We genotyped strains found in nasopharyngeal specimens (URT), bronchoalveolar lavage fluids (LRT), and strains identified in cases with infections lasting more than three weeks (protracted infection) to assess whether members of the HRV-A, -B and -C species were equally represented in the LRT and/or in the case of protracted infection. Samples were collected from a prospective cohort of lung transplant recipients screened routinely from September 2008 to November 2010, as well as hospital patients screened at the routine laboratory of the University of Geneva Hospitals between February and November 2009 (Table S1 ). VP4/VP2 sequencing was performed on all positive cases whenever possible. Sequences were obtained for 50 HRV-positive specimens collected from the lung transplant recipient cohort, and 94 specimens collected from hospital patients (56 from children, 36 from adults, and 1 with age not available). Phylogenetic analysis was performed on all sequences obtained, as well as corresponding sequences of HRV-A and -B reference types and proposed HRV-C reference types [22] . Of the 144 sequenced samples, 127 represented different infectious episodes with 71 (55.5%) due to HRV-A types, 10 (7.8%) to HRV-B types, and 47 (36.7%) to HRV-C types ( Figure 1 and Figures S1A, B , and C).