1
|
Nozuma S, Yoshimura A, Pai SC, Chen HJ, Matsuura E, Tanaka M, Kodama D, Dozono M, Matsuzaki T, Takashima H, Yang YC, Kubota R. Geographic characteristics of HTLV-1 molecular subgroups and genetic substitutions in East Asia: Insights from complete genome sequencing of HTLV-1 strains isolated in Taiwan and Japan. PLoS Negl Trop Dis 2024; 18:e0011928. [PMID: 38315729 PMCID: PMC10868808 DOI: 10.1371/journal.pntd.0011928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 02/15/2024] [Accepted: 01/21/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Although Japan is a major endemic area for human T-lymphotropic virus type 1 (HTLV-1) and the virus has been well-studied in this region, there is limited research on HTLV-1 in surrounding regions. In this study, we determined the complete genome sequences of HTLV-1 strains isolated from Taiwan and Japan and investigated the geographic characteristics of molecular subgroups and substitution mutations to understand the spread of HTLV-1 and its correlation with human migration. METHODOLOGY/PRINCIPAL FINDINGS The complete genome sequences of 26 HTLV-1 isolates from Taiwan were determined using next-generation sequencing and were compared with those of 211 isolates from Japan in terms of subgroup and genetic mutations. In total, 15/26 (58%) isolates from Taiwan belonged to the transcontinental subgroup and 11/26 (42%) isolates belonged to the Japanese subgroup. The transcontinental subgroup was significantly more prevalent among Taiwanese isolates than Japanese isolates (58% vs 18%, P < 0.0001). The mutation rate for the complete HTLV-1 sequence was as low as 0.2%. On examining individual base substitutions, the G-to-A mutation was predominant. Bayesian phylogenetic tree analysis estimated the time to the most recent common ancestor for the transcontinental and Japanese subgroups to be 28447 years. The transcontinental subgroups from Taiwan and Japan appeared to form clusters according to their respective regions. CONCLUSIONS/SIGNIFICANCE The transcontinental subgroup of HTLV-1 is predominant in Taiwan, while the Japanese subgroup is common in Japan. The difference in subgroup distribution may be attributed to the initial spread of the transcontinental subgroup in East Asia, followed by the influx of the Japanese subgroup.
Collapse
Affiliation(s)
- Satoshi Nozuma
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Akiko Yoshimura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Shun-Chung Pai
- Division of Quality, Taipei Blood Center, Taipei, Taiwan
| | - Hung-Jen Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Eiji Matsuura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Masakazu Tanaka
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Daisuke Kodama
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Mika Dozono
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Toshio Matsuzaki
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Hiroshi Takashima
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Ya-Chien Yang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ryuji Kubota
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| |
Collapse
|
2
|
Nunes da Silva A, Araújo THA, Boa-Sorte N, Farias G, Galvão-Barroso AK, de Carvalho A, Vicente AC, Galvão-Castro B, Rios Grassi MF. Epidemiological and molecular evidence of intrafamilial transmission through sexual and vertical routes in Bahia, the state with the highest prevalence of HTLV-1 in Brazil. PLoS Negl Trop Dis 2023; 17:e0011005. [PMID: 37769013 PMCID: PMC10593241 DOI: 10.1371/journal.pntd.0011005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/23/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
INTRODUCTION Familial clustering of HTLV-1 and related diseases has been reported in Brazil. However, intrafamilial transmission of HTLV-1 based on molecular analysis has been studied only in a few communities of Japanese immigrants and African-Brazilians. OBJECTIVE To investigate the familial clustering of HTLV-1 infection and to determine the likely routes of transmission through epidemiological and genetic analyzes. METHODS Medical records of 1,759 HTLV-1+ patients from de the Center for HTLV in Salvador, Brazil, were evaluated to identify first-degree relatives previously tested for HTLV-1. Familial clustering was assumed if more than one member of the same family was HTLV-1+. LTR regions of HTLV-1 sequences were analyzed for the presence of intrafamilial polymorphisms. Family pedigrees were constructed and analyzed to infer the likely transmission routes of HTLV-1. RESULTS In 154 patients at least one other family member had tested positive for HTLV-1 (a total of 182 first-degree relatives). Of the 91 couples (182 individuals), 51.6% were breastfed, and 67.4% reported never using a condom. Of the 42 mother-child pairs, 23.8% had a child aged 13 years or younger; all mothers reported breastfeeding their babies. Pedigrees of families with 4 or more members suggests that vertical transmission is a likely mode of transmission in three families. Three families may have had both vertical and sexual transmission routes for HTLV-1. The genetic signatures of the LTR region of 8 families revealed 3 families with evidence of vertical transmission, another 3 families (spouses) with sexual transmission, and one family with both transmission routes. HTLV-1 sequences belonged to Cosmopolitan subtype HTLV-1a Transcontinental subgroup A. CONCLUSION Sexual and vertical transmission routes contribute to the intrafamilial spread of HTLV-1 in the state of Bahia.
Collapse
Affiliation(s)
| | | | - Ney Boa-Sorte
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Brasil
| | - Giovanne Farias
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Brasil
| | | | | | | | - Bernardo Galvão-Castro
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Brasil
- Laboratório Avançado de Saúde Pública, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brasil
| | - Maria Fernanda Rios Grassi
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Brasil
- Laboratório Avançado de Saúde Pública, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brasil
| |
Collapse
|
3
|
Diakite M, Shaw-Saliba K, Lau CY. Malignancy and viral infections in Sub-Saharan Africa: A review. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2023; 3:1103737. [PMID: 37476029 PMCID: PMC10358275 DOI: 10.3389/fviro.2023.1103737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The burden of malignancy related to viral infection is increasing in Sub-Saharan Africa (SSA). In 2018, approximately 2 million new cancer cases worldwide were attributable to infection. Prevention or treatment of these infections could reduce cancer cases by 23% in less developed regions and about 7% in developed regions. Contemporaneous increases in longevity and changes in lifestyle have contributed to the cancer burden in SSA. African hospitals are reporting more cases of cancer related to infection (e.g., cervical cancer in women and stomach and liver cancer in men). SSA populations also have elevated underlying prevalence of viral infections compared to other regions. Of 10 infectious agents identified as carcinogenic by the International Agency for Research on Cancer, six are viruses: hepatitis B and C viruses (HBV and HCV, respectively), Epstein-Barr virus (EBV), high-risk types of human papillomavirus (HPV), Human T-cell lymphotropic virus type 1 (HTLV-1), and Kaposi's sarcoma herpesvirus (KSHV, also known as human herpesvirus type 8, HHV-8). Human immunodeficiency virus type 1 (HIV) also facilitates oncogenesis. EBV is associated with lymphomas and nasopharyngeal carcinoma; HBV and HCV are associated with hepatocellular carcinoma; KSHV causes Kaposi's sarcoma; HTLV-1 causes T-cell leukemia and lymphoma; HPV causes carcinoma of the oropharynx and anogenital squamous cell cancer. HIV-1, for which SSA has the greatest global burden, has been linked to increasing risk of malignancy through immunologic dysregulation and clonal hematopoiesis. Public health approaches to prevent infection, such as vaccination, safer injection techniques, screening of blood products, antimicrobial treatments and safer sexual practices could reduce the burden of cancer in Africa. In SSA, inequalities in access to cancer screening and treatment are exacerbated by the perception of cancer as taboo. National level cancer registries, new screening strategies for detection of viral infection and public health messaging should be prioritized in SSA's battle against malignancy. In this review, we discuss the impact of carcinogenic viruses in SSA with a focus on regional epidemiology.
Collapse
Affiliation(s)
- Mahamadou Diakite
- University Clinical Research Center, University of Sciences, Techniques, and Technologies, Bamako, Mali
| | - Kathryn Shaw-Saliba
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Chuen-Yen Lau
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| |
Collapse
|
4
|
Gessain A, Ramassamy JL, Afonso PV, Cassar O. Geographic distribution, clinical epidemiology and genetic diversity of the human oncogenic retrovirus HTLV-1 in Africa, the world's largest endemic area. Front Immunol 2023; 14:1043600. [PMID: 36817417 PMCID: PMC9935834 DOI: 10.3389/fimmu.2023.1043600] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
The African continent is considered the largest high endemic area for the oncogenic retrovirus HTLV-1 with an estimated two to five million infected individuals. However, data on epidemiological aspects, in particular prevalence, risk factors and geographical distribution, are still very limited for many regions: on the one hand, few large-scale and representative studies have been performed and, on the other hand, many studies do not include confirmatory tests, resulting in indeterminate serological results, and a likely overestimation of HTLV-1 seroprevalence. For this review, we included the most robust studies published since 1984 on the prevalence of HTLV-1 and the two major diseases associated with this infection in people living in Africa and the Indian Ocean islands: adult T-cell leukemia (ATL) and tropical spastic paraparesis or HTLV-1-associated myelopathy (HAM/TSP). We also considered most of the book chapters and abstracts published at the 20 international conferences on HTLV and related viruses held since 1985, as well as the results of recent meta-analyses regarding the status of HTLV-1 in West and sub-Saharan Africa. Based on this bibliography, it appears that HTLV-1 distribution is very heterogeneous in Africa: The highest prevalences of HTLV-1 are reported in western, central and southern Africa, while eastern and northern Africa show lower prevalences. In highly endemic areas, the HTLV-1 prevalence in the adult population ranges from 0.3 to 3%, increases with age, and is highest among women. In rural areas of Gabon and the Democratic Republic of the Congo (DRC), HTLV-1 prevalence can reach up to 10-25% in elder women. HTLV-1-associated diseases in African patients have rarely been reported in situ on hospital wards, by local physicians. With the exception of the Republic of South Africa, DRC and Senegal, most reports on ATL and HAM/TSP in African patients have been published by European and American clinicians and involve immigrants or medical returnees to Europe (France and the UK) and the United States. There is clearly a huge underreporting of these diseases on the African continent. The genetic diversity of HTLV-1 is greatest in Africa, where six distinct genotypes (a, b, d, e, f, g) have been identified. The most frequent genotype in central Africa is genotype b. The other genotypes found in central Africa (d, e, f and g) are very rare. The vast majority of HTLV-1 strains from West and North Africa belong to genotype a, the so-called 'Cosmopolitan' genotype. These strains form five clades roughly reflecting the geographic origin of the infected individuals. We have recently shown that some of these clades are the result of recombination between a-WA and a-NA strains. Almost all sequences from southern Africa belong to Transcontinental a-genotype subgroup.
Collapse
Affiliation(s)
- Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Jill-Léa Ramassamy
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Philippe V Afonso
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Olivier Cassar
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| |
Collapse
|
5
|
Prevalence and evolutionary analyses of human T-cell lymphotropic virus in Guangdong province, China: Transcontinental and Japanese subtype lineages dominate the prevalence. PLoS Negl Trop Dis 2021; 15:e0009043. [PMID: 33539355 PMCID: PMC7888662 DOI: 10.1371/journal.pntd.0009043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 02/17/2021] [Accepted: 12/18/2020] [Indexed: 11/19/2022] Open
Abstract
To systematically characterize the prevalence and evolution of human T-cell lymphotropic virus (HTLV) infection among voluntary blood donors (BDs) in Guangdong province, China. A three-year survey for HTLV epidemiology among BDs was performed in Guangdong during 2016–2018. Anti-HTLV-1/2 was screened by ELISA and ECLIA, and subsequently confirmed by western blot (WB) and nucleic acid testing (NAT). The prevalence of HTLV in donors from different cities was calculated. The identified HTLV-positive cases were phylogenetically genotyped and analyzed in a Bayesian phylogenetic framework. Among 3,262,271 BDs, 59 were confirmed positive for HTLV-1 (1.81 per 100,000) and no HTLV-2 infection was found. The prevalence of HTLV-1 varied significantly among 21 cities in Guangdong province, China. The highest prevalence was found in donors from Shanwei (13.94 per 100,000), which is a coastal city in eastern Guangdong. Viral genomic sequences genotyped from 55 HTLV-1 carriers showed that 39 were transcontinental subtype and 16 were Japanese subtype. Specially, 13 out of 39 transcontinental subtype sequences were characterized with L55P mutation and 21 out of 55 sequences were characterized with L19F mutation in viral gp46 protein. The L55P mutation seemed be specific to eastern Asia since it only presented in the sequences from Japan, mainland China, and Taiwan. Phylogenetic analysis of gp46 gene shows that HTLV-1a may have been introduced to Guangdong through four different introduction events and formed major transmission clusters: clades I(13,602 years ago), II(16, 010 years ago), III(15,639 years ago) and IV(16,517 years ago). In general, Guangdong is considered to be a low-prevalence region for HTLV-1 infection, but the prevalence is significantly higher in Shanwei city. Transcontinental and Japanese subtype lineages dominate the prevalence in Guangdong. In terms of blood safety, HTLV antibody screening for first-time blood donors can effectively reduce the risk of HTLV transmission. Human T-cell lymphotropic virus type 1 distributed all over the world. Since 1988, serological screening has been included in routine blood screening in certain developed countries and regions such as American countries and some parts of Western Europe and East Asia. However, data from some highly populated countries such as China are still not available. We performed a 3-year large-scale blood screening survey to systematically characterize the prevalence of HTLV infection among blood donors in Guangdong province in south China during 2016–2018. In general, Guangdong was considered to be a low-prevalence region for HTLV-1 infection, but the prevalence is significantly higher in Shanwei, a coastal city of eastern Guangdong. Transcontinental and Japanese subtype lineages dominate the prevalence in Guangdong. Moreover, similar molecular characteristics of prevalent HTLV-1 sequences in Mainland China, Taiwan and Japan suggested a same origin of these viruses.
Collapse
|
6
|
Cassar O, Desrames A, Marçais A, Gout O, Taylor GP, Hermine O, Soriano V, Mendoza CD, Dehan O, Mener ML, Afonso PV, Gessain A. Multiple recombinant events in human T-cell Leukemia virus Type 1: complete sequences of recombinant African strains. Emerg Microbes Infect 2020; 9:913-923. [PMID: 32249692 PMCID: PMC7269087 DOI: 10.1080/22221751.2020.1752117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Africa is the largest endemic area for HTLV-1, with many molecular genotypes. We previously demonstrated that some strains from North Africa (a-NA clade) originated from a recombinant event between Senegalese and West African strains. A series of 52 new HTLV-1 strains from 13 North and West African countries were sequenced in the LTR region and/or a env gene fragment. Four samples from French Guyanese of African origin were also added. Furthermore, 7 complete sequences from different genotypes were characterized. Phylogenetic analyses showed that most of the new African strains belong to the Cosmopolitan a-genotype. Ten new strains from the a-NA clade were found in Morocco, Western Sahara, Mali, Guinea, Côte d'Ivoire and Ghana. A new a-G-Rec clade, which arose from a distinct recombination event between Senegalese and West African strains, was identified in Guinea and Ghana. The complete sequences suggest that recombination occur in the LTR as well as the env/pol region of the genome, thus a-NA and a-G-Rec strains have a mosaic profile with genetic segments from either a-WA or a-Sen strains. Our work demonstrates that recombination in HTLV-1 may not be as rare an event as previously proposed.
Collapse
Affiliation(s)
- Olivier Cassar
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Université de Paris, Paris, France
| | - Alexandra Desrames
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Université de Paris, Paris, France
| | - Ambroise Marçais
- Service d'Hématologie, Hôpital Necker-Enfants Malades, Paris, France
| | - Olivier Gout
- Département de Neurologie, Fondation Rothschild, Paris, France
| | - Graham P Taylor
- Department of Infectious Disease, Imperial College, London, United Kingdom
| | - Olivier Hermine
- Service d'Hématologie, Hôpital Necker-Enfants Malades, Paris, France
| | - Vicente Soriano
- UNIR Health Sciences School and Medical Center, Madrid, Spain
| | - Carmen de Mendoza
- Internal Medicine Laboratory Puerta de Hierro Research Institute, University Hospital Majadahonda, Madrid, Spain
| | - Océane Dehan
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Université de Paris, Paris, France
| | - Margot Le Mener
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Université de Paris, Paris, France
| | - Philippe V Afonso
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Université de Paris, Paris, France
| | - Antoine Gessain
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Université de Paris, Paris, France
| |
Collapse
|
7
|
Afonso PV, Cassar O, Gessain A. Molecular epidemiology, genetic variability and evolution of HTLV-1 with special emphasis on African genotypes. Retrovirology 2019; 16:39. [PMID: 31842895 PMCID: PMC6916231 DOI: 10.1186/s12977-019-0504-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/07/2019] [Indexed: 02/01/2023] Open
Abstract
Human T cell leukemia virus (HTLV-1) is an oncoretrovirus that infects at least 10 million people worldwide. HTLV-1 exhibits a remarkable genetic stability, however, viral strains have been classified in several genotypes and subgroups, which often mirror the geographic origin of the viral strain. The Cosmopolitan genotype HTLV-1a, can be subdivided into geographically related subgroups, e.g. Transcontinental (a-TC), Japanese (a-Jpn), West-African (a-WA), North-African (a-NA), and Senegalese (a-Sen). Within each subgroup, the genetic diversity is low. Genotype HTLV-1b is found in Central Africa; it is the major genotype in Gabon, Cameroon and Democratic Republic of Congo. While strains from the HTLV-1d genotype represent only a few percent of the strains present in Central African countries, genotypes -e, -f, and -g have been only reported sporadically in particular in Cameroon Gabon, and Central African Republic. HTLV-1c genotype, which is found exclusively in Australo-Melanesia, is the most divergent genotype. This reflects an ancient speciation, with a long period of isolation of the infected populations in the different islands of this region (Australia, Papua New Guinea, Solomon Islands and Vanuatu archipelago). Until now, no viral genotype or subgroup is associated with a specific HTLV-1-associated disease. HTLV-1 originates from a simian reservoir (STLV-1); it derives from interspecies zoonotic transmission from non-human primates to humans (ancient or recent). In this review, we describe the genetic diversity of HTLV-1, and analyze the molecular mechanisms that are at play in HTLV-1 evolution. Similar to other retroviruses, HTLV-1 evolves either through accumulation of point mutations or recombination. Molecular studies point to a fairly low evolution rate of HTLV-1 (between 5.6E−7 and 1.5E−6 substitutions/site/year), supposedly because the virus persists within the host via clonal expansion (instead of new infectious cycles that use reverse transcriptase).
Collapse
Affiliation(s)
- Philippe V Afonso
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, CRNS-UMR 3569, Département de Virologie, Institut Pasteur, Bâtiment Lwoff, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.
| | - Olivier Cassar
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, CRNS-UMR 3569, Département de Virologie, Institut Pasteur, Bâtiment Lwoff, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Antoine Gessain
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, CRNS-UMR 3569, Département de Virologie, Institut Pasteur, Bâtiment Lwoff, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.
| |
Collapse
|
8
|
Low genetic diversity of the Human T-cell Lymphotropic Virus (HTLV-1) in an endemic area of the Brazilian Amazon basin. PLoS One 2018; 13:e0194184. [PMID: 29558516 PMCID: PMC5860735 DOI: 10.1371/journal.pone.0194184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 02/26/2018] [Indexed: 11/19/2022] Open
Abstract
The Human T-cell Lymphotropic Virus (HTLV-1) is a Deltaretrovírus that was first isolated in the 1970s, and associated with Adult T-cell Leucemia-Lymphoma (ATLL), and subsequently to Tropical Spastic Paraparesis-Myelopathy (TSP/HAM). The genetic diversity of the virus varies among geographic regions, although its mutation rate is very low (approximately 1% per thousand years) in comparison with other viruses. The present study determined the genetic diversity of HTLV-1 in the metropolitan region of Belém, in northern Brazil. Blood samples were obtained from patients at the UFPA Tropical Medicine Nucleus between January 2010 and December 2013. The DNA was extracted and the PX region of the HTLV was amplified using nested PCR. The positive samples were then digested using the Taq1 enzyme for the identification and differentiation of the HTLV-1 and HTLV-2. The 5'LTR region of the positive HTLV-1 samples were amplified by nested PCR, and then sequenced genetically. The phylogenetic analysis of the samples was based on the maximum likelihood method and the evolutionary profile was analyzed by the Bayesian approach. Overall, 78 samples tested positive for HTLV-1, and 44 were analyzed here. The aA (cosmopolitan-transcontinental) subtype was recorded in all the samples. The following evolutionary rates were recorded for the different subtypes-a: 2.10-3, b: 2.69. 10-2, c: 6.23. 10-2, d: 3.08. 10-2, e: 6. 10-2, f: 1.78. 10-3, g: 2.2. 10-2 mutations per site per year. The positive HTLV-1 samples tested in the present study were characterized by their low genetic diversity and high degree of stability.
Collapse
|
9
|
Reid MJC, Switzer WM, Schillaci MA, Ragonnet-Cronin M, Joanisse I, Caminiti K, Lowenberger CA, Galdikas BMF, Sandstrom PA, Brooks JI. Detailed phylogenetic analysis of primate T-lymphotropic virus type 1 (PTLV-1) sequences from orangutans (Pongo pygmaeus) reveals new insights into the evolutionary history of PTLV-1 in Asia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 43:434-50. [PMID: 27245152 PMCID: PMC11332081 DOI: 10.1016/j.meegid.2016.05.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/28/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
While human T-lymphotropic virus type 1 (HTLV-1) originates from ancient cross-species transmission of simian T-lymphotropic virus type 1 (STLV-1) from infected nonhuman primates, much debate exists on whether the first HTLV-1 occurred in Africa, or in Asia during early human evolution and migration. This topic is complicated by a lack of representative Asian STLV-1 to infer PTLV-1 evolutionary histories. In this study we obtained new STLV-1 LTR and tax sequences from a wild-born Bornean orangutan (Pongo pygmaeus) and performed detailed phylogenetic analyses using both maximum likelihood and Bayesian inference of available Asian PTLV-1 and African STLV-1 sequences. Phylogenies, divergence dates and nucleotide substitution rates were co-inferred and compared using six different molecular clock calibrations in a Bayesian framework, including both archaeological and/or nucleotide substitution rate calibrations. We then combined our molecular results with paleobiogeographical and ecological data to infer the most likely evolutionary history of PTLV-1. Based on the preferred models our analyses robustly inferred an Asian source for PTLV-1 with cross-species transmission of STLV-1 likely from a macaque (Macaca sp.) to an orangutan about 37.9-48.9kya, and to humans between 20.3-25.5kya. An orangutan diversification of STLV-1 commenced approximately 6.4-7.3kya. Our analyses also inferred that HTLV-1 was first introduced into Australia ~3.1-3.7kya, corresponding to both genetic and archaeological changes occurring in Australia at that time. Finally, HTLV-1 appears in Melanesia at ~2.3-2.7kya corresponding to the migration of the Lapita peoples into the region. Our results also provide an important future reference for calibrating information essential for PTLV evolutionary timescale inference. Longer sequence data, or full genomes from a greater representation of Asian primates, including gibbons, leaf monkeys, and Sumatran orangutans are needed to fully elucidate these evolutionary dates and relationships using the model criteria suggested herein.
Collapse
Affiliation(s)
- Michael J C Reid
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada.
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA, USA 30329.
| | - Michael A Schillaci
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada.
| | - Manon Ragonnet-Cronin
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, United Kingdom.
| | - Isabelle Joanisse
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Manitoba, R3E 3L5, Canada
| | - Kyna Caminiti
- Centre for Biosecurity, Public Health Agency of Canada, 100 Colonnade Road, Ottawa, Ontario, Canada.
| | - Carl A Lowenberger
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
| | - Birute Mary F Galdikas
- Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada; Orangutan Foundation International, 824 S. Wellesley Ave., Los Angeles, CA 90049, USA.
| | - Paul A Sandstrom
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Ontario, Canada.
| | - James I Brooks
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Manitoba, R3E 3L5, Canada.
| |
Collapse
|
10
|
Abstract
Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses. IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.
Collapse
|
11
|
Zehender G, Frati ER, Martinelli M, Bianchi S, Amendola A, Ebranati E, Ciccozzi M, Galli M, Lai A, Tanzi E. Dating the origin and dispersal of Human Papillomavirus type 16 on the basis of ancestral human migrations. INFECTION GENETICS AND EVOLUTION 2016; 39:258-264. [PMID: 26827632 DOI: 10.1016/j.meegid.2016.01.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 01/22/2016] [Accepted: 01/26/2016] [Indexed: 01/04/2023]
Abstract
A major limitation when reconstructing the origin and evolution of HPV-16 is the lack of reliable substitution rate estimates for the viral genes. On the basis of the hypothesis of human HPV-16 co-divergence, we estimated a mean evolutionary rate of 1.47×10(-7) (95% HPD=0.64-2.47×10(-7)) subs/site/year for the viral LCR region. The results of a Bayesian phylogeographical analysis suggest that the currently circulating HPV-16 most probably originated in Africa about 110 thousand years ago (Kya), before giving rise to four known geographical lineages: the Asian/European lineage, which most probably originated in Asia a mean 38 Kya, and the Asian/American and two African lineages, which probably respectively originated about 33 and 27 Kya. These data closely reflect current hypotheses concerning modern human expansion based on studies of mitochondrial DNA phylogeny. The correlation between ancient human migration and the present HPV phylogeny may be explained by the co-existence of modes of transmission other than sexual transmission.
Collapse
Affiliation(s)
- Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy.
| | - Elena Rosanna Frati
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Marianna Martinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Silvia Bianchi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Antonella Amendola
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Erika Ebranati
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; Campus Bio-Medico University, Rome, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Elisabetta Tanzi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| |
Collapse
|
12
|
Aiewsakun P, Katzourakis A. Endogenous viruses: Connecting recent and ancient viral evolution. Virology 2015; 479-480:26-37. [PMID: 25771486 DOI: 10.1016/j.virol.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/15/2014] [Accepted: 02/04/2015] [Indexed: 12/17/2022]
Abstract
The rapid rates of viral evolution allow us to reconstruct the recent history of viruses in great detail. This feature, however, also results in rapid erosion of evolutionary signal within viral molecular data, impeding studies of their deep history. Thus, the further back in time, the less accurate the inference becomes. Furthermore, reconstructing complex histories of transmission can be challenging, especially where extinct viral lineages are concerned. This problem has been partially solved by the discovery of viruses embedded in host genomes, known as endogenous viral elements (EVEs). Some of these endogenous viruses are derived from ancient relatives of extant viruses, allowing us to better examine ancient viral host range, geographical distribution and transmission routes. Moreover, our knowledge of viral evolutionary timescales and rate dynamics has also been greatly improved by their discovery, thereby bridging the gap between recent and ancient viral evolution.
Collapse
Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
| |
Collapse
|
13
|
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
|
14
|
Magri MC, Brigido LFDM, Morimoto HK, Caterino-de-Araujo A. Human T cell lymphotropic virus type 2a strains among HIV type 1-coinfected patients from Brazil have originated mostly from Brazilian Amerindians. AIDS Res Hum Retroviruses 2013; 29:1010-8. [PMID: 23484539 DOI: 10.1089/aid.2013.0014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human T cell lymphotropic virus type 2 (HTLV-2) is found mainly in Amerindians and in intravenous drug users (IDUs) from urban areas of the United States, Europe, and Latin America. Worldwide, HTLV-2a and HTLV-2b subtypes are the most prevalent. Phylogenetic analysis of HTLV-2 isolates from Brazil showed the HTLV-2a subtype, variant -2c, which spread from Indians to the general population and IDUs. The present study searched for the types of HTLV-2 that predominate among HIV-1-coinfected patients from southern and southeastern Brazil. Molecular characterization of the LTR, env, and tax regions of 38 isolates confirmed the HTLV-2c variant in 37 patients, and one HTLV-2b in a patient from Paraguay. Phylogenetic analysis of sequences showed different clades of HTLV-2 associated with risk factors and geographic region. These clades could represent different routes of virus transmission and/or little diverse evolutionary rates of virus. Taking into account the results obtained in the present study and the lack of the prototypic North American HTLV-2a strain and HTLV-2b subtypes commonly detected among HIV-coinfected individuals worldwide, we could speculate on the introduction of Brazilian HTLV-2 strains in such populations before the introduction of HIV.
Collapse
Affiliation(s)
- Mariana Cavalheiro Magri
- Laboratório de Investigaçõe Médica em Hepatologia por Vírus (LIM-47), Faculdade de Medicina, Universidade de São Paulo, São Paulo, S.P., Brazil
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, S.P., Brazil
| | - Luis Fernando de Macedo Brigido
- Laboratório de Retrovirus, Centro de Virologia, Instituto Adolfo Lutz, Secretaria de Estado da Saúde de São Paulo, São Paulo, S.P., Brazil
| | - Helena Kaminami Morimoto
- Departmento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina, Londrina, P.R., Brazil
| | - Adele Caterino-de-Araujo
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, S.P., Brazil
- Centro de Imunologia, Instituto Adolfo Lutz, Secretaria de Estado da Saúde de São Paulo, São Paulo, S.P., Brazil
| |
Collapse
|
15
|
Calvignac-Spencer S, Adjogoua EV, Akoua-Koffi C, Hedemann C, Schubert G, Ellerbrok H, Leendertz SAJ, Pauli G, Leendertz FH. Origin of human T-lymphotropic virus type 1 in rural Côte d'Ivoire. Emerg Infect Dis 2013; 18:830-3. [PMID: 22516514 PMCID: PMC3358045 DOI: 10.3201/eid1805.111663] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Simian T-lymphotropic virus type 1 (STLV-1) strains occasionally infect humans. However, the frequency of such infections is unknown. We show that direct transmission of STLV-1 from nonhuman primates to humans may be responsible for a substantial proportion of human T-lymphotropic virus type 1 infections in rural Côte d'Ivoire, where primate hunting is common.
Collapse
|
16
|
Andonov A, Coulthart MB, Pérez-Losada M, Crandall KA, Posada D, Padmore R, Giulivi A, Oger JJ, Peters AA, Dekaban GA. Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada. INFECTION GENETICS AND EVOLUTION 2012; 12:1822-30. [PMID: 22921499 DOI: 10.1016/j.meegid.2012.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 07/18/2012] [Accepted: 07/20/2012] [Indexed: 12/31/2022]
Abstract
The causes of the worldwide distribution of Human T-cell Lymphotropic Virus Type 1 (HTLV-1) remain incompletely understood, with competing hypotheses regarding the number and timing of events leading to intercontinental spread on historical and prehistoric timescales. Ongoing discovery of this virus in aboriginal populations of Asia and the Americas has been the main source of evidence for the latter. We conducted molecular phylogenetic and dating analyses for 13 newly reported HTLV-1 strains from Canada. We analyzed two full-length proviral genomes from aboriginal residents of Nunavut (an autonomous territory in Northern Canada including most of the Canadian Arctic), 11 long-terminal-repeat (LTR) sequences from aboriginal residents of British Columbia's Pacific coast, and 2 LTR sequences from non-aboriginal Canadians. Phylogenetic analysis demonstrated a well-supported affinity between the two Nunavut strains and two East Asian strains, suggesting the presence of an Asian-American sublineage within the widespread "transcontinental" subgroup A clade of HTLV-1 Cosmopolitan subtype a. This putative sublineage was estimated to be 5400-11,900 years in age, consistent with a long-term presence of HTLV-1 in aboriginal populations of the Canadian Arctic. Phylogenetic affinities of the other 11 Canadian HTLV-1 aboriginal strains were diverse, strengthening earlier evidence for multiple incursions of this virus into coastal aboriginal populations of British Columbia. Our results are consistent with the hypothesis of ancient presence of HTLV-1 in aboriginal populations of North America.
Collapse
Affiliation(s)
- Anton Andonov
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, Canada R3E 3R2
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Calvignac-Spencer S, Leendertz SAJ, Gillespie TR, Leendertz FH. Wild great apes as sentinels and sources of infectious disease. Clin Microbiol Infect 2012; 18:521-7. [PMID: 22448813 DOI: 10.1111/j.1469-0691.2012.03816.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Emerging zoonotic infectious diseases pose a serious threat to global health. This is especially true in relation to the great apes, whose close phylogenetic relationship with humans results in a high potential for microorganism exchange. In this review, we show how studies of the microorganisms of wild great apes can lead to the discovery of novel pathogens of importance for humans. We also illustrate how these primates, living in their natural habitats, can serve as sentinels for outbreaks of human disease in regions with a high likelihood of disease emergence. Greater sampling efforts and improvements in sample preservation and diagnostic capacity are rapidly improving our understanding of the diversity and distribution of microorganisms in wild great apes. Linking non-invasive diagnostic data with observational health data from great apes habituated to human presence is a promising approach for the discovery of pathogens of high relevance for humans.
Collapse
|
18
|
Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. Time-dependent rates of molecular evolution. Mol Ecol 2011; 20:3087-101. [PMID: 21740474 DOI: 10.1111/j.1365-294x.2011.05178.x] [Citation(s) in RCA: 350] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.
Collapse
Affiliation(s)
- Simon Y W Ho
- Centre for Macroevolution and Macroecology, Evolution Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia.
| | | | | | | | | | | | | |
Collapse
|
19
|
Gilbert C, Feschotte C. Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLoS Biol 2010; 8:e1000495. [PMID: 20927357 PMCID: PMC2946954 DOI: 10.1371/journal.pbio.1000495] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 08/16/2010] [Indexed: 11/18/2022] Open
Abstract
Because most extant viruses mutate rapidly and lack a true fossil record, their deep evolution and long-term substitution rates remain poorly understood. In addition to retroviruses, which rely on chromosomal integration for their replication, many other viruses replicate in the nucleus of their host's cells and are therefore prone to endogenization, a process that involves integration of viral DNA into the host's germline genome followed by long-term vertical inheritance. Such endogenous viruses are highly valuable as they provide a molecular fossil record of past viral invasions, which may be used to decipher the origins and long-term evolutionary characteristics of modern pathogenic viruses. Hepadnaviruses (Hepadnaviridae) are a family of small, partially double-stranded DNA viruses that include hepatitis B viruses. Here we report the discovery of endogenous hepadnaviruses in the genome of the zebra finch. We used a combination of cross-species analysis of orthologous insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds. We provide evidence that some of the avian hepadnavirus integration events are at least 19 My old, which reveals a much deeper ancestry of Hepadnaviridae than could be inferred based on the coalescence times of modern hepadnaviruses. Furthermore, the remarkable sequence similarity between endogenous and extant avian hepadnaviruses (up to 75% identity) suggests that long-term substitution rates for these viruses are on the order of 10(-8) substitutions per site per year, which is a 1,000-fold slower than short-term rates estimated based on the sequences of circulating hepadnaviruses. Together, these results imply a drastic shift in our understanding of the time scale of hepadnavirus evolution, and suggest that the rapid evolutionary dynamics characterizing modern avian hepadnaviruses do not reflect their mode of evolution on a deep time scale.
Collapse
Affiliation(s)
- Clément Gilbert
- Department of Biology, University of Texas, Arlington, Texas, United States of America
| | - Cédric Feschotte
- Department of Biology, University of Texas, Arlington, Texas, United States of America
| |
Collapse
|
20
|
Mylonas I, Brüning A, Kainer F, Friese K. HTLV infection and its implication in gynaecology and obstetrics. Arch Gynecol Obstet 2010; 282:493-501. [PMID: 20567840 DOI: 10.1007/s00404-010-1559-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 06/08/2010] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Worldwide, 20-30 million people are estimated to be infected with HTLV. HTLV-1 is endemic in Western Africa and Southern Japan, whereas HTLV-2 is considered to be spread among native American people. MATERIALS AND METHODS The impact of HTLV in gynaecology and obstetrics is being reviewed. Search strategy and selection criteria for identifying relevant data were performed by searching Medline, Current Contents, Web of Science, Embase and references from relevant articles. English and German gynaecological and infectious diseases textbooks as well as national and international guidelines and recommendations were also reviewed. RESULTS Transmission may occur by sexual intercourse or cellular blood products. Although materno-fetal transmission is debated, transmission through maternal breast milk has been confirmed. An HTLV-infection can lead to adult T-cell leukaemia (ATL) or cumulative opportunistic and neurological disorders that can occur with varying degrees of severity. Diagnosis can be done by antibody detection via the use of ELISA and western blot analysis as well as PCR diagnosis. CONCLUSION Due to inadequate treatment options and the lack of an effective vaccination, prevention is currently only possible by restricting transmission, including the usage of condoms during sexual intercourse or avoiding breastfeeding in HTLV-seropositive mothers. If, due to socio-economic reasons, breastfeeding cannot be avoided, short-term breastfeeding for a maximum of up to 6 months is suggested.
Collapse
Affiliation(s)
- Ioannis Mylonas
- First Department of Obstetrics and Gynaecology, Ludwig-Maximilians-University Munich, 80337 Munich, Germany.
| | | | | | | |
Collapse
|
21
|
Zheng H, Wolfe ND, Sintasath DM, Tamoufe U, Lebreton M, Djoko CF, Diffo JLD, Pike BL, Heneine W, Switzer WM. Emergence of a novel and highly divergent HTLV-3 in a primate hunter in Cameroon. Virology 2010; 401:137-45. [PMID: 20353873 PMCID: PMC2862145 DOI: 10.1016/j.virol.2010.03.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 02/08/2010] [Accepted: 03/02/2010] [Indexed: 01/01/2023]
Abstract
The recent discovery of human T-lymphotropic virus type 3 (HTLV-3) in Cameroon highlights the importance of expanded surveillance to better understand the prevalence and public health impact of this new retrovirus. HTLV diversity was investigated in 408 persons in rural Cameroon who reported simian exposures. Plasma from 29 persons (7.2%) had reactive serology. HTLV tax sequences were detected in 3 persons. Phylogenetic analysis confirmed HTLV-1 infection in two individuals and HTLV-3 infection in a third person (Cam2013AB). The complete proviral genome from Cam2013AB shared 98% identity and clustered tightly in distinct lineage with simian T-lymphotropic virus type 3 (STLV-3) subtype D recently identified in two guenon monkeys near this person's village. These results document a fourth HTLV-3 infection with a new and highly divergent strain we designate HTLV-3 (Cam2013AB) subtype D demonstrating the existence of a broad HTLV-3 diversity likely originating from multiple zoonotic transmissions of divergent STLV-3.
Collapse
Affiliation(s)
- HaoQiang Zheng
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
High prevalence, coinfection rate, and genetic diversity of retroviruses in wild red colobus monkeys (Piliocolobus badius badius) in Tai National Park, Cote d'Ivoire. J Virol 2010; 84:7427-36. [PMID: 20484508 DOI: 10.1128/jvi.00697-10] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simian retroviruses are precursors of all human retroviral pathogens. However, little is known about the prevalence and coinfection rates or the genetic diversity of major retroviruses-simian immunodeficiency virus (SIV), simian T-cell lymphotropic virus type 1 (STLV-1), and simian foamy virus (SFV)-in wild populations of nonhuman primates. Such information would contribute to the understanding of the natural history of retroviruses in various host species. Here, we estimate these parameters for wild West African red colobus monkeys (Piliocolobus badius badius) in the Taï National Park, Côte d'Ivoire. We collected samples from a total of 54 red colobus monkeys; samples consisted of blood and/or internal organs from 22 monkeys and additionally muscle and other tissue samples from another 32 monkeys. PCR analyses revealed a high prevalence of SIV, STLV-1, and SFV in this population, with rates of 82%, 50%, and 86%, respectively. Forty-five percent of the monkeys were coinfected with all three viruses while another 32% were coinfected with SIV in combination with either STLV or SFV. As expected, phylogenetic analyses showed a host-specific pattern for SIV and SFV strains. In contrast, STLV-1 strains appeared to be distributed in genetically distinct and distant clades, which are unique to the Taï forest and include strains previously described from wild chimpanzees in the same area. The high prevalence of all three retroviral infections in P. b. badius represents a source of infection to chimpanzees and possibly to humans, who hunt them.
Collapse
|
23
|
Sintasath DM, Wolfe ND, Zheng HQ, LeBreton M, Peeters M, Tamoufe U, Djoko CF, Diffo JLD, Mpoudi-Ngole E, Heneine W, Switzer WM. Genetic characterization of the complete genome of a highly divergent simian T-lymphotropic virus (STLV) type 3 from a wild Cercopithecus mona monkey. Retrovirology 2009; 6:97. [PMID: 19860877 PMCID: PMC2777865 DOI: 10.1186/1742-4690-6-97] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 10/27/2009] [Indexed: 11/18/2022] Open
Abstract
Background The recent discoveries of novel human T-lymphotropic virus type 3 (HTLV-3) and highly divergent simian T-lymphotropic virus type 3 (STLV-3) subtype D viruses from two different monkey species in southern Cameroon suggest that the diversity and cross-species transmission of these retroviruses are much greater than currently appreciated. Results We describe here the first full-length sequence of a highly divergent STLV-3d(Cmo8699AB) virus obtained by PCR-based genome walking using DNA from two dried blood spots (DBS) collected from a wild-caught Cercopithecus mona monkey. The genome of STLV-3d(Cmo8699AB) is 8913-bp long and shares only 77% identity to other PTLV-3s. Phylogenetic analyses using Bayesian and maximum likelihood inference clearly show that this highly divergent virus forms an independent lineage with high posterior probability and bootstrap support within the diversity of PTLV-3. Molecular dating of concatenated gag-pol-env-tax sequences inferred a divergence date of about 115,117 years ago for STLV-3d(Cmo8699AB) indicating an ancient origin for this newly identified lineage. Major structural, enzymatic, and regulatory gene regions of STLV-3d(Cmo8699AB) are intact and suggest viral replication and a predicted pathogenic potential comparable to other PTLV-3s. Conclusion When taken together, the inferred ancient origin of STLV-3d(Cmo8699AB), the presence of this highly divergent virus in two primate species from the same geographical region, and the ease with which STLVs can be transmitted across species boundaries all suggest that STLV-3d may be more prevalent and widespread. Given the high human exposure to nonhuman primates in this region and the unknown pathogenicity of this divergent PTLV-3, increased surveillance and expanded prevention activities are necessary. Our ability to obtain the complete viral genome from DBS also highlights further the utility of this method for molecular-based epidemiologic studies.
Collapse
Affiliation(s)
- David M Sintasath
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21205, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Sintasath DM, Wolfe ND, Lebreton M, Jia H, Garcia AD, Le Doux-Diffo J, Tamoufe U, Carr JK, Folks TM, Mpoudi-Ngole E, Burke DS, Heneine W, Switzer WM. Simian T-lymphotropic virus diversity among nonhuman primates, Cameroon. Emerg Infect Dis 2009; 15:175-84. [PMID: 19193260 PMCID: PMC2657614 DOI: 10.3201/eid1502.080584] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Broad virus diversity warrants active monitoring for cross-species transmission and highlights the risk for human disease. Cross-species transmission of retroviruses is common in Cameroon. To determine risk for simian T-cell lymphotropic virus (STLV) transmission from nonhuman primates to hunters, we examined 170 hunter-collected dried blood spots (DBS) from 12 species for STLV. PCR with generic tax and group-specific long terminal repeat primers showed that 12 (7%) specimens from 4 nonhuman primate species were infected with STLV. Phylogenetic analyses showed broad diversity of STLV, including novel STLV-1 and STLV-3 sequences and a highly divergent STLV-3 subtype found in Cercopithecus mona and C. nictitans monkeys. Screening of peripheral blood mononuclear cell DNA from 63 HTLV-seroreactive, PCR-negative hunters did not identify human infections with this divergent STLV-3. Therefore, hunter-collected DBS can effectively capture STLV diversity at the point where pathogen spillover occurs. Broad screening using this relatively easy collection strategy has potential for large-scale monitoring of retrovirus cross-species transmission among highly exposed human populations.
Collapse
Affiliation(s)
- David M Sintasath
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Gärtner K, Wiktorowicz T, Park J, Mergia A, Rethwilm A, Scheller C. Accuracy estimation of foamy virus genome copying. Retrovirology 2009; 6:32. [PMID: 19348676 PMCID: PMC2678077 DOI: 10.1186/1742-4690-6-32] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 04/06/2009] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Foamy viruses (FVs) are the most genetically stable viruses of the retrovirus family. This is in contrast to the in vitro error rate found for recombinant FV reverse transcriptase (RT). To investigate the accuracy of FV genome copying in vivo we analyzed the occurrence of mutations in HEK 293T cell culture after a single round of reverse transcription using a replication-deficient vector system. Furthermore, the frequency of FV recombination by template switching (TS) and the cross-packaging ability of different FV strains were analyzed. RESULTS We initially sequenced 90,000 nucleotides and detected 39 mutations, corresponding to an in vivo error rate of approximately 4 x 10-4 per site per replication cycle. Surprisingly, all mutations were transitions from G to A, suggesting that APOBEC3 activity is the driving force for the majority of mutations detected in our experimental system. In line with this, we detected a late but significant APOBEC3G and 3F mRNA by quantitative PCR in the cells. We then analyzed 170,000 additional nucleotides from experiments in which we co-transfected the APOBEC3-interfering foamy viral bet gene and observed a significant 50% drop in G to A mutations, indicating that APOBEC activity indeed contributes substantially to the foamy viral replication error rate in vivo. However, even in the presence of Bet, 35 out of 37 substitutions were G to A, suggesting that residual APOBEC activity accounted for most of the observed mutations. If we subtract these APOBEC-like mutations from the total number of mutations, we calculate a maximal intrinsic in vivo error rate of 1.1 x 10-5 per site per replication. In addition to the point mutations, we detected one 49 bp deletion within the analyzed 260000 nucleotides.Analysis of the recombination frequency of FV vector genomes revealed a 27% probability for a template switching (TS) event within a 1 kilobase (kb) region. This corresponds to a 98% probability that FVs undergo at least one additional TS event per replication cycle. We also show that a given FV particle is able to cross-transfer a heterologous FV genome, although at reduced efficiency than the homologous vector. CONCLUSION Our results indicate that the copying of the FV genome is more accurate than previously thought. On the other hand recombination among FV genomes appears to be a frequent event.
Collapse
Affiliation(s)
- Kathleen Gärtner
- Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Str 7, 97078, Würzburg, Germany
| | - Tatiana Wiktorowicz
- Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Str 7, 97078, Würzburg, Germany
| | - Jeonghae Park
- Department of Infectious Disease and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Ayalew Mergia
- Department of Infectious Disease and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Axel Rethwilm
- Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Str 7, 97078, Würzburg, Germany
| | - Carsten Scheller
- Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Str 7, 97078, Würzburg, Germany
| |
Collapse
|
26
|
Switzer WM, Salemi M, Qari SH, Jia H, Gray RR, Katzourakis A, Marriott SJ, Pryor KN, Wolfe ND, Burke DS, Folks TM, Heneine W. Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4. Retrovirology 2009; 6:9. [PMID: 19187529 PMCID: PMC2647524 DOI: 10.1186/1742-4690-6-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 02/02/2009] [Indexed: 12/21/2022] Open
Abstract
Background Human T-lymphotropic virus type 4 (HTLV-4) is a new deltaretrovirus recently identified in a primate hunter in Cameroon. Limited sequence analysis previously showed that HTLV-4 may be distinct from HTLV-1, HTLV-2, and HTLV-3, and their simian counterparts, STLV-1, STLV-2, and STLV-3, respectively. Analysis of full-length genomes can provide basic information on the evolutionary history and replication and pathogenic potential of new viruses. Results We report here the first complete HTLV-4 sequence obtained by PCR-based genome walking using uncultured peripheral blood lymphocyte DNA from an HTLV-4-infected person. The HTLV-4(1863LE) genome is 8791-bp long and is equidistant from HTLV-1, HTLV-2, and HTLV-3 sharing only 62–71% nucleotide identity. HTLV-4 has a prototypic genomic structure with all enzymatic, regulatory, and structural proteins preserved. Like STLV-2, STLV-3, and HTLV-3, HTLV-4 is missing a third 21-bp transcription element found in the long terminal repeats of HTLV-1 and HTLV-2 but instead contains unique c-Myb and pre B-cell leukemic transcription factor binding sites. Like HTLV-2, the PDZ motif important for cellular signal transduction and transformation in HTLV-1 and HTLV-3 is missing in the C-terminus of the HTLV-4 Tax protein. A basic leucine zipper (b-ZIP) region located in the antisense strand of HTLV-1 and believed to play a role in viral replication and oncogenesis, was also found in the complementary strand of HTLV-4. Detailed phylogenetic analysis shows that HTLV-4 is clearly a monophyletic viral group. Dating using a relaxed molecular clock inferred that the most recent common ancestor of HTLV-4 and HTLV-2/STLV-2 occurred 49,800 to 378,000 years ago making this the oldest known PTLV lineage. Interestingly, this period coincides with the emergence of Homo sapiens sapiens during the Middle Pleistocene suggesting that early humans may have been susceptible hosts for the ancestral HTLV-4. Conclusion The inferred ancient origin of HTLV-4 coinciding with the appearance of Homo sapiens, the propensity of STLVs to cross-species into humans, the fact that HTLV-1 and -2 spread globally following migrations of ancient populations, all suggest that HTLV-4 may be prevalent. Expanded surveillance and clinical studies are needed to better define the epidemiology and public health importance of HTLV-4 infection.
Collapse
Affiliation(s)
- William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Description of a "trans-Saharan" strain of human T-lymphotropic virus type 1 in West Africa. J Acquir Immune Defic Syndr 2008; 47:269-73. [PMID: 18398969 DOI: 10.1097/qai.0b013e31816649a4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The aim of this study was to assess the prevalence and the molecular epidemiology of human T-lymphotropic virus type 1 (HTLV-1) in a group of pregnant women living in Guinea Bissau. We studied 427 consecutive pregnant women attending 10 centers for HIV-1 infection monitoring in Bissau. HTLV-1 infection was found in 2.6% of the patients. Phylogenetic analysis of the long terminal repeat region showed that 10 isolates were of the cosmopolitan subtype (HTLV-1a) and that only 1 was of the widespread Central African subtype (HTLV-1b). All the cosmopolitan isolates belonged to the HTLV-1aD subgroup, which was first described in North Africa and clustered with other Senegal and Guinea isolates to form a significant West African clade. Our data show a high prevalence of HTLV-1 in Guinea Bissau and suggest the existence of a trans-Saharan strain distributed in North and West Africa, which probably crossed the desert in the past as a result of contacts between nomadic and sedentary populations or along trading routes.
Collapse
|
28
|
Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 2008; 9:267-76. [PMID: 18319742 DOI: 10.1038/nrg2323] [Citation(s) in RCA: 1006] [Impact Index Per Article: 62.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Understanding the factors that determine the rate at which genomes generate and fix mutations provides important insights into key evolutionary mechanisms. We review our current knowledge of the rates of mutation and substitution, as well as their determinants, in RNA viruses, DNA viruses and retroviruses. We show that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity.
Collapse
Affiliation(s)
- Siobain Duffy
- Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | | |
Collapse
|
29
|
Calvignac S, Terme JM, Hensley SM, Jalinot P, Greenwood AD, Hänni C. Ancient DNA identification of early 20th century simian T-cell leukemia virus type 1. Mol Biol Evol 2008; 25:1093-8. [PMID: 18296697 DOI: 10.1093/molbev/msn054] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The molecular identification of proviruses from ancient tissues (and particularly from bones) remains a contentious issue. It can be expected that the copy number of proviruses will be low, which magnifies the risk of contamination with retroviruses from exogenous sources. To assess the feasibility of paleoretrovirological studies, we attempted to identify proviruses from early 20th century bones of museum specimens while following a strict ancient DNA methodology. Simian T-cell leukemia virus type 1 sequences were successfully obtained and authenticated from a Chlorocebus pygerythrus specimen. This represents the first clear evidence that it will be possible to use museum specimens to better characterize simian and human T-tropic retrovirus genetic diversity and analyze their origin and evolution, in greater detail.
Collapse
Affiliation(s)
- Sébastien Calvignac
- Université de Lyon, Paléogénétique et Evolution Moléculaire, Institut de Génomique Fonctionnelle, INRA, CNRS, UCB-Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France
| | | | | | | | | | | |
Collapse
|
30
|
Abstract
During the rapid spread of HIV-1 in humans, the main (M) group of HIV-1 has evolved into ten distinct subtypes, undergone countless recombination events and diversified extensively. The impact of this extreme genetic diversity on the phenotype of HIV-1 has only recently become a research focus, but early findings indicate that the dominance of HIV-1 subtype C in the current epidemic might be related to the lower virulence of this subtype compared with other subtypes. Here, we explore whether HIV-1 has reached peak virulence or has already started the slow path to attenuation.
Collapse
Affiliation(s)
- Kevin K. Ariën
- the Department of Microbiology, HIV and Retrovirology Research Unit, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, B2000 Belgium
- Present Address: the Department of Clinical Chemistry, Microbiology and Immunology, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, Ghent, B-9000 Belgium
| | - Guido Vanham
- the Department of Microbiology, HIV and Retrovirology Research Unit, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, B2000 Belgium
| | - Eric J. Arts
- the Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 2109, Adelbert Rd, Cleveland, 44195 Ohio USA
| |
Collapse
|
31
|
Switzer WM, Qari SH, Wolfe ND, Burke DS, Folks TM, Heneine W. Ancient origin and molecular features of the novel human T-lymphotropic virus type 3 revealed by complete genome analysis. J Virol 2006; 80:7427-38. [PMID: 16840323 PMCID: PMC1563715 DOI: 10.1128/jvi.00690-06] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human T-lymphotropic virus type 3 (HTLV-3) is a new virus recently identified in two primate hunters in Central Africa. Limited sequence analysis shows that HTLV-3 is distinct from HTLV-1 and HTLV-2 but is genetically similar to simian T-lymphotropic virus type 3 (STLV-3). We report here the first complete HTLV-3 sequence obtained by PCR-based genome walking using uncultured peripheral blood lymphocytes from an HTLV-3-infected person. The HTLV-3(2026ND) genome is 8,917 bp long and is genetically equidistant from HTLV-1 and HTLV-2, sharing about 62% identity. Phylogenetic analysis of all gene regions confirms this relationship and shows that HTLV-3 falls within the diversity of STLV-3, suggesting a primate origin. However, HTLV-3(2026ND) is unique, sharing only 87% to 92% sequence identity with STLV-3. SimPlot and phylogenetic analysis did not reveal any evidence of genetic recombination with either HTLV-1, HTLV-2, or STLV-3. Molecular dating estimates that the ancestor of HTLV-3 is as old as HTLV-1 and HTLV-2, with an inferred divergence time of 36,087 to 54,067 years ago. HTLV-3 has a prototypic genomic structure, with all enzymatic, regulatory, and structural proteins preserved. Like STLV-3, HTLV-3 is missing a third 21-bp transcription element found in the long terminal repeats of HTLV-1 and HTLV-2 but instead contains a unique activator protein-1 transcription factor upstream of the 21-bp repeat elements. A PDZ motif, like that in HTLV-1, which is important for cellular signal transduction and transformation, is present in the C terminus of the HTLV-3 Tax protein. A basic leucine zipper region located in the antisense strand of HTLV-1, believed to play a role in viral replication and oncogenesis, was also found in the complementary strand of HTLV-3. The ancient origin of HTLV-3, the broad distribution of STLV-3 in Africa, and the propensity of STLVs to cross species into humans all suggest that HTLV-3 may be prevalent and support the need for expanded surveillance for this virus.
Collapse
Affiliation(s)
- William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G-45, Atlanta, GA 30333, USA.
| | | | | | | | | | | |
Collapse
|
32
|
Van Dooren S, Meertens L, Lemey P, Gessain A, Vandamme AM. Full-genome analysis of a highly divergent simian T-cell lymphotropic virus type 1 strain in Macaca arctoides. J Gen Virol 2005; 86:1953-1959. [PMID: 15958673 DOI: 10.1099/vir.0.80520-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Full-genome sequencing and analysis of the highly divergent simian T-cell lymphotropic virus type 1 (STLV-1) strain MarB43 in Macaca arctoides indicated that its open reading frame structure is compatible with proper functioning of its Gag, Pol, Env, Tax and Rex proteins. Detailed analysis of the coding potential, however, revealed that MarB43 is probably forced to use the human T-cell lymphotropic virus type 2/STLV-2 env-tax-rex splice-acceptor homologue and that the proximal pX auxiliary proteins p12(I), p13(II), p30(II) and p27(I) seem to have lost their function. Full-genome (gag-pol-env-tax), long terminal repeat and env phylogenetic analyses conclusively identified STLV-1 in M. arctoides as the currently most divergent STLV-1 strain. The long branching pattern of the monophyletic STLV-1 Macaca subspecies clades suggests that macaques might be the ancestral reservoir for primate T-cell lymphotropic virus type 1 in Asia. Full-genome molecular-clock analysis supports an archaic introduction of STLV-1 on the Asian continent, at least 269 000-156 000 years ago.
Collapse
Affiliation(s)
- Sonia Van Dooren
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Laurent Meertens
- Unité d'Epidémiologie des Virus Oncogènes, Département EEMI, Institut Pasteur, Paris, France
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Antoine Gessain
- Unité d'Epidémiologie des Virus Oncogènes, Département EEMI, Institut Pasteur, Paris, France
| | - Anne-Mieke Vandamme
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| |
Collapse
|