Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of adult T-cell leukemia/lymphoma (ATLL), HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), and other diseases. The mechanisms of virus pathogenesis are still obscure. The occurrence of defective proviruses in HTLV-1-infected cell lines and the peripheral blood mononuclear cells (PBMC) of infected individuals is a frequent feature of virus infection. We detected defective proviruses with large internal deletions in PBMC from ATLL and HAM/TSP patients and in asymptomatic HTLV-1 carriers. Seventeen PCR-amplified defective proviruses were sequenced, and three types of deletions were found. Besides truncated MA and the 5 end of the genome, truncated CA, truncated SU, and more frequently truncated TM linked to the pX region were detected. Reverse transcription-PCR analysis of PBMC from ATLL patients and asymptomatic carriers also revealed RNA transcripts with large internal deletions. Analysis of two RT-PCR cDNA clones confirmed a Gag-TM-pX structure of the transcripts. Most defective proviruses contained numerous internal stop codons, but some were capable of coding for the truncated MA linked to a variable out-of-frame peptide. Cloned defective proviruses with long open reading frames were subjected to in vitro transcription-translation followed by radioimmunoprecipitation, which showed expression of chimeric proteins between 8 and 12 kDa. Possible roles of defective proviruses and chimeric proteins are discussed, although there is no firm association with pathogenesis.The human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus which causes two distinct pathologies: adult T-cell leukemia/lymphoma (ATLL) (10, 27) and chronic progressive myelopathy-tropical spastic paraparesis (TSP), also called HTLV-1-associated myelopathy (HAM) (5, 26). Recent studies have suggested that HTLV-1 is also associated with other human diseases (23).Previous comparative studies of different HTLV-1 isolates indicated the following: the protein patterns of the viruses from cells of individuals with ATL and HAM/TSP were identical (6), DNA blotting (11, 33) and sequence comparisons of proviruses from ATLL and HAM/TSP revealed nearly 97% homology (4, 21), and restriction endonuclease analysis did not reveal any selected integration sites for the proviruses in the DNA of infected individuals (33). Occasional cases of ATLL associated with TSP-HAM pathology have been reported (14,24), and infection of a patient with blood from a HAM/TSP donor resulted in HAM/TSP in the recipient (8). Thus, different diseases in association with one virus remains a paradox of HTLV-1. The mechanisms by which the virus induces different diseases and the cofactors, either virus associated or host related, that contribute to different forms of disease manifestations or progression remain to be determined.Defective proviruses have been observed in cells from ATLL patients and could be important elements in pathogenesis (9,17,32). We have therefore compared the presence of defecti...