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cervical samples from a cohort of young women attending cervical screening with access to HPV vaccination in Luxembourg. DNA extracts of eighty-one cervical swabs from women (mean age 23 years) positive for HPV by AnyplexIIHPV28 VR (Seegene) were enriched by rolling circle amplification and sequenced on Illumina Miseq. Reads were mapped to 182 PaVE reference sequences of known HPV types using BBMap and assembled using VELVET. Complete HPV genomes obtained were aligned with genomes published in Genbank using MEGA6. Overall, an average of 1 per cent of reads mapped to HPV. Among the eightyone positive samples, NGS-RCA detected 186 different HPV types spanning thirty-six of the fifty-one known mucosal types. HPV types 42, 53, 51, 56, 90, and 31 were most frequently detected in twenty-two, fifteen, ten, ten, nine, and seven samples, respectively. Detection of HPV types by NGS-RCA was highly correlated with viral load of Anyplex. About sixty-seven consensus sequences of complete HPV genomes were assembled including two novel lineages of HPV66 and HPV90 and two novel sublineage of HPV67 and HPV73, respectively. NGS-RCA is a powerful method for obtaining complete HPV genomes from cervical samples with a high viral load (Ct< 30). After eight years of the vaccination programme in Luxembourg, vaccinerelated types 6, 11, 16, and 18 were infrequently detected in the targeted age group.

A45 Merkel-cell polyomavirus and human polyomavirus 6 in Argentina, Uruguay, and Spain: Deep characterization of the South American types