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Background  The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages.    Results  We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to  Simiiformes  (parvorders  Catarrhini  and  Platyrrhini ),  Tarsiiformes  and to the most primitive  Prosimians . Analysis of HERV-W orthologous loci in non-human  Catarrhini  primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of  Catarrhini  sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family  Cebidae ,  Platyrrhini  parvorder), identified as ERV1–1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in  Atelidae  and  Pitheciidae , representative of the other  Platyrrhini  families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of  Tarsiiformes  and  Prosimians .    Conclusions  Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1125-1) contains supplementary material, which is available to authorized users.

HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini