Phylogenetic patterns of human respiratory picornavirus species, including the newly identified group C rhinoviruses, during a 1-year surveillance of a hospitalized patient population in Italy

Abstract

Human rhinovirus species C (HRV-C) was the second most common HRV species detected in hospitalized patients in Italy with acute respiratory disease during a 1-year surveillance period. Sequencing of the picornavirus VP4/VP2 region allowed molecular typing of HRV-A and HRV-B and provisional typing of HRV-C.

FIG. 1.

A neighbor-joining phylogenetic tree analysis of the VP4/VP2 region of HRV (n = 195, accession numbers, HM366725 to HM366919) and HEV (n = 21, accession numbers HM370281 to HM370295; Pav260-Pav264, previously published accession numbers, GU722101 to GU722097) strains identified in Pavia, Italy. HEV branches were used to root the tree. Reference strains for HRV-A, HRV-B, HEV-C, and HEV-D were included in the tree reconstruction; these are indicated by black dots and the relevant accession numbers are in brackets. Strains showing more than 10% nucleotide divergence with respect to the reference strain (but less than 7% amino acid divergence) were marked with asterisks. Details of the HRV-C strains are shown in Fig. 2.

FIG. 2.

Phylogenetic tree based on amino acid (A) or nucleotide (B) HRV and HEV sequences. Eleven complete HRV-C genome sequences previously published with relevant accession numbers are in bold. HRV-PavC1 and HRV-PavC2 are two strain clusters temporally related to each other. (C) Predicted VP2 cre secondary structure of 67 HRV-C strains identified in Pavia. In the stem-loop, the nucleotide pairs joined by the thick line were detected in all 67 HRV-C strains (100%), as indicated in each circle. The other nucleotide pairs containing one variable nucleotide show the type(s) and, within the closed circle, the number of nucleotide substitutions detected in different strains. Above the loop, the conserved and variable nucleotides among the 14 nucleotides forming the loop are indicated along with the frequency of the variable nucleotide present in different strains.