Northern African Strains of Human T-Lymphotropic Virus Type 1 Arose from a Recombination Event

Abstract

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. IMPORTANCEA 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.

Multiple recombinant events in human T-cell Leukemia virus Type 1: complete sequences of recombinant African strains

“…The newly identified a-G-Rec clade exhibited a similar profile ( Figure 3B). When focusing on the nucleotide alignment, we found that a-G-Rec shared 4 specific nucleotides with a-Sen strains in the U3 region, and 4 specific nucleotides with a-WA strains in the R-U5 region, as we previously found for a-NA strains [14]. Together, this indicates that a-G-Rec strains likely derived from a recombination between a-WA and a-Sen, at the U3/R junction.…”

“…Only 4 strains (3 from Nigeria and one from Togo) belong to the b-genotype. Furthermore, as previously described [14], the large cosmopolitan HTLV-1a genotype can be subdivided into 4 subgroups: the transcontinental clade (a-TC), the Senegalese (a-Sen), the North African (a-NA), and the West African (a-WA) clades. As indicated by their names, these clades were globally related to a geographic region.…”

“…The a-NA group was previously identified as a recombinant group between a-WA and a-Sen [14]. Due to its close proximity to a-NA, we wondered whether the a-G-Rec group also emerged from a recombination event.…”

“…In 2014, we first suggested that recombination could also be at play in HTLV-1 evolution. Indeed, we demonstrated that HTLV-1 strains present in North Africa (a-NA clade) had originated from a recombination event between strains from the Senegalese (a-Sen) and the West African (a-WA) subgroups [14]. In order to better characterize these recombinant strains and their distribution in northwestern Africa, we sequenced (partially or entirely) a new series of 52 HTLV-1 strains from 13 North and West African countries and 4 strains from members of the Noir Marron community in French Guiana, who are descendent from African slaves [15].…”

Cocirculation of Two env Molecular Variants, of Possible Recombinant Origin, in Gorilla and Chimpanzee Simian Foamy Virus Strains from Central Africa

“…We first examined whether recombination, which is a frequent evolutionary event in retroviruses, could explain the diversity of env sequences (57)(58)(59)(60). Indeed, recombination is also frequent among SFVs.…”