An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics

Abstract

Human rhinovirus (HRV) is one of the most common human respiratory pathogens and is responsible for the majority of upper respiratory illnesses. Recently, a phylogeny was constructed from all known American Type Culture Collection (ATCC) HRV sequences. From this study, three HRV classifications (HRVA, HRVB, and HRVC) were determined and techniques for classifying new isolates of HRV were reported. The genetic change of this virus in specific populations over time is of great interest to understand the evolution and epidemiology of viruses. To facilitate the collections of HRV sequences over a number of years, a virology experiment was designed in which students test nasal lavage samples to look for HRV infection. Students will learn a variety of techniques including RNA isolation, cDNA synthesis, qPCR, and agarose gel electrophoresis as well as bioinformatic skills though examination of sequences from the HRV-field isolates. Furthermore, students can look at symptom data from subjects to investigate correlations between symptom severity and factors such as stress and sleep patterns. Such information can be used to examine hypotheses regarding HRV mutation, symptom severity and epidemiology.

Virology in the Classroom: Current Approaches and Challenges to Undergraduate- and Graduate-Level Virology Education

“…In a second, using as few as two lab sessions (or as many as four), students obtain nasal lavage samples, isolate RNA and synthesize complementary DNA, perform PCR and quantitative PCR, and analyze products using gel electrophoresis and sequencing/BLAST. Here, the idea is to look for human rhinovirus (HRV) nucleic acid in the samples, and look for any diversity in the recovered sequence and compare it to known HRV samples (21).…”

qPCR for second year undergraduates: A short, structured inquiry to illustrate differential gene expression

“…While there are many studies in the research literature utilizing qPCR, a review of the education literature in chemistry, biochemistry, and molecular biology reveals only a handful of published exercises adapted for use in the undergraduate setting. These laboratory exercises address multiple topics including detection of human rhinovirus in nasal lavage samples , determination of equine maternity , and examination of gene expression in response to vernalization in Arabidopsis among others . Common features of most of these exercises are their intended use with an upper level audience (third and fourth year students) and extensive time investment (9–12 hr of laboratory time).…”