MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during 2004-2005

Abstract

In New York State during winter 2004, there was a high incidence of influenza-like illness that tested negative both for influenza virus, by molecular methods, and for other respiratory viruses, by virus culture. Concern that a novel pathogen might be implicated led us to implement a new multiplex diagnostic tool. MassTag polymerase chain reaction resolved 26 of 79 previously negative samples, revealing the presence of rhinoviruses in a large proportion of samples, half of which belonged to a previously uncharacterized genetic clade. In some instances, knowledge of the detected viral and/or bacterial (co)infection could have altered clinical management.

Table 1

Pathogens in New York State respiratory specimens during the 2004–2005 influenza season

Figure 1

Dendrogram of isolates of rhinovirus from New York State (NYS) and of selected reference isolates of enterovirus and rhinovirus. The nucleotide sequence of VP4 was used to reconstruct a phylogenetic tree by use of the neighbor-joining method applying a Kimura 2-parameter model. Isolates from NYS that are related to human rhinovirus (HRV) group A (DQ875920 and DQ875923 [•]; DQ875923 and DQ875920) and HRV group B (DQ875922, DQ875927, and DQ875930 [♦]) are shown, as are isolates (DQ875921, DQ875924, DQ875925, DQ875926, DQ875928, DQ875929, DQ875931, and DQ875932 [▴]) that cluster as a distinct genetic clade, HRV-NY. The scale bar indicates nucleotide substitutions per site, and bootstrap values (percentage of 1000 pseudoreplicates) are shown at relevant branches