Polymerase chain reaction and sequencing for typing rhinovirus RNA

Primers were designed and tested for their ability to distinguish rhinoviruses from enteroviruses. A primer set derived from the 5'-UTR/VP coding region junction was able to amplify all the rhinovirus serotypes tested. Enteroviruses were either not amplified by these primer pairs or produced a band of larger size that could easily be discriminated from the rhinovirus-specific product. In contrast, primers embedded in the 5'-UTR region alone were able to amplify both rhinovirus and enterovirus RNA. It is shown that rhinoviruses could be specifically typed by sequencing the amplicon derived from the 5'-UTR set. The sequences of the 5'-UTR region of ten previously unsequenced rhinoviruses were derived. The sequences obtained cluster into two groups: 1B, 41, 15, 30, 63, 31, 56, and 44; and 17, 69, and 70. Amplicons from serotypes 17,69, and 70 also group by sequence with the equivalent region of HRV14 from the genetic database, while the others group with 2 and 89.