Figure. Identification of the major and minor 5′ terminally deleted or full-length enterovirus populations detected in the cardiac tissues of a patient with IDCM, Reims, France, September 2011. A) Gel electrophoresis analysis (4% agarose) of amplicons generated by using the rapid amplification of cDNA ends PCR strategy. Deleted control lane, synthetic RNA presenting with a 50-nt terminal deletion (3); IDCM lane, rapid amplification of cDNA ends PCR analysis of extracted RNA from heart tissues of the IDCM patient. B) Coverage data obtained by next-generation sequencing analysis of the cardiac tissue taken from IDCM patient. Reads obtained were filtered by bar code first to obtain 8,512,538 reads. A second discriminant step selected only reads containing both A and trP1 sequences, eliminating all artifacts resulting from early stops of the polymerase during amplification or sequencing. Following these steps, 7,354,283 reads were selected and aligned against the aligned human enterovirus group B genomes by using CLC Genomics software (CLC Bio, Aarhus, Denmark). Of these reads, only 538 were successfully aligned against enterovirus group B sequences and, more specifically, against coxsackieviruses B3 strain Nancy (Gen Bank accession no. JX312064.1). We observed that the persistent viral population in the cardiac samples consisted of a major proportion of deleted populations, with deletions ranging from 15 to 48 nt. C) Reads proportion obtained for each viral form from the IDCM patient. Coverage data were used to identify the full-length and deleted viral forms and indicate each populations’ proportions. IDCM, idiopathic dilated cardiomyopathy; FL, full-length; TD, terminally deleted.