nubiterrae) captured in the eastern United States. Arch Virol 1996; 141:959-67. [PMID: 8678841 DOI: 10.1007/bf01718170] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The S and M segments of a hantavirus, enzymatically amplified from tissues of Cloudland deer mice (Peromyscus maniculatus nubiterrae) captured during 1985 in West Virginia, diverged from strains of Four Corners virus from the southwestern United States by more than 16% and 6% at the nucleotide and amino acid levels, respectively. Phylogenetic analysis suggested that this virus strain (designated Monongahela) forms a possible evolutionary link between the Four Corners and New York hantaviruses.
Collapse
Affiliation(s)
- J W Song
- Laboratory of Central Nervous System Studies, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | | | | |
Collapse
|
7
|
Yamashita M, Ido E, Miura T, Hayami M. Molecular epidemiology of HTLV-I in the world. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES AND HUMAN RETROVIROLOGY : OFFICIAL PUBLICATION OF THE INTERNATIONAL RETROVIROLOGY ASSOCIATION 1996; 13 Suppl 1:S124-31. [PMID: 8797715 DOI: 10.1097/00042560-199600001-00021] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The geographic distribution of human T-cell lymphotropic/leukemia virus type I (HTLV-I) was initially believed to be limited to southwestern Japan, the Caribbean basin, and Africa. However, extensive searches in recent years have discovered its existence in other areas of the world as well as in isolated, ethnic populations such as South Amerindians, Australo-Melanesian aborigines, religiously segregated Jews, and Pygmies. Previous genetic analyses indicated that HTLV-I can be phylogenetically classified into three major lineages: Melanesian, Central African, and Cosmopolitan groups. Recently, more detailed characterization using long terminal repeat sequences (the most variable genomic region) has revealed that the Cosmopolitan group consists of four subtypes: (A) Transcontinental, (B) Japanese, (C) West African, and (D) North African. Most HTLV-I isolates of the same ethnic group from distant locations and those from different groups inhabiting the same area showed phylogenetic similarities. These observations indicate the present distribution of this virus should be interpreted from the anthropological backgrounds of the virus-possessing populations as well as spatial contact among them. Thus, the molecular epidemiology of HTLV-I and its simian counterpart, STLV-I, provides us with important clues for understanding not only the origin and dissemination of this retrovirus but past human movements over the globe.
Collapse
Affiliation(s)
- M Yamashita
- Laboratory of Pathogenic Virus, Kyoto University, Japan
| | | | | | | |
Collapse
|
8
|
Gessain A, de Thé G. Geographic and molecular epidemiology of primate T lymphotropic retroviruses: HTLV-I, HTLV-II, STLV-I, STLV-PP, and PTLV-L. Adv Virus Res 1996; 47:377-426. [PMID: 8895837 DOI: 10.1016/s0065-3527(08)60740-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- A Gessain
- Département du SIDA et des Rétrovirus, Institut Pasteur, Paris, France
| | | |
Collapse
|
9
|
Gessain A, Mahieux R, de Thé G. Genetic variability and molecular epidemiology of human and simian T cell leukemia/lymphoma virus type I. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES AND HUMAN RETROVIROLOGY : OFFICIAL PUBLICATION OF THE INTERNATIONAL RETROVIROLOGY ASSOCIATION 1996; 13 Suppl 1:S132-45. [PMID: 8797716 DOI: 10.1097/00042560-199600001-00022] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In the past few years, numerous investigators have demonstrated that human T cell leukemia/lymphoma virus type I (HTLV-I) possesses a great genetic stability, and recent data indicate that viral amplification via clonal expansion of infected cells, rather than by reverse transcription, could explain this remarkable genetic stability. In parallel, the molecular epidemiology of HTLV-I proviruses showed that the few nucleotide changes observed between isolates were specific for the geographical origin of the patients but not for the type of the associated pathologies (adult T cell leukemia/lymphoma, tropical spastic paraparesis/HTLV-I-associated myelopathy). Thus, based on sequence and/or restriction fragment length polymorphism analysis of more than 250 HTLV-I isolates originating from the main viral endemic areas, three major molecular geographical subtypes (or genotypes) emerged, strongly supported by phylogenetic analysis (high bootstrap values). Each of these genotypes (Cosmopolitan, Central African, and Melanesian) appeared to arise from ancient interspecies transmission between monkeys infected with simian T cell leukemia/lymphoma virus type I and humans. Furthermore, careful sequences analyses indicate that, within (or alongside) these three main genotypes, there are molecular subgroups defined clearly by several specific mutations but not always supported by phylogenetic analyses. Thus in Japan, there is evidence for two ancestral HTLV-I lineages: the classical Cosmopolitan genotype, representing approximately 25% of the HTLV-I present in Japan and clustering in the southern islands; and a related subgroup that we called the Japanese group. Similarly, within the Central African cluster, there are molecular subgroups defined by specific substitutions in either the env or the long terminal repeat. Furthermore, recent data from our laboratory indicate the presence of a new molecular phylogenetic group (fourth genotype) found among inhabitants of Central Africa, particularly in Pygmies. While geographical subtypes vary from 2 to 8% between themselves, HTLV-I quasi-species present within an individual appear to be much lower, with a variability of < 0.5%.
Collapse
Affiliation(s)
- A Gessain
- Départment du SIDA et des Rétrovirus, Institut Pasteur, Paris, France
| | | | | |
Collapse
|
10
|
Yanagihara R. Geographic-specific genotypes or topotypes of human T-cell lymphotropic virus type I as markers for early and recent migrations of human populations. Adv Virus Res 1994; 43:147-86. [PMID: 8191953 DOI: 10.1016/s0065-3527(08)60048-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R Yanagihara
- Laboratory of Central Nervous System Studies, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
| |
Collapse
|