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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.

Unlabelled: Although recombination is a major source of genetic variability in retroviruses, no recombinant strain had been observed for human T-lymphotropic virus type 1 (HTLV-1), the first isolated human-pathogenic retrovirus. Different genotypes exist for HTLV-1: Genotypes b and d to g are restricted to central Africa, while genotype c is only endemic in Australo-Melanesia. In contrast, the cosmopolitan genotype a is widely distributed. We applied a combination of phylogenetics and recombination analysis approaches to a set of new HTLV-1 sequences, which we collected from 19 countries throughout Africa, the continent where the virus has the largest endemic presence. This led us to demonstrate the presence of recombinants in HTLV-1. Indeed, the HTLV-1 strains currently present in North Africa have originated from a recombinant event between strains from Senegal and West Africa. This recombination is estimated to have occurred around 4,000 years ago. This recombination seems to have been generated during reverse transcription. In conclusion, we demonstrate that, albeit rare, recombination can occur in HTLV-1 and may play a role in the evolution of this retrovirus., Importance: A number of HTLV-1 subtypes have been described in different populations, but none of the genetic differences between these subtypes have been ascribed to recombination events. Here we report an HTLV-1 recombinant virus among infected individuals in North Africa. This demonstrates that, contrary to what was thought, recombination can occur and could play a role in the evolution of HTLV-1., (Copyright © 2014, American Society for Microbiology. All Rights Reserved.)

Background: The Human T-cell Leukemia Virus type 1 (HTLV-1) is the causative agent of several inflammatory diseases, including HTLV-1-associated inflammatory myopathies (HAIM). Little is known about the virological and immunological characteristics of this viral disease., Objectives: To characterize the histological and virological features of HAIM patients, in order to better understand the pathogenetic mechanisms and unravel new biological markers of this disease., Study Design: We conducted a retrospective study on 13 patients with HAIM, based on blood and muscle samples. We included blood samples from HTLV-1-infected individuals without myopathy as controls. Muscle biopsies were used for a broad immunohistological evaluation of tissue damage and inflammation, as well as identification of infected cells through in situ hybridization. DNA extracted from patients' PBMC was used to identify the virus genotype by sequencing and to assess the proviral load by quantitative PCR. Anti-viral antibodies in plasma samples were titrated by indirect immunofluorescence., Results: Patients originate from HTLV-1 endemic areas, the West Indies and West Africa. Histological alterations and inflammation in patients muscles were mostly moderate, with classical features of idiopathic myositis and rare HTLV-1-infected infiltrating cells. In all patients, HTLV-1 belonged to the A subtype, transcontinental subgroup. Anti-HTLV-1 antibodies titers were high, but the proviral load was not elevated compared to asymptomatic HTLV-1 carriers., Conclusion: We show here that muscle inflammation is moderate in HAIM, and accompanied by a low HTLV-1 proviral load, suggesting that the pathogenetic events do not exactly mirror those of other HTLV-1-associated inflammatory diseases., (Copyright © 2012 Elsevier B.V. All rights reserved.)